format-version: 1.2 data-version: 2024-01-09 date: 09:01:2024 14:43 remark: Please cite the OBI consortium http://purl.obolibrary.org/obo/obi where traditional citation is called for. However it is adequate that individual terms be attributed simply by use of the identifying PURL for the term, in projects that refer to them. ontology: obi property_value: defaultLanguage "en" xsd:string property_value: http://purl.org/dc/elements/1.1/contributor "Advisors for this project come from the IFOMIS group, Saarbruecken and from the Co-ODE group in Manchester" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Alan Ruttenberg" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Allyson Lister" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Barry Smith" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Bill Bug" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Bjoern Peters" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Carlo Torniai" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Chris Mungall" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Chris Stoeckert" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Chris Taylor" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Christian Bolling" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Cristian Cocos" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Daniel Rubin" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Daniel Schober" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Dawn Field" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Dirk Derom" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Elisabetta Manduchi" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Eric Deutsch" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Frank Gibson" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Gilberto Fragoso" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Helen C. Causton" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Helen Parkinson" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Holger Stenzhorn" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "James A. Overton" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "James Malone" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Jay Greenbaum" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Jeffrey Grethe" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Jennifer Fostel" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Jessica Turner" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Jie Zheng" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Joe White" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "John Westbrook" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Kevin Clancy" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Larisa Soldatova" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Lawrence Hunter" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Liju Fan" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Luisa Montecchi" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Matthew Brush" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Matthew Pocock" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Melanie Courtot" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Melissa Haendel" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Mervi Heiskanen" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Monnie McGee" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Norman Morrison" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Philippe Rocca-Serra" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Phillip Lord" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Pierre Grenon" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Richard Bruskiewich" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Richard Scheuermann" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Robert Stevens" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Ryan R. Brinkman" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Stefan Wiemann" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Susanna-Assunta Sansone" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Tanya Gray" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Tina Hernandez-Boussard" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Trish Whetzel" xsd:string property_value: http://purl.org/dc/elements/1.1/creator "Yongqun He" xsd:string property_value: http://purl.org/dc/elements/1.1/description "An ontology for representing biomedical investigations, including study designs, the collection and preparation of the targets of investigation, assays, instrumentation and reagents used, as well as the data generated and the types of analysis performed on the data to reach conclusions, and their documentation." xsd:string property_value: http://purl.org/dc/elements/1.1/format "OWL-DL" xsd:string property_value: http://purl.org/dc/elements/1.1/subject "An ontology for the annotation of biomedical and functional genomics experiments." xsd:string property_value: http://purl.org/dc/terms/license "http://creativecommons.org/licenses/by/4.0/" xsd:string property_value: http://purl.org/dc/terms/title "Ontology for Biomedical Investigations" xsd:string property_value: IAO:0000589 "Ontology for Biomedical Investigations" xsd:string property_value: owl:versionInfo "2024-01-09" xsd:string [Term] id: APOLLO_SV:00000008 name: software development def: "A planned process that has specified output a software product and that involves the creation of source code." [] is_a: OBI:0000011 ! planned process [Term] id: APOLLO_SV:00000032 name: count def: "A measurement datum that is the output of counting." [] is_a: IAO:0000109 ! measurement datum [Term] id: APOLLO_SV:00000033 name: counting def: "The planned process of finding the number of elements in a finite set of objects." [] is_a: OBI:0000011 ! planned process [Term] id: APOLLO_SV:00000522 name: source code repository def: "A document that comprises at least one source code module and provenance data about who contributed the set of files making up the module(s), and optionally comprises also multiple versions of files with detailed change history about who committed files and when, a license for the software, readme files, documentation, executables, etc." [] comment: Refers to the stuff that lives on GitHub, not to GitHub or the git software on which it is based is_a: IAO:0000310 ! document [Term] id: APOLLO_SV:00000796 name: dataset creating def: "A planned process that has a data set as its specified output." [] synonym: "data set creation" EXACT [] synonym: "dataset creation" EXACT [] is_a: OBI:0000011 ! planned process [Term] id: BFO:0000001 name: entity disjoint_from: ObsoleteClass ! Obsolete Class [Term] id: BFO:0000002 name: continuant def: "An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts." [] is_a: BFO:0000001 ! entity disjoint_from: BFO:0000003 ! occurrent [Term] id: BFO:0000003 name: occurrent def: "An entity that has temporal parts and that happens, unfolds or develops through time." [] is_a: BFO:0000001 ! entity [Term] id: BFO:0000004 name: independent continuant is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant [Term] id: BFO:0000005 name: obsolete dependent continuant def: "A continuant that is either dependent on one or other independent continuant bearers or inheres in or is borne by other entities." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: BFO:0000006 name: spatial region is_a: BFO:0000141 ! immaterial entity disjoint_from: BFO:0000029 ! site disjoint_from: BFO:0000029 ! site disjoint_from: BFO:0000140 ! continuant fiat boundary [Term] id: BFO:0000008 name: temporal region is_a: BFO:0000003 ! occurrent disjoint_from: BFO:0000011 ! spatiotemporal region disjoint_from: BFO:0000011 ! spatiotemporal region disjoint_from: BFO:0000015 ! process disjoint_from: BFO:0000035 ! process boundary [Term] id: BFO:0000009 name: two-dimensional spatial region is_a: BFO:0000006 ! spatial region disjoint_from: BFO:0000018 ! zero-dimensional spatial region disjoint_from: BFO:0000028 ! three-dimensional spatial region [Term] id: BFO:0000011 name: spatiotemporal region is_a: BFO:0000003 ! occurrent [Term] id: BFO:0000015 name: process is_a: BFO:0000003 ! occurrent [Term] id: BFO:0000016 name: disposition is_a: BFO:0000017 ! realizable entity disjoint_from: BFO:0000023 ! role [Term] id: BFO:0000017 name: realizable entity def: "A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances." [] is_a: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000019 ! quality [Term] id: BFO:0000018 name: zero-dimensional spatial region is_a: BFO:0000006 ! spatial region disjoint_from: BFO:0000028 ! three-dimensional spatial region [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant [Term] id: BFO:0000020 name: specifically dependent continuant is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant [Term] id: BFO:0000023 name: role def: "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." [] is_a: BFO:0000017 ! realizable entity [Term] id: BFO:0000024 name: fiat object part is_a: BFO:0000040 ! material entity [Term] id: BFO:0000026 name: one-dimensional spatial region is_a: BFO:0000006 ! spatial region disjoint_from: BFO:0000028 ! three-dimensional spatial region [Term] id: BFO:0000027 name: object aggregate is_a: BFO:0000040 ! material entity [Term] id: BFO:0000028 name: three-dimensional spatial region is_a: BFO:0000006 ! spatial region [Term] id: BFO:0000029 name: site is_a: BFO:0000141 ! immaterial entity [Term] id: BFO:0000030 name: object is_a: BFO:0000040 ! material entity [Term] id: BFO:0000031 name: generically dependent continuant is_a: BFO:0000002 ! continuant [Term] id: BFO:0000034 name: function is_a: BFO:0000016 ! disposition [Term] id: BFO:0000035 name: process boundary is_a: BFO:0000003 ! occurrent [Term] id: BFO:0000038 name: one-dimensional temporal region is_a: BFO:0000008 ! temporal region disjoint_from: BFO:0000148 ! zero-dimensional temporal region [Term] id: BFO:0000040 name: material entity def: "An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time." [] is_a: BFO:0000004 ! independent continuant disjoint_from: BFO:0000141 ! immaterial entity [Term] id: BFO:0000140 name: continuant fiat boundary is_a: BFO:0000141 ! immaterial entity [Term] id: BFO:0000141 name: immaterial entity is_a: BFO:0000004 ! independent continuant [Term] id: BFO:0000142 name: one-dimensional continuant fiat boundary is_a: BFO:0000140 ! continuant fiat boundary disjoint_from: BFO:0000146 ! two-dimensional continuant fiat boundary disjoint_from: BFO:0000146 ! two-dimensional continuant fiat boundary disjoint_from: BFO:0000147 ! zero-dimensional continuant fiat boundary [Term] id: BFO:0000144 name: process profile is_a: BFO:0000015 ! process disjoint_from: BFO:0000182 ! history [Term] id: BFO:0000145 name: relational quality is_a: BFO:0000019 ! quality [Term] id: BFO:0000146 name: two-dimensional continuant fiat boundary is_a: BFO:0000140 ! continuant fiat boundary [Term] id: BFO:0000147 name: zero-dimensional continuant fiat boundary is_a: BFO:0000140 ! continuant fiat boundary [Term] id: BFO:0000148 name: zero-dimensional temporal region synonym: "temporal instant." EXACT [] is_a: BFO:0000008 ! temporal region [Term] id: BFO:0000182 name: history is_a: BFO:0000015 ! process [Term] id: CHEBI:145810 name: insulin def: "A peptide hormone which consists of two polypeptide chains, A- and B- chains which are linked together by disulfide bonds. The amino acid sequence of insulin varies across species and certain segments of the molecule are highly conserved. In most species, the A chain consists of 21 amino acids and the B chain consists of 30 amino acids. In mammals, insulin is synthesised in the pancreas within the beta cells whereas in certain species of fish, the insulin-producing tissue is uniquely located in separate structures called Brockmann bodies." [] is_a: CHEBI:16670 ! peptide [Term] id: CHEBI:15377 name: water def: "An oxygen hydride consisting of an oxygen atom that is covalently bonded to two hydrogen atoms." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:15422 name: ATP def: "An adenosine 5'-phosphate in which the 5'-phosphate is a triphosphate group. It is involved in the transportation of chemical energy during metabolic pathways." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:15956 name: biotin def: "An organic heterobicyclic compound that consists of 2-oxohexahydro-1H-thieno[3,4-d]imidazole having a valeric acid substituent attached to the tetrahydrothiophene ring. The parent of the class of biotins." [] is_a: OBI:0002744 ! molecular label [Term] id: CHEBI:16113 name: cholesterol def: "A cholestanoid consisting of cholestane having a double bond at the 5,6-position as well as a 3beta-hydroxy group." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:16134 name: ammonia def: "An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:16247 name: phospholipid def: "A lipid containing phosphoric acid as a mono- or di-ester. The term encompasses phosphatidic acids and phosphoglycerides." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:16301 name: nitrite def: "The nitrogen oxoanion formed by loss of a proton from nitrous acid." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:16526 name: carbon dioxide def: "A one-carbon compound with formula CO2 in which the carbon is attached to each oxygen atom by a double bond. A colourless, odourless gas under normal conditions, it is produced during respiration by all animals, fungi and microorganisms that depend directly or indirectly on living or decaying plants for food." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:16670 name: peptide def: "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." [] is_a: CHEBI:33839 ! macromolecule [Term] id: CHEBI:166899 name: globulin type def: "One of the major classifications of proteins, which may be further divided into the euglobulins and the pseudoglobulins. The former group is insoluble in water but soluble in saline solutions and may be precipitated in water that has been half-saturated with a salt such as ammonium sulfate. The latter group is soluble in water and has properties that resemble those of the true globulins. Globulins are an important source of protein in seed plants and are found in minute amounts in cereals. Globulins found in animal fluids are enzymes, antibodies, and fibrous and contractile proteins usually contained in the blood plasma." [] is_a: CHEBI:33839 ! macromolecule [Term] id: CHEBI:16737 name: creatinine def: "A lactam obtained by formal cyclocondensation of creatine. It is a metabolite of creatine." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:168396 name: mycophenolic acid def: "A member of the class of 2-benzofurans that is 2-benzofuran-1(3H)-one which is substituted at positions 4, 5, 6, and 7 by methyl, methoxy, (2E)-5-carboxy-3-methylpent-2-en-1-yl, and hydroxy groups, respectively. It is an antibiotic produced by Penicillium brevi-compactum, P. stoloniferum, P. echinulatum and related species. An immunosuppressant, it is widely used (partiularly as its sodium salt and as the 2-(morpholin-4-yl)ethyl ester prodrug, mycophenolate mofetil) to prevent tissue rejection following organ transplants and for the treatment of certain autoimmune diseases." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:16919 name: creatine def: "A glycine derivative having methyl and amidino groups attached to the nitrogen." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:16990 name: bilirubin IXalpha def: "A member of the class of biladienes that is a linear tetrapyrrole with the dipyrrole units being of both exovinyl and endovinyl type. A product of heme degradation, it is produced in the reticuloendothelial system by the reduction of biliverdin and transported to the liver as a complex with serum albumin." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:16991 name: deoxyribonucleic acid def: "High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms." [] is_a: CHEBI:33696 ! nucleic acid [Term] id: CHEBI:17026 name: progesterone def: "A C21-steroid hormone in which a pregnane skeleton carries oxo substituents at positions 3 and 20 and is unsaturated at C(4)-C(5). As a hormone, it is involved in the female menstrual cycle, pregnancy and embryogenesis of humans and other species." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:17137 name: hydrogensulfite is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:17230 name: homocysteine def: "A sulfur-containing amino acid consisting of a glycine core with a 2-mercaptoethyl side-chain." [] is_a: CHEBI:33709 ! amino acid [Term] id: CHEBI:17234 name: glucose def: "An aldohexose used as a source of energy and metabolic intermediate." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:17347 name: testosterone def: "An androstanoid having 17beta-hydroxy and 3-oxo groups, together with unsaturation at C-4-C-5.." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:17423 name: methemoglobin def: "A hemoprotein that is the ferric (Fe(3+)) form of hemoglobin." [] is_a: CHEBI:33839 ! macromolecule [Term] id: CHEBI:17544 name: hydrogencarbonate def: "The carbon oxoanion resulting from the removal of a proton from carbonic acid." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:17650 name: cortisol def: "A 17alpha-hydroxy-C21-steroid that is pregn-4-ene substituted by oxo groups at positions 3 and 20 and hydroxy groups at positions 11, 17 and 21. Cortisol is a corticosteroid hormone or glucocorticoid produced by zona fasciculata of the adrenal cortex, which is a part of the adrenal gland. It is usually referred to as the \"stress hormone\" as it is involved in response to stress and anxiety, controlled by corticotropin-releasing hormone (CRH). It increases blood pressure and blood sugar, and reduces immune responses" [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:17709 name: 5'-adenylyl sulfate def: "An adenosine 5'-phosphate having a sulfo group attached to one the phosphate OH groups." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:17855 name: triglyceride def: "Any glyceride resulting from the condensation of all three hydroxy groups of glycerol (propane-1,2,3-triol) with fatty acids." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:17996 name: chloride def: "A halide anion formed when chlorine picks up an electron to form an an anion." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:20067 name: 3-hydroxybutyric acid def: "A straight-chain 3-hydroxy monocarboxylic acid comprising a butyric acid core with a single hydroxy substituent in the 3- position; a ketone body whose levels are raised during ketosis, used as an energy source by the brain during fasting in humans. Also used to synthesise biodegradable plastics." [] is_a: CHEBI:35366 ! fatty acid [Term] id: CHEBI:22868 name: bile salt def: "A sodium salt of the conjugate of any bile acid with either glycine or taurine." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:23367 name: molecular entity def: "Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity." [] is_a: BFO:0000040 ! material entity [Term] id: CHEBI:23528 name: cytochalasin is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:23965 name: estradiol def: "A 3-hydroxy steroid that is estra-1,3,5(10)-triene substituted by hydroxy groups at positions 3 and 17." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:23995 name: N-ethyl-N-nitrosourea def: "A member of the class of N-nitrosoureas that is urea in which one of the nitrogens is substituted by ethyl and nitroso groups." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:24636 name: proton def: "Nuclear particle of charge number +1, spin 1/2 and rest mass of 1.007276470(12) u." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:24875 name: iron cation is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:25078 name: luciferin def: "A low-molecular-mass compound present in bioluminescent organisms that emits light when oxidized in presence of enzyme luciferase." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:2637 name: amikacin def: "An amino cyclitol glycoside that is kanamycin A acylated at the N-1 position by a 4-amino-2-hydroxybutyryl group." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:26710 name: sodium chloride def: "An inorganic chloride salt having sodium(1+) as the counterion." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:27226 name: uric acid def: "An oxopurine that is the final oxidation product of purine metabolism." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:27889 name: lead(0) is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:28001 name: vancomycin def: "A complex glycopeptide from Streptomyces orientalis. It inhibits a specific step in the synthesis of the peptidoglycan layer in the Gram-positive bacteria Staphylococcus aureus and Clostridium difficile." [] is_a: CHEBI:16670 ! peptide [Term] id: CHEBI:28358 name: rac-lactic acid def: "A racemate comprising equimolar amounts of (R)- and (S)-lactic acid." [] is_a: BFO:0000040 ! material entity [Term] id: CHEBI:28619 name: acrylamide def: "A member of the class of acrylamides that results from the formal condensation of acrylic acid with ammonia." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:28689 name: dehydroepiandrosterone def: "An androstanoid that is androst-5-ene substituted by a beta-hydroxy group at position 3 and an oxo group at position 17. It is a naturally occurring steroid hormone produced by the adrenal glands." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:28774 name: 3,3',5'-triiodothyronine is_a: CHEBI:33709 ! amino acid [Term] id: CHEBI:28864 name: tobramycin def: "A amino cyclitol glycoside that is kanamycin B lacking the 3-hydroxy substituent from the 2,6-diaminoglucose ring." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:29101 name: sodium(1+) def: "A monoatomic monocation obtained from sodium." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:29103 name: potassium(1+) def: "A monoatomic monocation obtained from potassium." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:29191 name: hydroxyl is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:29237 name: deuterium atom def: "The stable isotope of hydrogen with relative atomic mass 2.014102 and a natural abundance of 0.0115 atom percent (from Greek deltaepsilonupsilontauepsilonrhoomicronnu, second)." [] is_a: CHEBI:23367 ! molecular entity is_a: CHEBI:33250 ! atom [Term] id: CHEBI:30660 name: thyroxine def: "An iodothyronine compound having iodo substituents at the 3-, 3'-, 5- and 5'-positions." [] is_a: CHEBI:33709 ! amino acid [Term] id: CHEBI:30682 name: ruthenium atom is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:31624 name: fluorescein (lactone form) def: "A xanthene dye that is highly fluorescent, detectable even when present in minute quantities. Used forensically to detect traces of blood, in analytical chemistry as an indicator in silver nitrate titrations and in microscopy." [] is_a: OBI:0002744 ! molecular label [Term] id: CHEBI:31642 name: gadodiamide hydrate def: "The hydrate of gadodiamide." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:31643 name: gadoteridol def: "A non-ionic gadolinium chelate having a macrocyclic tetraamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI)." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:31991 name: phenol red def: "3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 4-hydroxyphenyl groups. A pH indicator changing colour from yellow below pH 6.8 to bright pink above pH 8.2, it is commonly used as an indicator in cell cultures and in home swimming pool test kits. It is also used in the (now infrequently performed) phenolsulfonphthalein (PSP) test for estimation of overall blood flow through the kidney." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:32142 name: sodium citrate dihydrate def: "The dihydrate of trisodium citrate." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:33250 name: atom def: "A chemical entity constituting the smallest component of an element having the chemical properties of the element." [] is_a: BFO:0000040 ! material entity [Term] id: CHEBI:33262 name: elemental oxygen is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:33321 name: rare earth metal atom is_a: CHEBI:33250 ! atom [Term] id: CHEBI:33359 name: rhodium atom def: "A cobalt group element atom of atomic number 45." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:33375 name: gadolinium atom is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:33376 name: terbium atom is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:33696 name: nucleic acid def: "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." [] is_a: CHEBI:33839 ! macromolecule [Term] id: CHEBI:33697 name: ribonucleic acid def: "High molecular weight, linear polymers, composed of nucleotides containing ribose and linked by phosphodiester bonds; RNA is central to the synthesis of proteins." [] is_a: CHEBI:33696 ! nucleic acid [Term] id: CHEBI:33709 name: amino acid def: "A carboxylic acid containing one or more amino groups." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:33839 name: macromolecule def: "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." [] synonym: "polymer" EXACT [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:35143 name: hemoglobin is_a: CHEBI:33839 ! macromolecule [Term] id: CHEBI:35366 name: fatty acid def: "Any aliphatic monocarboxylic acid derived from or contained in esterified form in an animal or vegetable fat, oil or wax. Natural fatty acids commonly have a chain of 4 to 28 carbons (usually unbranched and even-numbered), which may be saturated or unsaturated. By extension, the term is sometimes used to embrace all acyclic aliphatic carboxylic acids." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:35729 name: gadolinium molecular entity is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:35780 name: phosphate ion def: "A phosphorus oxoanion that is the conjugate base of phosphoric acid." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:37333 name: gadodiamide def: "A non-ionic gadolinium chelate having a macrocyclic triamine framework. It is used as a paramagnetic contrast agent in magnetic resonance imaging (MRI)." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:37445 name: folic acids def: "A group of heterocyclic compounds based on the pteroic acid skeleton conjugated with one or more L-glutamic acid units." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:37586 name: sodium phosphate is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:37972 name: phosphorus-32 atom def: "The radioactive isotope of phosphorus with relative atomic mass 31.973907 and half-life of 14.26 days." [] is_a: CHEBI:33250 ! atom is_a: OBI:0001879 ! reagent [Term] id: CHEBI:37973 name: phosphorus-33 atom def: "The radioactive isotope of phosphorus with relative atomic mass 32.971725, half-life of 25.34 days and nuclear spin (1)/2." [] is_a: CHEBI:33250 ! atom is_a: OBI:0001879 ! reagent [Term] id: CHEBI:37987 name: Cy3 dye is_a: OBI:0002744 ! molecular label [Term] id: CHEBI:37989 name: Cy5 dye is_a: OBI:0002744 ! molecular label [Term] id: CHEBI:39025 name: high-density lipoprotein def: "A class of lipoproteins of small size (4-13 nm) and dense (greater than 1.063 g/ml) particles. They are synthesized in the liver without a lipid core, accumulate cholesterol esters from peripheral tissues and transport them to the liver for re-utilization or elimination from the body (the reverse cholesterol transport)." [] is_a: CHEBI:6495 ! lipoprotein [Term] id: CHEBI:39026 name: low-density lipoprotein def: "A class of lipoproteins of small size (18-25 nm) and low density (1.019-1.063 g/ml) particles with a core composed mainly of cholesterol esters and smaller amounts of triglycerides. The surface monolayer consists mostly of phospholipids, a single copy of apolipoprotein B-100, and free cholesterol molecules. The main function of LDL is to transport cholesterol and cholesterol esters from the liver. Excessive levels are associated with cardiovascular disease." [] is_a: CHEBI:6495 ! lipoprotein [Term] id: CHEBI:39027 name: very-low-density lipoprotein def: "A class of lipoproteins of large size (30-80 nm), very low density (0.93-1.006 g/ml) particles with a core composed mainly of triglycerides and a surface monolayer of phospholipids and cholesterol into which are imbedded the apolipoproteins B, E, and C. VLDL facilitate the transport of endogenously made triglycerides to extrahepatic tissues." [] is_a: CHEBI:6495 ! lipoprotein [Term] id: CHEBI:39123 name: calcium cation is_a: CHEBI:39124 ! calcium ion [Term] id: CHEBI:39124 name: calcium ion is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:39127 name: magnesium cation def: "Any magnesium ion that is positively charged." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:39867 name: valproic acid def: "A branched-chain saturated fatty acid that comprises of a propyl substituent on a pentanoic acid stem." [] is_a: CHEBI:35366 ! fatty acid [Term] id: CHEBI:42098 name: digoxigenin def: "A hydroxy steroid that consists of 5beta-cardanolide having a double bond at the 20(22)-position as well as hydroxy groups at the 3beta-, 12beta- and 14beta-positions. It has been isolated from the plant species of the genus Digitalis." [] is_a: OBI:0002744 ! molecular label [Term] id: CHEBI:42191 name: ethylenediaminetetraacetic acid is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:4551 name: digoxin def: "A cardenolide glycoside that is digitoxin beta-hydroxylated at C-12. A cardiac glycoside extracted from the foxglove plant, Digitalis lanata, it is used to control ventricular rate in atrial fibrillation and in the management of congestive heart failure with atrial fibrillation, but the margin between toxic and therapeutic doses is small." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:4705 name: double-stranded DNA is_a: CHEBI:16991 ! deoxyribonucleic acid [Term] id: CHEBI:472552 name: 5-bromo-2'-deoxyuridine def: "A pyrimidine 2'-deoxyribonucleoside compound having 5-bromouracil as the nucleobase." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:47774 name: low-density lipoprotein cholesterol def: "Cholesterol esters and free cholesterol which are contained in or bound to low-density lipoproteins (LDL)." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:47775 name: high-density lipoprotein cholesterol def: "Cholesterol esters and free cholesterol which are contained in or bound to high-density lipoproteins (HDL)." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:50076 name: chromium-51 def: "A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:51756 name: Alexa Fluor 532 is_a: OBI:0002744 ! molecular label [Term] id: CHEBI:51760 name: Alexa Fluor 546 is_a: OBI:0002744 ! molecular label [Term] id: CHEBI:52673 name: Alexa Fluor 555 def: "A fluorescent dye of absorption wavelength 555 nm and emission wavelength 565 nm, derived from a 3,6-diaminoxanthene-4,5-disulfate." [] is_a: OBI:0002744 ! molecular label [Term] id: CHEBI:53526 name: tritiated thymidine def: "Thymidine linked to the radioisotope tritium. Used to label DNA in the study of cellular and viral DNA synthesis." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:59050 name: dimethyl sulfate def: "The dimethyl ester of sulfuric acid." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:59051 name: diethyl pyrocarbonate def: "The diethyl ester of dicarbonic acid." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:59052 name: 1,1-dihydroxy-3-ethoxy-2-butanone def: "A butanone derivative having two hydroxy substituents at the 1-position and an ethoxy substituent at the 3-position." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:59053 name: N-cyclohexyl-N'-(2-(4-morpholinyl)ethyl)carbodiimide def: "A carbodiimide having cyclcohexyl and 2-(4-morpholinyl)ethyl as the two N-substituents." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:59054 name: N-methylisatoic anhydride def: "A 3,1-benzoxazin-1,4-dione having an N-methyl substituent." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:59055 name: (S)-1-(4-bromoacetamidobenzyl)EDTA def: "A tetracarboxylic acid consisting of ethylenediaminetetraacetic acid having a 4-bromoacetamidobenzyl group at the C1-position and (S)-configuration." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:59056 name: EDTA methidiumpropylamide def: "A combined intercalating and chelating reagent. The iron chelate, prepared by adding Fe(NH4)2(SO4)2, effects random oxidative cleavage of DNA in the presence of O2 and a reducing agent. This activity is useful as a footprinting probe." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:59424 name: bromophenol blue def: "3H-2,1-Benzoxathiole 1,1-dioxide in which both of the hydrogens at position 3 have been substituted by 3,5-dibromo-4-hydroxyphenyl groups. It is used as a laboratory indicator, changing from yellow below pH 3 to purple at pH 4.6, and as a size marker for monitoring the progress of agarose gel and polyacrylamide gel electrophoresis. It has also been used as an industrial dye." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:61057 name: tacrolimus hydrate def: "A hydrate that is the monohydrate form of tacrolimus." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:61073 name: oxygen radical def: "An inorganic radical in which a free electron resides on one or more oxygen atoms of an oxygen species." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:6495 name: lipoprotein def: "A clathrate complex consisting of a lipid enwrapped in a protein host without covalent binding in such a way that the complex has a hydrophilic outer surface consisting of all the protein and the polar ends of any phospholipids." [] is_a: CHEBI:33839 ! macromolecule [Term] id: CHEBI:81567 name: thyroid stimulating hormone is_a: CHEBI:33839 ! macromolecule [Term] id: CHEBI:81568 name: Luteinizing hormone is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:81569 name: Follicle stimulating hormone is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:86319 name: 25-hydroxyvitamin D2 def: "A hydroxycalciol that is vitamin D2 in which the hydrogen at position 25 has been replaced by a hydroxy group." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHEBI:9754 name: tris def: "A primary amino compound that is tert-butylamine in which one hydrogen attached to each methyl group is replaced by a hydroxy group. A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC." [] is_a: CHEBI:23367 ! molecular entity [Term] id: CHMO:0000087 name: fluorescence microscopy assay def: "Any type of light microscopy assay where the specimen can be made to fluoresce (emit energy as visible light) by illuminating it with light of specific wavelengths. These specimens are called fluorophores." [] synonym: "fluorescence imaging" EXACT [] synonym: "fluorescence microscopic imaging" EXACT [] synonym: "FM" EXACT [] is_a: CHMO:0000102 ! light microscopy assay is_a: OBI:0001501 ! fluorescence detection assay [Term] id: CHMO:0000089 name: confocal fluorescence microscopy assay def: "Microscopy where the specimen can be made to fluoresce (emit energy as visible light) by scanning a gas (Ar or Kr) laser spot of specific wavelength over its surface and using a spatial pinhole to eliminate out-of-focus fluorescence." [] synonym: "CLSM" EXACT [] synonym: "confocal fluorescence imaging" EXACT [] synonym: "confocal laser scanning fluorescence microscopy" EXACT [] synonym: "confocal laser scanning microscopy" EXACT [] synonym: "confocal-laser scanning microscopy" EXACT [] synonym: "fluorescence confocal microscopy" EXACT [] synonym: "fluorescence confocal scanning laser microscopy" EXACT [] synonym: "LSCM" EXACT [] synonym: "scanning confocal fluorescence microscopy" EXACT [] is_a: OBI:0002119 ! microscopy assay [Term] id: CHMO:0000102 name: light microscopy assay def: "Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image." [] synonym: "light microscopy" EXACT [] synonym: "OM" EXACT [] synonym: "optical microscopy" EXACT [] is_a: OBI:0002119 ! microscopy assay [Term] id: CHMO:0000701 name: liquid chromatography-tandem mass spectrometry def: "A method where a sample mixture is first separated by liquid chromatography before being ionised and characterised by mass-to-charge ratio and relative abundance using two mass spectrometers in series." [] synonym: "LC-MS-MS" EXACT [] synonym: "LC-MS/MS" EXACT [] synonym: "LC-MS2" EXACT [] synonym: "LC-MSMS" EXACT [] synonym: "LC/MS/MS" EXACT [] synonym: "LCMSMS" EXACT [] synonym: "liquid chromatography tandem mass spectrometry" EXACT [] synonym: "liquid chromatography tandem mass spectroscopy" EXACT [] synonym: "liquid chromatography-tandem mass spectroscopy" EXACT [] is_a: OBI:0003097 ! liquid chromatography mass spectrometry assay is_a: OBI:0003540 ! tandem mass spectrometry assay [Term] id: CL:0000000 name: cell def: "A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane." [] is_a: BFO:0000040 ! material entity [Term] id: CL:0000001 name: primary cultured cell def: "A cultured cell that is freshly isolated from a organismal source, or derives in culture from such a cell prior to the culture being passaged." [] is_a: CL:0000010 ! cultured cell [Term] id: CL:0000003 name: native cell def: "A cell that is found in a natural setting, which includes multicellular organism cells 'in vivo' (i.e. part of an organism), and unicellular organisms 'in environment' (i.e. part of a natural environment)." [] is_a: CL:0000000 ! cell [Term] id: CL:0000010 name: cultured cell def: "A cell in vitro that is or has been maintained or propagated as part of a cell culture." [] is_a: CL:0000578 ! experimentally modified cell in vitro [Term] id: CL:0000057 name: fibroblast def: "A connective tissue cell which secretes an extracellular matrix rich in collagen and other macromolecules. Flattened and irregular in outline with branching processes; appear fusiform or spindle-shaped." [] is_a: CL:0000000 ! cell [Term] id: CL:0000066 name: epithelial cell def: "A cell that is usually found in a two-dimensional sheet with a free surface. The cell has a cytoskeleton that allows for tight cell to cell contact and for cell polarity where apical part is directed towards the lumen and the basal part to the basal lamina." [] is_a: CL:0000000 ! cell [Term] id: CL:0000077 name: mesothelial cell def: "A flattened epithelial cell of mesenchymal origin that lines the serous cavity." [] is_a: CL:0000003 ! native cell is_a: CL:0000066 ! epithelial cell [Term] id: CL:0000084 name: T cell def: "A type of lymphocyte whose defining characteristic is the expression of a T cell receptor complex." [] is_a: CL:0000542 ! lymphocyte [Term] id: CL:0000097 name: mast cell def: "A cell that is found in almost all tissues containing numerous basophilic granules and capable of releasing large amounts of histamine and heparin upon activation. Progenitors leave bone marrow and mature in connective and mucosal tissue. Mature mast cells are found in all tissues, except the bloodstream. Their phenotype is CD117-high, CD123-negative, CD193-positive, CD200R3-positive, and FceRI-high. Stem-cell factor (KIT-ligand; SCF) is the main controlling signal of their survival and development." [] is_a: CL:0000000 ! cell [Term] id: CL:0000182 name: hepatocyte def: "The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated." [] is_a: CL:0000066 ! epithelial cell [Term] id: CL:0000232 name: erythrocyte def: "A red blood cell. In mammals, mature erythrocytes are biconcave disks containing hemoglobin whose function is to transport oxygen." [] is_a: CL:0000000 ! cell [Term] id: CL:0000233 name: platelet def: "A non-nucleated disk-shaped cell formed by extrusion from megakaryocytes, found in the blood of all mammals, and mainly involved in blood coagulation." [] is_a: CL:0000003 ! native cell [Term] id: CL:0000235 name: macrophage def: "A mononuclear phagocyte present in variety of tissues, typically differentiated from monocytes, capable of phagocytosing a variety of extracellular particulate material, including immune complexes, microorganisms, and dead cells." [] is_a: CL:0000000 ! cell [Term] id: CL:0000236 name: B cell def: "A lymphocyte of B lineage that is capable of B cell mediated immunity." [] is_a: CL:0000542 ! lymphocyte [Term] id: CL:0000451 name: dendritic cell def: "A cell of hematopoietic origin, typically resident in particular tissues, specialized in the uptake, processing, and transport of antigens to lymph nodes for the purpose of stimulating an immune response via T cell activation. These cells are lineage negative (CD3-negative, CD19-negative, CD34-negative, and CD56-negative)." [] is_a: CL:0000000 ! cell [Term] id: CL:0000540 name: neuron def: "The basic cellular unit of nervous tissue. Each neuron consists of a body, an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [] is_a: CL:0002319 ! neural cell [Term] id: CL:0000542 name: lymphocyte def: "A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin." [] is_a: CL:0000842 ! mononuclear cell [Term] id: CL:0000556 name: megakaryocyte def: "A giant cell 50 to 100 micron in diameter, with a greatly lobulated nucleus, found in the bone marrow; mature blood platelets are released from its cytoplasm." [] is_a: CL:0000003 ! native cell [Term] id: CL:0000558 name: reticulocyte def: "An immature erythrocyte that changes the protein composition of its plasma membrane by exosome formation and extrusion. The types of protein removed differ between species though removal of the transferrin receptor is apparent in mammals and birds." [] is_a: CL:0000000 ! cell [Term] id: CL:0000560 name: band form neutrophil def: "A late neutrophilic metamyelocyte in which the nucleus is indented to more than half the distance to the farthest nuclear margin but in no area being condensed to a single filament. The nucleus is in the form of a curved or coiled band, not having acquired the typical multilobar shape of the mature neutrophil. These cells are fMLP receptor-positive, CD11b-positive, CD35-negative, and CD49d-negative." [] is_a: CL:0000775 ! neutrophil [Term] id: CL:0000562 name: nucleate erythrocyte def: "An erythrocyte having a nucleus." [] is_a: CL:0000003 ! native cell is_a: CL:0000232 ! erythrocyte [Term] id: CL:0000576 name: monocyte def: "Myeloid mononuclear recirculating leukocyte that can act as a precursor of tissue macrophages, osteoclasts and some populations of tissue dendritic cells." [] is_a: CL:0000003 ! native cell is_a: CL:0000738 ! leukocyte is_a: CL:0000842 ! mononuclear cell [Term] id: CL:0000578 name: experimentally modified cell in vitro def: "A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure." [] is_a: CL:0000000 ! cell is_a: OBI:0000047 ! processed material [Term] id: CL:0000624 name: CD4-positive, alpha-beta T cell def: "A mature alpha-beta T cell that expresses an alpha-beta T cell receptor and the CD4 coreceptor." [] is_a: CL:0000789 ! alpha-beta T cell [Term] id: CL:0000625 name: CD8-positive, alpha-beta T cell def: "A T cell expressing an alpha-beta T cell receptor and the CD8 coreceptor." [] is_a: CL:0000789 ! alpha-beta T cell [Term] id: CL:0000738 name: leukocyte def: "An achromatic cell of the myeloid or lymphoid lineages capable of ameboid movement, found in blood or other tissue." [] is_a: CL:0000000 ! cell [Term] id: CL:0000767 name: basophil def: "Any of the immature or mature forms of a granular leukocyte that in its mature form has an irregularly shaped, pale-staining nucleus that is partially constricted into two lobes, and with cytoplasm that contains coarse, bluish-black granules of variable size. Basophils contain vasoactive amines such as histamine and serotonin, which are released on appropriate stimulation. A basophil is CD123-positive, CD193-positive, CD203c-positive, and FceRIa-positive." [] is_a: CL:0000000 ! cell [Term] id: CL:0000771 name: eosinophil def: "Any of the immature or mature forms of a granular leukocyte with a nucleus that usually has two lobes connected by one or more slender threads of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and which can be stained by the dye eosin. Eosinophils are CD9-positive, CD191-positive, and CD193-positive." [] is_a: CL:0000003 ! native cell is_a: CL:0000738 ! leukocyte [Term] id: CL:0000775 name: neutrophil def: "Any of the immature or mature forms of a granular leukocyte that in its mature form has a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes." [] is_a: CL:0000003 ! native cell is_a: CL:0000738 ! leukocyte [Term] id: CL:0000776 name: immature neutrophil def: "Any of the immature forms of a neutrophil in which neutrophilic specific granules are present but other phenotypic features of the mature form may be lacking." [] is_a: CL:0000775 ! neutrophil [Term] id: CL:0000786 name: plasma cell def: "A terminally differentiated, post-mitotic, antibody secreting cell of the B cell lineage with the phenotype CD138-positive, surface immunonoglobulin-negative, and MHC Class II-negative. Plasma cells are oval or round with extensive rough endoplasmic reticulum, a well-developed Golgi apparatus, and a round nucleus having a characteristic cartwheel heterochromatin pattern and are devoted to producing large amounts of immunoglobulin." [] is_a: CL:0000236 ! B cell [Term] id: CL:0000789 name: alpha-beta T cell def: "A T cell that expresses an alpha-beta T cell receptor complex." [] is_a: CL:0000084 ! T cell [Term] id: CL:0000794 name: CD8-positive, alpha-beta cytotoxic T cell def: "A CD8-positive, alpha-beta T cell that is capable of killing target cells in an antigen specific manner with the phenotype perforin-positive and granzyme B-positive." [] is_a: CL:0000625 ! CD8-positive, alpha-beta T cell [Term] id: CL:0000814 name: mature NK T cell def: "A mature alpha-beta T cell of a distinct lineage that bears natural killer markers and a T cell receptor specific for a limited set of ligands. NK T cells have activation and regulatory roles particularly early in an immune response." [] is_a: CL:0000789 ! alpha-beta T cell [Term] id: CL:0000836 name: promyelocyte def: "A precursor in the granulocytic series, being a cell intermediate in development between a myeloblast and myelocyte, that has distinct nucleoli, a nuclear-to-cytoplasmic ratio of 5:1 to 3:1, and containing a few primary cytoplasmic granules. Markers for this cell are fucosyltransferase FUT4-positive, CD33-positive, integrin alpha-M-negative, low affinity immunoglobulin gamma Fc region receptor III-negative, and CD24-negative." [] is_a: CL:0000003 ! native cell [Term] id: CL:0000842 name: mononuclear cell def: "A leukocyte with a single non-segmented nucleus in the mature form." [] is_a: CL:0000000 ! cell [Term] id: CL:0001064 name: malignant cell def: "A neoplastic cell that is capable of entering a surrounding tissue" [] is_a: CL:0000000 ! cell [Term] id: CL:0002192 name: metamyelocyte def: "A eosinophil precursor in the granulocytic series, being a cell intermediate in development between a myelocyte and a band form cell. The nucleus becomes indented where the indentation is smaller than half the distance to the farthest nuclear margin; chromatin becomes coarse and clumped; specific granules predominate while primary granules are rare." [] is_a: CL:0000003 ! native cell [Term] id: CL:0002193 name: myelocyte def: "A cell type that is the first of the maturation stages of the granulocytic leukocytes normally found in the bone marrow. Granules are seen in the cytoplasm. The nuclear material of the myelocyte is denser than that of the myeloblast but lacks a definable membrane. The cell is flat and contains increasing numbers of granules as maturation progresses." [] is_a: CL:0000003 ! native cell [Term] id: CL:0002319 name: neural cell def: "A cell that is part of the nervous system." [] is_a: CL:0000000 ! cell [Term] id: CL:0011114 name: segmented neutrophil of bone marrow def: "A segmented neutrophilic cell of the bone marrow reserve pool that expresses CD11b (integrin alpha-M) and high levels of CD16 (low affinity immunoglobulin gamma Fc region receptor III) on its cell surface." [] is_a: CL:0000775 ! neutrophil [Term] id: CL:2000001 name: peripheral blood mononuclear cell def: "A leukocyte with a single non-segmented nucleus in the mature form found in the circulatory pool of blood." [] is_a: CL:0000003 ! native cell is_a: CL:0000842 ! mononuclear cell [Term] id: CLO:0000001 name: cell line cell is_a: OBI:0001866 ! secondary cultured cell [Term] id: CLO:0000018 name: 非永生细胞系细胞 is_a: CLO:0000001 ! cell line cell [Term] id: CLO:0000019 name: 永生细胞系细胞 is_a: CLO:0000001 ! cell line cell [Term] id: CLO:0000031 name: 细胞系 is_a: OBI:0001905 ! secondary cultured cell population [Term] id: CLO:0009828 name: immortal cell line def: "A cell line that is expected to be capable of indefinite propagation in an vitro culture." [] is_a: CLO:0000031 ! 细胞系 [Term] id: CLO:0009829 name: mortal cell line def: "A cell line is able to support only a limited number of passages in vitro." [] is_a: CLO:0000031 ! 细胞系 [Term] id: COB:0000080 name: complex of molecular entities def: "A complex of two or more molecular entities that are not covalently bound." [] is_a: BFO:0000040 ! material entity [Term] id: ENVO:00001998 name: soil def: "Soil is an environmental material which is primarily composed of minerals, varying proportions of sand, silt, and clay, organic material such as humus, gases, liquids, and a broad range of resident micro- and macroorganisms." [] is_a: BFO:0000040 ! material entity [Term] id: ENVO:00002257 name: podzol def: "Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics." [] is_a: ENVO:00001998 ! soil [Term] id: ENVO:00010483 name: environmental material def: "A portion of environmental material is a fiat object part which forms the medium or part of the medium of an environmental system." [] is_a: BFO:0000040 ! material entity [Term] id: GAZ:00000448 name: geographic location def: "A reference to a place on the Earth, by its name or by its geographical location." [] is_a: BFO:0000029 ! site [Term] id: GO:0000785 name: chromatin def: "The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome." [] is_a: GO:0005575 ! cellular_component [Term] id: GO:0001046 name: core promoter sequence-specific DNA binding def: "Binding to a sequence of DNA that is part of a core promoter region. The core promoter is composed of the transcription start site and binding sites for the RNA polymerase and the basal transcription machinery. The transcribed region might be described as a gene, cistron, or operon." [] is_a: GO:0003674 ! molecular_function is_a: GO:0043565 ! sequence-specific DNA binding [Term] id: GO:0001047 is_a: OBI:0001588 ! binding [Term] id: GO:0001172 name: RNA-templated transcription def: "The synthesis of an RNA transcript from an RNA template." [] is_a: GO:0009987 ! cellular process [Term] id: GO:0001508 name: action potential def: "A process in which membrane potential cycles through a depolarizing spike, triggered in response to depolarization above some threshold, followed by repolarization. This cycle is driven by the flow of ions through various voltage gated channels with different thresholds and ion specificities." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0001788 name: antibody-dependent cellular cytotoxicity def: "Cytolysis of target cells by natural killer cells, eosinophils, neutrophils, monocytes, or macrophages following engagement of antibodies bound to the target cells by Fc receptors on the effector cells." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0001806 name: type IV hypersensitivity def: "An inflammatory response driven by T cell recognition of processed soluble or cell-associated antigens leading to cytokine release and leukocyte activation." [] is_a: GO:0002524 ! hypersensitivity [Term] id: GO:0001816 name: cytokine production def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0001906 name: cell killing def: "Any process in an organism that results in the killing of its own cells or those of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0001913 name: T cell mediated cytotoxicity def: "The directed killing of a target cell by a T cell through the release of granules containing cytotoxic mediators or through the engagement of death receptors." [] is_a: GO:0001906 ! cell killing [Term] id: GO:0002250 name: adaptive immune response def: "An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory)." [] is_a: GO:0006955 ! immune response [Term] id: GO:0002367 name: cytokine production involved in immune response def: "The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus contributing to an immune response, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0002390 is_a: GO:0001816 ! cytokine production [Term] id: GO:0002507 name: tolerance induction def: "A process that directly activates any of the steps required for tolerance, a physiologic state in which the immune system does not react destructively against the components of an organism that harbors it or against antigens that are introduced to it." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0002514 name: B cell tolerance induction def: "A process involving any mechanism for tolerance induction in B cells." [] is_a: GO:0002507 ! tolerance induction [Term] id: GO:0002517 name: T cell tolerance induction def: "A process involving any mechanism for tolerance induction in T cells." [] is_a: GO:0002507 ! tolerance induction [Term] id: GO:0002524 name: hypersensitivity def: "An inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0002534 name: cytokine production involved in inflammatory response def: "The synthesis or release of a cytokine following a inflammatory stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0003094 name: glomerular filtration def: "The process in which plasma is filtered through the glomerular membrane which consists of capillary endothelial cells, the basement membrane, and epithelial cells. The glomerular filtrate is the same as plasma except it has no significant amount of protein." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0003674 name: molecular_function def: "A molecular process that can be carried out by the action of a single macromolecular machine, usually via direct physical interactions with other molecular entities. Function in this sense denotes an action, or activity, that a gene product (or a complex) performs. These actions are described from two distinct but related perspectives: (1) biochemical activity, and (2) role as a component in a larger system/process." [] is_a: BFO:0000015 ! process [Term] id: GO:0003823 name: antigen binding def: "Binding to an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen." [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0003824 name: catalytic activity def: "Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic." [] is_a: GO:0003674 ! molecular_function [Term] id: GO:0003939 name: L-iditol 2-dehydrogenase activity def: "Catalysis of the reaction: L-iditol + NAD+ = L-sorbose + NADH + H+." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0003964 name: RNA-directed DNA polymerase activity def: "Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0003990 name: acetylcholinesterase activity def: "Catalysis of the reaction: acetylcholine + H2O = choline + acetate." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0003997 name: acyl-CoA oxidase activity def: "Catalysis of the reaction: acyl-CoA + O2 = trans-2,3-dehydroacyl-CoA + hydrogen peroxide." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0004021 name: L-alanine:2-oxoglutarate aminotransferase activity def: "Catalysis of the reaction: 2-oxoglutarate + L-alanine = L-glutamate + pyruvate." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0004035 name: alkaline phosphatase activity def: "Catalysis of the reaction: an orthophosphoric monoester + H2O = an alcohol + phosphate, with an alkaline pH optimum." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0004069 name: L-aspartate:2-oxoglutarate aminotransferase activity def: "Catalysis of the reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0004104 name: cholinesterase activity def: "Catalysis of the reaction: an acylcholine + H2O = choline + a carboxylic acid anion." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0004111 name: creatine kinase activity def: "Catalysis of the reaction: ATP + creatine = N-phosphocreatine + ADP + 2 H(+)." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0004353 name: glutamate dehydrogenase [NAD(P)+] activity def: "Catalysis of the reaction: L-glutamate + H2O + NAD(P)+ = 2-oxoglutarate + NH3 + NAD(P)H + H+." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0004364 name: glutathione transferase activity def: "Catalysis of the reaction: R-X + glutathione = H-X + R-S-glutathione. R may be an aliphatic, aromatic or heterocyclic group; X may be a sulfate, nitrile or halide group." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0004448 name: isocitrate dehydrogenase [NAD(P)+] activity def: "Catalysis of the reaction: isocitrate + NAD(P)+ = 2-oxoglutarate + CO2 + NAD(P)H." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0004457 name: lactate dehydrogenase activity def: "Catalysis of the reaction: lactate + NAD+ = H+ + NADH + pyruvate." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0004540 name: ribonuclease activity def: "Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0005216 name: ion channel activity def: "Enables the facilitated diffusion of an ion (by an energy-independent process) by passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism. May be either selective (it enables passage of a specific ion only) or non-selective (it enables passage of two or more ions of same charge but different size)." [] is_a: GO:0009987 ! cellular process [Term] id: GO:0005575 name: cellular_component def: "A location, relative to cellular compartments and structures, occupied by a macromolecular machine when it carries out a molecular function. There are two ways in which the gene ontology describes locations of gene products: (1) relative to cellular structures (e.g., cytoplasmic side of plasma membrane) or compartments (e.g., mitochondrion), and (2) the stable macromolecular complexes of which they are parts (e.g., the ribosome)." [] is_a: BFO:0000040 ! material entity [Term] id: GO:0005577 name: fibrinogen complex def: "A highly soluble, elongated protein complex found in blood plasma and involved in clot formation. It is converted into fibrin monomer by the action of thrombin. In the mouse, fibrinogen is a hexamer, 46 nm long and 9 nm maximal diameter, containing two sets of nonidentical chains (alpha, beta, and gamma) linked together by disulfide bonds." [] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0005694 name: chromosome def: "A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information." [] is_a: GO:0005575 ! cellular_component [Term] id: GO:0005739 name: mitochondrion def: "A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration." [] is_a: GO:0043227 ! membrane-bounded organelle [Term] id: GO:0006006 name: glucose metabolic process def: "The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0006260 name: DNA replication def: "The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0006306 name: DNA methylation def: "The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0006338 name: chromatin remodeling def: "A dynamic process of chromatin reorganization resulting in changes to chromatin structure. These changes allow DNA metabolic processes such as transcriptional regulation, DNA recombination, DNA repair, and DNA replication." [] is_a: GO:0009987 ! cellular process [Term] id: GO:0006909 name: phagocytosis def: "A vesicle-mediated transport process that results in the engulfment of external particulate material by phagocytes and their delivery to the lysosome. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0006955 name: immune response def: "Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat." [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0006974 name: cellular response to DNA damage stimulus def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism." [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0007049 name: cell cycle def: "The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0007596 name: blood coagulation def: "The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0008150 name: biological_process def: "A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence." [] is_a: BFO:0000015 ! process disjoint_from: OBI:0000011 ! planned process [Term] id: GO:0008228 name: opsonization def: "The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody." [] is_a: GO:0006909 ! phagocytosis [Term] id: GO:0008253 name: 5'-nucleotidase activity def: "Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0008283 name: cell population proliferation def: "The multiplication or reproduction of cells, resulting in the expansion of a cell population." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0009566 name: fertilization def: "The union of gametes of opposite sexes during the process of sexual reproduction to form a zygote. It involves the fusion of the gametic nuclei (karyogamy) and cytoplasm (plasmogamy)." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0009987 name: cellular process def: "Any process that is carried out at the cellular level, but not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0010467 name: gene expression def: "The process in which a gene's sequence is converted into a mature gene product (protein or RNA). This includes the production of an RNA transcript and its processing, translation and maturation for protein-coding genes." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0010573 name: vascular endothelial growth factor production def: "The appearance of vascular endothelial growth factor production due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0015925 name: galactosidase activity def: "Catalysis of the hydrolysis of galactosyl compounds, substances containing a group derived from a cyclic form of galactose or a galactose derivative." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016064 name: immunoglobulin mediated immune response def: "An immune response mediated by immunoglobulins, whether cell-bound or in solution." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0016160 name: amylase activity def: "Catalysis of the hydrolysis of amylose or an amylose derivative." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016231 name: beta-N-acetylglucosaminidase activity def: "Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-glucosamine residues in N-acetyl-beta-D-glucosaminides." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016570 name: histone modification def: "The covalent alteration of one or more amino acid residues within a histone protein." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0016788 name: hydrolase activity, acting on ester bonds def: "Catalysis of the hydrolysis of any ester bond." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0019814 name: immunoglobulin complex def: "A protein complex that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains, held together by disulfide bonds and sometimes complexed with additional proteins. An immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0019815 name: B cell receptor complex def: "An immunoglobulin complex that is present in the plasma membrane of B cells and that in its canonical form is composed of two identical immunoglobulin heavy chains and two identical immunoglobulin light chains and a signaling subunit, a heterodimer of the Ig-alpha and Ig-beta proteins." [] is_a: OBI:1110022 ! adaptive immune receptor [Term] id: GO:0019882 name: antigen processing and presentation def: "The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0019904 name: protein domain specific binding def: "Binding to a specific domain of a protein." [] is_a: OBI:0001588 ! binding [Term] id: GO:0030041 name: actin filament polymerization def: "Assembly of actin filaments by the addition of actin monomers to a filament." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0030097 name: hemopoiesis def: "The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0032601 name: connective tissue growth factor production def: "The appearance of connective tissue growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032602 name: chemokine production def: "The appearance of a chemokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. All chemokines possess a number of conserved cysteine residues involved in intramolecular disulfide bond formation. Some chemokines are considered pro-inflammatory and can be induced during an immune response to recruit cells of the immune system to a site of infection, while others are considered homeostatic and are involved in controlling the migration of cells during normal processes of tissue maintenance or development. Chemokines are found in all vertebrates, some viruses and some bacteria." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032604 name: granulocyte macrophage colony-stimulating factor production def: "The appearance of granulocyte macrophage colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032605 name: hepatocyte growth factor production def: "The appearance of hepatocyte growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032606 name: type I interferon production def: "The appearance of type I interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032607 name: interferon-alpha production def: "The appearance of interferon-alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032606 ! type I interferon production [Term] id: GO:0032608 name: interferon-beta production def: "The appearance of interferon-beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032609 name: interferon-gamma production def: "The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032610 name: interleukin-1 alpha production def: "The appearance of interleukin-1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032612 ! interleukin-1 production [Term] id: GO:0032611 name: interleukin-1 beta production def: "The appearance of interleukin-1 beta due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032612 ! interleukin-1 production [Term] id: GO:0032612 name: interleukin-1 production def: "The appearance of interleukin-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032613 name: interleukin-10 production def: "The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032614 name: interleukin-11 production def: "The appearance of interleukin-11 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032615 name: interleukin-12 production def: "The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032616 name: interleukin-13 production def: "The appearance of interleukin-13 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032617 name: obsolete interleukin-14 production def: "OBSOLETE. The appearance of interleukin-14 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032618 name: interleukin-15 production def: "The appearance of interleukin-15 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032619 name: interleukin-16 production def: "The appearance of interleukin-16 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032620 name: interleukin-17 production def: "The appearance of any member of the interleukin-17 family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032621 name: interleukin-18 production def: "The appearance of interleukin-18 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032622 name: interleukin-19 production def: "The appearance of interleukin-19 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032623 name: interleukin-2 production def: "The appearance of interleukin-2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032624 name: interleukin-20 production def: "The appearance of interleukin-20 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032625 name: interleukin-21 production def: "The appearance of interleukin-21 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032626 name: interleukin-22 production def: "The appearance of interleukin-22 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032627 name: interleukin-23 production def: "The appearance of interleukin-23 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032628 name: interleukin-24 production def: "The appearance of interleukin-24 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032629 name: interleukin-25 production def: "The appearance of interleukin-25 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032630 name: interleukin-26 production def: "The appearance of interleukin-26 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032631 name: interleukin-27 production def: "The appearance of interleukin-27 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032632 name: interleukin-3 production def: "The appearance of interleukin-3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032633 name: interleukin-4 production def: "The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032634 name: interleukin-5 production def: "The appearance of interleukin-5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032635 name: interleukin-6 production def: "The appearance of interleukin-6 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032636 name: interleukin-7 production def: "The appearance of interleukin-7 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032637 name: interleukin-8 production def: "The appearance of interleukin-8 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032638 name: interleukin-9 production def: "The appearance of interleukin-9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032639 name: TRAIL production def: "The appearance of TRAIL due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032640 name: tumor necrosis factor production def: "The appearance of tumor necrosis factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Tumor necrosis factor is an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis." [] synonym: "TNF alpha production" EXACT [] is_a: GO:0071706 ! tumor necrosis factor superfamily cytokine production [Term] id: GO:0032641 name: lymphotoxin A production def: "The chemical reactions and pathways resulting in the formation of the cytokine lymphotoxin A." [] synonym: "TNF beta production" EXACT [] is_a: GO:0071706 ! tumor necrosis factor superfamily cytokine production [Term] id: GO:0032905 name: transforming growth factor beta1 production def: "The appearance of transforming growth factor-beta1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032906 name: transforming growth factor beta2 production def: "The appearance of transforming growth factor-beta2 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032907 name: transforming growth factor beta3 production def: "The appearance of transforming growth factor-beta3 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0032991 name: protein-containing complex def: "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." [] synonym: "protein complex" EXACT [] is_a: BFO:0000040 ! material entity [Term] id: GO:0033036 name: macromolecule localization def: "Any process in which a macromolecule is transported to, or maintained in, a specific location." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0034061 name: DNA polymerase activity def: "Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and a 3'hydroxyl group." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0034343 name: type III interferon production def: "The appearance of type III interferon due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon lambda is the only member of the type III interferon found so far." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0035393 name: chemokine (C-X-C motif) ligand 9 production def: "The appearance of chemokine (C-X-C motif) ligand 9 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0035397 name: helper T cell enhancement of adaptive immune response def: "Positive regulation of an adaptive immune response mediated via cytokine production by helper T cell." [] is_a: GO:0002250 ! adaptive immune response [Term] id: GO:0035398 name: helper T cell enhancement of T cell mediated immune response def: "Positive regulation of a T cell mediated immune response mediated via cytokine production by a helper T cell." [] is_a: GO:0035397 ! helper T cell enhancement of adaptive immune response [Term] id: GO:0035399 name: helper T cell enhancement of B cell mediated immune response def: "Positive regulation of a B cell mediated immune response mediated via cytokine production by a helper T cell." [] is_a: GO:0035397 ! helper T cell enhancement of adaptive immune response [Term] id: GO:0035746 name: granzyme A production def: "The appearance of granzyme A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0035944 name: perforin production def: "The appearance of a perforin protein due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0036262 name: granulysin production def: "The appearance of granulysin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0036392 name: chemokine (C-C motif) ligand 20 production def: "The appearance of chemokine (C-C motif) ligand 20 (CCL20) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0042098 name: T cell proliferation def: "The expansion of a T cell population by cell division. Follows T cell activation." [] is_a: GO:0008283 ! cell population proliferation [Term] id: GO:0042101 name: T cell receptor complex def: "A protein complex that contains a disulfide-linked heterodimer of T cell receptor (TCR) chains, which are members of the immunoglobulin superfamily, and mediates antigen recognition, ultimately resulting in T cell activation. The TCR heterodimer is associated with the CD3 complex, which consists of the nonpolymorphic polypeptides gamma, delta, epsilon, zeta, and, in some cases, eta (an RNA splice variant of zeta) or Fc epsilon chains." [] is_a: OBI:1110022 ! adaptive immune receptor [Term] id: GO:0042110 name: T cell activation def: "The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0042571 name: immunoglobulin complex, circulating def: "An immunoglobulin complex that is secreted into extracellular space and found in mucosal areas or other tissues or circulating in the blood or lymph. In its canonical form, a circulating immunoglobulin complex is composed of two identical heavy chains and two identical light chains, held together by disulfide bonds. Some forms of are polymers of the basic structure and contain additional components such as J-chain and the secretory component." [] synonym: "antibody" EXACT [] is_a: GO:0019814 ! immunoglobulin complex is_a: OBI:1110022 ! adaptive immune receptor [Term] id: GO:0042575 name: DNA polymerase complex def: "A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA." [] is_a: GO:0032991 ! protein-containing complex is_a: OBI:0000427 ! enzyme [Term] id: GO:0042605 name: peptide antigen binding def: "Binding to an antigen peptide." [] is_a: GO:0003823 ! antigen binding [Term] id: GO:0042611 name: MHC protein complex def: "A transmembrane protein complex composed of an MHC alpha chain and, in most cases, either an MHC class II beta chain or an invariant beta2-microglobin chain, and with or without a bound peptide, lipid, or polysaccharide antigen." [] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0043227 name: membrane-bounded organelle def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [] is_a: GO:0005575 ! cellular_component [Term] id: GO:0043316 name: cytotoxic T cell degranulation def: "The regulated exocytosis of secretory granules containing preformed mediators such as perforin and granzymes by a cytotoxic T cell." [] is_a: GO:0001906 ! cell killing [Term] id: GO:0043565 name: sequence-specific DNA binding def: "Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding." [] is_a: OBI:0001588 ! binding [Term] id: GO:0044030 name: regulation of DNA methylation def: "Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0044807 name: macrophage migration inhibitory factor production def: "The appearance of macrophage migration inhibitory factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0044808 name: oncostatin M production def: "The appearance of oncostatin M due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0044809 name: chemokine (C-C motif) ligand 17 production def: "The appearance of chemokine (C-C motif) ligand 17 (CCL17) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0047823 name: D-glutamyltransferase activity def: "Catalysis of the reaction: L(or D)-glutamine + D-glutamyl-peptide = NH3 + 5-glutamyl-D-glutamyl-peptide." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0048869 name: cellular developmental process def: "A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0050896 name: response to stimulus def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0051276 name: chromosome organization def: "A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0052689 name: carboxylic ester hydrolase activity def: "Catalysis of the hydrolysis of a carboxylic ester bond." [] is_a: GO:0003824 ! catalytic activity [Term] id: GO:0070288 name: ferritin complex def: "A protein complex that binds iron and acts as a major iron storage system. Intracellular and extracellular ferritin complexes have different ratios of two types of ferritin monomer, the L (light) chain and H (heavy) chain." [] is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0070358 name: actin polymerization-dependent cell motility def: "A process involved in the controlled movement of a bacterial cell powered by the continuous polymerization of actin at one pole of the cell." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0071604 name: transforming growth factor beta production def: "The appearance of any member of the transforming growth factor-beta family of cytokines due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Transforming growth factor-beta family members include TGF-B1, TGF-B2, and TGF-B3." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0071605 name: monocyte chemotactic protein-1 production def: "The appearance of monocyte chemotactic protein-1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0071606 name: chemokine (C-C motif) ligand 4 production def: "The appearance of chemokine (C-C motif) ligand 4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0071607 name: macrophage inflammatory protein-1 gamma production def: "The appearance of macrophage inflammatory protein-1 gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0071608 name: macrophage inflammatory protein-1 alpha production def: "The appearance of macrophage inflammatory protein 1 alpha due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0071609 name: chemokine (C-C motif) ligand 5 production def: "The appearance of chemokine (C-C motif) ligand 5 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0071610 name: chemokine (C-C motif) ligand 1 production def: "The appearance of chemokine (C-C motif) ligand 1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0071611 name: granulocyte colony-stimulating factor production def: "The appearance of granulocyte colony-stimulating factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0071612 name: IP-10 production def: "The appearance of IP-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0071613 name: granzyme B production def: "The appearance of granzyme B due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0008150 ! biological_process [Term] id: GO:0071706 name: tumor necrosis factor superfamily cytokine production def: "The appearance of any member of the TNF superfamily due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0071735 name: IgG immunoglobulin complex def: "A protein complex composed of two identical immunoglobulin heavy chains of an IgG isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgG immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [] is_a: GO:0019814 ! immunoglobulin complex [Term] id: GO:0071742 name: IgE immunoglobulin complex def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgE isotype and two identical immunoglobulin light chains, held together by disulfide bonds. An IgE immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [] is_a: GO:0019814 ! immunoglobulin complex [Term] id: GO:0071745 name: IgA immunoglobulin complex def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgA isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and sometimes complexed with J chain or J chain and secretory component. An IgA immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [] is_a: GO:0019814 ! immunoglobulin complex [Term] id: GO:0071753 name: IgM immunoglobulin complex def: "A protein complex composed of two identical immunoglobulin heavy chains of the IgM isotype and two identical immunoglobulin light chains, held together by disulfide bonds, and in its circulating form complexed with J chain in polymeric forms. An IgM immunoglobulin complex may be embedded in the plasma membrane or present in the extracellular space, in mucosal areas or other tissues, or circulating in the blood or lymph." [] is_a: GO:0019814 ! immunoglobulin complex [Term] id: GO:0071924 name: chemokine (C-C motif) ligand 22 production def: "The appearance of chemokine (C-C motif) ligand 22 (CCL22) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0072535 name: tumor necrosis factor (ligand) superfamily member 11 production def: "The appearance of tumor necrosis factor superfamily member 11 (TNFSF11; RANKL) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0071706 ! tumor necrosis factor superfamily cytokine production [Term] id: GO:0097087 name: interleukin-17A production def: "The appearance of interleukin-17A due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032620 ! interleukin-17 production [Term] id: GO:0097088 name: interleukin-17F production def: "The appearance of interleukin-17F due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032620 ! interleukin-17 production [Term] id: GO:0097278 name: complement-dependent cytotoxicity def: "Cell killing caused by the membrane attack complex formed following complement activation." [] is_a: GO:0001906 ! cell killing [Term] id: GO:0097280 name: histamine secretion mediated by immunoglobulin def: "Histamine release triggered by the binding of an antigen to an immunoglobulin bound to the cell surface." [] is_a: GO:0006955 ! immune response [Term] id: GO:0097281 name: immune complex formation def: "The process that gives rise to an immune complex. Immune complexes are clusters of antibodies bound to antigen, to which complement may also be fixed, and which may precipitate or remain in solution. Examples are the clumping of cells such as bacteria or red blood cells in the presence of an antibody, precipitation of a toxin after an antibody binds to it, and clumping of viral particles as a result of antibody binding to the virus." [] is_a: GO:0016064 ! immunoglobulin mediated immune response [Term] id: GO:0097282 name: immunoglobulin-mediated neutralization def: "The inhibition of an antigen's biological effects by antibody binding to it. An example is neutralization of diphtheria toxin by preventing its entry into human cells via the binding of antibody specific for diphtheria toxin." [] is_a: GO:0016064 ! immunoglobulin mediated immune response [Term] id: GO:0097388 name: chemokine (C-C motif) ligand 19 production def: "The appearance of chemokine (C-C motif) ligand 19 (CCL19) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0097389 name: chemokine (C-C motif) ligand 21 production def: "The appearance of chemokine (C-C motif) ligand 21 (CCL21) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0097390 name: chemokine (C-X-C motif) ligand 12 production def: "The appearance of chemokine (C-X-C motif) ligand 12 (CXCL12) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0097391 name: chemokine (C-X-C motif) ligand 13 production def: "The appearance of chemokine (C-X-C motif) ligand 13 (CXCL13) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0097392 name: chemokine (C-X-C motif) ligand 16 production def: "The appearance of chemokine (C-X-C motif) ligand 16 (CXCL16) due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0032602 ! chemokine production [Term] id: GO:0140730 name: amphiregulin production def: "The appearance of amphiregulin due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Amphiregulin (AREG) is a ligand of the epidermal growth factor receptor (EGFR), a widely expressed transmembrane tyrosine kinase. AREG is synthesized as a membrane-anchored precursor protein that can engage in juxtacrine signaling on adjacent cells. Alternatively, after proteolytic processing by cell membrane proteases, mainly TACE/ADAM17, AREG is secreted and behaves as an autocrine or paracrine factor." [] is_a: GO:0001816 ! cytokine production [Term] id: GO:0140779 name: XCL1 production def: "The appearance of XCL1 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels." [] is_a: GO:0001816 ! cytokine production [Term] id: HP:0000855 name: Insulin resistance def: "Increased resistance towards insulin, that is, diminished effectiveness of insulin in reducing blood glucose levels." [] is_a: BFO:0000016 ! disposition [Term] id: HP:0002664 name: Neoplasm def: "An organ or organ-system abnormality that consists of uncontrolled autonomous cell-proliferation which can occur in any part of the body as a benign or malignant neoplasm (tumor)." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: IAO:0000001 name: conditional specification def: "A directive information entity that specifies what should happen if the trigger condition is fulfilled." [] is_a: IAO:0000033 ! directive information entity [Term] id: IAO:0000003 name: measurement unit label def: "A measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure." [] is_a: IAO:0000009 ! datum label [Term] id: IAO:0000005 name: objective specification def: "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." [] synonym: "goal specification" EXACT [] is_a: IAO:0000033 ! directive information entity [Term] id: IAO:0000006 name: narrative object def: "A narrative object is an information content entity that is a set of propositions." [] is_a: IAO:0000030 ! information content entity [Term] id: IAO:0000007 name: action specification def: "A directive information entity that describes an action the bearer will take." [] is_a: IAO:0000033 ! directive information entity [Term] id: IAO:0000008 name: obsolete_artifact is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000009 name: datum label def: "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" [] is_a: IAO:0000030 ! information content entity [Term] id: IAO:0000010 name: software def: "Software is a plan specification composed of a series of instructions that can be \ninterpreted by or directly executed by a processing unit." [] is_a: IAO:0000104 ! plan specification [Term] id: IAO:0000012 name: obsolete2_digital entity def: "A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000013 name: journal article def: "A report that is published in a journal." [] is_a: IAO:0000088 ! report [Term] id: IAO:0000015 name: information carrier def: "A quality of an information bearer that imparts the information content" [] is_a: BFO:0000019 ! quality [Term] id: IAO:0000017 name: model number def: "A model number is an information content entity specifically borne by catalogs, design specifications, advertising materials, inventory systems and similar that is about manufactured objects of the same class. The model number is an alternative term for the class. The manufactered objects may or may not also bear the model number. Model numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots." [] is_a: IAO:0000028 ! symbol [Term] id: IAO:0000018 name: obsolete_material_entity is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000019 name: obsolete2_binary digital entity def: "A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000024 name: obsolete_unit of measure def: "a unit of measure is the quality of some material entity compared to which another quality is some multiple of." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000025 name: programming language def: "A language in which source code is written that is intended to be executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it." [] is_a: IAO:0000104 ! plan specification [Term] id: IAO:0000027 name: data item def: "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." [] synonym: "data" EXACT [] is_a: IAO:0000030 ! information content entity [Term] id: IAO:0000028 name: symbol def: "An information content entity that is a mark(s) or character(s) used as a conventional representation of another entity." [] is_a: IAO:0000030 ! information content entity [Term] id: IAO:0000029 name: numeral def: "A symbol that denotes a number." [] is_a: IAO:0000028 ! symbol [Term] id: IAO:0000030 name: information content entity def: "A generically dependent continuant that is about some thing." [] is_a: BFO:0000031 ! generically dependent continuant [Term] id: IAO:0000031 name: integer numeral def: "A numeral that denotes an integer" [] is_a: IAO:0000029 ! numeral [Term] id: IAO:0000032 name: scalar measurement datum def: "A scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label." [] is_a: IAO:0000109 ! measurement datum [Term] id: IAO:0000033 name: directive information entity def: "An information content entity whose concretizations indicate to their bearer how to realize them in a process." [] is_a: IAO:0000030 ! information content entity [Term] id: IAO:0000034 name: time trigger is_a: IAO:0000001 ! conditional specification [Term] id: IAO:0000035 name: obsolete_study interpretation def: "A study interpretation is a textual entity about the implications of a study result. Examples include discussion of whether a hypothesis is false, whether the study failed to address the hypothesis, and whether the study results have led to new hypotheses" [] synonym: "conclusion" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000037 name: dot plot def: "A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions." [] is_a: IAO:0000038 ! graph [Term] id: IAO:0000038 name: graph def: "A diagram that presents one or more tuples of information by mapping those tuples in to a two dimensional space in a non arbitrary way." [] is_a: IAO:0000309 ! diagram [Term] id: IAO:0000047 name: obsolete2_text based digital entity def: "A text based digital entity is a digital entity that is encoded so that it only contains text characters." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000055 name: rule def: "A rule is an executable which guides, defines, restricts actions." [] is_a: IAO:0000001 ! conditional specification [Term] id: IAO:0000057 name: contour plot is_a: IAO:0000038 ! graph [Term] id: IAO:0000059 name: obsolete2_report figure def: "A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000064 name: algorithm def: "A plan specification which describes the inputs and output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata." [] is_a: IAO:0000104 ! plan specification [Term] id: IAO:0000065 name: software interpreter def: "A software interpreter is a software application that executes some specified input software." [] is_a: IAO:0000064 ! algorithm [Term] id: IAO:0000078 name: curation status specification def: "The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] is_a: IAO:0000102 ! data about an ontology part [Term] id: IAO:0000079 name: density plot def: "A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel." [] is_a: IAO:0000038 ! graph [Term] id: IAO:0000088 name: report def: "A document assembled by an author for the purpose of providing information for the audience. A report is the output of a documenting process and has the objective to be consumed by a specific audience. Topic of the report is on something that has completed. A report is not a single figure. Examples of reports are journal article, patent application, grant progress report, case report (not patient record)." [] is_a: IAO:0000310 ! document [Term] id: IAO:0000091 name: obsolete_report element def: "A report element is a narrative object in which information is presented and consumed by a human being, and is part of a report. Examples of report elements are figure (dot plot), table, text portion (may include a movie or audio clip on a web page)." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000093 name: obsolete2_binary executable def: "Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000096 name: source code module def: "A source code module is a directive information entity that specifies, using a programming language, some algorithm." [] is_a: IAO:0000033 ! directive information entity [Term] id: IAO:0000097 name: obsolete_report table def: "A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000098 name: data format specification def: "A data format specification is the information content borne by the document published defining the specification.\nExample: The ISO document specifying what encompasses an XML document; The instructions in a XSD file" [] is_a: IAO:0000033 ! directive information entity [Term] id: IAO:0000100 name: data set def: "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." [] is_a: IAO:0000027 ! data item [Term] id: IAO:0000101 name: image def: "An image is an affine projection to a two dimensional surface, of measurements of some quality of an entity or entities repeated at regular intervals across a spatial range, where the measurements are represented as color and luminosity on the projected on surface." [] is_a: IAO:0000308 ! figure [Term] id: IAO:0000102 name: data about an ontology part def: "Data about an ontology part is a data item about a part of an ontology, for example a term" [] is_a: IAO:0000027 ! data item [Term] id: IAO:0000104 name: plan specification def: "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." [] comment: 2/3/2009 Comment from OBI review.\n\nAction specification not well enough specified.\nConditional specification not well enough specified.\nQuestion whether all plan specifications have objective specifications.\n\nRequest that IAO either clarify these or change definitions not to use them is_a: IAO:0000033 ! directive information entity [Term] id: IAO:0000105 name: obsolete2_digital document def: "A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000109 name: measurement datum def: "A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device." [] is_a: IAO:0000027 ! data item [Term] id: IAO:0000128 name: obsolete_identifier is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000129 name: version number def: "A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name." [] is_a: IAO:0000028 ! symbol [Term] id: IAO:0000131 name: serial number def: "A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots." [] is_a: IAO:0000028 ! symbol [Term] id: IAO:0000132 name: lot number def: "A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots." [] synonym: "batch number" EXACT [] is_a: IAO:0000028 ! symbol [Term] id: IAO:0000140 name: setting datum def: "A settings datum is a datum that denotes some configuration of an instrument." [] is_a: IAO:0000027 ! data item [Term] id: IAO:0000141 name: obsolete_digital quality is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000144 name: conclusion textual entity def: "A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers." [] is_a: IAO:0000300 ! textual entity is_a: OBI:0001909 ! conclusion based on data [Term] id: IAO:0000178 name: material information bearer def: "A material entity in which a concretization of an information content entity inheres." [] is_a: BFO:0000040 ! material entity [Term] id: IAO:0000179 name: histogram def: "A histogram is a report graph which is a statistical description of a\ndistribution in terms of occurrence frequencies of different event classes." [] is_a: IAO:0000038 ! graph [Term] id: IAO:0000180 name: heatmap def: "A heatmap is a report graph which is a graphical representation of data\nwhere the values taken by a variable(s) are shown as colors in a\ntwo-dimensional map." [] is_a: IAO:0000038 ! graph [Term] id: IAO:0000181 name: Venn diagram def: "A Venn diagram is a report graph showing all hypothetically possible\nlogical relations between a finite collection of sets." [] is_a: IAO:0000038 ! graph [Term] id: IAO:0000182 name: obsolete_survival curve def: "A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000183 name: dendrogram def: "A dendrogram is a report graph which is a tree diagram\nfrequently used to illustrate the arrangement of the clusters produced by a\nclustering algorithm." [] is_a: IAO:0000038 ! graph [Term] id: IAO:0000184 name: scatter plot def: "A scatterplot is a graph which uses Cartesian coordinates to display values for two variables for a set of data. The data is displayed as a collection of points, each having the value of one variable determining the position on the horizontal axis and the value of the other variable determining the position on the vertical axis." [] synonym: "scattergraph" EXACT [] is_a: IAO:0000038 ! graph [Term] id: IAO:0000185 name: photograph def: "A photograph is created by projecting an image onto a photosensitive surface such as a chemically treated plate or film, CCD receptor, etc." [] is_a: IAO:0000101 ! image [Term] id: IAO:0000186 name: photographic print def: "A photographic print is a material entity upon which a photograph generically depends." [] is_a: IAO:0000178 ! material information bearer [Term] id: IAO:0000225 name: obsolescence reason specification def: "The reason for which a term has been deprecated. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value." [] is_a: IAO:0000102 ! data about an ontology part [Term] id: IAO:0000300 name: textual entity def: "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." [] synonym: "text" EXACT [] is_a: IAO:0000030 ! information content entity [Term] id: IAO:0000301 name: citation def: "A textual entity intended to identify a particular publication." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000302 name: author identification def: "A textual entity intended to identify a particular author" [] is_a: IAO:0000590 ! written name [Term] id: IAO:0000303 name: institutional identification def: "A textual entity intended to identify a particular institution" [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000304 name: caption def: "A textual entity that describes a figure" [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000305 name: document title def: "A textual entity that names a document" [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000306 name: table def: "A textual entity that contains a two-dimensional arrangement of texts repeated at regular intervals across a spatial range, such that the spatial relationships among the constituent texts expresses propositions" [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000307 name: table of abbreviations def: "A table where the constituent texts are abbreviations and their expansions" [] is_a: IAO:0000306 ! table [Term] id: IAO:0000308 name: figure def: "An information content entity consisting of a two dimensional arrangement of information content entities such that the arrangement itself is about something." [] is_a: IAO:0000030 ! information content entity [Term] id: IAO:0000309 name: diagram def: "A figure that expresses one or more propositions" [] is_a: IAO:0000308 ! figure [Term] id: IAO:0000310 name: document def: "A collection of information content entities intended to be understood together as a whole" [] is_a: IAO:0000030 ! information content entity [Term] id: IAO:0000311 name: publication def: "A document that has been accepted by a publisher" [] is_a: IAO:0000310 ! document [Term] id: IAO:0000312 name: publication about an investigation def: "A publication that is about an investigation" [] synonym: "scientific publication" EXACT [] is_a: IAO:0000311 ! publication [Term] id: IAO:0000313 name: patent def: "A document that has been accepted by a patent authority" [] is_a: IAO:0000310 ! document [Term] id: IAO:0000314 name: document part def: "An information content entity that is part of a document." [] is_a: IAO:0000030 ! information content entity [Term] id: IAO:0000315 name: abstract def: "A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes." [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000316 name: introduction to a publication about an investigation def: "A part of a publication about an investigation that is about the objective specification (why the investigation is being done)" [] synonym: "background" EXACT [] synonym: "introduction" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000317 name: methods section def: "A part of a publication about an investigation that is about the study design of the investigation" [] synonym: "experimental" EXACT [] synonym: "experimental procedures" EXACT [] synonym: "experimental section" EXACT [] synonym: "methods" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000318 name: results section def: "A part of a publication about an investigation that is about a study design execution" [] synonym: "results" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000319 name: discussion section of a publication about an investigation def: "A part of a publication about an investigation that is about the study interpretation of the investigation" [] synonym: "discussion" EXACT [] synonym: "discussion section" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000320 name: references section def: "A part of a document that has citations as parts" [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000321 name: author list def: "A part of a document that enumerates the authors of the document" [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000322 name: institution list def: "A part of a document that has parts that are institution identifications associated with the authors of the document" [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000323 name: author contributions section def: "A part of a publication that is about the specific contributions of each author" [] synonym: "author contributions" EXACT [] synonym: "contributions by the authors" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000324 name: acknowledgements section def: "Part of a publication that is about the contributions of people or institutions other than the authors." [] synonym: "acknowledgements" EXACT [] synonym: "acknowledgments" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000325 name: footnote def: "A part of a document that is about a specific other part of the document. Usually footnotes are spatially segregated from the rest of the document." [] synonym: "endnote" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000326 name: supplementary material to a document def: "A part of a document that is segregated from the rest of the document due to its size" [] synonym: "additional information" EXACT [] synonym: "appendix" EXACT [] synonym: "supplemental information" EXACT [] synonym: "supplementary material" EXACT [] synonym: "supporting information" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000327 name: table of contents def: "A table that relates document parts to specific locations in a document (usually page numbers). This is also a document part (subsumption there should be inferred)." [] is_a: IAO:0000306 ! table [Term] id: IAO:0000328 name: table of figures def: "A table that relates figures in a document to specific locations in that document (usually page numbers). This is also a document part (subsumption there should be inferred)." [] is_a: IAO:0000306 ! table [Term] id: IAO:0000329 name: running title def: "A shorter version of a document title" [] is_a: IAO:0000305 ! document title [Term] id: IAO:0000330 name: copyright section def: "A document part that describes legal restrictions on making or distributing copies of the document" [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000400 name: cartesian spatial coordinate datum def: "A cartesian spatial coordinate datum is a representation of a point in a spatial region, in which equal changes in the magnitude of a coordinate value denote length qualities with the same magnitude" [] is_a: IAO:0000027 ! data item [Term] id: IAO:0000401 name: one dimensional cartesian spatial coordinate datum def: "A cartesion spatial coordinate datum that uses one value to specify a position along a one dimensional spatial region" [] is_a: IAO:0000400 ! cartesian spatial coordinate datum [Term] id: IAO:0000402 name: two dimensional cartesian spatial coordinate datum def: "A cartesion spatial coordinate datum that uses two values to specify a position within a two dimensional spatial region" [] is_a: IAO:0000400 ! cartesian spatial coordinate datum [Term] id: IAO:0000403 name: three dimensional cartesian spatial coordinate datum def: "A cartesion spatial coordinate datum that uses three values to specify a position within a three dimensional spatial region" [] is_a: IAO:0000400 ! cartesian spatial coordinate datum [Term] id: IAO:0000408 name: length measurement datum def: "A scalar measurement datum that is the result of measurement of length quality" [] is_a: IAO:0000032 ! scalar measurement datum [Term] id: IAO:0000409 name: denotator type def: "A denotator type indicates how a term should be interpreted from an ontological perspective." [] is_a: IAO:0000102 ! data about an ontology part [Term] id: IAO:0000414 name: mass measurement datum def: "A scalar measurement datum that is the result of measurement of mass quality" [] is_a: IAO:0000032 ! scalar measurement datum [Term] id: IAO:0000415 name: hypothesis textual entity def: "A textual entity that expresses an assertion that is intended to be tested." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000416 name: time measurement datum def: "A scalar measurement datum that is the result of measuring a temporal interval" [] is_a: IAO:0000032 ! scalar measurement datum [Term] id: IAO:0000422 name: postal address def: "A textual entity that is used as directive to deliver something to a person, or organization" [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000429 name: email address is_a: IAO:0000030 ! information content entity [Term] id: IAO:0000442 name: author role def: "A role inhering in a person or organization that is realized when the bearer participates in the work which is the basis of the document, in the writing of the document, and signs it with their name." [] is_a: BFO:0000023 ! role [Term] id: IAO:0000443 name: data item extraction from journal article def: "A planned process in which journal articles are read or processed and data items are extracted, typically for further analysis or indexing" [] is_a: OBI:0000011 ! planned process [Term] id: IAO:0000572 name: documenting def: "A planned process in which a document is created or added to by including the specified input in it." [] is_a: OBI:0000011 ! planned process [Term] id: IAO:0000573 name: line graph def: "A line graph is a type of graph created by connecting a series of data\npoints together with a line." [] synonym: "line chart" EXACT [] is_a: IAO:0000038 ! graph [Term] id: IAO:0000574 name: assigning a centrally registered identifier def: "A planned process in which a new CRID is created, associated with an entity, and stored in the CRID registry thereby registering it as being associated with some entity" [] synonym: "assigning a CRID" EXACT [] is_a: OBI:0000011 ! planned process [Term] id: IAO:0000575 name: associating information with a centrally registered identifier in its registry def: "A planned process in which a CRID registry associates an information content entity with a CRID symbol" [] synonym: "associating information with a CRID in the CRID registry" EXACT [] is_a: OBI:0000011 ! planned process [Term] id: IAO:0000576 name: obsolete_establishing a CRID registry def: "a planned process with the objective to establish a system that allows to refer to specific entities of a certain kind and store information about them, by establishing a CRID registry and plan specifications for the process of 1) assigning a CRID and 2) looking up a CRID." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: IAO:0000577 name: centrally registered identifier symbol def: "A symbol that is part of a CRID and that is sufficient to look up a record from the CRID's registry." [] synonym: "CRID symbol" EXACT [] is_a: IAO:0000028 ! symbol [Term] id: IAO:0000578 name: centrally registered identifier def: "An information content entity that consists of a CRID symbol and additional information about the CRID registry to which it belongs." [] synonym: "CRID" EXACT [] is_a: IAO:0000030 ! information content entity [Term] id: IAO:0000579 name: centrally registered identifier registry def: "A CRID registry is a dataset of CRID records, each consisting of a CRID symbol and additional information which was recorded in the dataset through a assigning a centrally registered identifier process." [] synonym: "CRID registry" EXACT [] is_a: IAO:0000100 ! data set [Term] id: IAO:0000580 name: looking up a centrally registered identifier def: "A planned process in which a request to a CRID registry is made to return the information associated with a CRID symbol" [] synonym: "looking up a CRID" EXACT [] is_a: OBI:0000011 ! planned process [Term] id: IAO:0000582 name: time stamped measurement datum is_a: IAO:0000109 ! measurement datum [Term] id: IAO:0000584 name: time sampled measurement data set def: "A data set that is an aggregate of data recording some measurement at a number of time points. The time series data set is an ordered list of pairs of time measurement data and the corresponding measurement data acquired at that time." [] synonym: "experimental time series" EXACT [] is_a: IAO:0000100 ! data set [Term] id: IAO:0000590 name: written name def: "A textual entity that denotes a particular in reality." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000591 name: software method def: "A software method (also called subroutine, subprogram, procedure, method, function, or routine) is software designed to execute a specific task." [] is_a: IAO:0000010 ! software [Term] id: IAO:0000592 name: software module def: "A software module is software composed of a collection of software methods." [] is_a: IAO:0000010 ! software [Term] id: IAO:0000593 name: software library def: "A software library is software composed of a collection of software modules and/or software methods in a form that can be statically or dynamically linked to some software application." [] is_a: IAO:0000010 ! software [Term] id: IAO:0000594 name: software application def: "A software application is software that can be directly executed by some processing unit." [] is_a: IAO:0000010 ! software [Term] id: IAO:0000595 name: software script def: "A software script is software whose instructions can be executed using a software interpreter." [] is_a: IAO:0000010 ! software [Term] id: IAO:0000605 name: abbreviation textual entity def: "A textual entity listing abbreviations and their expansions that are used in a document." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000606 name: abbreviations section def: "A part of a document where abbreviations and their long-forms used within the document are listed." [] synonym: "abbreviations" EXACT [] synonym: "abbreviations list" EXACT [] synonym: "abbreviations used" EXACT [] synonym: "list of abbreviations" EXACT [] synonym: "list of abbreviations used" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000607 name: author information section def: "A part of a document about the authors that provides biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document." [] synonym: "author information" EXACT [] synonym: "authors’ information" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000608 name: author information textual entity def: "A textual entity expression information about an author of a document. This information may include biographical information and may discuss how the authors' professional experiences are relevant to the work described in the document." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000609 name: author summary section def: "A part of a document, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers." [] synonym: "author summary" EXACT [] synonym: "summary" EXACT [] synonym: "synopsis" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000610 name: author summary textual entity def: "A textual entity, distinct from the abstract, that describes the significance and broader context of the document content. The author summary is often written in a non-technical manner and is aimed at both scientists and non-scientist readers, e.g as described in the article submission guidelines for PLoS Genetics (http://journals.plos.org/plosgenetics/s/submission-guidelines)." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000611 name: availability section def: "A part of a document about a resource described in the document, e.g. software, that describes where and/or how that resource can be obtained." [] synonym: "availability" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000612 name: availability textual entity def: "A textual entity expressing the location of a resource, e.g. software, or the manner in which a resource can be obtained." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000613 name: case report section def: "A part of a document about the medical history of a specific patient as it relates to the topic of the document." [] synonym: "case presentation" EXACT [] synonym: "case report" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000614 name: case report textual entity def: "A textual entity that expresses a detailed account of a portion of the medical history for a specific patient." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000615 name: conclusion section def: "A part of a document used to summarize the findings discussed in the document. The conclusion section is typically found near the end of a document." [] synonym: "concluding remarks" EXACT [] synonym: "conclusion" EXACT [] synonym: "conclusions" EXACT [] synonym: "findings" EXACT [] synonym: "summary" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000616 name: conflict of interest section def: "A part of a document used to declare any competing interests regarding the authors and/or funding organization for the work described in the document." [] synonym: "competing interests" EXACT [] synonym: "conflict of interest" EXACT [] synonym: "conflict of interest statement" EXACT [] synonym: "declaration of competing interests" EXACT [] synonym: "disclosure of potential conflicts of interest" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000617 name: conflict of interest textual entity def: "A textual entity that expresses a situation involving one or more of the authors, or the funding source of a document whereby the authors or funding source stand to potentially gain (typically financially) from the results reported in the document." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000618 name: consent section def: "A part of a document about the consent process that was used to enroll patients in a study." [] synonym: "consent" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000619 name: consent textual entity def: "A textual entity that documents the consenting process used to enroll patients in a study." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000620 name: ethical approval section def: "A part of a document about the governance body responsible for approving the work discussed in a document on an ethical basis." [] synonym: "ethical approval" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000621 name: ethical approval textual entity def: "A textual entity that documents the ethical approval of some study design." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000622 name: figures section def: "A part of a document that contains one or more figures." [] synonym: "figures" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000623 name: funding source declaration section def: "A part of a document used to detail information regarding the source of funding used in support of the generation of the document content." [] synonym: "funding" EXACT [] synonym: "funding information" EXACT [] synonym: "funding sources" EXACT [] synonym: "funding statement" EXACT [] synonym: "funding/support" EXACT [] synonym: "source of funding" EXACT [] synonym: "sources of funding" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000624 name: funding source declaration textual entity def: "A textual entity documenting the source of funding that supported some study." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000625 name: future directions section def: "A part of a document detailing extensions of the described work that may be implemented at some future point in time." [] synonym: "future challenges" EXACT [] synonym: "future considerations" EXACT [] synonym: "future developments" EXACT [] synonym: "future directions" EXACT [] synonym: "future outlook" EXACT [] synonym: "future perspectives" EXACT [] synonym: "future plans" EXACT [] synonym: "future prospects" EXACT [] synonym: "future research" EXACT [] synonym: "future research directions" EXACT [] synonym: "future studies" EXACT [] synonym: "future work" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000626 name: future directions textual entity def: "A textual entity expressing ideas regarding future work relevant to work described in a document that could be done." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000627 name: genome announcement section def: "A document part announcing the publication of a novel draft genome sequence." [] synonym: "genome announcement" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000628 name: genome announcement textual entity def: "A textual entity that describes the generation and public release of a novel, draft genome sequence." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000629 name: keyword textual entity def: "A textual entity listing keywords indicating the major theme(s) of a document." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000630 name: keywords section def: "A part of a document where keywords selected by the author to categorize the major theme(s) of a document are listed." [] synonym: "keywords" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000631 name: study limitations section def: "A part of a document about biases or short comings related to the study design and execution." [] synonym: "limitations" EXACT [] synonym: "study limitations" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000632 name: study limitations textual entity def: "A textual entity addressing a shortcoming or bias of a study design or execution." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000633 name: materials section def: "A part of a document about the materials required to reproduce the content of the document." [] synonym: "materials" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000634 name: notes section def: "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." [] synonym: "footnotes" EXACT [] synonym: "notes" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000635 name: patients section def: "A part of a document about the patients that participated in a study." [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000636 name: patients textual entity def: "A textual entity expressing information regarding the patients used in a study." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000637 name: pre-publication history section def: "A part of the document about the publication history of a document. This section typically details dates of document submission to a journal and dates of any re-submissions as well as reviewer comments and responses to reviewers by the authors." [] synonym: "notice of republication" EXACT [] synonym: "pre-publication history" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000638 name: pre-publication history textual entity def: "A textual entity that expresses the pre-publication history (submission dates, reviewer comments, etc) for a document, often including a hyperlink to a web page detailing the information." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000639 name: related work section def: "A part of a document about work in other publications that is relevant to the content of the document." [] synonym: "related literature" EXACT [] synonym: "related work" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000640 name: related work textual entity def: "A textual entity that discusses work from other publications and expresses their relevancy to the content of a document." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000641 name: requirements section def: "A part of a document about a resource described in the document, e.g. software, that describes the requirements necessary to use the resource, e.g. operating systems, hardware, etc. in the case of a software resource." [] synonym: "requirements" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000642 name: requirements textual entity def: "A textual entity that expresses the requirements necessary to use a resource, e.g. software." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000643 name: statistical analysis textual entity def: "A textual entity documenting statistical analysis tools and techniques employed." [] is_a: IAO:0000300 ! textual entity [Term] id: IAO:0000644 name: statistical analysis section def: "A part of the document used to describe the statistical methodologies employed in the work presented in the document." [] synonym: "statistical analysis" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000645 name: tables section def: "A part of a document that contains one or more tables." [] synonym: "tables" EXACT [] is_a: IAO:0000314 ! document part [Term] id: IAO:0000646 name: postal code def: "An identifier that denotes some postal delivery route, some aggregate of postal delivery routes or a geographical region and was created for the purpose of sorting and delivering mail." [] is_a: IAO:0020000 ! identifier [Term] id: IAO:0000647 name: Postal delivery route def: "A plan specification that if realized, is realized by the delivery of mail to some facility or mailbox within some geographical region." [] is_a: IAO:0000104 ! plan specification [Term] id: IAO:0000648 name: zone improvement plan code def: "A postal code that is used in the United States for the purpose of sorting and delivering mail, and that denotes some postal delivery route or some aggregate of postal delivery routes." [] synonym: "ZIP code" EXACT [] is_a: IAO:0000646 ! postal code [Term] id: IAO:0000650 name: database extract, transform, and load process def: "A planned process which takes as input a database and fills another database by extracting concretizations of information entities from the first, transforming them, and loading the transformed concretizations into the second." [] synonym: "ETL" EXACT [] is_a: OBI:0000011 ! planned process [Term] id: IAO:0020000 name: identifier def: "An identifier is an information content entity that is the outcome of a dubbing process and is used to refer to one instance of entity shared by a group of people to refer to that individual entity." [] is_a: IAO:0000030 ! information content entity [Term] id: IAO:8000000 name: ontology module synonym: "ontology file" EXACT [] is_a: IAO:0000102 ! data about an ontology part [Term] id: IAO:8000001 name: base ontology module def: "An ontology module that comprises only of asserted axioms local to the ontology, excludes import directives, and excludes axioms or declarations from external ontologies." [] is_a: IAO:8000000 ! ontology module [Term] id: IAO:8000002 name: editors ontology module def: "An ontology module that is intended to be directly edited, typically managed in source control, and typically not intended for direct consumption by end-users." [] synonym: "source ontology module" EXACT [] is_a: IAO:8000000 ! ontology module [Term] id: IAO:8000003 name: main release ontology module def: "An ontology module that is intended to be the primary release product and the one consumed by the majority of tools." [] is_a: IAO:8000000 ! ontology module [Term] id: IAO:8000004 name: bridge ontology module def: "An ontology module that consists entirely of axioms that connect or bridge two distinct ontology modules. For example, the Uberon-to-ZFA bridge module." [] is_a: IAO:8000000 ! ontology module [Term] id: IAO:8000005 name: import ontology module def: "A subset ontology module that is intended to be imported from another ontology." [] synonym: "import file" EXACT [] is_a: IAO:8000006 ! subset ontology module [Term] id: IAO:8000006 name: subset ontology module def: "An ontology module that is extracted from a main ontology module and includes only a subset of entities or axioms." [] synonym: "ontology slim" EXACT [] synonym: "subset ontology" EXACT [] is_a: IAO:8000000 ! ontology module [Term] id: IAO:8000007 name: curation subset ontology module def: "A subset ontology that is intended as a whitelist for curators using the ontology. Such a subset will exclude classes that curators should not use for curation." [] is_a: IAO:8000006 ! subset ontology module [Term] id: IAO:8000008 name: analysis subset ontology module def: "An ontology module that is intended for usage in analysis or discovery applications." [] is_a: IAO:8000006 ! subset ontology module [Term] id: IAO:8000009 name: single layer subset ontology module def: "A subset ontology that is largely comprised of a single layer or strata in an ontology class hierarchy. The purpose is typically for rolling up for visualization. The classes in the layer need not be disjoint." [] synonym: "ribbon subset" EXACT [] is_a: IAO:8000006 ! subset ontology module [Term] id: IAO:8000010 name: exclusion subset ontology module def: "A subset of an ontology that is intended to be excluded for some purpose. For example, a blacklist of classes." [] synonym: "antislim" EXACT [] is_a: IAO:8000006 ! subset ontology module [Term] id: IAO:8000011 name: external import ontology module def: "An imported ontology module that is derived from an external ontology. Derivation methods include the OWLAPI SLME approach." [] synonym: "external import" EXACT [] is_a: IAO:8000005 ! import ontology module [Term] id: IAO:8000012 name: species subset ontology module def: "A subset ontology that is crafted to either include or exclude a taxonomic grouping of species." [] synonym: "taxon subset" EXACT [] is_a: IAO:8000006 ! subset ontology module [Term] id: IAO:8000013 name: reasoned ontology module def: "An ontology module that contains axioms generated by a reasoner. The generated axioms are typically direct SubClassOf axioms, but other possibilities are available." [] is_a: IAO:8000000 ! ontology module [Term] id: IAO:8000014 name: generated ontology module def: "An ontology module that is automatically generated, for example via a SPARQL query or via template and a CSV." [] is_a: IAO:8000000 ! ontology module [Term] id: IAO:8000015 name: template generated ontology module def: "An ontology module that is automatically generated from a template specification and fillers for slots in that template." [] is_a: IAO:8000014 ! generated ontology module [Term] id: IAO:8000016 name: taxonomic bridge ontology module is_a: IAO:8000004 ! bridge ontology module [Term] id: IAO:8000017 name: ontology module subsetted by expressivity is_a: IAO:8000006 ! subset ontology module [Term] id: IAO:8000018 name: obo basic subset ontology module def: "A subset ontology that is designed for basic applications to continue to make certain simplifying assumptions; many of these simplifying assumptions were based on the initial version of the Gene Ontology, and have become enshrined in many popular and useful tools such as term enrichment tools.\n\nExamples of such assumptions include: traversing the ontology graph ignoring relationship types using a naive algorithm will not lead to cycles (i.e. the ontology is a DAG); every referenced term is declared in the ontology (i.e. there are no dangling clauses).\n\nAn ontology is OBO Basic if and only if it has the following characteristics:\nDAG\nUnidirectional\nNo Dangling Clauses\nFully Asserted\nFully Labeled\nNo equivalence axioms\nSingly labeled edges\nNo qualifier lists\nNo disjointness axioms\nNo owl-axioms header\nNo imports" [] is_a: IAO:8000017 ! ontology module subsetted by expressivity [Term] id: IAO:8000019 name: ontology module subsetted by OWL profile is_a: IAO:8000017 ! ontology module subsetted by expressivity [Term] id: IAO:8000020 name: EL++ ontology module is_a: IAO:8000019 ! ontology module subsetted by OWL profile [Term] id: IDO:0000450 name: pathogenic disposition def: "A disposition to initiate processes that result in a disorder." [] is_a: BFO:0000016 ! disposition [Term] id: IDO:0000528 name: pathogen def: "A material entity with a pathogenic disposition." [] is_a: BFO:0000040 ! material entity [Term] id: IDO:0000562 name: antibacterial def: "A material entity bearing an antibacterial disposition." [] is_a: BFO:0000040 ! material entity [Term] id: IDO:0000586 name: infection def: "A part of an extended organism that itself has as part a population of one or more infectious agents and that (1) exists as a result of processes initiated by members of the infectious agent population and is (2) clinically abnormal in virtue of the presence of this infectious agent population, or (3) has a disposition to bring clinical abnormality to immunocompetent organisms of the same Species as the host (the organism corresponding to the extended organism) through transmission of a member or offspring of a member of the infectious agent population." [] is_a: BFO:0000040 ! material entity [Term] id: IDO:0000666 name: human pathogenicity disposition def: "A disposition to initiate processes that result in a disorder in a human organism." [] is_a: IDO:0000450 ! pathogenic disposition [Term] id: MRO:0000013 name: HLA-DR protein complex is_a: MRO:0001455 ! human MHC class II protein complex [Term] id: MRO:0000966 name: H2-Db protein complex is_a: MRO:0001759 ! mouse MHC class I protein complex with H2-b haplotype [Term] id: MRO:0000967 name: H2-Dd protein complex is_a: MRO:0001460 ! mouse MHC class I protein complex [Term] id: MRO:0000971 name: H2-IA protein complex is_a: MRO:0001461 ! mouse MHC class II protein complex [Term] id: MRO:0000973 name: H2-IAd protein complex is_a: MRO:0000971 ! H2-IA protein complex [Term] id: MRO:0000975 name: H2-IAg7 protein complex is_a: MRO:0000971 ! H2-IA protein complex [Term] id: MRO:0000991 name: H2-Kb protein complex is_a: MRO:0001759 ! mouse MHC class I protein complex with H2-b haplotype [Term] id: MRO:0000992 name: H2-Kd protein complex is_a: MRO:0001460 ! mouse MHC class I protein complex [Term] id: MRO:0000994 name: H2-Ks protein complex is_a: MRO:0001460 ! mouse MHC class I protein complex [Term] id: MRO:0000997 name: H2-Ld protein complex is_a: MRO:0001460 ! mouse MHC class I protein complex [Term] id: MRO:0001149 name: HLA-C protein complex is_a: MRO:0001454 ! human MHC class I protein complex [Term] id: MRO:0001167 name: HLA-DP protein complex is_a: MRO:0001455 ! human MHC class II protein complex [Term] id: MRO:0001355 name: MHC class I protein complex is_a: GO:0042611 ! MHC protein complex [Term] id: MRO:0001356 name: MHC class II protein complex is_a: GO:0042611 ! MHC protein complex [Term] id: MRO:0001434 name: cattle MHC class I protein complex is_a: MRO:0001355 ! MHC class I protein complex [Term] id: MRO:0001435 name: cattle MHC class II protein complex is_a: MRO:0001356 ! MHC class II protein complex [Term] id: MRO:0001454 name: human MHC class I protein complex is_a: MRO:0001355 ! MHC class I protein complex [Term] id: MRO:0001455 name: human MHC class II protein complex is_a: MRO:0001356 ! MHC class II protein complex [Term] id: MRO:0001460 name: mouse MHC class I protein complex is_a: MRO:0001355 ! MHC class I protein complex [Term] id: MRO:0001461 name: mouse MHC class II protein complex is_a: MRO:0001356 ! MHC class II protein complex [Term] id: MRO:0001465 name: pig MHC class I protein complex is_a: MRO:0001355 ! MHC class I protein complex [Term] id: MRO:0001498 name: mouse MHC protein complex with H2-p haplotype is_a: GO:0042611 ! MHC protein complex [Term] id: MRO:0001530 name: HLA protein complex with A2 serotype is_a: GO:0042611 ! MHC protein complex [Term] id: MRO:0001533 name: HLA protein complex with A24 serotype is_a: GO:0042611 ! MHC protein complex [Term] id: MRO:0001537 name: HLA protein complex with A28 serotype is_a: GO:0042611 ! MHC protein complex [Term] id: MRO:0001538 name: HLA protein complex with A29 serotype is_a: GO:0042611 ! MHC protein complex [Term] id: MRO:0001557 name: HLA protein complex with B27 serotype is_a: GO:0042611 ! MHC protein complex [Term] id: MRO:0001622 name: HLA protein complex with DQ3 serotype is_a: GO:0042611 ! MHC protein complex [Term] id: MRO:0001759 name: mouse MHC class I protein complex with H2-b haplotype is_a: MRO:0001460 ! mouse MHC class I protein complex [Term] id: MRO:0001790 name: rat MHC class I protein complex is_a: MRO:0001355 ! MHC class I protein complex [Term] id: MRO:0001793 name: rat MHC class II protein complex with RT1-A haplotype is_a: MRO:0001356 ! MHC class II protein complex [Term] id: MRO:0002026 name: H2-Dq protein complex is_a: MRO:0001460 ! mouse MHC class I protein complex [Term] id: MRO:0002027 name: H2-Kq protein complex is_a: MRO:0001460 ! mouse MHC class I protein complex [Term] id: NCBITaxon:10090 name: Mus musculus synonym: "house mouse" EXACT [] synonym: "mouse" EXACT [] is_a: NCBITaxon:39107 ! Murinae [Term] id: NCBITaxon:10116 name: Rattus norvegicus synonym: "brown rat" EXACT [] synonym: "Norway rat" EXACT [] synonym: "rat" EXACT [] synonym: "rats" EXACT [] is_a: NCBITaxon:39107 ! Murinae [Term] id: NCBITaxon:10239 name: Viruses is_a: OBI:0100026 ! organism [Term] id: NCBITaxon:10292 name: Herpesviridae is_a: NCBITaxon:10239 ! Viruses [Term] id: NCBITaxon:10358 name: Cytomegalovirus is_a: NCBITaxon:10292 ! Herpesviridae [Term] id: NCBITaxon:10376 name: Human gammaherpesvirus 4 synonym: "Epstein Barr virus" EXACT [] synonym: "Epstein-Barr virus" EXACT [] synonym: "Epstein-Barr virus EBV" EXACT [] synonym: "Human herpesvirus 4" EXACT [] synonym: "Human herpesvirus type 4" EXACT [] is_a: NCBITaxon:10292 ! Herpesviridae [Term] id: NCBITaxon:10407 name: Hepatitis B virus synonym: "hepatitis B virus (HBV)" EXACT [] synonym: "hepatitis B virus HBV" EXACT [] synonym: "hepatitis B virus, HBV" EXACT [] synonym: "Human hepatitis B virus" EXACT [] synonym: "human hepatitis B virus HBV" EXACT [] is_a: NCBITaxon:2732514 ! Revtraviricetes [Term] id: NCBITaxon:11050 name: Flaviviridae synonym: "Flavivirus (arbovirus group B)" EXACT [] is_a: NCBITaxon:2732406 ! Kitrinoviricota [Term] id: NCBITaxon:11103 name: Hepacivirus C synonym: "Hepatitis C virus" EXACT [] synonym: "hepatitis C virus HCV" EXACT [] synonym: "human hepatitis C virus" EXACT [] synonym: "human hepatitis C virus HCV" EXACT [] synonym: "human hepatitis virus C HCV" EXACT [] synonym: "post-transfusion hepatitis non A non B virus" EXACT [] is_a: NCBITaxon:11050 ! Flaviviridae [Term] id: NCBITaxon:11646 name: Lentivirus synonym: "Lentivirinae" EXACT [] is_a: NCBITaxon:2732514 ! Revtraviricetes [Term] id: NCBITaxon:11676 name: Human immunodeficiency virus 1 synonym: "human immunodeficiency virus 1 HIV-1" EXACT [] synonym: "human immunodeficiency virus HIV-1" EXACT [] synonym: "human immunodeficiency virus type 1 HIV 1" EXACT [] synonym: "human immunodeficiency virus type 1 HIV1" EXACT [] synonym: "human immunodeficiency virus type 1, HIV-1" EXACT [] synonym: "human immunodeficiency virus type I HIV-1" EXACT [] synonym: "human immunodeficiency virus type-1 HIV-1" EXACT [] synonym: "human immunodeficiency virus-1 HIV-1" EXACT [] is_a: NCBITaxon:11646 ! Lentivirus [Term] id: NCBITaxon:11709 name: Human immunodeficiency virus 2 synonym: "HIV type 2" EXACT [] synonym: "Human immunodeficiency virus type 2" EXACT [] synonym: "human immunodeficiency virus type 2 HIV-2" EXACT [] synonym: "human immunodeficiency virus type 2, HIV-2" EXACT [] synonym: "Human immunodeficiency virus-2" EXACT [] is_a: NCBITaxon:11646 ! Lentivirus [Term] id: NCBITaxon:117571 name: Euteleostomi synonym: "bony vertebrates" EXACT [] is_a: NCBITaxon:7742 ! Vertebrata [Term] id: NCBITaxon:1206794 name: Ecdysozoa is_a: NCBITaxon:33213 ! Bilateria [Term] id: NCBITaxon:12637 name: Dengue virus is_a: NCBITaxon:11050 ! Flaviviridae [Term] id: NCBITaxon:160 name: Treponema pallidum is_a: NCBITaxon:2 ! Bacteria [Term] id: NCBITaxon:197562 name: Pancrustacea is_a: NCBITaxon:6656 ! Arthropoda [Term] id: NCBITaxon:2 name: Bacteria synonym: "eubacteria" EXACT [] is_a: OBI:0100026 ! organism [Term] id: NCBITaxon:2157 name: Archaea is_a: OBI:0100026 ! organism [Term] id: NCBITaxon:2559587 name: Riboviria synonym: "RNA viruses" EXACT [] synonym: "RNA viruses and viroids" EXACT [] is_a: NCBITaxon:10239 ! Viruses [Term] id: NCBITaxon:2732406 name: Kitrinoviricota is_a: NCBITaxon:2559587 ! Riboviria [Term] id: NCBITaxon:2732514 name: Revtraviricetes is_a: NCBITaxon:2559587 ! Riboviria [Term] id: NCBITaxon:2759 name: Eukaryota synonym: "eucaryotes" EXACT [] synonym: "eukaryotes" EXACT [] is_a: OBI:0100026 ! organism [Term] id: NCBITaxon:314146 name: Euarchontoglires is_a: NCBITaxon:40674 ! Mammalia [Term] id: NCBITaxon:32523 name: Tetrapoda synonym: "tetrapods" EXACT [] is_a: NCBITaxon:117571 ! Euteleostomi [Term] id: NCBITaxon:32524 name: Amniota synonym: "amniotes" EXACT [] is_a: NCBITaxon:32523 ! Tetrapoda [Term] id: NCBITaxon:33154 name: Opisthokonta is_a: NCBITaxon:2759 ! Eukaryota [Term] id: NCBITaxon:33208 name: Metazoa synonym: "metazoans" EXACT [] synonym: "multicellular animals" EXACT [] is_a: NCBITaxon:33154 ! Opisthokonta [Term] id: NCBITaxon:33213 name: Bilateria is_a: NCBITaxon:33208 ! Metazoa [Term] id: NCBITaxon:3702 name: Arabidopsis thaliana synonym: "mouse-ear cress" EXACT [] synonym: "thale cress" EXACT [] synonym: "thale-cress" EXACT [] is_a: NCBITaxon:2759 ! Eukaryota [Term] id: NCBITaxon:37124 name: Chikungunya virus is_a: NCBITaxon:2732406 ! Kitrinoviricota [Term] id: NCBITaxon:388799 name: HIV-1 group O is_a: NCBITaxon:11676 ! Human immunodeficiency virus 1 [Term] id: NCBITaxon:39107 name: Murinae is_a: NCBITaxon:9989 ! Rodentia [Term] id: NCBITaxon:40674 name: Mammalia synonym: "mammals" EXACT [] is_a: NCBITaxon:32524 ! Amniota [Term] id: NCBITaxon:44689 name: Dictyostelium discoideum is_a: NCBITaxon:2759 ! Eukaryota [Term] id: NCBITaxon:4890 name: Ascomycota synonym: "ascomycetes" EXACT [] synonym: "sac fungi" EXACT [] is_a: NCBITaxon:33154 ! Opisthokonta [Term] id: NCBITaxon:4896 name: Schizosaccharomyces pombe synonym: "fission yeast" EXACT [] is_a: NCBITaxon:4890 ! Ascomycota [Term] id: NCBITaxon:4932 name: Saccharomyces cerevisiae synonym: "baker's yeast" EXACT [] synonym: "brewer's yeast" EXACT [] synonym: "S. cerevisiae" EXACT [] is_a: NCBITaxon:716545 ! saccharomyceta [Term] id: NCBITaxon:5140 name: Neurospora is_a: NCBITaxon:716545 ! saccharomyceta [Term] id: NCBITaxon:5820 name: Plasmodium is_a: NCBITaxon:2759 ! Eukaryota [Term] id: NCBITaxon:6239 name: Caenorhabditis elegans is_a: NCBITaxon:1206794 ! Ecdysozoa [Term] id: NCBITaxon:6656 name: Arthropoda synonym: "arthropods" EXACT [] is_a: NCBITaxon:1206794 ! Ecdysozoa [Term] id: NCBITaxon:6668 name: Daphnia synonym: "common water fleas" EXACT [] is_a: NCBITaxon:197562 ! Pancrustacea [Term] id: NCBITaxon:7147 name: Diptera synonym: "flies" EXACT [] is_a: NCBITaxon:197562 ! Pancrustacea [Term] id: NCBITaxon:7157 name: Culicidae synonym: "mosquitos" EXACT [] is_a: NCBITaxon:7147 ! Diptera [Term] id: NCBITaxon:716545 name: saccharomyceta is_a: NCBITaxon:4890 ! Ascomycota [Term] id: NCBITaxon:7227 name: Drosophila melanogaster synonym: "fruit fly" EXACT [] is_a: NCBITaxon:7147 ! Diptera [Term] id: NCBITaxon:7742 name: Vertebrata synonym: "Vertebrata" EXACT [] synonym: "vertebrates" EXACT [] is_a: NCBITaxon:33213 ! Bilateria [Term] id: NCBITaxon:784 name: Orientia tsutsugamushi is_a: NCBITaxon:2 ! Bacteria [Term] id: NCBITaxon:7955 name: Danio rerio synonym: "leopard danio" EXACT [] synonym: "zebra danio" EXACT [] synonym: "zebra fish" EXACT [] synonym: "zebrafish" EXACT [] is_a: NCBITaxon:117571 ! Euteleostomi [Term] id: NCBITaxon:8353 name: Xenopus synonym: "Xenopus" EXACT [] is_a: NCBITaxon:32523 ! Tetrapoda [Term] id: NCBITaxon:9031 name: Gallus gallus synonym: "bantam" EXACT [] synonym: "chicken" EXACT [] synonym: "chickens" EXACT [] synonym: "Gallus domesticus" EXACT [] is_a: NCBITaxon:32524 ! Amniota [Term] id: NCBITaxon:9606 name: Homo sapiens synonym: "human" EXACT [] synonym: "human being" EXACT [] is_a: NCBITaxon:314146 ! Euarchontoglires [Term] id: NCBITaxon:9989 name: Rodentia synonym: "rodent" EXACT [] is_a: NCBITaxon:314146 ! Euarchontoglires [Term] id: OBA:0000001 name: biological attribute is_a: BFO:0000019 ! quality [Term] id: OBA:2060180 name: limb coordination efficacy def: "The process efficacy of a limb coordination." [] is_a: OBA:0000001 ! biological attribute [Term] id: OBA:2060181 name: upper limb coordination efficacy def: "The process efficacy of a upper limb coordination." [] is_a: OBA:2060180 ! limb coordination efficacy [Term] id: OBA:2060182 name: lower limb coordination efficacy def: "The process efficacy of a lower limb coordination." [] is_a: OBA:2060180 ! limb coordination efficacy [Term] id: OBA:2060184 name: whole organism stability def: "The stability of a multicellular organism." [] is_a: OBA:0000001 ! biological attribute [Term] id: OBA:2060185 name: facial muscle performance def: "The functionality of a facial muscle." [] is_a: OBA:0000001 ! biological attribute [Term] id: OBA:2060186 name: peripheral nervous system function def: "The functionality of a peripheral nervous system." [] is_a: OBA:0000001 ! biological attribute [Term] id: OBA:2060187 name: knee joint functionality def: "The functionality of a knee joint." [] is_a: OBA:0000001 ! biological attribute [Term] id: OBA:2060188 name: ankle joint functionality def: "The functionality of a ankle joint." [] is_a: OBA:0000001 ! biological attribute [Term] id: OBA:2060189 name: tendon of biceps brachii functionality def: "The functionality of a tendon of biceps brachii." [] is_a: OBA:0000001 ! biological attribute [Term] id: OBA:2060190 name: brachioradialis functionality def: "The functionality of a brachioradialis." [] is_a: OBA:0000001 ! biological attribute [Term] id: OBI:0000006 name: role of being consumer safety officer def: "the role of a human being that is realized by enforcing regulations to ensure consumer safety" [] is_a: OBI:0000273 ! role of regulator of consumables and medical devices [Term] id: OBI:0000010 name: fluorescent reporter intensity def: "A measurement datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter." [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0000011 name: planned process def: "A process that realizes a plan which is the concretization of a plan specification." [] is_a: BFO:0000015 ! process [Term] id: OBI:0000014 name: regulator role def: "a regulatory role involved with making and/or enforcing relevant legislation and governmental orders" [] synonym: "regulator" EXACT [] is_a: OBI:0000017 ! regulatory role [Term] id: OBI:0000015 name: biological feature identification objective def: "Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature." [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0000016 name: regulation-assigned role def: "Regulation-assigned role is a regulatory role defined by legislation or governmental orders" [] is_a: OBI:0000017 ! regulatory role [Term] id: OBI:0000017 name: regulatory role def: "a role which inheres in material entities and is realized in the processes of making, enforcing or being defined by legislation or orders issued by a governmental body." [] is_a: BFO:0000023 ! role [Term] id: OBI:0000018 name: material supplier role def: "a role realized through the process of supplying materials such as animal subjects, reagents or other materials used in an investigation." [] synonym: "material provider role" EXACT [] synonym: "supplier" EXACT [] is_a: OBI:0000947 ! service provider role [Term] id: OBI:0000020 name: contract research organization role def: "a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution" [] synonym: "contract research organization" EXACT [] is_a: OBI:0000116 ! worker role [Term] id: OBI:0000021 name: list-mode data file def: "A list-mode data file is a binary digital entity where events are stored sequentially, parameter by parameter." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0000023 name: classified data set def: "A data set that is produced as the output of a class prediction data transformation and consists of a data set with assigned class labels." [] synonym: "data set with assigned class labels" EXACT [] is_a: IAO:0000100 ! data set [Term] id: OBI:0000025 name: reference substance role def: "a role inhering in a material entity that is realized when characteristics or responses elicited by the substance are used for comparison or reference." [] synonym: "reference substance" EXACT [] is_a: BFO:0000023 ! role [Term] id: OBI:0000026 name: cytological stain role def: "A dye role that is realized when the stain is used to colour cells and or cellular components for the purposes of visualization" [] synonym: "cytological stain" EXACT [] is_a: OBI:0000250 ! dye role [Term] id: OBI:0000029 name: centrifuge pellet role def: "pellet role is a role which inheres in a material entity and is realized by a material separation process using gravitational force generated by a centrifuge in which the material bearing the pellet role is the heavier or heaviest component of the output material.." [] is_a: BFO:0000023 ! role [Term] id: OBI:0000032 name: clinical research coordinator role def: "a worker role comprised of handling the administrative duties of a trial or study." [] synonym: "clinical research coordinator" EXACT [] is_a: OBI:0000116 ! worker role [Term] id: OBI:0000034 name: supernatant role def: "supernatant role is a role which inheres in a material entity and is realized by a material separation process using gravitational force in which the material bearing the supernatant role is the liquid component of the output material." [] is_a: BFO:0000023 ! role [Term] id: OBI:0000038 name: chromatography column def: "Chromatography column in chemistry is a tube and contents (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms." [] is_a: OBI:0000932 ! material separation device [Term] id: OBI:0000040 name: drug role def: "a role borne by a molecular entity and is realized in a process of absorption by an organism alters, or effects (or is assumed to effect) a function(s) which inhere in an organism" [] synonym: "drug" EXACT [] is_a: BFO:0000023 ! role [Term] id: OBI:0000041 name: pump valve switch def: "A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow." [] is_a: OBI:0000968 ! device [Term] id: OBI:0000043 name: xenotransplantation def: "is the transplantation of living cells, tissues or \\norgans from one species to another such as from pigs to humans" [] is_a: OBI:0000105 ! transplantation [Term] id: OBI:0000044 name: physical document def: "A physical document is an object serving as a record of information by means of symbolic marks." [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000045 name: waiting def: "A planned process where an agent does not take any new actions towards a particular objective for a period of time until a set of conditions is met." [] is_a: OBI:0600009 ! exposure of material to environment [Term] id: OBI:0000047 name: processed material def: "Is a material entity that is created or changed during material processing." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0000048 name: chromatography device def: "A device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a \"mobile phase\" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated." [] synonym: "chromatography instrument" EXACT [] is_a: OBI:0000832 ! measurement device is_a: OBI:0000932 ! material separation device is_a: OBI:0002089 ! physical store [Term] id: OBI:0000049 name: mass spectrometer def: "A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum" [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000050 name: obsolete_platform def: "A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000051 name: liquid chromatography mass spectrometry platform def: "A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI." [] is_a: OBI:0000832 ! measurement device is_a: OBI:0000932 ! material separation device [Term] id: OBI:0000052 name: microarray platform def: "A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI." [] is_a: OBI:0001034 ! environmental control device [Term] id: OBI:0000054 name: ratio of collected to emitted light def: "A measurement datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role" [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0000055 name: software optimization objective def: "Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software." [] is_a: OBI:0000242 ! software testing objective [Term] id: OBI:0000056 name: notified body role def: "Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive" [] synonym: "notified body" EXACT [] is_a: OBI:0000273 ! role of regulator of consumables and medical devices [Term] id: OBI:0000057 name: allotransplantation def: "is the transplantation of organs between members of the same species." [] is_a: OBI:0000105 ! transplantation [Term] id: OBI:0000059 name: gamma counter def: "A processed material which measures gamma radiation" [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000060 name: trial monitor role def: "a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study" [] synonym: "trial monitor" EXACT [] is_a: OBI:0000102 ! responsible party role [Term] id: OBI:0000064 name: positive reference substance role def: "a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a \"100%\" response" [] synonym: "positive reference substance" EXACT [] is_a: OBI:0000025 ! reference substance role [Term] id: OBI:0000065 name: polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether def: "triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant properties" [] is_a: CHEBI:23367 ! molecular entity [Term] id: OBI:0000066 name: investigation def: "a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s)." [] synonym: "study" EXACT [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000067 name: evaluant role def: "a role that inheres in a material entity that is realized in an assay in which data is generated about the bearer of the evaluant role" [] is_a: BFO:0000023 ! role [Term] id: OBI:0000068 name: reporting party role def: "a study personnel role played by a party who reports the outcome of a study component" [] synonym: "reporting party" EXACT [] synonym: "submitter" EXACT [] is_a: OBI:0000202 ! investigation agent role [Term] id: OBI:0000070 name: assay def: "A planned process that has the objective to produce information about a material entity (the evaluant) by examining it." [] synonym: "any method" EXACT [] synonym: "measuring" EXACT [] synonym: "scientific observation" EXACT [] synonym: "study assay" EXACT [] is_a: OBI:0000011 ! planned process disjoint_from: OBI:0000339 ! planning disjoint_from: OBI:0200000 ! data transformation disjoint_from: OBI:0600013 ! information acquisition [Term] id: OBI:0000071 name: quantitative confidence value def: "A data item which is used to indicate the degree of uncertainty about a measurement." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0000073 name: sample preparation for assay def: "A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI." [] synonym: "study" EXACT [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000075 name: diagnosis textual entity def: "diagnosis is an assessment of a disease or injury, its likely prognosis and treatment." [] is_a: IAO:0000300 ! textual entity [Term] id: OBI:0000076 name: unplanned occurrence effecting an investigation def: "a process which is external in origin to the investigation that has an impact on the outcome." [] is_a: BFO:0000015 ! process [Term] id: OBI:0000078 name: eMedical record def: "An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0000079 name: culture medium def: "a processed material that provides the needed nourishment for microorganisms or cells grown in vitro." [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000083 name: electronic case report tabulation def: "An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0000084 name: polystyrene tube def: "A polystyrene tube is a test tube made of polystyrene" [] is_a: OBI:0000836 ! test tube [Term] id: OBI:0000086 name: reagent role def: "A role inhering in a biological or chemical entity that is intended to be applied in a scientific technique to participate (or have molecular components that participate) in a chemical reaction that facilitates the generation of data about some entity distinct from the bearer, or the generation of some specified material output distinct from the bearer." [] comment: (copied from ReO)\nReagents are distinguished from instruments or devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in or have parts that participate in some chemical interaction or reaction during their intended participation in some technique. By contrast, instruments do not participate in a chemical reaction/interaction during the technique.\n\nReagents are distinguished from study subjects/evaluants in that study subjects and evaluants are that about which conclusions are drawn and knowledge is sought in an investigation - while reagents, by definition, are not. It should be noted, however, that reagent and study subject/evaluant roles can be borne by instances of the same type of material entity - but a given instance will realize only one of these roles in the execution of a given assay or technique. For example, taq polymerase can bear a reagent role or an evaluant role. In a DNA sequencing assay aimed at generating sequence data about some plasmid, the reagent role of the taq polymerase is realized. In an assay to evaluate the quality of the taq polymerase itself, the evaluant/study subject role of the taq is realized, but not the reagent role since the taq is the subject about which data is generated.\n\nIn 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). synonym: "reagent" EXACT [] is_a: OBI:0003610 ! reactant role [Term] id: OBI:0000089 name: role of regulator of chemical manufacturer def: "a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture" [] synonym: "regulator of chemical manufacture" EXACT [] is_a: OBI:0000014 ! regulator role [Term] id: OBI:0000091 name: detector reagent role def: "a role which inheres in a molecular entity and is realized by the process of recording or registering a stimulus." [] is_a: BFO:0000023 ! role [Term] id: OBI:0000092 name: role of certified IRB professional def: "a role of which inheres in a Homo sapiens and realized during administration and oversight of the daily activities of Institutional Review Boards (IRBs) in the USA" [] synonym: "certified IRB professional" EXACT [] is_a: OBI:0000016 ! regulation-assigned role [Term] id: OBI:0000093 name: patient role def: "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" [] synonym: "patient" EXACT [] is_a: BFO:0000023 ! role [Term] id: OBI:0000094 name: material processing def: "A planned process which results in physical changes in a specified input material" [] synonym: "material transformation" EXACT [] is_a: OBI:0000011 ! planned process disjoint_from: OBI:0600010 ! material acquisition [Term] id: OBI:0000096 name: protocol testing objective def: "Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols." [] is_a: OBI:0000208 ! methodology testing objective [Term] id: OBI:0000097 name: participant under investigation role def: "A role that is realized through the execution of a study design in which the bearer of the role participates and in which data about that bearer is collected." [] is_a: BFO:0000023 ! role [Term] id: OBI:0000100 name: obsolete_role of being first subject treated def: "First subject treated role is a study subject role borne by the subject realized in the application of the process specified in intervention study design with no previous study subject realizing the role prior in the study" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000101 name: measured expression level def: "A measurement datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA transcripts." [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0000102 name: responsible party role def: "a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study" [] synonym: "responsible party" EXACT [] is_a: OBI:0000202 ! investigation agent role [Term] id: OBI:0000103 name: principal investigator role def: "a responsible party role played by a person responsible for the overall conduct of a study" [] synonym: "principal investigator" EXACT [] is_a: OBI:0000102 ! responsible party role [Term] id: OBI:0000105 name: transplantation def: "a protocol application to replace an organ or tissue of an organism" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000109 name: obsolete biological vector role def: "a biological vector role is a material to be added role that is realized by the process of transmitting material to the organism that is the target of the transmission." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000110 name: pH indicator dye role def: "the role of a dye that is realized when the dye is used in an experiment to measure the pH in a material entity" [] synonym: "pH indicator dye" EXACT [] is_a: OBI:0000250 ! dye role [Term] id: OBI:0000112 name: specimen role def: "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" [] is_a: BFO:0000023 ! role [Term] id: OBI:0000113 name: sequence feature identification objective def: "Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide." [] is_a: OBI:0000015 ! biological feature identification objective [Term] id: OBI:0000115 name: intervention design def: "An intervention design is a study design in which a controlled process applied to the subjects (the intervention) serves as the independent variable manipulated by the experimentalist. The treatment (perturbation or intervention) defined can be defined as a combination of values taken by independent variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0000116 name: worker role def: "a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline" [] synonym: "worker" EXACT [] is_a: OBI:0000202 ! investigation agent role [Term] id: OBI:0000117 name: Bernoulli trial def: "An assay where the output data is a datum with one of two values denoting success and failure." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000118 name: gene list def: "A data set of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis." [] is_a: IAO:0000100 ! data set [Term] id: OBI:0000119 name: number of particles in subset def: "A measurement datum measuring the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role" [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0000125 name: number of lost events electronic def: "A measurement datum measuring the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer instrument. The datum has a qualitative role." [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0000129 name: calibration substance role def: "A reference substance role that is realized when characteristics or responses elicited by the bearer are used to ensure an instrument is within protocol specification of accuracy or performance" [] is_a: OBI:0000025 ! reference substance role [Term] id: OBI:0000131 name: molecular feature identification objective def: "Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications." [] is_a: OBI:0000015 ! biological feature identification objective [Term] id: OBI:0000134 name: hardware testing objective def: "Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner." [] is_a: OBI:0000208 ! methodology testing objective [Term] id: OBI:0000136 name: incubator def: "A device in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled" [] is_a: OBI:0001034 ! environmental control device [Term] id: OBI:0000140 name: obsolete_label role def: "Label role is a role which inheres in a material entity and which is realized in a detection of label assay" [] synonym: "label" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: OBI:0002743 [Term] id: OBI:0000143 name: baseline participant role def: "a reference participant role which is realized by making the reference to qualities at the start of the study or intervention" [] synonym: "baseline participant" EXACT [] is_a: OBI:0000220 ! reference subject role [Term] id: OBI:0000144 name: role of independent data monitoring committee def: "a trial monitor role charged recommending whether to continue, modify, or end the trial" [] synonym: "independent data monitoring committee" EXACT [] is_a: OBI:0000060 ! trial monitor role [Term] id: OBI:0000145 name: pathologist role def: "a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline" [] synonym: "Pathologist" EXACT [] is_a: OBI:0000116 ! worker role [Term] id: OBI:0000146 name: supernatant collection system harvesting frame def: "A device that is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125." [] is_a: OBI:0000967 ! container [Term] id: OBI:0000151 name: filter paper def: "A device manufacture with the intent to provide a porous unsized paper used for filtering." [] is_a: OBI:0000932 ! material separation device [Term] id: OBI:0000153 name: cell co-culturing def: "A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one." [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000154 name: role of Institutional Review Board def: "the role of a organization that is realized by members reviewing study designs for their agreement with regulations" [] synonym: "Internal Review Board" EXACT [] is_a: OBI:0000014 ! regulator role [Term] id: OBI:0000158 name: eSource document def: "an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures" [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0000161 name: crossover population role def: "a role realized when a participant serves as reference to itself" [] synonym: "crossover population" EXACT [] is_a: OBI:0000220 ! reference subject role [Term] id: OBI:0000162 name: complete nutrient role def: "A nutrient role that inheres in a material entity and is realized in the use of that material entity by an organism to provide all needed nourishment." [] synonym: "complete nutrient" EXACT [] is_a: OBI:0000204 ! nutrient role [Term] id: OBI:0000163 name: radiolabel role def: "a molecular label role which inheres in a material entity which is realized by the process of radioactivity detection" [] synonym: "radiolabel" EXACT [] is_a: OBI:0002743 ! molecular label role [Term] id: OBI:0000164 name: clonal cDNA library def: "Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.\n\nALT DEF (PRS):: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications." [] is_a: OBI:0000731 ! recombinant vector [Term] id: OBI:0000167 name: electronic case report form def: "An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0000169 name: placebo role def: "a negative reference substance is a reference role in which the substance playing the reference substance role is physically similar in appearance to the test substance" [] synonym: "placebo" EXACT [] is_a: OBI:0000214 ! negative reference substance role [Term] id: OBI:0000171 name: autotransplantation def: "is the transplantation of tissue from one part of \\nthe body to another in the same individual. )" [] is_a: OBI:0000105 ! transplantation [Term] id: OBI:0000172 name: parameter threshold def: "A measurement datum measuring the minimal signal that must be detected to generate an electrical event, as compared to the maximal detected signal in a flow cytometer instrument. The datum has a qualitative role" [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0000174 name: study group role def: "a study population role where the bearer is a population of material entities and the role is realized in the implementation of a study design wherein the entities bearing the study population role are observed or subjected to intervention according to the study design and are biological replicates, i.e. they receive the same treatment under the protocol" [] synonym: "study group population" EXACT [] is_a: BFO:0000023 ! role [Term] id: OBI:0000175 name: p-value def: "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." [] is_a: OBI:0000071 ! quantitative confidence value [Term] id: OBI:0000181 name: population def: "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" [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0000182 name: NMR 3D molecular structure determination assay def: "A 3D molecular structure determination assay that uses magnetic properties of atomic nuclei to determine the 3D structure and dynamics of molecules in the input sample." [] is_a: OBI:0003117 ! 3D molecular structure determination assay [Term] id: OBI:0000185 name: imaging assay def: "An assay that produces a picture of an entity." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000186 name: protocol optimization objective def: "Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol." [] is_a: OBI:0000096 ! protocol testing objective [Term] id: OBI:0000188 name: role of pathology review board def: "a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation" [] synonym: "pathology review board" EXACT [] is_a: OBI:0000116 ! worker role [Term] id: OBI:0000192 name: microtiter plate def: "A microtiter_plate is a flat plate with multiple wells used as small test tubes." [] synonym: "microplate" EXACT [] is_a: OBI:0000967 ! container [Term] id: OBI:0000196 name: role of impartial witness def: "a role which inheres in a Homo sapiens and is realized during a clinical trial - the impartial witness is independent of the trial and cannot be unfairly influenced by people involved with the trial" [] synonym: "impartial witness" EXACT [] is_a: OBI:0000016 ! regulation-assigned role [Term] id: OBI:00001975 name: chromatin immunoprecipitation def: "An immunoprecipitation in which chromatin (i.e. packaged DNA which can include protein and RNA complexes) is cut into short regions, reversibly cross linked, and antibodies or tags are used to select for pieces of chromatin with desired characteristics." [] synonym: "ChIP" EXACT [] is_a: OBI:0000690 ! immunoprecipitation [Term] id: OBI:0000198 name: biological replicate role def: "a reference participant role realized by equivalent treatment of participants" [] synonym: "biological replicate" EXACT [] is_a: OBI:0000220 ! reference subject role [Term] id: OBI:0000201 name: radioactivity detection def: "An assay that measures the amount of radiation in the radioactive spectrum (alpha, beta or gamma rays) emitted from an input material." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000202 name: investigation agent role def: "A role borne by an entity and that is realized in a process that is part of an investigation in which an objective is achieved. These processes include, among others: planning, overseeing, funding, reviewing." [] comment: Philly2013: Historically, this role would have been borne only by humans or organizations. However, we now also want to enable investigations run by robot scientists such as ADAM (King et al, Science, 2009) synonym: "investigator" EXACT [] synonym: "study person role" EXACT [] is_a: BFO:0000023 ! role [Term] id: OBI:0000204 name: nutrient role def: "a role that inheres in a material entity and is realized in the use of that material entity by an organism when it is used in that organism's metabolism and provides nourishment." [] synonym: "nutrient" EXACT [] is_a: BFO:0000023 ! role [Term] id: OBI:0000205 name: obsolete_dropout role def: "Dropout is a study subject role borne by an entity realized by a process of leaving the study earlier than the protocol specified and where the bearer of the dropout role had been borne study subject role prior to bearing dropout role." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000207 name: obsolete health care provider role def: "a worker role of providing medical care either within or outside the study timeline" [] synonym: "health care provider" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: OMRSE:00000012 [Term] id: OBI:0000208 name: methodology testing objective def: "Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies." [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0000210 name: analytical cytology data file def: "A digital entity intended to capture data in analytical cytology domain." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0000211 name: proxy respondent role def: "Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel" [] synonym: "proxy respondent" EXACT [] is_a: OBI:0000116 ! worker role [Term] id: OBI:0000213 name: fluorescence compensation matrix def: "A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0000214 name: negative reference substance role def: "a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used to establish a \"no effect\" response" [] synonym: "negative reference substance" EXACT [] is_a: OBI:0000025 ! reference substance role [Term] id: OBI:0000215 name: role of legally acceptable representative def: "a role which inheres in a human or organization who are able subject to applicable law to consent, on behalf of a prospective subject, to the subject`s participation in as clinical trial." [] synonym: "legally acceptable representative" EXACT [] is_a: OBI:0000016 ! regulation-assigned role [Term] id: OBI:0000218 name: investigation results report def: "An investigation report is a report on the results of an investigation." [] is_a: IAO:0000088 ! report [Term] id: OBI:0000219 name: cellular feature identification objective def: "Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation." [] is_a: OBI:0000015 ! biological feature identification objective [Term] id: OBI:0000220 name: reference subject role def: "a reference subject role which inheres in an organism or entity of organismal origin so that the characteristics or responses of the participant playing the reference participant role are used for comparison or reference" [] synonym: "reference participant" EXACT [] is_a: OBI:0000097 ! participant under investigation role [Term] id: OBI:0000221 name: vital dye role def: "A dye role that is realized when used to detect live cells in an experiment" [] synonym: "vital dye" EXACT [] is_a: OBI:0000250 ! dye role [Term] id: OBI:0000223 name: obsolete_blinded medication role def: "Is a role which inheres in a material entity which is manufactured to be similar in appearance to a test material entity in e.g. a clinical trial to prevent participants from detecting which is the active and inactive substance" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000224 name: sub-investigator role def: "a worker role authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline" [] synonym: "sub-investigator" EXACT [] is_a: OBI:0000116 ! worker role [Term] id: OBI:0000227 name: data encoding def: "a documenting process to encode an information entity into a digital document" [] is_a: IAO:0000572 ! documenting [Term] id: OBI:0000231 name: enzymatic cleavage def: "a material processing that digests the fraction of input material that is susceptible to that enzyme" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000232 name: hardware optimization objective def: "Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware." [] is_a: OBI:0000134 ! hardware testing objective [Term] id: OBI:0000233 name: obsolete_defined_material def: "Place holder class, Utility class to gather the defined classes" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000234 name: trial statistician role def: "a worker role that analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated." [] synonym: "trial statistician" EXACT [] is_a: OBI:0000116 ! worker role [Term] id: OBI:0000235 name: standard error def: "A quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution." [] is_a: OBI:0000071 ! quantitative confidence value [Term] id: OBI:0000237 name: antigen role def: "A role of a material entity that is being recognized in whole or in part by receptors of the immune system such as antibodies or T cell receptors." [] is_a: BFO:0000023 ! role [Term] id: OBI:0000242 name: software testing objective def: "Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software." [] is_a: OBI:0000208 ! methodology testing objective [Term] id: OBI:0000243 name: sponsor role def: "a responsible party role involved with any of the following activities: initiating, managing and funding a study" [] synonym: "sponsor" EXACT [] is_a: OBI:0000102 ! responsible party role [Term] id: OBI:0000245 name: organization def: "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." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0000248 name: feed role def: "a role that inheres in a material entity and is realized in the use of that material entity by lab animal to provide all needed nourishment." [] synonym: "feed" EXACT [] is_a: OBI:0000162 ! complete nutrient role [Term] id: OBI:0000249 name: technical replicate role def: "technical replicate role is realized when two portions from one evaluant are used in replicate runs of an assay" [] synonym: "technical replicate" EXACT [] is_a: OBI:0000220 ! reference subject role [Term] id: OBI:0000250 name: dye role def: "A molecular label role which inheres in a material entity and which is realized in the process of detecting a molecular dye that imparts color to some material of interest." [] synonym: "dye" EXACT [] is_a: OBI:0002743 ! molecular label role [Term] id: OBI:0000251 name: cluster def: "A data set which is a subset of data that are a similar to each other in some way." [] is_a: IAO:0000100 ! data set [Term] id: OBI:0000252 name: cohort role def: "a cohort role is a biological replicate role played by a group of study participants who share a common characteristic of interest to the study." [] is_a: OBI:0000198 ! biological replicate role [Term] id: OBI:0000253 name: artificially induced nucleic acid hybridization def: "Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules." [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000257 name: DNA extraction def: "A DNA extraction is a nucleic acid extraction where the desired output material is DNA." [] is_a: OBI:0666667 ! nucleic acid extraction [Term] id: OBI:0000260 name: plan def: "A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process." [] is_a: BFO:0000017 ! realizable entity [Term] id: OBI:0000264 name: obsolete_sample population def: "A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers." [] synonym: "recruited population" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000268 name: organism feature identification objective def: "Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle." [] is_a: OBI:0000015 ! biological feature identification objective [Term] id: OBI:0000269 name: number of lost events computer def: "A measurement datum recording the number of measurement events lost due to overloading of the analysis chip in a flow cytometer instrument. The datum has a qualitative role" [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0000272 name: protocol def: "A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process." [] synonym: "study protocol" EXACT [] is_a: IAO:0000104 ! plan specification [Term] id: OBI:0000273 name: role of regulator of consumables and medical devices def: "a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices" [] synonym: "drug regulatoy authority" EXACT [] is_a: OBI:0000014 ! regulator role [Term] id: OBI:0000274 name: adding a material entity into a target def: "is a process with the objective to place a material entity bearing the 'material to be added role' into a material bearing the 'target of material addition role'." [] is_a: OBI:0000652 ! material combination [Term] id: OBI:0000275 name: analyte role def: "A measurand role borne by a molecular entity or an atom and realized in an analyte assay which achieves the objective to measure the magnitude/concentration/amount of the analyte in the entity bearing evaluant role." [] is_a: OBI:0002444 ! measurand role [Term] id: OBI:0000278 name: disease stage def: "a part of an occurrence of a disease process which is associated with position in the normal progression of the disease" [] is_a: GO:0008150 ! biological_process [Term] id: OBI:0000281 name: intraperitoneal injection def: "is the injection of a material entity (bearing the administered substance role) into the peritoneum (bearing the target role) of an organism using a syringe" [] is_a: OBI:0000426 ! injection is_a: OBI:0000429 ! intraperitoneal administration [Term] id: OBI:0000286 name: precipitate def: "a precipitate is a material entity which is output of a precipitation process" [] synonym: "precipited material" EXACT [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000288 name: protein-protein interaction detection assay def: "An assay that determines interactions between proteins, such as protein-protein binding." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000291 name: transcription factor binding site assay def: "An assay tthat determines DNA regions specifically recognized by proteins that function as transcription factors" [] synonym: "TF binding" EXACT [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0000296 name: obsolete_enrollment def: "enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000310 name: adverse event trigger def: "revisit?" [] is_a: IAO:0000001 ! conditional specification [Term] id: OBI:0000318 name: eluate def: "a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase" [] synonym: "eluted material" EXACT [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000319 name: material to be added role def: "A role of a material entity that is realized in an \"adding a material entity into a target\" process where the bearer of the role is added into another material entity (the target)." [] is_a: BFO:0000023 ! role [Term] id: OBI:0000323 name: obsolete_peritoneum def: "is the serous membrane that forms the lining of the abdominal cavity" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000338 name: drawing a conclusion based on data def: "A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion" [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000339 name: planning def: "a process of creating or modifying a plan specification" [] is_a: BFO:0000015 ! process [Term] id: OBI:0000340 name: obsolete_documenting is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: IAO:0000572 [Term] id: OBI:0000341 name: histological sample preparation def: "histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay" [] is_a: OBI:0000094 ! material processing is_a: OBI:0000659 ! specimen collection process [Term] id: OBI:0000343 name: inductive reasoning def: "a interpreting data that is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns." [] is_a: OBI:0000338 ! drawing a conclusion based on data [Term] id: OBI:0000345 name: mass analyzer def: "A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields in vacuum where the two laws of Lorentz force law and Newton's second law of motion apply." [] is_a: OBI:0000832 ! measurement device is_a: OBI:0000932 ! material separation device [Term] id: OBI:0000355 name: hypothesis driven investigation def: "is an investigation with the goal to test one or more hypothesis" [] is_a: OBI:0000066 ! investigation [Term] id: OBI:0000356 name: hypothesis generating investigation def: "is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis" [] is_a: OBI:0000066 ! investigation [Term] id: OBI:0000361 name: ion source def: "An ion source is a device that is part of a mass spectrometer that ionizes the material under analysis. The ions are then transported by magnetic or electric fields to the mass analyzer. Techniques for ionization have been key to determining what types of samples can be analyzed by mass spectrometry. Electron ionization and chemical ionization are used for gases and vapors. In chemical ionization sources, the material is ionized by chemical ion-molecule reactions during collisions in the source. Two techniques often used with liquid and solid biological samples include electrospray ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp (Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson (Editor) (ISBN 0-941901-31-9)))." [] is_a: OBI:0000968 ! device [Term] id: OBI:0000364 name: ion detector def: "An ion detector is a device that measures and records the charge induced or current produced when an ion passes by or hits a surface. Example: In a scanning instrument the signal produced in the detector during the course of the scan versus where the instrument is in the scan (at what m/Q) will produce a mass spectrum, a record of ions as a function of m/Q." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000366 name: metabolite profiling assay def: "An assay that detects and identifies chemical entities resulting from biochemical and cellular metabolism" [] synonym: "metabolite assay" EXACT [] synonym: "metabolomic assay" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000367 name: light emission function def: "A light emission function is an excitation function to excite a material to a specific excitation state that it emits light." [] is_a: OBI:0000374 ! excitation function [Term] id: OBI:0000368 name: record function def: "A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation" [] is_a: BFO:0000034 ! function [Term] id: OBI:0000369 name: magnify function def: "A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000370 name: contain function def: "A contain function is a function to constrain a material entities location in space" [] is_a: BFO:0000034 ! function [Term] id: OBI:0000371 name: heat function def: "A heat function is a function that increases the internal kinetic energy of a material" [] is_a: BFO:0000034 ! function [Term] id: OBI:0000372 name: material separation function def: "A material separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000373 name: ionize process def: "a physical process of converting an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions. This excludes chemical processes of dissociation." [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000374 name: excitation function def: "A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000375 name: freeze function def: "A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000376 name: synthesizing function def: "A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000377 name: perturb function def: "A perturb function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000378 name: filter function def: "A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entity while allowing entities which have different qualities to pass through" [] is_a: OBI:0000372 ! material separation function [Term] id: OBI:0000379 name: mechanical function def: "A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force)." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000380 name: gas filter function def: "A gas filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a gas-solid mixture" [] is_a: OBI:0000378 ! filter function [Term] id: OBI:0000381 name: liquid filter function def: "A liquid filter function is a filter function which prevents the flow of solid objects, defined by specific qualities, in a liquid-solid mixture" [] is_a: OBI:0000378 ! filter function [Term] id: OBI:0000383 name: transfer function def: "A transfer function is a function to displace a material from one location to another." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000384 name: electricity supply function def: "An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity or as a stimulus during a neuroscience experiment." [] synonym: "power supply" EXACT [] is_a: OBI:0000391 ! energy supply function [Term] id: OBI:0000385 name: ionization function def: "An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000387 name: cool function def: "A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of material." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000388 name: connection function def: "A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000389 name: isoelectric focusing device def: "An isoelectric focusing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separation medium and the charged material to be separated." [] synonym: "isoelectric focusing unit" EXACT [] is_a: OBI:0002089 ! physical store [Term] id: OBI:0000390 name: thermostatic circulator def: "A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid" [] is_a: OBI:0002089 ! physical store [Term] id: OBI:0000391 name: energy supply function def: "An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy" [] is_a: BFO:0000034 ! function [Term] id: OBI:0000392 name: information processor function def: "An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process." [] synonym: "data processor function" EXACT [] is_a: BFO:0000034 ! function [Term] id: OBI:0000393 name: signal conversion function def: "A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon." [] synonym: "transduction function" EXACT [] is_a: OBI:0000392 ! information processor function [Term] id: OBI:0000394 name: blot module def: "A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised" [] is_a: OBI:0000968 ! device [Term] id: OBI:0000395 name: signal amplification function def: "A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differential magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal." [] is_a: OBI:0000393 ! signal conversion function [Term] id: OBI:0000397 name: image acquisition function def: "An image acquisition function is a function to acquire an image of a material" [] is_a: OBI:0000453 ! measure function [Term] id: OBI:0000398 name: image creation device def: "An image creation device is a device which captures a digitized image of an object" [] synonym: "image acquisition device" EXACT [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000399 name: solid support function def: "A solid support function is a function of a device on which an entity is kept in a defined position and prevented in its movement" [] is_a: BFO:0000034 ! function [Term] id: OBI:0000400 name: display function def: "A display function is a function to present information by translating that information through some lookup process into visual form." [] is_a: OBI:0000392 ! information processor function [Term] id: OBI:0000401 name: environment control function def: "An environmental control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000403 name: sort function def: "A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order." [] is_a: OBI:0000372 ! material separation function [Term] id: OBI:0000404 name: gel dryer def: "A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels" [] is_a: OBI:0002089 ! physical store [Term] id: OBI:0000405 name: primer role def: "a complementary nucleotide probe role which inheres in nucleic acid molecular entity and is realized by the use of the entity bearing the role to initiate chain elongation." [] is_a: OBI:0000857 ! complementary nucleotide probe role [Term] id: OBI:0000406 name: PCR product def: "is double stranded DNA that is the specified output of a polymerase chain reaction" [] is_a: CHEBI:4705 ! double-stranded DNA is_a: OBI:0000809 ! amplified DNA [Term] id: OBI:0000407 name: viral RNA extraction def: "The extraction of RNA from an input material that specifically isolates viral RNA" [] is_a: OBI:0666666 ! RNA extraction [Term] id: OBI:0000409 name: nucleic acid template role def: "a reference substance role which inheres in nucleic acid material entity and is realized in the process of using the nucleic acid bearing the template role as a reference during synthesis of a reverse copy." [] is_a: OBI:0000025 ! reference substance role [Term] id: OBI:0000410 name: recombinant plasmid def: "a plasmid in which extraneous DNA has been inserted." [] is_a: OBI:0000430 ! plasmid is_a: OBI:0000731 ! recombinant vector [Term] id: OBI:0000411 name: cloning vector role def: "A material to be added role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning." [] is_a: OBI:0000319 ! material to be added role [Term] id: OBI:0000413 name: cell cycle synchronization def: "a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000415 name: polymerase chain reaction def: "PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified." [] synonym: "PCR" EXACT [] is_a: OBI:0600058 ! enzymatic amplification [Term] id: OBI:0000416 name: cloning insert role def: "cloning insert role is a role which inheres in DNA or RNA and is realized by the process of being inserted into a cloning vector in a cloning process." [] is_a: BFO:0000023 ! role [Term] id: OBI:0000418 name: measuring glucose concentration in blood serum assay def: "An assay that determines the concentration of glucose molecules in a blood serum sample" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:0000419 name: reverse transcriptase def: "enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase\nactivity)" [] is_a: OBI:0000427 ! enzyme [Term] id: OBI:0000420 name: obsolete_trypsinized material def: "A material entity that has undergone a process of digestion with trypsin" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000422 name: syringe def: "A processed material which is used to introduce or draw fluids from a material entity. A syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw" [] is_a: OBI:0000968 ! device [Term] id: OBI:0000423 name: extract def: "an extract is a material entity which results from an extraction process" [] synonym: "extracted material" EXACT [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000424 name: transcription profiling assay def: "An assay that determines gene expression and transcription activity using ribonucleic acids collected from a material entity." [] synonym: "gene expression profiling" EXACT [] synonym: "transcription profiling" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000425 name: averaging objective def: "An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0000426 name: injection def: "injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as syringe or injector connection, attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue." [] is_a: OBI:0000274 ! adding a material entity into a target [Term] id: OBI:0000427 name: enzyme def: "(protein or rna) or has_part (protein or rna) and\nhas_function some GO:0003824 (catalytic activity)" [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0000429 name: intraperitoneal administration def: "The administration of a substance into the peritoneum of an organism" [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0000430 name: plasmid def: "plasmid = DNA and has_quality circular and has_function\n(is_realized_as some gene expression) GO:0010467" [] is_a: CHEBI:4705 ! double-stranded DNA [Term] id: OBI:0000431 name: injection into organ section def: "A process in which an input substance is injected into a organ section." [] is_a: OBI:0000426 ! injection [Term] id: OBI:0000432 name: polyacrylamide gel def: "a material entity resulting from the polymerization of acrylamide with TEMED in some buffer solution" [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000433 name: DNA sequence feature detection assay def: "An assay with the objective to determine a sequence feature of DNA" [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000434 name: adding material objective def: "is the specification of an objective to add a material into a target material. The adding is asymmetric in the sense that the target material largely retains its identity" [] is_a: OBI:0000686 ! material combination objective [Term] id: OBI:0000435 name: genotyping assay def: "An assay which generates data about a genotype from a specimen of genomic DNA. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions." [] synonym: "genotype profiling" EXACT [] synonym: "SNP analysis" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0000436 name: needle def: "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." [] is_a: OBI:0000968 ! device [Term] id: OBI:0000437 name: analyte measurement objective def: "an assay objective to determine the presence or concentration of an analyte in the evaluant" [] is_a: OBI:0000441 ! assay objective [Term] id: OBI:0000438 name: DNA sequence variation detection assay def: "An assay that measures changes (expansion, amplification, deletion, mutation) in the sequence of a DNA molecule." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000439 name: agarose gel def: "a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution" [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000441 name: assay objective def: "an objective specification to determine a specified type of information about an evaluated entity (the material entity bearing evaluant role)" [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0000442 name: obsolete_heart def: "The heart is a muscular organ found in all vertebrates that is responsible for pumping blood throughout the blood vessels by repeated, rhythmic contractions" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000443 name: analyte assay def: "An assay with the objective to capture information about the presence, concentration, or amount of an analyte in an evaluant." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000444 name: target of material addition role def: "A role of a material entity that is realized in an \"adding a material entity into a target\" process where the bearer of the role (the target) receives the addition of another material entity." [] is_a: BFO:0000023 ! role [Term] id: OBI:0000445 name: mass measurement assay def: "An assay that determines the mass of an evaluant" [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000446 name: obsolete_identification def: "a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000447 name: intracellular electrophysiology recording assay def: "An electrophysiology assay where the recording location of the electrode is intracellular." [] is_a: OBI:0002176 ! electrophysiology assay [Term] id: OBI:0000448 name: packed column def: "A packed column is a chromatography column where the particles of the solid stationary phase or the support coated with a liquid stationary phase may fill the whole inside volume of the tube." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000449 name: obsolete_defined_output def: "This is only a placeholder for defined classes, as are its siblings _defined_material and _defined protocol application. Its children should be defined classes constructed as output of a process." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000450 name: regulatory agency def: "A regulatory agency is a organization that has responsibility over or for the legislation (acts and regulations) for a given sector of the government." [] is_a: OBI:0000245 ! organization [Term] id: OBI:0000451 name: normalized data set def: "A data set that is produced as the output of a normalization data transformation." [] is_a: IAO:0000100 ! data set [Term] id: OBI:0000453 name: measure function def: "Measure function is a function that is borne by a processed material and realized in a process in which information about some entity is expressed relative to some reference." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000454 name: extracellular electrophysiology recording assay def: "An electrophysiology assay where the recording location of the electrode is extracellular." [] is_a: OBI:0002176 ! electrophysiology assay [Term] id: OBI:0000455 name: consume data function def: "Process data function is a function that is borne by in a material entity by virtue of its structure. When realized the material entity consumes data." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000456 name: material transformation objective def: "an objective specifiction that creates an specific output object from input materials." [] synonym: "artifact creation objective" EXACT [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0000457 name: manufacturing def: "A planned process with the objective to produce a processed material which will have a function for future use." [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000458 name: manufacturing objective def: "is the objective to manufacture a material of a certain function (device)" [] is_a: OBI:0000456 ! material transformation objective [Term] id: OBI:0000463 name: column chromatography detector def: "There is a wide range of detectors available for both GC and LC each having their own particular areas of application. In general the more catholic the response, the less sensitive the detector and the most sensitive detectors are those that have a specific response. The performance of all detectors should be properly specified so that the user can determine which is most suitable for a specific application. Such specifications are also essential to compare the performance of different detectors supplied by alternative instrument manufactures. Detector specifications should be presented in a standard form and in standard units, so that detectors can be compared that function on widely different principles." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000464 name: Bruker autosampler def: "A Bruker autosampler is an autosampler made by Bruker." [] is_a: OBI:0000555 ! autosampler [Term] id: OBI:0000465 name: organic acid column def: "An organic acid column is a chromatography column which enables (reversed-phase) separation of hydrophilic aliphatic and aromatic organic acids with UV detection. Organic acid columns allow retention of polar and apolar organic acids and are hydrolysis resistant." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000466 name: thermal conductivity detector def: "The most commonly used detector in preparative GC is the thermal conductivity detector (hot wire detector). Even this detector, however, is often too sensitive and has too high a flow impedance. Under such circumstances, the procedure mentioned above must be employed. The eluent from the preparative column is split and a small portion diverted through the detector (sometimes with further dilution with carrier gas to reduce sensitivity)." [] synonym: "TCD, hot wire detector" EXACT [] is_a: OBI:0000637 ! gas chromatography detector [Term] id: OBI:0000467 name: Bruker US 2 NMR magnet def: "An actively-shielded superconducting magnet from Bruker that combines Bruker BioSpin's advanced, proprietary UltraShield active shielding and UltraStabilized sub-cooling technologies. This shielded and stabilized (US2) magnet system delivers high sensitivity and spectral dispersion." [] is_a: OBI:0000597 ! Bruker NMR magnet [Term] id: OBI:0000468 name: protein column def: "A protein column is a chromatography column used for the separation of complex protein mixtures. Protein columns enable sample desalting, followed by chromatographic separation or fractionation of complex protein samples, e.g. immunodepleted serum or plasma proteins." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000469 name: solvent mixer def: "A liquid chromatography device that mixes different solvents, e.g. under high pressure and in differrent volumes ranging from 5 ml to 5 L capacity. Powerful magnetic mixers provide vigorous agitation required for high pressure reaction chemistry." [] is_a: OBI:0000485 ! chromatography instrument [Term] id: OBI:0000470 name: mass spectrometry assay def: "An assay that identifies the amount and type of material entities present in a sample by fragmenting the sample and measuring the mass-to-charge ratio of the resulting particles." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000471 name: study design execution def: "a planned process that carries out a study design" [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000473 name: Bruker NMR Case sample changer def: "The NMR Case is an economical NMR sample changer for laboratories with modest automation needs. It expands the maximum number of samples your spectrometer can process during unattended operation to 24. The NMR Case consists of multiple components. The NMR Case exchange module installed atop your cryostat. The two front legs are adjustable, making the NMR Case compatible with many different cryostats." [] is_a: OBI:0000464 ! Bruker autosampler [Term] id: OBI:0000474 name: nano pump system def: "A pump system optimized for nano flow chromatography." [] is_a: OBI:0000589 ! chromatography pump system [Term] id: OBI:0000475 name: Bruker AutoClean system def: "NMR tubes are often used once and discarded, creating needless waste. With the Bruker BioSpin Autoclean system you can now recycle 5mm, 3mm, or 5mm/3mm step-down (Wilmad 520-1B) NMR tubes. AutoClean NMR Tube Washing System is a simple way to recoup the substantial investment your organization makes in quality NMR tubes, and cut back on needless waste material." [] is_a: OBI:0000498 ! NMR tube washing system [Term] id: OBI:0000476 name: manual injection system def: "The traditional hardware system that allows a human to inject a sample into an inlet by hand, using a syringe." [] is_a: OBI:0000504 ! sample injection system [Term] id: OBI:0000477 name: Varian GEMINI spectrometer def: "An older Varian Broadband NMR spectrometer." [] is_a: OBI:0000611 ! Varian NMR instrument [Term] id: OBI:0000478 name: column connector def: "A device that connects two or more columns together in a functional way with leak-tight connection, low dead volume, low thermal mass and high inertness." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000479 name: solid NMR probe def: "An NMR probe that is designed to hold a solid sample." [] is_a: OBI:0000516 ! NMR probe [Term] id: OBI:0000480 name: Bruker high resolution probe def: "BRUKER BIOSPIN's experienced Research & Development group not only delivers top-performance probes for the more common experiments, but also a wealth of special probes for almost any application. For high resolution (HR) NMR we offer probes with a variety of important characteristics and features." [] synonym: "HR Probe" EXACT [] is_a: OBI:0000561 ! Bruker NMR probe [Term] id: OBI:0000481 name: chromatography detector def: "A chromatography detector is a device that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a chromatographic process and thus permits the senses to appreciate the nature of the separation. Defining characteristics are Dynamic Range, Response Index or Linearity, Linear Dynamic range, Detector Response, Detector Noise Level, Detector Sensitivity or Minimum Detectable Concentration, Total System Dispersion, Sensor Dimensions, Detector Time Constant, Pressure Sensitivity, Flow Sensitivity, Operating Temperature Range." [] is_a: OBI:0000485 ! chromatography instrument [Term] id: OBI:0000482 name: normal phase column def: "A normal phase column is a chromatography column in which the stationary phase is more polar than the mobile phase. Its counterpart is the reversed phase column." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000483 name: APOLLO console def: "The APOLLO is a compact, modular, multiple-DSP, Windows XP Professional-based console that can be equipped with up to 8 DDS-based RF transmitter channels configurable from 2 kHz to 3.5 GHz. Each transmitter channel produces a nominal 1V output and has the most agile frequency, phase and amplitude control of any system on the market. An array of additional options are available including multiple RF transmitters, linear high-power RF amplifiers, digital receiver arrays, low noise figure preamplifiers, a gradient control system, shim unit, MAS spin-speed controller, variable temperature unit, digital lock system and probe/coil interface. With its numerous options, the Apollo can be configured for any NMR, NQR or MRI application." [] is_a: OBI:0000599 ! tecmag NMR console [Term] id: OBI:0000484 name: NMR sample holder def: "An NMR sample holder is the part of an NMR instrument, which carries the NMR probe,sample tube and the nmr sample." [] is_a: OBI:0000968 ! device [Term] id: OBI:0000485 name: chromatography instrument def: "Any instrument that is used to carry out a chromatography experiment." [] is_a: OBI:0000932 ! material separation device [Term] id: OBI:0000486 name: continuous wave NMR instrument def: "Continuous wave NMR spectrometers are similar to optical spectrometers, but the sample is held in a strong magnetic field, where the frequency of the source is slowly scanned (in some instruments, the source frequency is held constant, and the field is scanned)." [] is_a: OBI:0000566 ! NMR instrument [Term] id: OBI:0000487 name: fourier transformation NMR instrument def: "In fourier transformation NMR, all frequencies in a spectrum are irradiated simultaneously with a radio frequency pulse. Following the pulse, the nuclei return to thermal equilibrium. A time domain emission signal is recorded by the instrument as the nuclei relax. A frequency domain spectrum is obtained by Fourier transformation." [] is_a: OBI:0000566 ! NMR instrument [Term] id: OBI:0000489 name: nitrogen phosphorous detector def: "The nitrogen phosphorus detector (NPD) (sometimes called the thermionic detector) is a very sensitive, specific detector the design of which, is based on the FID. Physically the sensor appears to be very similar to the FID but, in fact, operates on an entirely different principle. The nitrogen phosphorous detector (sometimes called the thermionic detector) is a very sensitive but specific detector that responds almost exclusively to nitrogen and phosphorous compounds. It is based on the flame ionization detector but differs in that it contains a rubidium or cesium silicate (glass) bead situated in a heater coil, a little distance from the hydrogen flame. If the detector is to respond to both nitrogen and phosphorous then the hydrogen flow should be minimal so that the gas does not ignite at the jet. If the detector is to respond to phosphorous only, a large flow of hydrogen is used which is burnt at the jet. The heated bead emits electrons by thermionic emission. These electrons are collected under a potential of a few volts by an appropriately placed anode, and provides a background current. When a solute containing nitrogen or phosphorous is eluted from the column, the partially combusted nitrogen and phosphorous materials are adsorbed on the surface of the bead. The adsorbed material reduces the work function of the surface and, as consequence, the emission of electrons is increased which raises the current collected at the electrode. The sensitivity of the detector to phosphorous is about 10-12 gram per ml and for nitrogen about 10-11 gram per ml at a signal to nose ratio of 2. The alkali bead as a finite life and needs regular replacement." [] is_a: OBI:0000637 ! gas chromatography detector [Term] id: OBI:0000490 name: cation exchange column def: "A cation exchange column is a chromatography column that is used in cation exchange chromatography." [] is_a: OBI:0000560 ! ion exchange column [Term] id: OBI:0000491 name: direct detection NMR probe def: "An NMR probe designed to allow the direct detection of acquisition nuclei." [] is_a: OBI:0000516 ! NMR probe [Term] id: OBI:0000492 name: Bruker B-ACS system def: "The Bruker Automatic Sample Changer (B-ACS 60/120), used in conjunction with Bruker DISNMR, UXNMR or XWIN-NMR software, provides dialog-guided facilities which allow the user to easily and effectively perform automatic (continuous) experiments. Features include a 60 or 120 sample capacity, random accessing of samples, positive sample identification with the optional bar code reader, and temperature control of individual samples with the optional sample heater unit." [] is_a: OBI:0000464 ! Bruker autosampler [Term] id: OBI:0000493 name: rapid resolution column def: "A rapid resolution column is a chromatography column as marketed by Agilent, which is used with a rapid resolution cartridge to ensure a fast chromatography process with good separation resolution." [] is_a: OBI:0000932 ! material separation device [Term] id: OBI:0000494 name: liquid chromatography autosampler def: "Designed to perform capillary LC with injection of sample volumes ranging from nL to L." [] is_a: OBI:0000485 ! chromatography instrument [Term] id: OBI:0000495 name: vacuum degasser def: "A degassing system used for degassing solvents in liquid chromatography. Dissolved gasses, usually nitrogen and oxygen from the air, tend to be evolved in the mobile phase as the pressure is reduced when the mobile phase leaves the liquid chromatography column and enters the detector. Gasses in the mobile phase in the detector can produce completely unacceptable noise and, thus, must be removed. The dissolved gasses were originally removed under vacuum but, unfortunately, are soon replaced if the solvent is left in contact with air at atmospheric pressure. For this reason degassing is now usually carried out by bubbling helium through the mobile phase reservoirs. Secondly, vacuum is used in the thermionic detector. This consists of a device, very similar in design to the thermionic valve which is attached to a vacuum and a small quantity of the eluent from a gas chromatography column allowed to bleed through it. Helium is used as the carrier gas. The presence of solute vapor causes the thermionic current to fall. This type of detector tends to become contaminated rather readily." [] is_a: OBI:0000589 ! chromatography pump system [Term] id: OBI:0000496 name: capillary column def: "A capillary column is a thin tube with a small inner diameter, usually around 0.5 mm." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000497 name: sample inlet def: "The column inlet (or injector) provides the means to introduce a sample into a continuous flow of carrier gas. The inlet is a piece of hardware attached to the column head." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000498 name: NMR tube washing system def: "An automatic cleaning system for NMR tubes that removes previous probe and sample residues in order to allow for tube recycling." [] is_a: OBI:0000968 ! device [Term] id: OBI:0000499 name: NMR console def: "A component of an NMR instrument that controls the activities of the other components." [] is_a: OBI:0000968 ! device [Term] id: OBI:0000500 name: dual loop autosampler def: "A dual loop autosampler is an autosampler that is designed for handling both analytical (10 mL/min flow rate) to preparative scale sample purification (100 mL/min flow rate)." [] is_a: OBI:0000494 ! liquid chromatography autosampler [Term] id: OBI:0000501 name: variable wavelength detector def: "A chromatography detector, that can detect signals within a certain range at user-defined wavelengths." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000503 name: Bruker LC-NMR platform def: "The LC-NMR/MS setup was first introduced by Bruker BioSpin in 1999. An LC-NMR system including a Bruker Peak Sampling Unit (BPSU-36) was coupled with a Bruker Daltonics esquire series ion trap mass spectrometer via a Bruker NMR-MS interface (BNMI). Since October 2004 the Bruker Daltonics microTOF-LC time-of-flight mass spectrometer can also be integrated in an LC-NMR setup." [] is_a: OBI:0000596 ! Bruker NMR instrument [Term] id: OBI:0000504 name: sample injection system def: "An automated chromatography system that injects the sample into the chromatography columns in order to increase speed and minimize human involvement in the purification process for better reproducibility." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000505 name: multiple wavelength detector def: "A chromatography detector, that can detect many discrete wavelengths in parallel and produces a multiple wavelength chromatographic profile." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000506 name: photoionization detector def: "The selective determination of aromatic hydrocarbons or organo-heteroatom species is the job of the photoionization detector (PID). This device uses ultraviolet light as a means of ionizing an analyte exiting from a GC column. The ions produced by this process are collected by electrodes. The current generated is therefore a measure of the analyte concentration. f the amount of ionization is reproducible for a given compound, pressure, and light source then the current collected at the PID's reaction cell electrodes is reproducibly proportional to the amount of that compound entering the cell. The reason why the compounds that are routinely analyzed are either aromatic hydrocarbons or heteroatom containing compounds (like organosulfur or organophosphorus species) is because these species have ionization potentials (IP) that are within reach of commercially available UV lamps. The available lamp energies range from 8.3 to 11.7 ev, that is, lambda max ranging from 150 nm to 106 nm. Although most PIDs have only one lamp, lamps in the PID are exchanged depending on the compound selectivity required in the analysis." [] synonym: "PID" EXACT [] is_a: OBI:0000637 ! gas chromatography detector [Term] id: OBI:0000507 name: gas generator def: "An instrument that generates gases for use with the gas chromatograph. Previously gas was obtained from gas tanks or gas cylinders. However, over the past decade the use of gas generators have become more popular as it avoids having gases at high pressure in the laboratory which is perceived by some as potentially dangerous. In addition, the use of a hydrogen generator avoids the use of a cylinder of hydrogen at high pressure which is also perceived by some as a serious fire hazard despite the fact that they have been used in laboratories, quite safely for nearly a century." [] is_a: OBI:0000542 ! gas chromatography equipment [Term] id: OBI:0000508 name: column jacket def: "A column jacket is a piece of column chromatography equipment that covers a column in order to ensure thermoisolation and create a controllable thermostatic microenvironment." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000509 name: electron capture detector def: "The electron capture detector is a GC detector that uses a radioactive Beta emitter (electrons) to ionize some of the carrier gas and produce a current between a biased pair of electrodes. When organic molecules that contain electronegative functional groups, such as halogens, phosphorous, and nitro groups pass by the detector, they capture some of the electrons and reduce the current measured between the electrodes." [] synonym: "ECD" EXACT [] is_a: OBI:0000637 ! gas chromatography detector [Term] id: OBI:0000510 name: reversed phase column def: "A reversed phase column is a chromatography column in which the mobile phase is more polar than the stationary phase. Its counterpart is the normal phase column." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000511 name: injector lubricant def: "A lubricant used in liquid chromatography that eases sample injector penetration." [] is_a: OBI:0000601 ! chromatography consumable [Term] id: OBI:0000512 name: isolation of cell population def: "a process in which a population of cells with certain characteristics is isolated from a larger population" [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0000513 name: DISCOVERY console def: "The Discovery console is a Windows XP Professional-based, integrated console designed especially for Solid-State NMR. The console includes everything needed to interface to any magnet and solids probe - from computer to cables to duplexing network." [] is_a: OBI:0000599 ! tecmag NMR console [Term] id: OBI:0000514 name: Bruker AMX series NMR instrument def: "A series of older Bruker NMR magnets, now out of production. The Bruker AMX500 has proven an extremely reliable workhorse, with excellent lineshape yielding superior water suppression even without gradients. The Oxford 11.7 Tesla 5.2 cm bore magnet rests on a TMC vibration damping table. Homogeneity is controlled by a BSN-18 and BSN-2 with 19 shim controls. In addition to the 5 mm triple resonance probe, the AMX is equipped with a 10mm broadband observe probe." [] is_a: OBI:0000596 ! Bruker NMR instrument [Term] id: OBI:0000515 name: chromatofocusing column def: "A chromatofocusing column is a chromatography column in which a resin is equilibrated at one pH and eluted at a second pH. The use of a weak ion-exchange resin causes a pH gradient to be formed at the solvent front owing to the buffering action of the resin. This pH gradient in turn leads to an ordering of proteins by isoelectric point. Molecules of charge sign opposite the resin bind; those of charge sign like the resin do not bind." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000516 name: NMR probe def: "Part of an NMR instrument that detects the signals emitted from a sample. No single probe can perform the full range of experiments, and probes that are designed to perform more than one type of measurement usually suffer from performance compromises. The probe represents a rather fragile single point of failure that can render an NMR system completely unusable if the probe is dropped or otherwise damaged. Probes are usually characterised by Sample diameter and Frequency.n alt The instrument that transmits and receives radiofrequency to and from the NMR sample." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000517 name: NMR magnet def: "A magnet which induces a certain frequency (MHz) and which has a certain bore diameter.n alt The NMR signal is a natural physical property of the certain atomic nuclei but it can only be detected with an external magnetic field. A magnet is a fundamental part of an NMR instrument which induces an electromagnetic force field (RF pulse) and by this excites and aligns the spins of the electrons of the NMR acquisition nucleus. It is usually a big (superconducting) electromagnet which is cooled by liquid helium and can be adjusted to a frequency between 200 and 950 MHz. The magnetic field strength is measured in Tesla or Gauss." [] is_a: OBI:0000968 ! device [Term] id: OBI:0000518 name: trap column def: "A trap column is a chromatography column which is used prior to a, e.g. mass spectrometry, separation to clean up or concentrate controlled amounts of samples prior to elution to a detector." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000519 name: flow probe def: "An NMR probe that allows the automatized flow-through of a sample. The sample is aspirated via a syringe pump into the Flow probe, the NMR spectrum is acquired and when the experiment is complete, the sample is returned to back to an external source (well plate) or flushed to waste. Sometimes pulsed field gradients (PFG) can be established in flow probes." [] is_a: OBI:0000516 ! NMR probe [Term] id: OBI:0000520 name: clinical chemistry assay def: "An analyte assay which uses analytical methods to produce measurements and data on the concentration of chemical parameters (analytes) present in a bodily fluid collected from an organism." [] synonym: "chemical pathology" EXACT [] synonym: "detection of analyte in blood sample" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0000521 name: flame ionization detector def: "A flame ionization detector is a GC detector that consist of a hydrogen/air flame and a collector plate which are normally heated independently of the chromatographic oven. Heating is necessary in order to prevent condensation of water generated by the flame and also to prevent any hold-up of solutes as they pass from the column to the flame. There is an electrode above the flame to collect the ions formed at a hydrogen/air flame. The number of ions hitting the collector is measured and a signal is generated. Flame ionization detectors are most widely used and generally applicable for gas chromatography and hence is used for routine and general purpose analysis. It is easy to use but destructive of the sample." [] synonym: "FID" EXACT [] is_a: OBI:0000637 ! gas chromatography detector [Term] id: OBI:0000522 name: vial def: "A container made from solid material and primarily used for holding liquid." [] is_a: OBI:0000967 ! container [Term] id: OBI:0000523 name: magic angle spinning rotor def: "A rotor device that holds the NMR sample and enables the adjustment of the orientation of the rotation axis for a sample in a NMR instrument in the magic angle." [] synonym: "MAS rotor" EXACT [] is_a: OBI:0000968 ! device [Term] id: OBI:0000524 name: Varian VXR spectrometer def: "A Varian NMR spectrometer." [] is_a: OBI:0000611 ! Varian NMR instrument [Term] id: OBI:0000525 name: splitless GC injector def: "Injected sample enters column immediately (while split valve to split vent is closed). Here a sample is introduced into a heated small chamber via a syringe through a septum - the heat facilitates volatilization of the sample and sample matrix. The carrier gas then either sweeps the entirety (splitless mode) or a portion (split mode) of the sample into the column. In split mode, a part of the sample/carrier gas mixture in the injection chamber is exhausted through the split vent." [] is_a: OBI:0000504 ! sample injection system [Term] id: OBI:0000526 name: preparative autosampler def: "For preparative LC with injection of sample volumes ranging from L to mL ranges." [] is_a: OBI:0000494 ! liquid chromatography autosampler [Term] id: OBI:0000527 name: flow high resolution probe def: "Hyphenated analytical techniques combining mass spectrometry and chromatography are well-established laboratory tools. The combination of chromatography and NMR has also made its way into the analytical laboratory. Further developments even combine all three techniques into an LC-NMR/NMR-MS system. The use of solid phase extraction provides an efficient interface between chromatography and NMR with demands for special type of flow probes." [] synonym: "flow HR-probe" EXACT [] is_a: OBI:0000480 ! Bruker high resolution probe [Term] id: OBI:0000528 name: liquid chromatography valve def: "A sample valve that must be able to sustain pressures up to 10,000 p.s.i., although it is most likely to operate on a continuous basis, at pressures of 3,000 p.s.i. or less. The higher the operating pressure the tighter the valve seating surfaces must be forced together to eliminate any leak. It follows that any abrasive material, however fine, that passes into the valve can cause the valve seating to become scored each time it is rotated which will ultimately lead to leaks. This will cause the sample size to vary between samples and eventually affect the accuracy of the analysis. It follows that any solid material must be carefully removed from any sample before filling the valve. The sample volume of an internal loop valve is situated in the connecting slot of the valve rotor and can be used only for relatively small sample volumes. Internal sample loop valves provide samples with volumes ranging from 0.1 ml to about 0.5 ml. Valve operation is shown in figure 6. The left-hand side diagram shows the load position. The sample occupies the rotor slot and has been filled by passing the sample from an appropriate syringe through the rotor slot to waste. While loading the sample, the mobile phase supply is passed through the valve directly to the column. To place the sample onto the column, the valve is then rotated and the valve slot containing the sample is now placed between the solvent supply and the column. As a result, the sample is passed into the column by the flow of solvent." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000529 name: JEOL NMR probe def: "An NMR probe that is manufactured by JEOL." [] is_a: OBI:0000516 ! NMR probe [Term] id: OBI:0000530 name: Bruker UltraShield Plus NMR magnet def: "An NMR magnet of which Brukers claims it is the latest and most advanced self-shielding NMR magnet technology ever developed. These magnets are the ultimate advancement in high performance, actively-shielded NMR solutions. They offer unprecedented shielding performance whilst ensuring no compromise in system homogeneity, stability or cryogenic specifications." [] is_a: OBI:0000597 ! Bruker NMR magnet [Term] id: OBI:0000531 name: Bruker CryoProbe def: "The Bruker BioSpin CryoProbe is a high-performance cryogenically cooled probe developed for high-resolution applications. It has improved signal/noise (S/N) ratios obtained by reducing the operating temperature of the coil and the pre-amplifier. As a result, the efficiency of the coil is improved and the noise of the coil and the pre-amplifier are reduced.The dramatic increase in the S/N ratio by a factor of 3-4, as compared to conventional probes, leads to a possible reduction in experiment time of up to 16 or a reduction in required sample concentration by a factor of up to 4. The CryoProbes possess key characteristics for NMR analysis:n Significant S/N gains (with moderately salty samples also)n Short pulse widthsn Short ring down timesn Linear behavior in power responsen Gradient capabilityn CryoProbes are available as Triple Resonance, Dual, Selective X Detection, MicroImaging, and Quad Nucleus Probes configurations at 400 MHz and highern All high resolution probes have a lock circuitn All high resolution probes have Z-gradient." [] is_a: OBI:0000561 ! Bruker NMR probe [Term] id: OBI:0000532 name: column cartridge def: "A device that binds the chromatography column and additional connector elements and / or valves or syringes into one physical unity for further processing." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000533 name: affinity column def: "An affinity column is a chromatography column that is used in affinity chromatography. Differences in the affinity of molecules to be separated to a stationary phase are used for discriminate retention." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000534 name: tecmag NMR instrument def: "An NMR instrument that is manufactured by tecmag." [] is_a: OBI:0000566 ! NMR instrument [Term] id: OBI:0000535 name: gel filtration column def: "A Gel filtration column is a chromatography column for size-exclusion chromatography, in which the stationary phase is a gel. The main application of gel filtration chromatography is the fractionation of proteins and other water-soluble polymers." [] is_a: OBI:0000618 ! size exclusion column [Term] id: OBI:0000536 name: fraction collector def: "A fraction detector is a device that allows regular or specified samples to be taken from a column eluate and stored in a retrievable form. The storage vessels are usually small sample tubes or vials that are oriented in a rotating disk or in a moving belt, there movement usually being controlled by a microprocessor. On receiving a signal from the microprocessor, the next vial is placed under the column outlet and the eluate collected until receiving another signal from the computer. Once the properties of the chromatogram that describes the separation has been ascertained, then the collection program can be defined. The fractions can be collected on a basis of time either at regular intervals or a specific times to collect specific peaks. Alternatively the fractions can be collected by monitoring the detector output and when a peak starts to elute the fraction collector is activated and the peak collected in a specific vial. When the peak returns to base line the column eluate is then directed to waste until the next peak starts eluting. Fraction collectors are in common use with most liquid chromatographs. They are used to collect samples for further purification, subsequent examination by spectroscopic techniques or for biological or organoleptic testing." [] is_a: OBI:0000485 ! chromatography instrument [Term] id: OBI:0000537 name: copy number variation profiling assay def: "An assay that determines lost or amplified genomic regions of DNA by comparing genomic DNA originating from tissues from the same or different individuals using specific techniques such as CGH, array CGH, SNP genotyping" [] synonym: "CNV analysis" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000538 name: in-line filter def: "A solvent filter that sits between the pump and the injection valve that prevents dust particles, general debris and, to some extent, bacteria from entering the chromatography system. Contaminants can interfere with the low-pressure gradient former or the pump and particles entering valves may interfere with the proper function. The result could cause an increased baseline noise, non-repeatable gradient forming, unreliable flow rate or other interferences. Solvent in-line filters are low-pressure filters and will allow a high flow rate due to a large surface area and large porosity." [] is_a: OBI:0000592 ! chromatography detector filter [Term] id: OBI:0000539 name: imaging NMR probe def: "An NMR probe that is designed for generating pictures from sample states via NMR imaging." [] is_a: OBI:0000516 ! NMR probe [Term] id: OBI:0000540 name: isolation of adherent cells def: "a material separation process in which cells that stick to the container in which they are grown as a cell culture are separated from those in the liquid component of the culture. The output of this process are adherent cells." [] is_a: OBI:0000512 ! isolation of cell population [Term] id: OBI:0000541 name: Bruker AC series NMR instrument def: "A series of older Bruker NMR magnets, now out of production." [] is_a: OBI:0000596 ! Bruker NMR instrument [Term] id: OBI:0000542 name: gas chromatography equipment def: "Any device used in a gas chromatography experiment." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000543 name: syringe filter def: "A small membrane filter of defined pore size, that filters samples from a syringe." [] is_a: OBI:0000592 ! chromatography detector filter [Term] id: OBI:0000544 name: Bruker SampleRail system def: "This Instrument system automatically prepares an NMR sample, inserts it into an NMR magnet, performs NMR experiments on the sample, and transports it back to the preparation system. The SampleRail fulfills the transporting tasks from the preparation system into the NMR magnet and back." [] is_a: OBI:0000968 ! device [Term] id: OBI:0000545 name: column compartment def: "For chromatography analyses, the ability to maintain a stable column environment regardless of ambient temperature fluctuations is critical for maintaining retention time precision. In order to ensure such stable conditions at different chromatography steps a column compartment can be installed that ensures e.g. stable temperature of the column in a given step." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000546 name: capillary pump system def: "A pump system optimized for capillary chromatography." [] is_a: OBI:0000589 ! chromatography pump system [Term] id: OBI:0000547 name: evaporative light scattering detector def: "The evaporative light scattering detector, as its name implies, utilizes a spray that continuously atomizes the column eluent into small droplets. These droplets are allowed to evaporate, leaving the solutes as fine particulate matter suspended in the atomizing gas." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000548 name: isolation of PBMCs def: "a process in which cells with a single nucleus are isolated from a blood sample" [] is_a: OBI:0000512 ! isolation of cell population [Term] id: OBI:0000549 name: column cartridger def: "A chromatography device where the column cartridge is inserted into and stabilised." [] is_a: OBI:0000485 ! chromatography instrument [Term] id: OBI:0000550 name: nitrogen generator def: "A gas generator that generates nitrogen gas." [] is_a: OBI:0000507 ! gas generator [Term] id: OBI:0000551 name: needle assembly def: "The needle assembly attached to the autosampler, comprises the injector needle that feeds a sample or carrier gas into the inlet" [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000552 name: reverse transcribed polymerase chain reaction def: "reverse transcribe pcr is a process which allow amplification of cDNA during a pcr reaction while the cDNA results from a retrotranscription of messenger RNA isolated from a material entity." [] synonym: "reverse transcription polymerase chain reaction" EXACT [] synonym: "RT-PCR" EXACT [] is_a: OBI:0600058 ! enzymatic amplification [Term] id: OBI:0000553 name: Bruker Capillary LC-NMR platform def: "Capillary LC-NMR is a hyphenated technique coupling capillary liquid chromatography and NMR, which increases sensitivity dramatically through the use of miniaturization of the chromatographic techniques and NMR detection volume. LC-NMR hyphenated systems separate a mixture into its pure components and couple the output to NMR for automatic sample analysis. The ever increasing need to measure lower sample amounts and lower level impurities demands the highest NMR sensitivity. Traditional LC-NMR systems with relatively large peak volumes are not optimized for such low levels of detection. Bruker BioSpin, together with Waters and Protasis has developed a Capillary LC-NMR system. The latest capillary LC attributes and highest capillary flow probe sensitivity combine with state of the art NMR systems technology. Greater mass sensitivity and faster spectral analysis with smaller sample volumes is possible. This system is ideal for analysis of metabolites and impurities associated with the drug development process." [] is_a: OBI:0000596 ! Bruker NMR instrument [Term] id: OBI:0000554 name: gas chromatography oven def: "A gas chromatography oven is an oven with a heated connection between the GC and the MS instrument in a GCMS-analysis, that keeps compounds in the gas phase as they leave the GC oven." [] is_a: OBI:0000542 ! gas chromatography equipment [Term] id: OBI:0000555 name: autosampler def: "An optional part of an NMR instrument used to hold samples prior to NMR analysis and that sequentially loads these samples into the analytical part of the NMR instrument. n alt The autosampler is an automatic sample changer device." [] is_a: OBI:0000968 ! device [Term] id: OBI:0000556 name: isocratic pump system def: "A pump system optimized for isocratic chromatography." [] is_a: OBI:0000589 ! chromatography pump system [Term] id: OBI:0000557 name: flash pump system def: "Any pump system used in flash column chromatography to push the solvent through the column. Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography)." [] is_a: OBI:0000589 ! chromatography pump system [Term] id: OBI:0000558 name: Varian UNITY INOVA spectrometer def: "The UNITY INOVA is also the easiest spectrometer to use and is also the choice of those interested in using advanced NMR techniques in their own research, but without becoming, or hiring, an NMR expert. A complete set of turnkey operating environments is available for the UNITY INOVA covering the structure and dynamics of biological macromolecules, small molecules, solids, and imaging. These packages put the combined NMR expertise of the entire Varian NMR community at your fingertips." [] is_a: OBI:0000611 ! Varian NMR instrument [Term] id: OBI:0000559 name: liquid NMR probe def: "An NMR probe that is designed to hold a liquid sample." [] is_a: OBI:0000516 ! NMR probe [Term] id: OBI:0000560 name: ion exchange column def: "An ion exchange column is a chromatography column that is used in ion exchange chromatography and anion or cation exchange resins to enable separation." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000561 name: Bruker NMR probe def: "An NMR probe that is manufactured by Bruker." [] is_a: OBI:0000516 ! NMR probe [Term] id: OBI:0000562 name: anion trap column def: "An anion trap column is a trap column and ion-exchange column which contains cationic anion-exchange resins." [] is_a: OBI:0000518 ! trap column [Term] id: OBI:0000563 name: fluorescene detector def: "A single wavelength detector, where the excitation light wavelength is normally a mercury lamp generated high intensity UV light at 253.7 nm. Many substances that fluoresce will be excited by light of this wavelength and hence be detected." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000564 name: tecmag EAGLE probe def: "The Eagle is a 4 mm 1H/X solid-state MAS probe with a top spinning speed of 18 kHz. Its simple design is robust, reliable and easy to spin. Configurations are available for 200 to 600 MHz wide bore magnets on Tecmag, Bruker, Chemagnetics, JEOL and Varian spectrometers." [] is_a: OBI:0000479 ! solid NMR probe [Term] id: OBI:0000565 name: electrical conductivity detector def: "The electrical conductivity detector measures the conductivity of the mobile phase. There is usually background conductivity which must be backed-off by suitable electronic adjustments. If the mobile phase contains buffers, the detector gives a base signal that completely overwhelms that from any solute usually making detection impossible. Thus, the electrical conductivity detector a bulk property detector. and senses all ions whether they are from a solute or from the mobile phase. In order to prevent polarization of the sensing electrodes, AC voltages must be used and so it is the impedance not the resistance of the electrode system that is actually measured. From a physical chemistry stand point the conductivity of a solution is more important than its resistance. However, it is the resistance (impedance) of the electrode system that determines the current across it. The resistance of any conductor varies directly as its length and inversely as its cross sectional area." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000566 name: NMR instrument def: "An Instrument which is used to carry out a NMR analysis of some sample." [] synonym: "magnetic resonance imaging scanner" EXACT [] synonym: "MRI scanner" EXACT [] synonym: "NMR instrument" EXACT [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000567 name: Bruker UltraShield NMR magnet def: "An NMR magnet manufactured by Bruker that ensures field homogeneity without amplified effects from vibrations or thermal changes. This magnet technology uses active shielding and optimizes coil design." [] is_a: OBI:0000597 ! Bruker NMR magnet [Term] id: OBI:0000568 name: piston-seal def: "The seal made by a piston in a diaphragm pump. The unique property of the reciprocating diaphragm pump is that the actuating piston does not come into direct contact with the mobile phase and thus, the demands on the piston-cylinder seal are not so great. The diaphragm has a relatively high surface area and thus, the movement of the diaphragm is relatively small and consequently the pump can be operated at a fairly high frequency. High frequency pumping results in a very significant reduction in pulse amplitude and, in addition, high frequency pulses are more readily damped by the column system. Nevertheless, it must be emphasized that diaphragm pumps are not pulseless." [] is_a: OBI:0000601 ! chromatography consumable [Term] id: OBI:0000569 name: mass selective detector def: "A mass selective detector is a GC detector that uses mass spectrometry. It is based upon the ionization of solute molecules in the ion source and the separation of the ions generated on the basis of their mass/charge ratio by an analyzer unit. This may be a magnetic sector analyzer, a quadruple mass filter, or an ion trap. Ions are detected by a dynode electron multiplier." [] synonym: "mass spectrometry detector" EXACT [] is_a: OBI:0000637 ! gas chromatography detector [Term] id: OBI:0000570 name: spin column def: "A spin column is a chromatography column which is suitable for putting it into a centrifuge. A spin column enforces separation through increased G-forces while spinning the column in a centrifuge. It is often used in DNA gel extraction kits." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000571 name: manufacturer role def: "Manufacturer role is a role which inheres in a person or organization and which is realized by a manufacturing process." [] is_a: BFO:0000023 ! role [Term] id: OBI:0000572 name: transfer line def: "A combination of devices that are used in connection with a sampling head for transferring components of an applied sample to the analyzing part of a chromatography system." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000573 name: gradient pump system def: "A pump system optimized for gradient chromatography." [] is_a: OBI:0000589 ! chromatography pump system [Term] id: OBI:0000574 name: high temperature column def: "A high temperature column is a chromatography column which is suitable for and withstands very high temperatures in chromatography ovens." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000575 name: Bruker Ultrastabilized NMR magnet def: "An NMR magnet manufactured by Bruker for Ultra-High Field NMR, available from 750 MHz to 900 MHz, which provides reliable operation at reduced temperature and ambient pressure via being rigidly mounted and stabilized." [] is_a: OBI:0000597 ! Bruker NMR magnet [Term] id: OBI:0000576 name: scattered molecular aggregate def: "a material entity that consists of all the molecules of a specific type that are located in some bounded region and which is part of a more massive material entity that has parts that are other such aggregates" [] synonym: "Collective" EXACT [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0000577 name: obsolete_molecular concentration def: "A concentration is a relational quality that inheres in a material entity towards molecular scattered aggregate that is part of it by virtue of some ratio of masses of the two or the counts of the grains of the two or volume occupied by the larger material entity." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000578 name: NMR sample tube def: "The sample-tube holds the NMR sample and sits in the nmr probe. It is usually a glass tube of 5-20mm diameter." [] is_a: OBI:0000836 ! test tube [Term] id: OBI:0000579 name: Varian UNITY spectrometer def: "The predecessor series of the Varian UNITY INOVA spectrometer." [] is_a: OBI:0000611 ! Varian NMR instrument [Term] id: OBI:0000580 name: AVANCE II spectrometer def: "A spectrometer suitable for metabolomics and in vivo NMR studies but structural analysis of small molecules and low molecular weight proteins can also be performed. To accomplish these studies there are six probe-heads available. A successor, the AVANCE III came out recently." [] is_a: OBI:0000596 ! Bruker NMR instrument [Term] id: OBI:0000581 name: y-column connector def: "A column connector that connects one column on one side with two columns at the other side, hence building a Y shaped structure." [] is_a: OBI:0000478 ! column connector [Term] id: OBI:0000582 name: Bruker LC-NMR/MS platform def: "Includes the connection to a high-resolution TOF-LC-MS system." [] is_a: OBI:0000596 ! Bruker NMR instrument [Term] id: OBI:0000583 name: refractive index detector def: "For analyzing non-UV absorbing substances, such as carbohydrates, lipids and polymers. This is also the detector of choice for gel permeation chromatography. The refractive index detector is one of the least sensitive LC detectors. It is very sensitive to changes in ambient temperature, pressure changes, flow-rate changes and can not be used for gradient elution. Despite these many disadvantages, this detector is extremely useful for detecting those compounds that are nonionic, do not adsorb in the UV, and do not fluoresce. There are many optical systems used in refractive index detectors but one of the most common is the differential refractive index detector." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000584 name: anion exchange column def: "An anion exchange column is a chromatography column that is used in anion exchange chromatography and which enables the separation of anion mixtures." [] is_a: OBI:0000560 ! ion exchange column [Term] id: OBI:0000586 name: plunger column def: "A plunger column is a chromatography column with adjustable heigth control. By means of an adjustable endpiece (plunger) the user can adjust the column length without disturbing the packed bed. Plunger columns can equalize volume changes and thus avoids dead volumes within the column." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000588 name: flame photometric detector def: "The determination of sulfur or phosphorus containing compounds is the job of the flame photometric detector (FPD). This device uses the chemiluminescent reactions of these compounds in a hydrogen/air flame as a source of analytical information that is relatively specific for substances containing these two kinds of atoms. The emitting species for sulfur compounds is excited S2. The lambda max for emission of excited S2 is approximately 394 nm. The emitter for phosphorus compounds in the flame is excited HPO (lambda max = doublet 510-526 nm). In order to selectively detect one or the other family of compounds as it elutes from the GC column, an interference filter is used between the flame and the photomultiplier tube (PMT) to isolate the appropriate emission band. The drawback here being that the filter must be exchanged between chromatographic runs if the other family of compounds is to be detected." [] synonym: "FPD" EXACT [] is_a: OBI:0000637 ! gas chromatography detector [Term] id: OBI:0000589 name: chromatography pump system def: "Better flow rates can be achieved by using a pump or by using compressed gas (e.g. air, nitrogen, or argon) to push the solvent through the column (flash column chromatography)." [] is_a: OBI:0000485 ! chromatography instrument [Term] id: OBI:0000590 name: Bruker 1mm MicroProbe def: "Over the past few years there has been a significantly growing demand for miniaturization in all areas ofmodern research and development. Evoked by many exciting applications, there is a need for analytical methods which require less amounts of sample. Bruker BioSpin meets this challenge with a revolutionary NMR probe design: The 1mm MicroProbe. It operates with disposable 1mm capillary sample tubes and the sample volume of 5 microliters enables the use of lowest amounts of sample to run all high resolution NMR experiments with outstanding sensitivity and up to 16 times faster measurements. Due to the TXI-type probe design, the z-gradient coil and the automatic matching and tuning accessory, the 1mm MicroProbe can be used for a wide variety of NMR experiments. The key advantages of this probe include:n up to 4 times higher mass sensitivity than 5mm conventional probes (with respect to the same sample amount)n excellent solvent suppression propertiesn virtually no salt effectn discrete samples in tubes that can be sealed and storedn automation accessory for sample preparation and handling available." [] is_a: OBI:0000561 ! Bruker NMR probe [Term] id: OBI:0000591 name: Bruker BEST NMR system def: "The introduction of biological screening and combinatorial chemistry for chemical synthesis has also introduced new requirements for NMR automation, e.g., the use of well plates for sample input, increased demands on throughput, and the need for quick and simple interpretation of the acquired NMR data." [] synonym: "Bruker Efficient Sample Transfer NMR" EXACT [] is_a: OBI:0000464 ! Bruker autosampler [Term] id: OBI:0000592 name: chromatography detector filter def: "An optical filter that is used to obtain monochromatic light of a defined wavelength from detector lamps." [] is_a: OBI:0000601 ! chromatography consumable [Term] id: OBI:0000593 name: cation trap column def: "A cation trap column is a trap column and ion-exchange column which contains anionic cation-exchange resins." [] is_a: OBI:0000518 ! trap column [Term] id: OBI:0000594 name: column adapter def: "An Adapter that enabled the connection of a column to additional devices." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000595 name: pulsed amperometric detector def: "A chromatography detector as used by high-performance anion exchange chromatography that provides sensitive and specific detection of carbohydrates. Pulsed Electrochemical Detection (PED) allows simple, sensitive, and direct detection of numerous polar aliphatic compounds, especially carbohydrates. This technique exploits the electrocatalytic activity of noble metal electrode surfaces to oxidize various polar functional groups. In PED, multi-step potential-time waveforms at Au and Pt electrodes realize amperometric/coulometric detection while maintaining uniform and reproducible electrode activity. The response mechanisms in PED are dominated by the surface properties of the electrode, and, as a consequence, members of each chemical class of compounds produce virtually identical voltammetric responses. Thus, the full potential is realized when combined with high performance liquid chromatography (HPLC)." [] synonym: "PAD" EXACT [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000596 name: Bruker NMR instrument def: "An NMR instrument that is manufactured by Bruker." [] is_a: OBI:0000566 ! NMR instrument [Term] id: OBI:0000597 name: Bruker NMR magnet def: "An NMR magnet that is manufactured by Bruker." [] is_a: OBI:0000517 ! NMR magnet [Term] id: OBI:0000598 name: ozone-induced chemiluminescence detector def: "Although there are many direct ozone chemiluminescent reactions with various gaseous molecules, the incorporation of a conversion step to convert various non-chemiluminescent analytes to a species capable of reacting with ozone to produce chemiluminescence broadens the horizon of this technique tremendously. The conversion of nearly all nitrogen- and sulfur-containing compounds to their respective chemiluminescent species for universal nitrogen and sulfur detection has made nitrogen/sulfur chemiluminescence detection the most widely used analytical methods based upon ozone-induced chemiluminescence. In addition to non-chromatographic applications, nitrogen/sulfur chemiluminescence detection has been adapted to various chromatographic techniques from gas chromatography to liquid and supercritical fluid chromatography as specialized element-specific detectors. The characteristics of these detectors are evaluated and compared to other element-selective detection techniques. The unique features of the chemiluminescence detectors have made them powerful tools in many diverse fields of analytical chemistry." [] is_a: OBI:0000637 ! gas chromatography detector [Term] id: OBI:0000599 name: tecmag NMR console def: "An NMR console manufactured by tecmac." [] is_a: OBI:0000499 ! NMR console [Term] id: OBI:0000600 name: JEOL NMR instrument def: "An NMR instrument that is manufactured by JEOL." [] is_a: OBI:0000566 ! NMR instrument [Term] id: OBI:0000601 name: chromatography consumable def: "A chromatography consumable is a consumable that is used in a chromatography experiment." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000602 name: column frit def: "A part of the column content that separates column packing compartments. In radial columns the packing is supported between two cylindrical frits and the gap between represents the bed height or column length. The outer frit is the column inlet and consequently the sample initially has a large area of stationary phase with which to interact. Frits are porous metal products to prevent unwanted particles from entering the chromatography system. These particles may come from the sample, the solvent or debris generated by the chromatography system itself. Such particles entering the system may lead to clogging of capillaries, interference with the chromatography by changing chromatographic parameters or disturbance of the detector function. Characteristics of a frit, besides the diameter and the thickness, is the porosity (pore distribution, density)." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000603 name: liquid chromatography column def: "A liquid chromatography column is a chromatography column that is used in liquid chromatography, i.e. a column that is provided with a liquid sample mix." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000604 name: detector lamp def: "A lamp used in a chromatography detector that excites sample molecules at certain frequencies / emission wavelengths, e.g. Mercury Vapor Lamp (253.7 nm), Zinc Vapor Lamp (2123.9 nm and 307.6 nm), Cadmium Vapor Lamp (228.8, 326.1,340.3, and 346.6 nm). To obtain monochromatic light an appropriate light filter would be needed." [] is_a: OBI:0000601 ! chromatography consumable [Term] id: OBI:0000605 name: chart recorder def: "The chart recorder is a device that transduces signal-intensities into a graphical peak output: As the separated components of the gas sample emerge into the detector, the change in voltage in the detecting bridge circuit causes a representative peak to be drawn on a chart recorder. The position of the peak along the time axis of the chart measures the component's retention time, which identifies the component. This is directly related to carrier gas flow rate, temperature and column packing and dimensions. The area under each peak is proportional to the concentration of the component of the sample. The area of the peaks inscribed on the chart recorder can be determined by multiplying the height of the peak in mm, by the width of the peak in mm at 1/2 the peak height. The calibration curves for use with the chart recorder are therefore peak area plotted against concentration." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000606 name: open tubular column def: "An open tubular column is a chromatography column in which the particles of the solid stationary phase or the support coated with a liquid stationary phase are concentrated on or along the inside tube wall leaving an open, unrestricted path for the mobile phase in the middle part of the tube." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000607 name: high resolution magic angle spin probe def: "Samples that are neither solid nor liquid, being of biological, chemical, or pharmaceutical interest, reveal highly resolved spectra when magic angle spinning is applied. The correct solution is a gradient, such that the field varies along the spinner axis. This so-called Magic Angle Gradient is employed in Brukers high resolution Magic Angle Spinning (hr-MAS) probes, and is implemented in such a way that it is compatible with the stator and does not interfere with the sample eject or insert. Bruker BioSpin has developed a series of dedicated probes for standard bore magnets to accommodate the rapidly expanding field of hr-MAS. These probes are available in double (e.g. 1H and 13C) and triple resonance (e.g. 1H, 13C, 15N) modes and come equipped with a deuterium lock channel. The probes have automatic sample ejection and insertion capability, with the availability of an optional sample changer, enabling fully automated sample runs. Probes can be equipped with an optional B0 gradient, directed along the magic angle, so that gradient spectroscopy can be done used." [] synonym: "high resolution MAS, hr-MAS" EXACT [] is_a: OBI:0000480 ! Bruker high resolution probe [Term] id: OBI:0000608 name: hydrogen generator def: "A gas generator that generates hydrogen gas." [] is_a: OBI:0000507 ! gas generator [Term] id: OBI:0000609 name: glass column def: "A glass column is a chromatography column made out of glass that is usually used for larger scale and preparative liquid chromatography separations." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000610 name: auto injector def: "A gas chromatography device that can auto-inject a small number of samples an inlet." [] is_a: OBI:0000504 ! sample injection system [Term] id: OBI:0000611 name: Varian NMR instrument def: "An NMR instrument that is manufactured by Varian." [] is_a: OBI:0000566 ! NMR instrument [Term] id: OBI:0000612 name: Bruker MATCH tube holder system def: "The Bruker Multiple Adjustable Tube Clamp Holder MATCH system is a holder for 100 mm long NMR sample tubes with diameters ranging from micro tubes up to 5 mm NMR tubes. The MATCH insert fits into a standard 10 mm Bruker spinner and is suitable for all non-spinning applications.n The MATCH system provides an easy and cost efficient means of optimizing the signal-to-noise ratio of each sample. By matching the NMR tube diameter to the size of the sample, most of the sample can be placed in the active column of the NMR coil. This leads to an enhanced signal detection compared to diluting the same sample quantity in a larger tube." [] synonym: "Bruker Multiple Adjustable Tube Clamp Holder" EXACT [] is_a: OBI:0000484 ! NMR sample holder [Term] id: OBI:0000613 name: Bruker SPE-NMR platform def: "A Solid Phase Extraction (SPE) system provides an interface between liquid chromatography (LC) and NMR. For the process of LC-SPE NMR a chromatographic separation is done and the peaks of interest are trapped on an individual SPE cartridge after the column. The peak selection is done either by UV detection or by evaluation of the on-line registered MS or MSn spectra." [] is_a: OBI:0000596 ! Bruker NMR instrument [Term] id: OBI:0000614 name: guard column def: "Guard columns are installed between the injection valve and the analytical or preparative column and here will remove contaminants and prolong the lifetime of the columns." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000615 name: protein expression profiling assay def: "An assay that determines protein expression and translation activity using protein extracts collected from a material entity." [] synonym: "proteomic analysis" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000616 name: high resolution probe with automatic tuning and matching def: "The Automatic Tuning and Matching (ATM) option for AVANCE spectrometers is available for double resonance probes in fixed-frequency and broadband tunable configurations with either direct or indirect detection. Thus, for multinuclear operation, as often required for applications in inorganic chemistry, ATM facilitates the accurate setting of 90 degree pulse widths on both observe and decoupling channels for each chosen nucleus and each individual sample - even with full automation. Triple resonance probes in fixed-frequency configurations, as typically used for inverse detection with high-field systems." [] synonym: "High Resolution Probes with Automatic Tuning and Matching, HR_probe_with_ATM" EXACT [] is_a: OBI:0000480 ! Bruker high resolution probe [Term] id: OBI:0000617 name: fluorine-induced chemiluminescence detector def: "A gas chromatographic detection system based on the low pressure, gas phase chemiluminescence of the reaction mixture of molecular fluorine with organo-sulfur, -selenium, and -tellurium compounds separated from (gas phase) headspace samples. This detector was originally developed in the research group of John Birks at the University of Colorado, USA and was manufactured and sold by Sievers Instruments (Boulder Colorado, USA). This system can be divided up into three parts: the chromatograph, transfer line, and reaction cell; PMT and photon counting electronics; and the molecular fluorine generator." [] is_a: OBI:0000637 ! gas chromatography detector [Term] id: OBI:0000618 name: size exclusion column def: "A size exclusion column is a chromatography column as used in size exclusion chromatography and which enables the separation of mixtures according to differrences in molecular size." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000619 name: chromatography splitter def: "An adjustable restriction that is placed in the waste outlet to allow the necessary pressure to develop at the column inlet to force a flow (q ml/min) through the column. If the flow of mobile phase is Q ml/min then the waste flow will be (Q-q) ml/min. by adjusting the waste flow, the proportion of the sample entering the capillary column can be varied over a wide range of values and the necessary minimum permissible volume for the particular column in use can be selected for analysis. Unfortunately, the fraction taken in this way may not be representative of the original sample. This is due to the individual solutes in the mixture having different diffusivities and, thus, they distribute themselves across the sampling tube in an irregular manner. In general, the components with higher diffusivities (e.g., those solutes of lower molecular weight) will diffuse away from the bulk sample more quickly than those having lower diffusivities." [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0000620 name: Bruker micro imaging probe def: "For medical, biological and material sciences research, avance imaging systems provide optimal object handling and performance with a variety of samples types. Two classes of imaging probes are available: in vivo probes for handling and sustaining live objects such as animals and plants, and conventional imaging probes for materials samples." [] is_a: OBI:0000561 ! Bruker NMR probe [Term] id: OBI:0000621 name: custom made column def: "A custom made column ia a chromatography column which is specifically tailored according to the needs of the separation as requested by a scientist or working group." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000622 name: gel permeation column def: "A gel permeation column is a chromatography column which is used in gel permeation chromatography and which employs as the stationary phase a swollen gel made by polymerizing and cross-linking styrene in the presence of a diluent which is a nonsolvent for the styrene polymer. The polymer to be analyzed is introduced at the top of the column and then is elutriated with a solvent. The polymer molecules diffuse through the gel at rates depending on their molecular size." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000623 name: NMR spectroscopy assay def: "An assay that exploits the magnetic properties of certain nuclei (those with a spin) to resonate when placed in particular magnetic field conditions. Instruments recording NMR spectrum and sets of analysis can be used to deduce identity of chemical as well as composition of complex chemical mixtures." [] synonym: "Nuclear magnetic resonance spectroscopy" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000624 name: Bruker SampleJet system def: "Bruker BioSpin introduces the SampleJet, a robot for NMR tube automation. The SampleJet has been consciously designed to meet the growing customer demand for simplicity, versatility and higher throughput in NMR sample tube automation.n The SampleJet utilizes the modern-day industry standard for sample arrangements-the 96 well plate array. Therefore, the samples may be handled by standard lab automation devices before or after the NMR measurement." [] is_a: OBI:0000464 ! Bruker autosampler [Term] id: OBI:0000625 name: JEOL ECX NMR spectrometer def: "The ECX series of NMR spectrometers is designed for any laboratory needing an easy-to-use, reliable, routine NMR system. The ECX NMR series is available from 300 to 500 MHz. The console is designed around a modular, digital NMR electronics chassis controlled by an intelligent acquisition computer. For unprecedented flexibility, the JEOL NMR system offers a Windows XP, Mac OSX or LINUX. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world." [] is_a: OBI:0000600 ! JEOL NMR instrument [Term] id: OBI:0000626 name: DNA sequencing assay def: "A sequencing assay which determines information on the sequence of a DNA molecule." [] synonym: "nucleotide sequencing" EXACT [] is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0000627 name: quaternary pump system def: "A pump system that pump and mix up to four different solvents in parallel." [] is_a: OBI:0000589 ! chromatography pump system [Term] id: OBI:0000628 name: carbon nanotube column def: "Carbon nanotubes (CNTs) are known to have high thermal and mechanical stability and have the potential to be high-performance separation media that utilize the nanoscale interactions. CNT can be applied in long capillary tubes for the development of gas chromatography columns. A film of CNTs can be deposited by chemical vapor deposition (CVD) to form the stationary phase in the open tubular format. Altering the CVD conditions can vary the thickness and the morphology of the CNT film, which opens the possibility of selectivity tuning. The ability to fabricate long tubes coated with CNTs can be readily employed in other gas- and liquid-phase separations as well." [] is_a: OBI:0000038 ! chromatography column [Term] id: OBI:0000629 name: Bruker solid magic angle spinning probe def: "Magic angle spinning, nowadays a routine technique for solids NMR, still offers the capability of innovation. The high mechanical performance of MAS probes in conjunction with efficient rf pulse techniques open new exciting fields in solids NMR of biological samples and in the field of quadrupolar nuclei." [] synonym: "solid MAS probe" EXACT [] is_a: OBI:0000561 ! Bruker NMR probe [Term] id: OBI:0000630 name: hematology assay def: "An assay that studies blood and blood producing organs using a variety of techniques and instruments" [] synonym: "blood analysis" EXACT [] synonym: "haematology" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000631 name: Varian MERCURY spectrometer def: "MERCURYplus spectrometers provide superior control, stability, and performance for high-productivity environments. Surface-mount electronics enable a small footprint without compromising data quality. Modular design allows flexible configuration. Direct digital synthesis, linear amplifiers, and other innovative RF and digital technologies enable push-button operation." [] is_a: OBI:0000611 ! Varian NMR instrument [Term] id: OBI:0000632 name: Bruker Metabolic Profiler def: "An NMR platform for conducting metabonomics studies, traditional metabolism studies, and analysis of complex mixtures, featuring an Avance NMR spectrometer and a microTOF from Bruker Daltonics. By combining the structural resolving power of NMR with mass accuracy of the microTOF Bruker offers a complete system for metabolic research. The Metabolic Profiler provides a simple, easy to use and inexpensive base-system to acquire the spectroscopic data, needed to do basic metabolic profiling including metabonomic statistical analysis." [] is_a: OBI:0000596 ! Bruker NMR instrument [Term] id: OBI:0000633 name: column heater def: "The glass liner can be fitted with a separate heater and the volatilization temperature can, thus, be controlled. This flash heater system is available in most chromatographs. By using a syringe with a long needle, the tip can be made to penetrate past the liner and discharge its contents directly into the column packing. This procedure is called 'on-column injection' and, as it reduces peak dispersion on injection and thus, provides higher column efficiencies, is often the preferred procedure." [] is_a: OBI:0000485 ! chromatography instrument [Term] id: OBI:0000634 name: DNA methylation profiling assay def: "An assay that measures the state of methylation of DNA molecules using genomic DNA collected from a material entity using a range of techniques and instrument such as DNA sequencers and often relying on treatment with bisulfites to ensure cytosine conversion." [] synonym: "DNA methylation profiling" EXACT [] is_a: OBI:0002020 ! epigenetic modification assay [Term] id: OBI:0000635 name: JEOL CapNMR probe def: "The JEOL ECA and ECX NMR spectrometers now support the MRM/Protasis CapNMR Probe for well plate-based and microvial-based NMR analysis. The CapNMR probe is available at proton frequencies ranging from 300 MHz to 800 MHz in both indirect configurations (e.g. 1H{13C} and 1H {31P}) and also in triple resonance configurations (e.g. 1H{13C, 15N}, 1H{31P, 15N}). Both employ a high-strength z-directed field gradient. The flowprobes come with the choice of two flowcell volumes: a 5 μl flowcell with an NMR active volume of 2.5 μl, and a 10 μl flowcell with an NMR active volume of 5 μl. The fluidic connections are 75 μm i.d. and 1/32 o.d. FEP Teflon with hastelloy unions for exceptional solvent compatibility." [] is_a: OBI:0000529 ! JEOL NMR probe [Term] id: OBI:0000636 name: acquisition computer def: "A Computer used for NMR, can be divided into central processing unit (CPU), consisting of instruction, interpretation and arithmetic unit plus fast access memory, and peripheral devices such as bulk data storage and input and output devices (including, via the interface, the spectrometer). Under software control, the computer controls the RF pulses and gradients necessary to acquire data, and process the data to produce spectra or images. Note that devices such as the spectrometer may themselves incorporate small computers." [] is_a: OBI:0400107 ! computer [Term] id: OBI:0000637 name: gas chromatography detector def: "A gas chromatography detector is a chromatography detector that locates in the dimensions of space and time, the positions of the components of a mixture that has been subjected to a gas chromatographic process and thus permits the senses to appreciate the nature of the separation. There is no LC detector that has an equivalent performance to the flame ionization detector (FID) used in GC. In general, LC detectors have sensitivities of two to three orders of magnitude less than their GC counterparts and linear dynamic ranges one to two orders of magnitude lower. Only highly specific LC detectors have sensitivities that can approach those of GC detectors." [] synonym: "FID" EXACT [] is_a: OBI:0000481 ! chromatography detector [Term] id: OBI:0000638 name: gas purifier def: "Gas purifiers are instruments used for the removal of gas impurities like hydrocarbons, oxygen, and moisture from carrier gas and fuel gases for GC or GC-MS systems." [] is_a: OBI:0000542 ! gas chromatography equipment [Term] id: OBI:0000639 name: material separation objective def: "is an objective to transform a material entity into spatially separated components." [] is_a: OBI:0000456 ! material transformation objective [Term] id: OBI:0000640 name: indirect detection probe def: "An NMR probe designed to allow the indirect detection of acquisition nuclei." [] is_a: OBI:0000516 ! NMR probe [Term] id: OBI:0000641 name: JEOL ECA NMR spectrometer def: "The ECA series of NMR spectrometers is a high performance, research grade NMR system configurable to a wide range off applications. The ECA NMR is available from 300 to 930 MHz field strengths and is 1GHz ready. The system is designed around a modular, digital NMR electronics chassis controlled from a UNIX or Windows workstation and acquisition system. Both the workstation and spectrometer may be connected to a standard network, allowing seamless remote operation anywhere in the world." [] is_a: OBI:0000600 ! JEOL NMR instrument [Term] id: OBI:0000642 name: atomic emission detector def: "Instead of measuring simple gas phase (carbon containing) ions created in a flame as with the flame ionization detector, or the change in background current because of electronegative element capture of thermal electrons as with the electron capture detector, the AED has a much wider applicability because it is based on the detection of atomic emissions. The strength of the AED lies in the detector's ability to simultaneously determine the atomic emissions of many of the elements in analytes that elute from a GC capillary column (called eluants or solutes in some books). As eluants come off the capillary column they are fed into a microwave powered plasma (or discharge) cavity where the compounds are destroyed and their atoms are excited by the energy of the plasma. The light that is emitted by the excited particles is separated into individual lines via a photodiode array. The associated computer then sorts out the individual emission lines and can produce chromatograms made up of peaks from eluants that contain only a specific element." [] synonym: "AED" EXACT [] is_a: OBI:0000637 ! gas chromatography detector [Term] id: OBI:0000648 name: clustered data set def: "A data set that is produced as the output of a class discovery data transformation and consists of a data set with assigned discovered class labels." [] synonym: "data set with assigned discovered class labels" EXACT [] is_a: IAO:0000100 ! data set [Term] id: OBI:0000649 name: data set of features def: "A data set that is produced as the output of a descriptive statistical calculation data transformation and consists of producing a data set that represents one or more features of interest about the input data set." [] is_a: IAO:0000100 ! data set [Term] id: OBI:0000650 name: differential expression analysis data transformation def: "A differential expression analysis data transformation is a data transformation that has an objective of differential expression analysis. Frequently this data transformation involves summarizing or otherwise aggregating signals from various samples categorized into groups, and calculating measures of group differences from these aggregated signals." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0000651 name: urine specimen def: "a portion of urine collected from an organism" [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0000652 name: material combination def: "is a material processing with the objective to combine two or more material entities as input into a single material entity as output." [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000653 name: fuzzy clustering objective def: "A fuzzy clustering objective is a data transformation objective where the aim is to assign input objects (typically vectors of attributes) a probability that a point belongs to a class, where the number of class and their specifications are not known a priori." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0000654 name: device setting def: "a quality inheres_in some device and is concretization of some (device_setting_specification and is_about a quality of the device" [] is_a: BFO:0000019 ! quality [Term] id: OBI:0000655 name: blood specimen def: "a material entity derived from a portion of blood collected from an organism" [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:0000656 name: data set of predicted values according to fitted curve def: "A data set which is the output of a curve fitting data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints." [] is_a: IAO:0000100 ! data set [Term] id: OBI:0000658 name: data representational model def: "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." [] synonym: "data structure" EXACT [] synonym: "data structure specification" EXACT [] is_a: IAO:0000033 ! directive information entity [Term] id: OBI:0000659 name: specimen collection process def: "A planned process with the objective of collecting a specimen." [] synonym: "specimen collection" EXACT [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000660 name: background corrected data set def: "A data set that is produced as the output of a background correction data transformation." [] is_a: IAO:0000100 ! data set [Term] id: OBI:0000661 name: enzyme-linked immunosorbent assay def: "An analyte assay where binding of an enzyme linked antibody to a material entity that is immobilized on solid support is detected utilizing a chemiluminescent reaction. Depending on the setup, the enzyme-linked antibody could be binding directly to the analyte, or it serves as a secondary antibody detecting binding of the primary antibody to the analyte." [] synonym: "ELISA" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0000662 name: error corrected data set def: "A data set that is produced as the output of an error correction data transformation and consists of producing a data set which has had erroneous contributions from the input to the data transformation removed (corrected for)." [] is_a: IAO:0000100 ! data set [Term] id: OBI:0000663 name: class prediction data transformation def: "A class prediction data transformation (sometimes called supervised classification) is a data transformation that has objective class prediction." [] synonym: "supervised classification data transformation" EXACT [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0000664 name: BrdU incorporation assay def: "A cell proliferation assay in which cells are cultured in the presence of BrdU which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle), substituting for thymidine during DNA replication, which can be quantified by BrdU specific antibodies." [] is_a: OBI:0000891 ! cell proliferation assay [Term] id: OBI:0000665 name: obsolete intracellular cytokine staining assay def: "The measurement of cytokines within the cytoplasm of a cell by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer." [] synonym: "ICCS" EXACT [] synonym: "ICS" EXACT [] synonym: "intracellular cytokine staining (ICS)" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: OBI:0000916 [Term] id: OBI:0000666 name: background correction data transformation def: "A background correction data transformation (sometimes called supervised classification) is a data transformation that has the objective background correction." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0000667 name: obsolete MHC multimer staining assay def: "An MHC multimer assay is an assay that detects T cells capable of binding the MHC:ligand complexes present in the multimer. The multimer is fluorescently labelled. The T cells bound to multimers are counted in a flow cytometer" [] synonym: "MHC tetramer assay" EXACT [] synonym: "MHC tetramer/multimer staining" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: OBI:1110179 [Term] id: OBI:0000668 name: error correction data transformation def: "An error correction data transformation is a data transformation that has the objective of error correction, where the aim is to remove (correct for) erroneous contributions from the input to the data transformation." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0000669 name: tritiated thymidine incorporation assay def: "A cell proliferation assay in which cells are cultured in the presence of tritiated thymidine which is incorporated into newly synthesized DNA of replicating cells (during the S phase of the cell cycle). The radioactivity of tritiated thymidine in a cell is a proxy for cells that were actively replicating." [] is_a: OBI:0000891 ! cell proliferation assay [Term] id: OBI:0000671 name: sample from organism def: "a material obtained from an organism in order to be a representative of the whole" [] is_a: OBI:0000747 ! material sample is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0000673 name: statistical hypothesis test def: "A statistical hypothesis test data transformation is a data transformation that has objective statistical hypothesis test." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0000674 name: center value def: "A data item that is produced as the output of a center calculation data transformation and represents the center value of the input data." [] synonym: "median" EXACT [] is_a: IAO:0000027 ! data item [Term] id: OBI:0000675 name: statistical hypothesis test objective def: "is a data transformation objective where the aim is to estimate statistical significance with the aim of proving or disproving a hypothesis by means of some data transformation." [] synonym: "hypothesis test objective" EXACT [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0000676 name: reduced dimension data set def: "A data set that is produced as the output of a data vector reduction data transformation and consists of producing a data set which has fewer vectors than the input data set." [] is_a: IAO:0000100 ! data set [Term] id: OBI:0000678 name: portioning objective def: "A material separation objective aiming to separate material into multiple portions, each of which contains a similar composition of the input material." [] is_a: OBI:0000639 ! material separation objective disjoint_from: OBI:0000681 ! separation into different composition objective [Term] id: OBI:0000679 name: average value def: "A data item that is produced as the output of an averaging data transformation and represents the average value of the input data." [] synonym: "arithmetic mean" EXACT [] is_a: IAO:0000027 ! data item [Term] id: OBI:0000680 name: whole organism preparation def: "A material entity which is the output of a process in which one or more whole organisms are prepared in a way to make it easier to study them, and in which the great majority of organismal parts are maintained" [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0000681 name: separation into different composition objective def: "A material separation objective aiming to separate a material entity that has parts of different types, and end with at least one output that is a material with parts of fewer types (modulo impurities)." [] is_a: OBI:0000639 ! material separation objective [Term] id: OBI:0000682 name: obsolete_study result def: "Study result is an information content entity that is a specified data output of a study." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000684 name: specimen collection objective def: "A objective specification to obtain a material entity for potential use as an input during an investigation." [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0000685 name: creating a mixture of molecules in solution def: "is a process with the objective to prepare a liquid solution of one or more chemicals at desired concentrations." [] is_a: OBI:0000652 ! material combination [Term] id: OBI:0000686 name: material combination objective def: "is an objective to obtain an output material that contains several input materials." [] is_a: OBI:0000456 ! material transformation objective [Term] id: OBI:0000687 name: nucleotide overhang cloning def: "Nucleotide overhang cloning is the process of inserting nucleic acid into a vector using nucleotide overhangs used to prevent self ligation" [] is_a: OBI:0600064 ! recombinant vector cloning [Term] id: OBI:0000688 name: rodent care protocol def: "A rodent care protocol is an animal protocol in which the animals being taken care of are rodents." [] is_a: OBI:0000715 ! animal care protocol [Term] id: OBI:0000689 name: 454 Genome Sequence 20 def: "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." [] synonym: "GS 20" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0000690 name: immunoprecipitation def: "is a process which realizes a material separation objective by relying on antibodies to specifically binding to material entity" [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0000691 name: ABI 377 automated sequencer def: "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: OBI:0400103 ! DNA sequencer [Term] id: OBI:0000692 name: recombination enzyme based cloning def: "a recombination enzyme based cloning is a recombinant vector cloning process that uses complementary nucleotide sequences in both the insert genetic material and the cloning vector with a recombination enzyme to directly create a recombinant vector" [] is_a: OBI:0600064 ! recombinant vector cloning [Term] id: OBI:0000693 name: MeDIP-seq assay def: "A DNA methylation profiling assay that identifies methylated sites in genomic DNA and determines the methylation pattern that affect gene transcription using immunoprecipitation of methylated genomic DNA, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods." [] synonym: "Methylated DNA immunoprecipitation sequencing assay" EXACT [] is_a: OBI:0000634 ! DNA methylation profiling assay is_a: OBI:0001954 ! ChIP assay is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0000694 name: animal feeding def: "animal feeding is a process in which animals are provided with food" [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000695 name: chain termination sequencing assay def: "A DNA sequencing assay which rely on the use of dideoxynucleotides used in 4 distinct sequencing reaction on the same DNA sample. The dideoxynucleotides, once incorporated in the complementary DNA strand being synthesized by the DNA polymerase prevent any further chain elongation. The newly generated sequences are resolved on a polyacrylamide gel using electrophoresis and labels (either fluorochrome or radioactivity) are used to determine the nucleotide present at a given position" [] synonym: "dye terminator sequencing" EXACT [] synonym: "Sanger sequencing" EXACT [] is_a: OBI:0000734 ! DNA sequencing by synthesis assay [Term] id: OBI:0000696 name: AB SOLiD System def: "is a DNA sequencer which is manufactured by Applied Biosystems and which enable DNA sequencing by ligation" [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0000697 name: Helicos sequencing assay def: "A DNA sequencing by synthesis assay that identifiies the sequnece of billions of DNA molecules immobilized to a surface using DNA polymerase and fluorescently labeled nucleotides added one at a time. The sequencing process does not require an amplification step and is typically able to produce reads of 25 base pair length." [] synonym: "true single molecule sequencing" EXACT [] is_a: OBI:0000734 ! DNA sequencing by synthesis assay [Term] id: OBI:0000698 name: obsolete_DNA ligase def: "A DNA ligase is an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule" [] synonym: "ligase" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000699 name: survival assessment assay def: "An assay that measures the occurrence of death events in one or more organisms over time" [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000700 name: support vector machine def: "A support vector machine is a data transformation with a class prediction objective based on the construction of a separating hyperplane that maximizes the margin between two data sets of vectors in n-dimensional space." [] synonym: "SVM" EXACT [] is_a: OBI:0000663 ! class prediction data transformation [Term] id: OBI:0000701 name: self-organizing map def: "A self-organizing map (SOM) is an artificial neural network with objective class discovery that uses a neighborhood function to preserve the topological properties of a dataset to produce low-dimensional (typically 2) discretized representation of the training data set. A set of artificial neurons learn to map points in an input space to coordinates in an output space. The input space can have different dimensions and topology from the output space, and the SOM will attempt to preserve these." [] synonym: "SOM" EXACT [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200175 ! class discovery data transformation [Term] id: OBI:0000702 name: 454 Genome Sequencer FLX def: "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." [] synonym: "454 GS FLX" EXACT [] synonym: "GS-FLX" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0000703 name: Illumina Genome Analyzer II def: "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: OBI:0400103 ! DNA sequencer [Term] id: OBI:0000704 name: decision tree induction objective def: "A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0000705 name: Edman degradation def: "A sequencing assay in which the amino acid sequence of input peptides or proteins is determined by iteratively cleaving of the amino-terminal (N-terminal) residue without disrupting the peptide bonds and identifying it by e.g. chromatography or electropheresis." [] is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0000706 name: SOLiD sequencing assay def: "A DNA sequencing by ligation assay that identifies sequence information using primers to hybridize to the P1 adapter sequence within the library template, fluorescently labeled di-base probes to compete for ligation to the sequencing primer, multiple cycles of ligation, detection and cleavage to determine the eventual read length, following a series of ligation cycles, the extension product is removed and the template is reset with a primer complementary to the n-1 position for a second round of ligation cycles." [] is_a: OBI:0000723 ! DNA sequencing by ligation assay [Term] id: OBI:0000707 name: decision tree building data transformation def: "A decision tree building data transformation is a data transformation that has objective decision tree induction." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0000708 name: laboratory animal care def: "a process that realizes an animal care protocol that specifies how animals are kept and maintained" [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000709 name: yeast artificial chromosome vector def: "a double-stranded DNA that was engineered to contain a yeast origin of replication, encodes for a selectable gene product, contains a cloning site, and has yeast telomerase sequences" [] synonym: "YAC" EXACT [] is_a: CHEBI:4705 ! double-stranded DNA is_a: OBI:0000737 ! cloning vector [Term] id: OBI:0000710 name: Li-Cor 4300 DNA Analysis System def: "is a DNA sequencer which is manufactured by Li-Cor corporation and enable automated chain termination based DNA sequencing" [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0000711 name: library preparation def: "is a process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors." [] synonym: "library construction" EXACT [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000712 name: pathogen challenge def: "The administration of a live pathogenic organism to a host." [] is_a: OBI:0003456 ! in vivo challenge [Term] id: OBI:0000713 name: GenePattern software def: "a software that provides access to more than 100 tools for gene expression analysis, proteomics, SNP analysis and common data processing tasks." [] is_a: IAO:0000010 ! software [Term] id: OBI:0000714 name: graph of vertices def: "A construct that consists of many nodes connected with edges. The edges represent a relationship between the objects represented by the nodes. A graph can be equivalently represented as a matrix." [] is_a: IAO:0000038 ! graph [Term] id: OBI:0000715 name: animal care protocol def: "An animal care protocol is a protocol which specifies the environment in which animals are being kept in captivity for research purposes" [] is_a: OBI:0000272 ! protocol [Term] id: OBI:0000716 name: ChIP-seq assay def: "An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA sequencing step to identify which parts of DNA are part of the isolated chromatin" [] synonym: "chromatin immunoprecipitation sequencing assay" EXACT [] is_a: OBI:0001954 ! ChIP assay [Term] id: OBI:0000717 name: HeliScope Single Molecule Sequencer def: "is a DNA sequencer manufacturer by Helicos Corporation to carry out Single Molecule sequencing using reversible termination chemistry" [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0000718 name: pathogen role def: "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" [] is_a: BFO:0000023 ! role [Term] id: OBI:0000719 name: vaccine production def: "A planned process with the objective to create a vaccine." [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000720 name: immunologic adjuvant role def: "The role a material entity plays when it is co-administered with an immunogen in order to enhance the immune response to the immunogen." [] is_a: OBI:1110092 ! adjuvant role [Term] id: OBI:0000721 name: glucose tolerance test def: "An assay that measures glucose clearance from blood over time by repeated glucose measurement in blood serum or plasma after the administration of a glucose bolus in-vivo. This assay can be used to evaluate the severity of insulin resistance or the efficiency of glucose clearance." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000722 name: paired-end library def: "is a collection of short paired tags from the two ends of DNA fragments are extracted and covalently linked as ditag constructs" [] synonym: "mate-paired library" EXACT [] synonym: "paired-end tag (PET) library" EXACT [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000723 name: DNA sequencing by ligation assay def: "A DNA sequencing assay that performs chain extension during the sequencing reaction step using DNA ligase" [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0000724 name: Solexa sequencing assay def: "A DNA sequencing by synthesis assay that identifies sequence information using DNA polymerase and reversible terminator, requiring immobilization of genomic DNA fragments onto a surface and a specific clonal amplification step known as bridge PCR. Reliance on a reversible terminator allows cycles of DNA chain extension by DNA polymerase and imaging without the need of electrophoretic separation of newly synthesized DNA fragment as with Sanger sequencing." [] synonym: "reversible terminator sequencing" EXACT [] is_a: OBI:0000734 ! DNA sequencing by synthesis assay [Term] id: OBI:0000725 name: host role def: "host role is a role played by an organism and realized by providing nourishment, shelter or a means of reproduction to another organism within the organism playing the host role" [] is_a: BFO:0000023 ! role [Term] id: OBI:0000726 name: peak matching def: "Peak matching is a data transformation performed on a dataset of a graph of ordered data points (e.g. a spectrum) with the objective of pattern matching local maxima above a noise threshold" [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0000727 name: k-nearest neighbors def: "A k-nearest neighbors is a data transformation which achieves a class discovery or partitioning objective, in which an input data object with vector y is assigned to a class label based upon the k closest training data set points to y; where k is the largest value that class label is assigned." [] synonym: "k-NN" EXACT [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200171 ! partitioning data transformation is_a: OBI:0200175 ! class discovery data transformation [Term] id: OBI:0000728 name: rodent care def: "rodent care is the process by which rodents are being provided with a controlled living environment while kept in captivity for the purpose of research." [] is_a: OBI:0000708 ! laboratory animal care [Term] id: OBI:0000729 name: cloning plasmid def: "A cloning plasmid is a plasmid that was engineered to contain a bacterial origin of replication, encodes for a selectable gene product and contains a cloning site." [] is_a: OBI:0000430 ! plasmid is_a: OBI:0000737 ! cloning vector [Term] id: OBI:0000730 name: pyrosequencing assay def: "A DNA sequencing by synthesis assay which sequences a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T nucleotides are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. ssDNA template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5-prime phosphosulfate (APS) and luciferin." [] is_a: OBI:0000734 ! DNA sequencing by synthesis assay [Term] id: OBI:0000731 name: recombinant vector def: "A recombinant vector is created by a recombinant vector cloning process, and contains nucleic acids that can be amplified. It retains functions of the original cloning vector." [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000732 name: restriction enzyme def: "an enzyme that has a specific target cleavage sites within nucleic acids" [] is_a: PR:000000001 ! protein [Term] id: OBI:0000734 name: DNA sequencing by synthesis assay def: "A DNA sequencing assay that relies on DNA polymerase activity to perform chain extension during the sequencing reaction step." [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0000735 name: NTP-2000 def: "a material consisting of 14.5% protein, 8.5% fat and 9.5% fiber produced to feed rodents" [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000736 name: single fragment library def: "is a collection of short tags from DNA fragments, are extracted and covalently linked as single tag constructs" [] synonym: "fragment library" EXACT [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000737 name: cloning vector def: "A cloning vector is an engineered material that is used as an input material for a recombinant vector cloning process to carry inserted nucleic acids. It contains an origin of replication for a specific destination host organism, encodes for a selectable gene product and contains a cloning site." [] is_a: OBI:0000047 ! processed material is_a: OBI:1110108 ! material to be added [Term] id: OBI:0000738 name: restriction enzyme based cloning def: "restriction enzyme based cloning is a recombinant vector cloning process that has as an input genetic material that was cleaved with restriction enzymes, and a cloning vector that was cleaved with complementary restriction enzymes. It uses ligase to chemically join the input genetic material and the cloning vector to create a recombinant vector." [] is_a: OBI:0600064 ! recombinant vector cloning [Term] id: OBI:0000739 name: Student's t-test def: "Studen't t-test is a data transformation with the objective of a statistical hypothesis test in which the test statistic has a Student's t distribution if the null hypothesis is true. It is applied when the population is assumed to be normally distributed but the sample sizes are small enough that the statistic on which inference is based is not normally distributed because it relies on an uncertain estimate of standard deviation rather than on a precisely known value." [] is_a: OBI:0000673 ! statistical hypothesis test [Term] id: OBI:0000740 name: material sample role def: "A material sample role is a specimen role borne by a material entity that is the output of a material sampling process." [] is_a: OBI:0000112 ! specimen role [Term] id: OBI:0000741 name: topologically preserved clustered data set def: "A clustered data set in which the topology, i.e. the spatial properties between data points, is preserved from the original input data from which it was derived." [] is_a: OBI:0000648 ! clustered data set [Term] id: OBI:0000742 name: nucleic acid restriction enzyme digest def: "A nucleic acid digest is a material that is the output of a process in which nucleic acids are combined with a restriction enzyme resulting in digested fragments with defined ends based on the enzymes cleavage site" [] is_a: CHEBI:33696 ! nucleic acid is_a: OBI:0000047 ! processed material [Term] id: OBI:0000743 name: immune response assay def: "An assay that determines information about an immune response" [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000744 name: material sampling process def: "A specimen gathering process with the objective to obtain a specimen that is representative of the input material entity" [] synonym: "sample collection" EXACT [] synonym: "sampling" EXACT [] is_a: OBI:0000659 ! specimen collection process [Term] id: OBI:0000747 name: material sample def: "A material entity that has the material sample role" [] synonym: "sample" EXACT [] synonym: "sample population" EXACT [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0000748 name: bisulfite sequencing assay def: "A DNA methylation profiling assay which determines the methylation status of genomic DNA using DNA sequencing techniques preceded by a bisulfite based chemical modification of genomic DNA at CpG island location." [] is_a: OBI:0000626 ! DNA sequencing assay is_a: OBI:0000634 ! DNA methylation profiling assay [Term] id: OBI:0000749 name: CART def: "A CART (classification and regression trees) is a data transformation method for producing a classification or regression model with a tree-based structure." [] synonym: "classification and regression trees" EXACT [] is_a: OBI:0000707 ! decision tree building data transformation [Term] id: OBI:0000750 name: study design independent variable def: "a directive information entity that is part of a study design. Independent variables are entities whose values are selected to determine its relationship to an observed phenomenon (the dependent variable). In such an experiment, an attempt is made to find evidence that the values of the independent variable determine the values of the dependent variable (that which is being measured). The independent variable can be changed as required, and its values do not represent a problem requiring explanation in an analysis, but are taken simply as given. The dependent variable on the other hand, usually cannot be directly controlled" [] synonym: "experimental factor" EXACT [] synonym: "independent variable" EXACT [] synonym: "study factor" EXACT [] is_a: IAO:0000033 ! directive information entity [Term] id: OBI:0000751 name: study design dependent variable def: "dependent variable specification is part of a study design. The dependent variable is the event studied and expected to change when the independent variable varies." [] synonym: "dependent variable" EXACT [] is_a: IAO:0000033 ! directive information entity [Term] id: OBI:0000784 name: anticoagulant-containing test tube def: "A 'blue top' test tube that contains anticoagulant for storing blood specimens'" [] is_a: OBI:0000836 ! test tube [Term] id: OBI:0000785 name: study design controlled variable def: "Controlled variable specification is a part of a study design. They are the entities that could vary, but are kept constant to prevent their influence on the effect of the independent variable on the dependent." [] synonym: "controlled variable" EXACT [] is_a: IAO:0000033 ! directive information entity [Term] id: OBI:0000787 name: human antithrombin-III in blood assay def: "An assay that measures the amount of antithrombin III in blood." [] synonym: "AT-III assay" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0000788 name: fluorescently labeled MHC multimer def: "A complex of two or more linked MHC molecules including a fluorescent label that can be loaded with a ligand, and is used in flow cytometry assay to bind to T cell receptors of T cells specific for the ligand" [] is_a: OBI:0001936 ! molecular-labeled material [Term] id: OBI:0000789 name: survival rate def: "A measurement data that represents the percentage of people or animals in a study or treatment group who are alive for a given period of time after diagnosis or initiation of monitoring." [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0000790 name: recombinant BAC cloning def: "Recombinant BAC cloning is a process with the objective to insert genetic material into an F plasmid based bacterial artificial chromosome for future replication of the inserted material" [] is_a: OBI:0600064 ! recombinant vector cloning [Term] id: OBI:0000791 name: multiple testing correction objective def: "A multiple testing correction objectives is a data transformation objective where the aim is to correct for a set of statistical inferences considered simultaneously" [] synonym: "multiple comparison correction objective" EXACT [] is_a: OBI:0200186 ! error correction objective [Term] id: OBI:0000792 name: statistical model validation def: "A data transformation which assesses how the results of a statistical analysis will generalize to an independent data set." [] is_a: OBI:0200171 ! partitioning data transformation [Term] id: OBI:0000793 name: double blind study execution def: "A double blind study execution is defined as any study execution in which neither the subjects nor the investigators are informed of which study arm the subjects are part of during the portion of the trial when the subjects are being treated" [] is_a: OBI:0000822 ! single blind study execution [Term] id: OBI:0000794 name: obsolete transcription factor binding site is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: SO:0000235 [Term] id: OBI:0000795 name: glucometer def: "A measurement device with the function to measure and record the level/amount of glucose in a blood sample" [] synonym: "glucose meter" EXACT [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000796 name: purification objective def: "The objective to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest" [] synonym: "isolation objective" EXACT [] is_a: OBI:0000681 ! separation into different composition objective [Term] id: OBI:0000797 name: obsolete_primary structure of protein def: "The primary structure of a protein that is completely defined by the set of its amino acid residue parts and the linear order induced by the peptide bonds that hold them together" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000798 name: capsule shell def: "a small rounded gelatinous container" [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0000799 name: recombinant phage cloning def: "Recombinant phage cloning is the process of using a phage plus some insert nucleic acid for the purposes of amplification of the insert material achieved by phage assembly in vitro." [] is_a: OBI:0600064 ! recombinant vector cloning [Term] id: OBI:0000800 name: cross linking def: "A process in which bonds are created that link one polymer to another" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000801 name: spike train datum def: "A measurement datum which represents information about an ordered series of action potentials in an organism's CNS measured over time." [] synonym: "spike train measurement" EXACT [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0000802 name: prothrombin time assay def: "An assay that measures the prothrombin ratio, which is the prothrombin time for a patient, divided by the result for control plasma. Most commonly the test is preformed using blood plasma. Blood is drawn into a test tube containing liquid citrate, which acts as an anticoagulant. An excess of calcium is added to enable the blood to clot again.Tissue factor (also known as factor III or thromboplastin) is added, and the time the sample takes to clot is measured optically as the prothrombin time, which is compared to a control sample." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000803 name: denaturing def: "Is a process in which the tertiary or secondary structure of a polymer is disrupted" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000804 name: informing investigator of subject study arm def: "A planned process with the objective to make the investigator aware of which study arm a patient is participating in." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000805 name: antithrombin-III berichrome assay def: "An antithrombin-III (AT-III) assay in which exogenous bovine thrombin and heparin are added to test plasma to form a thrombin-heparin-AT complex. The residual thrombin not bound then hydrolyzes the p-nitroalanine substrate to produce a yellow color, which is read at 405 nm. The intensity of color produced is inversely proportional to the AT present. A calibration is done with standard human plasma reagent and results for a given specimen are reported as a percentage relative to the standard" [] synonym: "AT-III assay" EXACT [] is_a: OBI:0000787 ! human antithrombin-III in blood assay [Term] id: OBI:0000806 name: material maintenance objective def: "An objective specification maintains some or all of the qualities of a material over time." [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0000807 name: presentation of stimulus def: "A planned process with the objective to expose an organism to a stimulus." [] synonym: "stimulation of organism" EXACT [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000808 name: spectrolyse heparin antifactor-Xa assay def: "An assay that quantitatively measures heparin in human plasma using Factor Xa and Antithrombin III in excess, where the rate of Factor Xa inhibition is directly proportional to the heparin concentration. The residual Factor Xa activity, measured with a Factor Xa-specific chromogenic substrate, is inversely proportional to the heparin concentration." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000809 name: amplified DNA def: "DNA that has been produced in an enzymatic amplification process" [] is_a: CHEBI:16991 ! deoxyribonucleic acid is_a: OBI:0000047 ! processed material [Term] id: OBI:0000810 name: informed consent process def: "A planned process with the objective to inform a person or their legal representative of legally and ethically relevant facts about a process that the person in question is asked to participate in, and which results in a documented decision as to whether the person in question will participate." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000811 name: primary structure of DNA macromolecule def: "a quality of a DNA molecule that inheres in its bearer due to the order of its DNA nucleotide residues." [] is_a: SO:0000001 ! region [Term] id: OBI:0000812 name: measuring neural activity in the caudate nucleus assay def: "An assay that measures neural activity in the caudate nucleus" [] is_a: OBI:0000454 ! extracellular electrophysiology recording assay [Term] id: OBI:0000813 name: to be treated with active ingredient role def: "A study subject role which begins to exist when a subject is assigned to be one of those who will receive active ingredient, and is realized in a study execution in which they receive the active ingredient" [] is_a: OBI:0000097 ! participant under investigation role [Term] id: OBI:0000814 name: guar gum def: "Guar gum, also called guaran, is a galactomannan. It is primarily the ground endosperm of guar beans. The guar seeds are dehusked, milled and screened to obtain the guar gum.[1] It is typically produced as a free flowing, pale, off-white colored, coarse to fine ground powder." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0000815 name: Berichrom(r) Antithrombin III (A) Kit def: "For the chromogenic determination of antithrombin III. Autoanalyzer method for undiluted samples. For the quantitative chromogenic determination of the functional activity of antithrombin III in plasma on autoanalyzers for the diagnosis of diminished AT III synthesis, increased consumption, and for monitoring substitution therapy. Berichrom(r) Antithrombin III (A) is used for the rapid determination of the physiologically active antithrombin III and permits the diagnosis of congenital and acquired antithrombin III deficiency, a condition frequently associated with an increased risk of thrombosis. Acquired antithrombin III deficiencies frequently occur due to consumption following major operations or due to disseminated intravascular coagulation (DIC) in cases of septicaemia, nephroses, liver parenchymal damage (hepatitis, drug intoxication, alcoholism) and estrogen-containing contraceptives. The test permits early detection of patients at increased risk for thrombosis. Kit contains: 6 x for 5.0 mL Thrombin (bovine), 3 x for 3.0 mL Substrate Reagent, 1 x 30.0 mL Buffer Solution" [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000816 name: micro electrode def: "An electrode of very fine caliber consisting usually of a fine wire or a glass tube of capillary diameter drawn to a fine point and filled with saline or a metal used in physiological experiments to stimulate or record action currents of extracellular or intracellular origin in the nervous system." [] synonym: "micro electrode measuring device" EXACT [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000817 name: fucoidan def: "Fucoidan is a sulfated polysaccharide (MW: average 20,000) found mainly in various species of brown seaweed such as kombu, limu moui,bladderwrack, wakame, mozuku, and hijiki (variant forms of fucoidan have also been found in animal species, including the sea cucumber)." [] is_a: CHEBI:23367 ! molecular entity [Term] id: OBI:0000818 name: calibration def: "A planned process with the objective to establish the relationship between data produced by a measurement device and physical qualities. This is done by using the measurement device under defined conditions, and either tuning it to adjust the measured output, or record the output and use it as a reference in future measurements." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000819 name: anticoagulant tube storage of blood specimen def: "Storage of a blood specimen in a tube with anticoagulant" [] is_a: OBI:0302893 ! storage [Term] id: OBI:0000820 name: activated partial thromboplastin time assay def: "An assay that evaluates blood coagulation by measuring the time required for the appearance of fibrin strands following the mixing blood or plasma with phospholipid platelet substitute (e.g., crude cephalins, soybean phosphatides). It is a test of the intrinsic pathway (factors VIII, IX, XI, and XII) and the common pathway (fibrinogen, prothrombin, factors V and X) of blood coaguation . It is used as a screening test and to monitor heparin therapy." [] synonym: "aPTT assay" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000821 name: filled capsule def: "A pill in the form of a small rounded gelatinous container with medicine inside." [] is_a: OBI:0000827 ! pill [Term] id: OBI:0000822 name: single blind study execution def: "A single blind study execution is defined as any study execution in which the subjects are not informed of which study arm they are part of during the portion of the trial when the subjects are being treated" [] is_a: OBI:0000826 ! treatment portion of study execution [Term] id: OBI:0000823 name: thrombin time assay def: "An assay that measures the time between the addition of the thrombin and the clot formation in plasma." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000824 name: recombinant YAC cloning def: "Recombinant YAC cloning is a process with the objective to insert genetic material into a yeast artificial chromosome vector for future replication of the inserted material" [] is_a: OBI:0600064 ! recombinant vector cloning [Term] id: OBI:0000825 name: to be treated with placebo role def: "A study subject role which begins to exist when a subject is assigned to be one of those who will receive a placebo, and realized in a study execution in which they receive the placebo" [] is_a: OBI:0000097 ! participant under investigation role [Term] id: OBI:0000826 name: treatment portion of study execution def: "A planned process, part of a study design execution, during which the treatment of subjects is ongoing" [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000827 name: pill def: "A dose of medicine or placebo in the form of a small pellet." [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000828 name: research organization def: "An organization formed with a goal to have its members conduct investigations" [] is_a: OBI:0000245 ! organization [Term] id: OBI:0000830 name: obsolete_primary structure of sequence macromolecule def: "A quality inhering in a molecule that is completely defined by the linear sequence of a set of residues which are connected by directional, linear bonds" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000831 name: DNA residue methylation def: "a quality of a DNA residue that has a methyl group attached to it" [] is_a: PATO:0001241 ! physical object quality [Term] id: OBI:0000832 name: measurement device def: "A device in which a measure function inheres." [] is_a: OBI:0000968 ! device [Term] id: OBI:0000834 name: high molecular weight DNA extract def: "The output of an extraction process in which DNA molecules above a molecular weight cutoff are purified in order to exclude DNA from organellas." [] is_a: OBI:0001051 ! DNA extract [Term] id: OBI:0000835 name: manufacturer def: "A person or organization that has a manufacturer role." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0000836 name: test tube def: "A test tube is a device consisting of a glass or plastic tubing, open at the top, usually with a rounded U-shaped bottom which has the function to contain material" [] synonym: "collection tube" EXACT [] synonym: "sample tube" EXACT [] is_a: OBI:0000522 ! vial [Term] id: OBI:0000837 name: oral ingestion of pill def: "An adding a material entity to target with the entity is a pill and the target is the mouth" [] is_a: OBI:0000952 ! oral administration [Term] id: OBI:0000838 name: material maintenance def: "A planned process with the objective to maintain some or all of the characteristics of an input material over time." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000839 name: labeled oligonucleotide def: "a labeled oligonucleotide is a short nucleic acid which underwent a labeling process resulting in a radioactive isotope such as P32 or P33 added to its backbone for instance by end labeling with polynucleotide kinase which added radiolabeled ATP to the 5' end of oligonucleotide" [] is_a: OBI:0001936 ! molecular-labeled material [Term] id: OBI:0000840 name: unblinding process def: "A planned process that is the part of the study execution in which the subjects are told what study arm they are in and in which the investigators are told which subjects are in which trials." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000841 name: subject agrees they understand informed consent document def: "A planned process in which a subject receives an informed consent document and agrees that they have understood it." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000842 name: informing subject of study arm def: "A planned process with the objective to make the subject aware of which study arm they are participating in." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000843 name: Sysmex CA-6000 Coagulation Analyzer def: "The Sysmex CA-6000 automated coagulation analyzer is a random access instrument that is capable of performing 20 clot-based and chromogenic assays" [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000844 name: obsolete hospital def: "A medical organization at which sick or injured people are given clinical care" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: OMRSE:00000056 [Term] id: OBI:0000845 name: primary structure of RNA molecule def: "The primary structure of an RNA molecule that is completely defined by the set of its nucleic residue parts and the linear order induced by the peptide bonds that hold them together" [] is_a: SO:0000001 ! region [Term] id: OBI:0000847 name: test substance role def: "A role born by a material entity and realized in a process where the substance is used as specified as the independent variable for an investigation" [] is_a: BFO:0000023 ! role [Term] id: OBI:0000848 name: polyA RNA extraction def: "A RNA extraction process typically involving the use of poly dT oligomers in which the desired output material is polyA RNA." [] is_a: OBI:0666666 ! RNA extraction [Term] id: OBI:0000849 name: organellar RNA extraction def: "A RNA extraction process in which the desired output material is RNA in the organelle(s)." [] is_a: OBI:0666666 ! RNA extraction [Term] id: OBI:0000851 name: obsolete_diethyl pyrocarbonate is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000852 name: record of missing knowledge def: "An information content entity created to indicate that information about something is not available to the person recording it." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0000854 name: western blot assay def: "An analyte assay that detects specific peptides in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules." [] is_a: OBI:0001978 ! immunoblot assay [Term] id: OBI:0000855 name: total RNA extraction def: "A RNA extraction process in which total cellular and organelle RNA are extracted." [] is_a: OBI:0666666 ! RNA extraction [Term] id: OBI:0000856 name: obsolete intracellular material detection by flow cytometry assay def: "An assay in which the presence of a material inside a cell is measured by permeabilizing the cell membrane to allow entry of specific antibodies, and counting the stained cells using a flow cytometer." [] synonym: "intracellular staining" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: OBI:0000916 [Term] id: OBI:0000857 name: complementary nucleotide probe role def: "A role played by a nucleic acid molecule that is used in a planned process for its ability to bind a nucleic acid molecules with complementary nucleotide sequence" [] is_a: BFO:0000023 ! role [Term] id: OBI:0000858 name: record of unknown sex def: "a record indicating that the biological sex of an organism is not known." [] is_a: OBI:0000852 ! record of missing knowledge [Term] id: OBI:0000859 name: cytoplasmic RNA extraction def: "A RNA extraction process in which the desired output material is RNA in the cytoplasm." [] is_a: OBI:0666666 ! RNA extraction [Term] id: OBI:0000860 name: northern blot assay def: "An assay that determines the presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing gel, transfered by a blotting procedure to a solid support. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager." [] synonym: "northern blot" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0000861 name: Likelihood-ratio test def: "Likelihood-ratio is a data transformation which tests whether there is evidence of the need to move from a simple model to a more complicated one (where the simple model is nested within the complicated one); tests of the goodness-of-fit between two models." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0000862 name: nuclear RNA extract def: "A RNA extract that is the output of an extraction process in which RNA molecules found in the nucleus, including mRNA precursors (pre-mRNA), are extracted." [] is_a: OBI:0000880 ! RNA extract [Term] id: OBI:0000865 name: 96-well neutralization assay def: "A serum neutralization of viral infectivity assay which is performed in a 96-well plate." [] synonym: "microneutralization assay" EXACT [] is_a: OBI:0000872 ! serum neutralization of viral infectivity assay [Term] id: OBI:0000867 name: establishing cancer cell line def: "is a planned process in which the objective is to generate a cell line from a natural population of cancer cells which are already immortal" [] comment: Helen Parkinson is_a: OBI:0001867 ! establishing cell line [Term] id: OBI:0000868 name: pattern matching objective def: "A pattern matching objective aims to detect the presence of the constituents of a given pattern. In contrast to pattern recognition, the pattern is rigidly specified. Patterns are typicall sequences or trees." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0000869 name: polyA RNA extract def: "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." [] is_a: OBI:0000880 ! RNA extract [Term] id: OBI:0000870 name: single-nucleotide-resolution nucleic acid structure mapping assay def: "An assay that provides information about the secondary structure of nucleic acids using chemical or enzymatic probing to establish the extent of base-pairing or solvent accessiblity." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000871 name: viral hemagglutination assay def: "An assay that quantifies viruses by their hemagglutination activity." [] synonym: "HA" EXACT [] synonym: "HI" EXACT [] synonym: "viral haemagglutinin assay" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0000872 name: serum neutralization of viral infectivity assay def: "An analyte assay that measures virus-neutralizing abilities of different sera. Different dilutions of serum are mixed with virus and used to infect cells. At the lower dilutions, antibodies will block infection, but at higher dilutions, there will be too few antibodies to have an effect.The neutralization titer is expressed as the reciprocal of the highest dilution at which virus infection is blocked." [] synonym: "influenza neutralization assay" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0000873 name: pre-mortem specimen def: "a specimen that was taken from a live organism" [] is_a: OBI:0001506 ! specimen with pre- or post-mortem status disjoint_from: OBI:0000902 ! post mortem specimen [Term] id: OBI:0000874 name: detection of specific nucleic acid polymers with complementary probes def: "An analyte assay in which a specified input material (the evaluant) is examined for the presence or quantity of specified nucleic acid polymers, which are identified based on the use of complementary nucleic acid probes." [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0000875 name: viral hemagglutination inhibition assay def: "An assay that measures the ability of an evaluant to inhibit hemagglutination by a virus. Hemagglutinin is a viral protein which binds to sialic acid receptors on cells or to erythrocytes, causing the cells to clump. Loss of clumping indicates that the evaluant blocks binding of hemagglutinin to sialic acid receptors." [] synonym: "biological activity" EXACT [] synonym: "HAI" EXACT [] synonym: "hemagglutination inhibition" EXACT [] synonym: "HIA" EXACT [] synonym: "viral haemagglutinin inhibition assay" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000876 name: cytoplasmic RNA extract def: "A RNA extract that is the output of a RNA extraction process in which RNA molecules found in the cytoplasm are extracted." [] is_a: OBI:0000880 ! RNA extract [Term] id: OBI:0000877 name: cell line immortalization def: "an establishing cell line process whereby a mortal cell line is intentionally genetically modified to be capable of indefinite propagation and re-established as a new immortal cell line" [] comment: A immortalizing genetic transformation of an existing population of cell line cells is required as part of this process, as are additional steps for selecting and propagating the cells output form this process into a cell line. synonym: "'establishing immortal cell line through directed genetic modification'" EXACT [] is_a: OBI:0001867 ! establishing cell line [Term] id: OBI:0000879 name: random primed DNA labeling def: "a labeling in which random primers are used to uniformly label input DNA" [] is_a: OBI:0600038 ! addition of molecular label [Term] id: OBI:0000880 name: RNA extract def: "an extract which is the output of an extraction process in which RNA molecules are isolated from a specimen." [] is_a: OBI:0001010 ! nucleic acid extract [Term] id: OBI:0000882 name: cell-cell killing assay def: "A cytometry assay that monitors a cell population to track how many are killed by other cells." [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0000883 name: in vivo cell killing assay def: "A cell killing assay that measures if and how many target cells are killed within an organism." [] is_a: OBI:0000882 ! cell-cell killing assay [Term] id: OBI:0000885 name: secondary structure of sequence macromolecule def: "A quality inhering in a molecule that refers to general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure.\nSecondary structure was introduced by Kaj Ulrik Linderstrøm-Lang in the 1952 Lane medical lectures at Stanford." [] is_a: PATO:0001241 ! physical object quality [Term] id: OBI:0000888 name: nuclear RNA extraction def: "A RNA extraction process in which the desired output material is RNA in the nucleus." [] is_a: OBI:0666666 ! RNA extraction [Term] id: OBI:0000889 name: survival curve def: "A survival curve is a report graph which is a graphical representation of data where the percentage of survival is plotted as a function of time." [] is_a: IAO:0000573 ! line graph [Term] id: OBI:0000891 name: cell proliferation assay def: "A cytometry assay which measures the degreee to which input cells are replicating." [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0000892 name: Southern blot assay def: "An analyte assay that detects the presence of a specific sequence in a DNA sample, which has been digested by restriction enzymes, resolved by gel electrophoresis, and blotted to a solid support, followed by hybridization of a probe raised against a specific sequence and detected with fluorescence or radioactivity." [] synonym: "Southern blot" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0000893 name: real time polymerase chain reaction assay def: "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." [] synonym: "kinetic polymerase chain reaction" EXACT [] synonym: "Q-PCR" EXACT [] synonym: "qPCR" EXACT [] synonym: "quantitative real time polymerase chain reaction" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0000894 name: protein extract def: "a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation," [] is_a: OBI:0000423 ! extract [Term] id: OBI:0000895 name: total RNA extract def: "A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen." [] is_a: OBI:0000880 ! RNA extract [Term] id: OBI:0000896 name: secondary structure of RNA molecule is_a: OBI:0000885 ! secondary structure of sequence macromolecule [Term] id: OBI:0000897 name: DEPC structure mapping assay def: "A single-nucleotide-resolution nucleic acid structure mapping assay which determines nucleic acid secondary structure at a nucleotide resolution scale using DEPC as reagent and chemical probe" [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0000899 name: organellar RNA extract def: "A RNA extract that is the output of an extraction process in which RNA molecules found in an organelle, e.g., mitochondrion, ER, or chloroplast, excluding the nucleus, are extracted." [] is_a: OBI:0000880 ! RNA extract [Term] id: OBI:0000902 name: post mortem specimen def: "a specimen that was taken from a dead organism" [] is_a: OBI:0001506 ! specimen with pre- or post-mortem status [Term] id: OBI:0000903 name: in vitro cell killing assay def: "A cell killing assay that measures if and how many target cells are actively killed by other cells in a cell culture." [] is_a: OBI:0000882 ! cell-cell killing assay is_a: OBI:0003587 ! cell culture assay [Term] id: OBI:0000904 name: reporter cell line analyte detection bioassay def: "An analyte assay in which a cell line whose growth is known to be affected by the presence of a specific type of material (the anlyte) is cultured in the presence of an input material (the evaluant) in order to detect presence of the analyte in the evaluant." [] is_a: OBI:0000443 ! analyte assay is_a: OBI:0003587 ! cell culture assay [Term] id: OBI:0000905 name: sequence feature annotation def: "Information about a sequence region" [] comment: place holder for sequence ontology term is_a: IAO:0000030 ! information content entity [Term] id: OBI:0000906 name: induced hemagglutination def: "The clumping or clustering of red blood cells caused by certain viruses, antibodies, or other substances" [] synonym: "hemeagglutination" EXACT [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000907 name: supplying def: "A planned process with the objective to provide material entities to be used in an investigation." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000908 name: labeled DNA extract def: "a labeled specimen that is the output of a labeling process and has grain labeled DNA to be able to detect DNA in future experiments." [] is_a: OBI:0001143 ! labeled nucleic acid extract [Term] id: OBI:0000909 name: cloacal specimen def: "A specimen obtained by inserting a swab deeply into the vent of the cloaca of\nan organism and vigorously swabbing the wall. The swab should be deeply\nstained with fecal material and is then placed in transport medium." [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0000910 name: radio immuno assay def: "An assay in which a radioactive labeled antigen or antibody is used to determine the interaction between an antigen and its receptor. This can be used to detect the presence of an antigen of interest in an input sample or determine the specificity of an input antibody." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000911 name: real time reverse-transcription polymerase chain reaction assay def: "An assay that uses a reverse transcription step (an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase) before a PCR assay." [] synonym: "qRT-PCR" EXACT [] synonym: "RRT-PCR" EXACT [] synonym: "RT-rt PCR" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0000912 name: X-ray crystallography 3D molecular structure determination assay def: "A 3D molecular structure determination assay in which the diffraction of pattern of X-ray beams in a crystal of purified material entities is used to resolve the 3-dimensional structure of the material entity of interest." [] is_a: OBI:0003117 ! 3D molecular structure determination assay [Term] id: OBI:0000913 name: promoter activity detection by reporter gene assay def: "An assay in which the activity of a promoter in a cell is monitored by using a reporter gene that was inserted in a genomic location under control of the promoter and whose expression can be easily detected based on qualities or functions of the gene." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000914 name: nasopharyngeal aspirate specimen def: "A speciemn which derives from nasopharyngeal mucosa after\naspiration." [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0000915 name: freezing storage def: "A storage process in temperature that maintenance the frozen status of the stored entities." [] is_a: OBI:0302893 ! storage [Term] id: OBI:0000916 name: flow cytometry assay def: "A cytometry assay in which an input cell population is put in solution, is passed by a laser, and optical sensors are used to detect scattering of the laser light and/or fluorescence of specific markers to count and characterize the particles in solution." [] synonym: "FACS" EXACT [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0000917 name: nasal swab specimen def: "A specimen obtained using a cotton swab on a stick, passed up the nostril to obtain a sample of\nexudate and epithelial debris for microbiological or cellular examination." [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0000918 name: Dulbecco's modified Eagle medium def: "A culture medium containing iron, phenol red, amino acids, salts, glucose and vitamins." [] synonym: "D-MEM" EXACT [] synonym: "DMEM" EXACT [] is_a: OBI:0000079 ! culture medium [Term] id: OBI:0000919 name: animal euthanization def: "A process in which is the end of life of animal is brought about in accordance with local regulations on treatment of animal subjects and using a method which causes minimal pain and distress to the animal subject" [] comment: may later be refined with more specific list of organisms synonym: "animal sacrifice" EXACT [] is_a: OBI:0600006 ! killing [Term] id: OBI:0000920 name: cytometric bead array assay def: "An analyte assay in which a series of beads coated with antibodies, antigens, or other small molecules are used to detect an analyte of interest." [] synonym: "Luminex assay" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0000921 name: labeled RNA extract def: "a labeled specimen that is the output of a labeling process and has grain labeled RNA to be able to detect RNA in future experiments." [] is_a: OBI:0001143 ! labeled nucleic acid extract [Term] id: OBI:0000922 name: frozen specimen def: "A specimen that has been frozen in order to store it." [] is_a: OBI:0001472 ! specimen with known storage state disjoint_from: OBI:0000950 ! paraffin specimen disjoint_from: OBI:0000965 ! lyophilized specimen disjoint_from: OBI:0000971 ! fresh specimen disjoint_from: OBI:0000981 ! agar stab specimen [Term] id: OBI:0000923 name: surface plasmon resonance binding assay def: "A binding assay that uses the detection of electromagnetic waves in a surface to detect material entities adsorbed to the surface, which change the local optical index of refraction." [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0000924 name: labeled specimen def: "A specimen that has been modified in order to be able to detect it in future experiments" [] is_a: OBI:0000953 ! processed specimen is_a: OBI:0001936 ! molecular-labeled material [Term] id: OBI:0000925 name: infectious agent def: "is a material entity bearing the disposition to infect an organism" [] is_a: OBI:0100026 ! organism [Term] id: OBI:0000926 name: obsolete_ambidexterious handedness is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000927 name: lyophilization storage def: "a storage process with input material entity and output freeze dried material for long time storage" [] comment: can link to freezing-dying equipment, such as freeze-dryer, rotary evaporator, if needed is_a: OBI:0302893 ! storage [Term] id: OBI:0000928 name: material combination function def: "A material separation function is a function that decreases the resolution between two or more material entities." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000929 name: obsolete_training service provider role def: "a service provider role which is realized by a servicer provider organization performing some training" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000930 name: calorimeter def: "A measurement device that is used to calculate the heat flow of a chemical reaction or physical change." [] synonym: "calorimetry instrument?" EXACT [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000931 name: study intervention def: "A planned process that is the part of the execution of an intervention design study which is varied between two or more subjects in the study." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000932 name: material separation device def: "A device with a separation function realized in a planed process" [] is_a: OBI:0000968 ! device [Term] id: OBI:0000933 name: positron emission tomography scanner def: "A device that produces a three-dimensional image or picture of functional processes in the body. It detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule." [] synonym: "PET scanner?" EXACT [] is_a: OBI:0000398 ! image creation device [Term] id: OBI:0000934 name: intramuscular injection def: "is the injection of a material entity (bearing the administered substance role) into the muscle (bearing the target role) of an organism using a syringe" [] is_a: OBI:0000426 ! injection is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0000935 name: micromanipulator def: "A device that is used to physically interact with a sample under a microscope, where a level of precision of movement is necessary that cannot be achieved by the unaided human hand." [] is_a: OBI:0000968 ! device [Term] id: OBI:0000936 name: obsolete_material access provider role def: "a service provider role which is realized by a servicer provider organization performing access to some material" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000937 name: obsolete_left handedness is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000938 name: categorical measurement datum def: "A measurement datum that is reported on a categorical scale." [] synonym: "nominal mesurement datum" EXACT [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0000939 name: training process def: "a process that achieves a training objective" [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0000940 name: optical microscope def: "A microscope that produces an image of an object by targeting it with an electro-magnetic beam in the visible frequency range" [] is_a: OBI:0400169 ! microscope [Term] id: OBI:0000941 name: service consumer role def: "a role which inheres in a person who uses a service" [] is_a: BFO:0000023 ! role [Term] id: OBI:0000942 name: intradermal injection def: "is the injection of a material entity (bearing the administered substance role) into the dermis (bearing the target role) of an organism using a syringe" [] is_a: OBI:0000426 ! injection is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0000943 name: chemical cleavage def: "chemical cleavage is a protocol application relying on a chemical compound to cause the fragmentation of an input material that is susceptible to that chemical agent" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0000944 name: handedness assay def: "An assay that measures the unequal distribution of fine motor skill between the left and right hands typically in human subjects by means of some questionnaire and scoring procedure." [] synonym: "handedness test" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000945 name: vibration isolation table def: "A device that supports another device such as a precision instrument by isolating it from vibration that is transmitted from the floor." [] is_a: OBI:0001034 ! environmental control device [Term] id: OBI:0000946 name: sterilization function def: "a function to remove viable organisms from an input material" [] is_a: BFO:0000034 ! function [Term] id: OBI:0000947 name: service provider role def: "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" [] is_a: BFO:0000023 ! role [Term] id: OBI:0000948 name: oscilloscope def: "A device that measures and displayes signal voltages, usually as a two-dimensional graph of one or more electrical potential differences (vertical axis) plotted as a function of time or of some other voltage (horizontal axis)." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0000949 name: accessed material role def: "is realized in a planned process where the bearer participates" [] is_a: BFO:0000023 ! role [Term] id: OBI:0000950 name: paraffin specimen def: "a specimen that is output of a paraffin storage process in which specimen is embedded in paraffin" [] is_a: OBI:0001472 ! specimen with known storage state disjoint_from: OBI:0000965 ! lyophilized specimen disjoint_from: OBI:0000971 ! fresh specimen disjoint_from: OBI:0000981 ! agar stab specimen [Term] id: OBI:0000951 name: compound treatment design def: "an intervention design in which the treatment is the administration of a compound" [] is_a: OBI:0000115 ! intervention design [Term] id: OBI:0000952 name: oral administration def: "An administering substance in vivo into the mouth of an organism" [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0000953 name: processed specimen def: "A specimen that has been intentionally physically modified." [] comment: A tissue sample that has been sliced and stained for a histology study. is_a: OBI:0000047 ! processed material is_a: OBI:0100051 ! specimen [Term] id: OBI:0000954 name: subcutaneous injection def: "is the injection of a material entity (bearing the administered substance role) into the hypodermis (bearing the target role) of an organism using a syringe" [] is_a: OBI:0000426 ! injection is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0000955 name: electrode puller def: "A device used in the first step in making electrodes, that applies constant tension on a glass capillary tube and eventually breaks it while heating it; this produces a very fine point on the capillary tube." [] is_a: OBI:0000968 ! device [Term] id: OBI:0000956 name: obsolete_handedness is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: PATO:0002201 [Term] id: OBI:0000957 name: self reported handedness assessment def: "An assay where a person makes a statement that indicates what handedness he has from a choice of different categories." [] is_a: OBI:0000944 ! handedness assay [Term] id: OBI:0000959 name: vibrotome def: "A preparation device that uses a vibrating razor blade to cut through tissue." [] is_a: OBI:0000932 ! material separation device [Term] id: OBI:0000960 name: reagent application function def: "A function that is realized when a reagent is automatically added to some research material." [] is_a: BFO:0000034 ! function [Term] id: OBI:0000961 name: addition of molecular tracer function def: "A reagent application function that is realized when a molecular tracer, such as an antibody or probe is automatically transferred to a biological specimen." [] is_a: OBI:0000960 ! reagent application function [Term] id: OBI:0000962 name: training objective def: "An objective specification which is fulfilled by the provision of some training." [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0000963 name: categorical label def: "A label that is part of a categorical datum and that indicates the value of the data item on the categorical scale." [] is_a: IAO:0000009 ! datum label [Term] id: OBI:0000964 name: in live cell assay def: "An assay in which a measurement is made by observing entities located in a live cell." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000965 name: lyophilized specimen def: "a specimen that is output of a lyophilization storage process in which specimen is lyophilized for storage." [] is_a: OBI:0001472 ! specimen with known storage state disjoint_from: OBI:0000971 ! fresh specimen disjoint_from: OBI:0000981 ! agar stab specimen [Term] id: OBI:0000966 name: in live organism assay def: "An assay in which a measurement is made by observing entities located in an organism." [] synonym: "in vivo assay" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000967 name: container def: "A device that can be used to restrict the location of material entities over time" [] is_a: OBI:0000968 ! device [Term] id: OBI:0000968 name: device def: "A material entity that is designed to perform a function in a scientific investigation, but is not a reagent." [] synonym: "instrument" EXACT [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0000969 name: dose specification def: "a directive information entity that describes the dose that will be administered to a target" [] is_a: IAO:0000033 ! directive information entity [Term] id: OBI:0000970 name: scalar score from composite inputs def: "A measurement datum which is the result of combining multiple datum. For example, a mean or summary score." [] synonym: "questionaire score" EXACT [] is_a: IAO:0000032 ! scalar measurement datum [Term] id: OBI:0000971 name: fresh specimen def: "a specimen that is output of a specimen creation process used for an investigation without storage." [] is_a: OBI:0001472 ! specimen with known storage state disjoint_from: OBI:0000981 ! agar stab specimen [Term] id: OBI:0000972 name: obsolete_electrically powered device def: "a processed material created to have a function and which requires electrical power to execute" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000973 name: sequence data def: "A measurement datum that representing the primary structure of a macromolecule(it's sequence) sometimes associated with an indicator of confidence of that measurement." [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0000974 name: obsolete_right handedness is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000975 name: cell-cell binding detection by flow cytometry assay def: "A binding assay which uses a flow cytometer to detect pairs of cells that are bound to each other by staining them with different fluorescent labels." [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0000976 name: handedness categorical measurement datum def: "A datum used to record the answer to a self assessment of whether a person uses their left hand, right hand primarily or each hand equally" [] is_a: OBI:0000938 ! categorical measurement datum [Term] id: OBI:0000977 name: paraffin storage def: "a storage process with input organism or anatomical entity and paraffin and output material embedded in paraffin for long term storage" [] comment: need to specify paraffin or wax is one of specified input of the process is_a: OBI:0302893 ! storage [Term] id: OBI:0000978 name: in container assay def: "An assay in which a measurement is made by observing entities located in a container." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0000980 name: obsolete_protocol service provider role def: "a service provider role which is realized by a servicer provider organization performing a protocol execution" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000981 name: agar stab specimen def: "a specimen that is output of a process that cell culture inoculated into agar for long term storage." [] is_a: OBI:0001472 ! specimen with known storage state [Term] id: OBI:0000982 name: computed tomography scanner def: "An image acquisition device that generates a three-dimensional image of the inside of an object from a large series of two-dimensional X-ray images taken around a single axis of rotation." [] synonym: "CT scanner" EXACT [] synonym: "X-ray computed tomography scanner" EXACT [] is_a: OBI:0000398 ! image creation device [Term] id: OBI:0000983 name: intranasal mucosal administration def: "The administration of a substance into the intranasal mucosis of an organism" [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0000984 name: dose def: "A measurement datum that measures the quantity of something that may be administered to an organism or that an organism may be exposed to. Quantities of nutrients, drugs, vaccines and toxins are referred to as doses." [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0000985 name: growth condition intervention design def: "A study design in which the independent variable is the environmental condition in which the specimen is growing" [] is_a: OBI:0000115 ! intervention design [Term] id: OBI:0000986 name: obsolete_DNA sequencing training service def: "A training process with the objective to provide a trainee with the skill to run DNA sequencing experiments" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000987 name: obsolete_general scalar measurement datum is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000988 name: obsolete performing a diagnosis def: "The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0000989 name: PCR instrument def: "A device that is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence." [] is_a: OBI:0400116 ! thermal cycler [Term] id: OBI:0000990 name: electron microscope def: "A microscope that produces an image of an object by targeting it with an electron beam" [] is_a: OBI:0400169 ! microscope [Term] id: OBI:0000991 name: Edinburgh score def: "A score that measures the dominance of a person's right or left hand in everyday activities." [] is_a: OBI:0000970 ! scalar score from composite inputs [Term] id: OBI:0000992 name: DNA sequencing service def: "A DNA sequencing process provided as a service - which is the realization of some DNA sequencing in which the service provider role is realized." [] is_a: OBI:0001904 ! sequencing service [Term] id: OBI:0000993 name: service provision objective def: "An objective which is fulfilled by the provision of some service e.g. a training service" [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0000994 name: intravenous injection def: "is the injection of a material entity (bearing the administered substance role) into the vein (bearing the target role) of an organism using a syringe" [] is_a: OBI:0000426 ! injection is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0000995 name: administration of material to specimen def: "The directed combination of a material entity with a specimen." [] is_a: OBI:0000274 ! adding a material entity into a target [Term] id: OBI:0000996 name: device creation objective def: "an objective which aims to create a device with a specified function" [] is_a: OBI:0000456 ! material transformation objective [Term] id: OBI:0000997 name: growth environment def: "The collection of material entities and their qualities that are located near a live organism, tissue or cell and can influence its growth." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0001000 name: questionnaire def: "A document with a set of printed or written questions with a choice of answers, devised for the purposes of a survey or statistical study." [] is_a: IAO:0000310 ! document [Term] id: OBI:0001001 name: Edinburgh handedness assay def: "An assay that uses a set of questions (the Edinburgh Handedness inventory) to generate a score that can be used to assess the dominance of a person's right or left hand in everyday activities. The inventory can be used by an observer assessing the person, or by a person self-reporting hand use. The latter method tends to be less reliable due to a person over-attributing tasks to the dominant hand." [] is_a: OBI:0000944 ! handedness assay [Term] id: OBI:0001002 name: Faraday cage def: "A device formed by conducting material or by a mesh of such material, that blocks out external static electric fields." [] synonym: "Faraday shield" EXACT [] is_a: OBI:0001034 ! environmental control device [Term] id: OBI:0001003 name: agar stab storage def: "a storage process with input cell culture and agar and output agar stab for long time storage" [] comment: need to specify that agar is one of input for this process is_a: OBI:0302893 ! storage [Term] id: OBI:0001005 name: RNASE CL3 structure mapping assay def: "A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse CL3 as reagent and enzymatic probe." [] synonym: "single nucleotide resolution mapping assay using RNAse CL3" EXACT [] is_a: OBI:0001014 ! single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing [Term] id: OBI:0001006 name: CMCT structure mapping assay def: "A single-nucleotide-resolution nucleic acid structure mapping assay which uses CMCT as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure" [] synonym: "single nucleotide resolution mapping assay using CMCT probe" EXACT [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0001007 name: image creation def: "A planned process that captures an image of an object." [] synonym: "image acquisition" EXACT [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0001008 name: MPE-Fe(II) structure mapping assay def: "A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using Fe-MP as reagent and chemical probe." [] synonym: "single nucleotide resolution mapping assay using Fe-MP probe" EXACT [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0001009 name: obsolete_qualitative binding detection assay def: "A binding assay where the specified output determines if two or more material entities do or do not have the disposition to form a complex above a threshold level of significance. The threshold can be defined through detection limits of the instrument, the use of experimental controls that establish what is considered significant binding, or a predefined cutoff based on what binding is considered significant in a certain context." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0001010 name: nucleic acid extract def: "An extract that is the output of an extraction process in which nucleic acid molecules are isolated from a specimen." [] is_a: OBI:0000423 ! extract is_a: OBI:0000953 ! processed specimen [Term] id: OBI:0001011 name: ENU structure mapping assay def: "A single-nucleotide-resolution nucleic acid structure mapping assay that determines the secondary structure of a nucleic acid at the nucleotide resolution scale which uses ENU as reagent and chemical probe" [] synonym: "single nucleotide resolution mapping assay using ENU probe" EXACT [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0001012 name: RNASE V1 structure mapping assay def: "A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse V1 as reagent and enzymatic probe" [] synonym: "single nucleotide resolution mapping assay using RNAse V1" EXACT [] is_a: OBI:0001014 ! single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing [Term] id: OBI:0001013 name: kethoxal structure mapping assay def: "A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using kethoxal as reagent and chemical probe" [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0001014 name: single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing def: "A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using proteins acting as enzymatic probes." [] is_a: OBI:0000870 ! single-nucleotide-resolution nucleic acid structure mapping assay [Term] id: OBI:0001015 name: DMS structure mapping assay def: "A single-nucleotide-resolution nucleic acid structure mapping assay which determins nucleic acid secondary structure at a nucleotide resolution scale using DMS as reagent and chemical probe" [] synonym: "single nucleotide resolution mapping assay using DMS probe" EXACT [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0001016 name: DNASE 1 structure mapping assay def: "A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay which uses DNAse 1 as reagent and enzymatic probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure" [] synonym: "DNAse footprinting assay" EXACT [] synonym: "single nucleotide resolution mapping assay using DNAse I" EXACT [] is_a: OBI:0001014 ! single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing [Term] id: OBI:0001017 name: single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing def: "A single-nucleotide-resolution nucleic acid structure mapping assay that determines structural information about the RNA species under study using small chemical compounds acting as chemical probes." [] is_a: OBI:0000870 ! single-nucleotide-resolution nucleic acid structure mapping assay [Term] id: OBI:0001018 name: Rhodium DNA structure mapping assay def: "A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhodium as reagent and chemical probe." [] synonym: "single nucleotide resolution mapping assay using Rhodium probe" EXACT [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0001019 name: RNA ADA I RNA structure mapping assay def: "A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNA adenosine deaminase I as reagent and enzymatic probe." [] synonym: "single nucleotide resolution mapping assay using RNA adenosine deaminase I" EXACT [] is_a: OBI:0001014 ! single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing [Term] id: OBI:0001020 name: Lead structure mapping assay def: "A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using lead as reagent and chemical probe" [] synonym: "single nucleotide resolution mapping assay using Lead probe" EXACT [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0001021 name: RNASE T2 structure mapping assay def: "A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAse T2 as reagent and enzymatic probe" [] synonym: "single nucleotide resolution mapping assay using RNAse T2" EXACT [] is_a: OBI:0001014 ! single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing [Term] id: OBI:0001022 name: gene dosage assay def: "An assay that measures changes in phenotype due to increased or decreased dosage of a single allele of a gene." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0001023 name: Fe-BABE RNA structure mapping assay def: "A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic secondary structure at a nucleotide resolution scale using Fe-BABE as reagent and chemical probe." [] synonym: "single nucleotide resolution mapping assay using Fe-BABE probe" EXACT [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0001024 name: RNASE U2 structure mapping assay def: "A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using RNAase U2 as reagent and enzymatic probe" [] synonym: "single nucleotide resolution mapping assay using RNAse U2" EXACT [] is_a: OBI:0001014 ! single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing [Term] id: OBI:0001025 name: binding constant determination assay def: "A binding assay where the specified output is a binding constant" [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001026 name: NMIA RNA structure mapping assay def: "A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at the nucleotide resolution scale using NMIA as reagent and chemical probe" [] synonym: "SHAPE mapping assay" EXACT [] synonym: "single nucleotide resolution mapping assay using NMIA probe" EXACT [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0001027 name: Terbium RNA structure mapping assay def: "A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Terbium as reagent and chemical probe" [] synonym: "single nucleotide resolution mapping assay using Terbium probe" EXACT [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0001028 name: feature extraction def: "A planed process with objective of obtaining quantified values from an image." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0001029 name: OH-radical structure mapping assay def: "A single-nucleotide-resolution nucleic acid structure mapping assay hat determines nucleic acid secondary structure at a nucleotide resolution scale using hydroxyl radical as reagent and chemical probe" [] synonym: "MOHCA assay" EXACT [] synonym: "OH footprinting assay" EXACT [] synonym: "single nucleotide resolution mapping assay using OH-radical probe" EXACT [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0001030 name: RNASE T1 structure mapping assay def: "A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale uses RNAse T1 as reagent and enzymatic probe." [] synonym: "single nucleotide resolution mapping assay using RNAse T1" EXACT [] is_a: OBI:0001014 ! single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing [Term] id: OBI:0001031 name: array image creation def: "An image creation process that generate an image from the array." [] synonym: "array image acquisition" EXACT [] is_a: OBI:0001007 ! image creation [Term] id: OBI:0001032 name: light emission device def: "A device which has a function to emit light." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001033 name: perturbation device def: "A perturbation device is a device which is designed to perform a perturb function" [] is_a: OBI:0000968 ! device [Term] id: OBI:0001034 name: environmental control device def: "An environmental control device is a device which has the function to control some aspect of the environment such as temperature, or humidity." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001035 name: Nuclease S1 structure mapping assay def: "A single-nucleotide-resolution deoxyribonucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using DNAse 1 as reagent and enzymatic probe." [] synonym: "single nucleotide resolution mapping assay using Nuclease S1" EXACT [] is_a: OBI:0001014 ! single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing [Term] id: OBI:0001036 name: specimen fixation function def: "a function that allows specific identification of individual speciment from one another." [] is_a: BFO:0000034 ! function [Term] id: OBI:0001037 name: obsolete_specimen fixation function def: "A specimen fixation function is a function that holds or fastens an entity in a fixed position." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0001038 name: Ruthenium structure mapping assay def: "A single-nucleotide-resolution nucleic acid structure mapping assay that determines nucleic acid secondary structure at a nucleotide resolution scale using Rhutenium as reagent and chemical probe" [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0001039 name: inline probing RNA structure mapping assay def: "A single-nucleotide-resolution ribonucleic acid structure mapping assay that determines nucleic acid secondary structure at nucleotide resolution scale using intromolecular reactivity" [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing [Term] id: OBI:0001040 name: current amplification function def: "A current amplification function is an amplification function that increases the amplitude of a current." [] is_a: BFO:0000034 ! function [Term] id: OBI:0001041 name: stabilization function def: "A stabilization function is a function that holds or isolates an entity such as an instrument or specimen steadfast or at an unfluctuating level or quantity." [] synonym: "isolation function" EXACT [] is_a: BFO:0000034 ! function [Term] id: OBI:0001042 name: pump function def: "a transfer unction where the transfer requires work to move the entity, often against a gradient." [] is_a: OBI:0000383 ! transfer function [Term] id: OBI:0001043 name: cell transfer function def: "is a transfer function that displaces cells from one place to another" [] is_a: OBI:0000383 ! transfer function [Term] id: OBI:0001044 name: angiograph def: "A device that records the patterns of pulse waves inside blood vessels." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001045 name: capillary blotter def: "A device that is used to transfer nucleic acids from agarose gels onto a membrane, based on the movement of buffer from a reservoir through the gel and the blotting membrane to a stack of dry blotting paper by capillary force. The molecules are carried to the blotting membrane on which they are adsorbed." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001046 name: bioreactor def: "A device or system that supports a biologically active environment." [] is_a: OBI:0001034 ! environmental control device [Term] id: OBI:0001047 name: pH meter def: "A device that is used to measure the pH (acidity or alkalinity) of a liquid." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001048 name: digital camera def: "An image acquisition device that takes video or still photographs, or both, digitally by recording images via an electronic image sensor." [] is_a: OBI:0000398 ! image creation device [Term] id: OBI:0001049 name: chip spotting device def: "A device for dropping and immobilizing a solution of biomolecules, for example, nucleic acids such as probe DNA, mRNA, and peptide nucleic acid (PNA), and proteins on a DNA microarray surface to manufacture a DNA microarray." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001050 name: RNA extraction/purification instrument def: "A device that is used to isolate and collect RNA for subsequent molecular analysis." [] is_a: OBI:0001114 ! nucleic acid extraction/purification instrument [Term] id: OBI:0001051 name: DNA extract def: "The output of an extraction process in which DNA molecules are purified in order to exclude DNA from organellas." [] is_a: OBI:0001010 ! nucleic acid extract [Term] id: OBI:0001052 name: two-photon laser/detector def: "A light source used in fluorescence imaging that allows the imaging of living tissue up to a depth of 1 mm, based on the concept that two photons of low energy can excite a fluorophore in a quantum event, resulting in the emission of a fluorescence photon, typically at a higher energy than either of the two excitatory photons." [] is_a: OBI:0400065 ! light source [Term] id: OBI:0001053 name: electrophoresis system def: "A device that moves charged particles through a medium by using an electric field induced by electrodes." [] is_a: OBI:0000932 ! material separation device [Term] id: OBI:0001054 name: PET synthesizer def: "A device that is used to produce targeted molecular pharmaceuticals for use in positron emission tomography." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001055 name: spinning-disk confocal microscope def: "A confocal microscope that uses a Nipkow disk, a mechanical, geometrically operating image scanning device." [] is_a: OBI:0001079 ! confocal microscope [Term] id: OBI:0001056 name: DNA synthesizer def: "An oligonucleotide synthesizer that is used to custom-build DNA molecules to contain a particular sequence of nucleotides." [] is_a: OBI:0400113 ! oligonucleotide synthesizer [Term] id: OBI:0001057 name: high performance liquid chromatography instrument def: "A liquid chromatography instrument that consists of a reservoir of mobile phase, a pump, an injector, a separation column, and a detector. The pump (rather than gravity) provides the higher pressure required to propel the mobile phase and analyte through the densely packed column." [] is_a: OBI:0001139 ! liquid chromatography instrument [Term] id: OBI:0001058 name: microplate reader def: "A measurement device that detects biological, chemical or physical events of samples in microtiter plates." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001059 name: ELISA microplate reader def: "A microplate reader that is used for enzyme-linked immunosorbent assays (ELISA)." [] is_a: OBI:0001058 ! microplate reader [Term] id: OBI:0001060 name: spot cutter def: "A robotic device that is used to excise spots from gels." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001061 name: microwave synthesis system def: "A device that is used to apply microwave irradiation to chemical reactions." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001062 name: densitometer def: "A device that measures the degree of darkness (the optical density) of a photographic or semitransparent material or of a reflecting surface." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001063 name: automatic staining machine def: "A device that is used to automatically stain tissue sections on slides or tissue specimens." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001064 name: automatic tissue processor def: "A device for processing histological tissue having a tissue carrier basket suspended from a turntable overlying a plurality of beakers suspended from a carrier plate. The turntable is raised, indexed, and lowered by a suitable driving mechanism to move the tissue basket sequentially through the beakers. Timers can each be programmed to control the movement of the turntable to provide various different cycles for processing the tissue. Some of the beakers are received in individual thermal baths to heat and control the temperature of the substances received in the beakers for treating the tissue." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001065 name: stereo microscope def: "An optical microscope that uses two separate optical paths with two objectives and two eyepieces to provide slightly different viewing angles to the left and right eyes." [] is_a: OBI:0000940 ! optical microscope [Term] id: OBI:0001066 name: top loading balance def: "A balance that consists of a metal plate on which to place an object and a digital readout of the measurement of its mass." [] is_a: OBI:0001135 ! balance [Term] id: OBI:0001067 name: perfusion station def: "A device or system in which perfusion units are integrated." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001068 name: SPECT scanner def: "A nuclear medicine tomographic imaging device that uses gamma rays to provide 3D information, typically presented as cross-sectional slices through the specimen but with the ability to be freely reformatted or manipulated as required." [] is_a: OBI:0000398 ! image creation device [Term] id: OBI:0001069 name: array manufacturer role def: "a manufacturer role which is played by the person or organization that manufactured the array" [] is_a: OBI:0000571 ! manufacturer role [Term] id: OBI:0001070 name: scintillation counter def: "A device that is used to measure ionizing radiation." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001071 name: programmable array microscope def: "A confocal microscope that uses a programmable spatial light modulator for generating an arbitrary pattern of conjugate illumination and detection apertures." [] is_a: OBI:0001079 ! confocal microscope [Term] id: OBI:0001072 name: cryostat def: "A device consisting of a vessel, similar in construction to a vacuum flask, that is used to maintain cold cryogenic temperatures. FIX THIS DEFINITION" [] is_a: OBI:0000967 ! container is_a: OBI:0001034 ! environmental control device [Term] id: OBI:0001073 name: microtome knife maker def: "A glass cutting and breaking device that is used to produce glass knives used in ultramicrotomy." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001074 name: cryofixation device def: "A device that is used for the fixation or stabilization of biological materials as the first step in specimen preparation for electron microscopy." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001075 name: hybridization oven def: "A device that creates an appropriate environment for nucleic acid hybridization." [] is_a: OBI:0000136 ! incubator is_a: OBI:0002089 ! physical store [Term] id: OBI:0001076 name: incubator shaker def: "An incubating device that provides shaking motion for biomedical applications (e.g., cell cultures)." [] is_a: OBI:0002089 ! physical store [Term] id: OBI:0001077 name: small-animal image acquisition device def: "A device that is used to image small laboratory animals (e.g., rats and mice) in vivo." [] is_a: OBI:0000398 ! image creation device [Term] id: OBI:0001078 name: infrared image acquisition device def: "An image acquisition device that is responsive to an infrared emissive target within a given field of view." [] is_a: OBI:0000398 ! image creation device [Term] id: OBI:0001079 name: confocal microscope def: "A microscope that is used to increase micrograph contrast and/or reconstruct three-dimensional images by using a spatial pinhole to eliminate out-of-focus light in specimens that are thicker than the focal plane." [] is_a: OBI:0400169 ! microscope [Term] id: OBI:0001080 name: patch clamp device def: "A device used in electrophysiology that allows the study of single or multiple ion channels in cells." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001081 name: gel imaging system def: "A device that is used to acquire images of laboratory gels." [] is_a: OBI:0000398 ! image creation device [Term] id: OBI:0001082 name: protein separation apparatus def: "A device that is used for the separation of proteins." [] is_a: OBI:0000932 ! material separation device [Term] id: OBI:0001083 name: multichannel electronic pipette def: "A multichannel pipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense the aspirated volume or a series of aliquots in successive dispensing operations." [] is_a: OBI:0001118 ! multichannel pipette [Term] id: OBI:0001084 name: vitrification apparatus def: "A device that is used to effect the transition of a substance into a glass." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001085 name: radiography instrument def: "An image acquisition device that uses ionizing electromagnetic radiation such as X-rays to view objects." [] is_a: OBI:0000398 ! image creation device [Term] id: OBI:0001086 name: radiation measurement device def: "A device that consists of a radiosensitive detector and a means of recording the effects of radiation on the detector." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001087 name: lyophilizer def: "A device that is used to freeze dry material." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001088 name: tandem mass spectrometer def: "A mass spectrometer in which ions are subjected to two or more sequential stages of analysis (which may be separated spatially or temporally) according to the quotient mass/charge." [] is_a: OBI:0000049 ! mass spectrometer [Term] id: OBI:0001089 name: microhardness tester def: "A hardness testing device that is used in light-optical microscopes." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001090 name: multimode microplate reader def: "A microplate reader that can detect multiple types of absorbance, luminescence or fluorescence." [] is_a: OBI:0001058 ! microplate reader [Term] id: OBI:0001091 name: mechanical balance def: "A balance that is used to compare the weights of two bodies, to determine the difference in mass (or weight)." [] is_a: OBI:0001135 ! balance [Term] id: OBI:0001092 name: computer cluster def: "A group of linked computers, working together closely so that in many respects they form a single computer." [] is_a: OBI:0400107 ! computer [Term] id: OBI:0001093 name: microtome knife sharpener def: "A device that is used to sharpen knives used in microtomy." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001094 name: plate shaker def: "A device that provides shaking motion for microplates." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001095 name: coagulation analyzer def: "A device for automatically analyzing blood coagulation in a clinical laboratory." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001096 name: laser capture microdissection microscope def: "A microscope that uses low-energy laser beams and special transfer film to lift single cells from a tissue." [] is_a: OBI:0400169 ! microscope [Term] id: OBI:0001097 name: liquid extraction robot def: "A liquid handling device that provides automatic liquid extraction." [] is_a: OBI:0400112 ! liquid handler [Term] id: OBI:0001098 name: ultrasound machine def: "A device that is used to visualize subcutaneous body structures including tendons, muscles, joints, vessels and internal organs." [] is_a: OBI:0000398 ! image creation device [Term] id: OBI:0001099 name: immunoblot scanner def: "A device that is used for the imaging of immunoblots." [] is_a: OBI:0000398 ! image creation device [Term] id: OBI:0001100 name: microcentrifuge def: "A type of centrifuge that is designed for small tubes (0.2 ml to 2.0 ml), has a compact design, and has a small footprint." [] is_a: OBI:0400106 ! centrifuge [Term] id: OBI:0001101 name: electronic repeater pipette def: "A micropipette that can be programmed by the user to aspirate a volume of liquid reagent or sample and dispense a series of aliquots in successive dispensing operations." [] is_a: OBI:0001128 ! micropipette [Term] id: OBI:0001102 name: electron paramagnetic resonance spectrometer def: "An spectrophotometer that is used to investigate chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion." [] is_a: OBI:0400115 ! spectrophotometer [Term] id: OBI:0001103 name: rocker def: "A device that provides three-dimensional motion for biomedical applications (e.g., gel trays)." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001104 name: analytical balance def: "A balance with weighing pan(s) inside a transparent enclosure that is used to measure mass to a very high degree of precision and accuracy." [] is_a: OBI:0001135 ! balance [Term] id: OBI:0001105 name: scanning force microscope def: "A microscope that forms images of surfaces using a physical probe that scans the specimen." [] is_a: OBI:0400169 ! microscope [Term] id: OBI:0001106 name: pulsed-field gel electrophoresis system def: "A gel electrophoresis system in which the gel matrix is subjected to an electric field that periodically changes direction." [] is_a: OBI:0001121 ! gel electrophoresis system [Term] id: OBI:0001107 name: tissue embedding station def: "A device that is used to perform paraffin embedding of tissue specimens." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001108 name: nucleic acid sequencer def: "An device that is used to determine the order of nucleotides in nucleic acid sequences." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001109 name: bead array reader def: "A device that is used to acquire and image bead array data." [] is_a: OBI:0000398 ! image creation device [Term] id: OBI:0001110 name: real-time PCR machine def: "An PCR instrument that enables both detection and quantification of one or more specific sequences in a DNA sample." [] is_a: OBI:0000989 ! PCR instrument [Term] id: OBI:0001111 name: paraffin oven def: "A device that is used for the warming of paraffin embedding medium." [] is_a: OBI:0000967 ! container is_a: OBI:0001034 ! environmental control device [Term] id: OBI:0001112 name: autoclave def: "A device that is used to sterilize equipment and supplies by subjecting them to high pressure steam at 121 C or more, typically for 15 to 20 minutes depending on the size of the load and the contents." [] is_a: OBI:0001034 ! environmental control device [Term] id: OBI:0001113 name: microplate washer def: "A device that is used to wash immunoassays in microwell strips and plates with professional accuracy. WHAT IS PROFESSIONAL ACCURACY??" [] is_a: OBI:0000968 ! device [Term] id: OBI:0001114 name: nucleic acid extraction/purification instrument def: "A device that is used to isolate and collect nucleic acids (DNA or RNA) for subsequent molecular analysis." [] is_a: OBI:0000932 ! material separation device [Term] id: OBI:0001115 name: ELISA microplate washer def: "A microplate washer that is used for enzyme-linked immunosorbent assays (ELISA)." [] is_a: OBI:0001113 ! microplate washer [Term] id: OBI:0001116 name: vacuum manifold def: "A device that is used for the vacuum-driven processing of multiwell strips or plates, or spin columns. IS THIS AN INSTRUMENT? IS THE DEFINTION CORRECT - TO DISTRIBUTE PRESSURE EVENLY." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001117 name: DNA extraction/purification instrument def: "A device that is used to isolate and collect DNA for subsequent molecular analysis." [] is_a: OBI:0001114 ! nucleic acid extraction/purification instrument [Term] id: OBI:0001118 name: multichannel pipette def: "A pipetting system that has a plurality of tip fittings and is used for multi-well plate applications." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001119 name: cell harvester def: "A device that is used to harvest cells from microplates and deposit samples on a filter mat. NOT AN INSTRUMENT?" [] is_a: OBI:0000968 ! device [Term] id: OBI:0001120 name: portable fluorometer def: "A compact fluorometer that can be carried or moved with ease." [] is_a: OBI:0400143 ! fluorometer [Term] id: OBI:0001121 name: gel electrophoresis system def: "An electrophoresis system in which an electric field is applied to a gel matrix" [] is_a: OBI:0001053 ! electrophoresis system [Term] id: OBI:0001122 name: diffractometer def: "A measurement device for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (e.g. X rays or neutrons) interacts with it." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001123 name: microdissection instrument def: "A device that is used for the dissection of tissues under magnification." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001124 name: micropipette puller def: "A device that is used to fabricate glass micropipettes." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001125 name: laser scanning confocal microscope def: "A confocal microscope that obtains high-resolution optical images with depth selectivity, in which a laser beam passes through a light source aperture and then is focused by an objective lens into a small (ideally diffraction limited) focal volume within or on the surface of a specimen." [] is_a: OBI:0001079 ! confocal microscope [Term] id: OBI:0001126 name: digital microscope def: "A microscope that uses optics and a charge-coupled device (CCD) camera to output a digital image to a monitor." [] is_a: OBI:0400169 ! microscope [Term] id: OBI:0001127 name: freeze substitution system def: "A device or system for dehydrating and then chemically fixing electron microscopy samples at low temperatures in preparation for various treatments including embedding in resins." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001128 name: micropipette def: "A microinjection device that is used to measure very small volumes of liquids." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001129 name: voltage clamp device def: "A device that is used to measure the ion currents across the membrane of excitable cells, such as neurons, while holding the membrane voltage at a set level." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001130 name: vacuum oven def: "A device that heats materials in a vacuum." [] is_a: OBI:0000967 ! container is_a: OBI:0001034 ! environmental control device [Term] id: OBI:0001131 name: slide warmer def: "A device that is used to heat microscope slides." [] is_a: OBI:0001034 ! environmental control device [Term] id: OBI:0001132 name: capillary electrophoresis instrument def: "An electrophoresis system that is used to separate ionic species by their charge and frictional forces and mass." [] is_a: OBI:0001053 ! electrophoresis system [Term] id: OBI:0001133 name: denaturing high-performance liquid chromatography instrument def: "A high performance liquid chromatography instrument that employs temperature-dependent separation of DNA containing mismatched base pairs from PCR-amplified DNA fragments for chromatographic mutation analysis." [] is_a: OBI:0000932 ! material separation device [Term] id: OBI:0001134 name: agarose gel electrophoresis system def: "A gel electrophoresis system that is used to separate DNA or RNA molecules by size, achieved by moving negatively charged nucleic acid molecules through an agarose matrix with an electric field." [] is_a: OBI:0001121 ! gel electrophoresis system [Term] id: OBI:0001135 name: balance def: "A measuring instrument that is used to determine the weight or mass of an object." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001136 name: surface plasmon resonance instrument def: "A tool for measuring adsorption of material onto planar metal (typically gold and silver) surfaces or onto the surface of metal nanoparticles." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001137 name: protein sequencer def: "An device that is used to determine the order of amino acids in protein sequences." [] is_a: OBI:0000832 ! measurement device [Term] id: OBI:0001138 name: X-ray source def: "A device that is used to generate X-rays." [] synonym: "x-ray generator" EXACT [] is_a: OBI:0000968 ! device [Term] id: OBI:0001139 name: liquid chromatography instrument def: "A chromatography device that dissolves a mixture in liquid mobile phase to separate the analyte to be measured from other molecules in the mixture and allows it to be isolated" [] is_a: OBI:0000048 ! chromatography device [Term] id: OBI:0001140 name: spike-in quality control role def: "a reference substance role that is borne by a material entity with a known amount which is mixed into the evaluant of assays for quality control or data normalization purposes" [] is_a: OBI:0000025 ! reference substance role [Term] id: OBI:0001141 name: individual organism identifier def: "a CRID symbol used to distinguish one individual organism from another." [] is_a: IAO:0000577 ! centrally registered identifier symbol [Term] id: OBI:0001142 name: dye swap quality control role def: "a reference substance role that is borne by a material entity used in a dye swap design experiment for quality control or data normalization purposes" [] is_a: OBI:0000025 ! reference substance role [Term] id: OBI:0001143 name: labeled nucleic acid extract def: "a labeled specimen that is the output of a labeling process and has grain labeled nucleic acid for detection of the nucleic acid in future experiments." [] synonym: "labeled extract" EXACT [] is_a: OBI:0000924 ! labeled specimen [Term] id: OBI:0001144 name: binding constant def: "A quantitative binding datum that is expressed as a scalar number and a unit, which can be utilized in equations that model the binding process independent of the specific assay performed." [] is_a: OBI:0003142 ! quantitative binding datum [Term] id: OBI:0001145 name: 3D structure determination of bound molecular complex assay def: "A 3D molecular structure determination assay in which a complex of 2 or more molecular enties is characterized which provides information on their binding configuration." [] is_a: OBI:0003117 ! 3D molecular structure determination assay [Term] id: OBI:0001146 name: binding assay def: "An assay with the objective to characterize the disposition of two or more material entities to form a complex." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0001147 name: cell culture expansion def: "a process that results in the increase of cell numbers" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0001148 name: gene knock out def: "a genetic transformation that renders a gene non-functional, e.g. due to a point mutation, or the removal of all, or part of, the gene using recombinant methods." [] is_a: OBI:0600043 ! genetic transformation [Term] id: OBI:0001149 name: gene knock in def: "a genetic transformation that involves the insertion of a protein coding cDNA sequence at a particular locus in an organism's chromosome. Typically, this is done in mice since the technology for this process is more refined, and because mouse embryonic stem cells are easily manipulated. The difference between knock-in technology and transgenic technology is that a knock-in involves a gene inserted into a specific locus, and is a \"targeted\" insertion." [] is_a: OBI:0600043 ! genetic transformation [Term] id: OBI:0001150 name: chromosomal substitution def: "A genetic transformation in which all, or part, of a chromosome from a donor replaces that of the recipient. It does not include chromosome recombination. For single gene insertion, use the term 'gene knock in'." [] is_a: OBI:0600043 ! genetic transformation [Term] id: OBI:0001151 name: genetically modified material def: "a material entity, organism or cell, that is the output of a genetic transformation process." [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0001152 name: transfection def: "a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA or RNA into a cell" [] is_a: OBI:0600043 ! genetic transformation [Term] id: OBI:0001153 name: genetic transformation objective def: "a material transformation objective aims to create genetically modified organism or cell" [] is_a: OBI:0000456 ! material transformation objective [Term] id: OBI:0001154 name: induced mutagenesis def: "A genetic transformation that is the modification of the genetic material (either coding or non-coding) of an organism caused by mutagenic processes, compounds, or irradiation." [] is_a: OBI:0600043 ! genetic transformation [Term] id: OBI:0001155 name: 3D structural organization datum def: "A measurement datum that describes the structural orientation of a material entity in 3D space." [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0001156 name: age since planting measurement datum def: "An age measurement datum that is the result of the measurement of the age of an organism since planting, the process of placing a plant in media (e.g. soil) to allow it to grow, which excludes sowing." [] is_a: OBI:0001167 ! age measurement datum [Term] id: OBI:0001157 name: age since hatching measurement datum def: "An age measurement datum that is the result of the measurement of the age of an organism since hatching, the process of emergence from an egg." [] is_a: OBI:0001167 ! age measurement datum [Term] id: OBI:0001158 name: age determination assay def: "An assay that determines the duration of part of the life of an organism, where the initial time point is the beginning of some transitional state (such as birth or when planted)." [] synonym: "age measurement assay" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0001159 name: age since egg laying measurement datum def: "An age measurement datum that is the result of the measurement of the age of an organism since egg laying, the process of the production of egg(s) by an organism." [] is_a: OBI:0001167 ! age measurement datum [Term] id: OBI:0001160 name: assay validation objective def: "an objective specification to check the accuracy or the quality of the results of an assay by comparison with independent results" [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0001161 name: age since germination measurement datum def: "An age measurement datum that is the result of the measurement of the age of an organism since germination, the process consisting of physiological and developmental changes by a seed, spore, pollen grain (microspore), or zygote that occur after release from dormancy, and encompassing events prior to and including the first visible indications of growth." [] is_a: OBI:0001167 ! age measurement datum [Term] id: OBI:0001162 name: validation by reverse transcription PCR design def: "a study design in which checks the accuracy or the quality of the result of an assay by comparing with reverse transcription PCR results" [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001163 name: age since eclosion measurement datum def: "An age measurement datum that is the result of the measurement of the age of an organism since eclosion, the process of emergence of an adult insect from its pupa or cocoon." [] is_a: OBI:0001167 ! age measurement datum [Term] id: OBI:0001164 name: age since sowing measurement datum def: "An age measurement datum that is the result of the measurement of the age of an organism since sowing, the process of placing a seed or spore in some media with the intention to invoke germination." [] is_a: OBI:0001167 ! age measurement datum [Term] id: OBI:0001165 name: age since coitus measurement datum def: "An age measurement datum that is the result of the measurement of the age of an organism since coitus, the process of copulation that occurs during the process of sexual reproduction." [] is_a: OBI:0001167 ! age measurement datum [Term] id: OBI:0001166 name: validation by real time PCR design def: "a study design in which the accuracy or the quality of the result of an assay is checked by comparing with real time PCR results" [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001167 name: age measurement datum def: "A time measurement datum that is the result of measurement of age of an organism" [] is_a: IAO:0000416 ! time measurement datum [Term] id: OBI:0001168 name: age since fertilization measurement datum def: "An age measurement datum that is the result of the measurement of the age of an organism since fertilization, the process of the union of gametes of opposite sexes during the process of sexual reproduction to form a zygote." [] is_a: OBI:0001167 ! age measurement datum [Term] id: OBI:0001169 name: age since birth measurement datum def: "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." [] is_a: OBI:0001167 ! age measurement datum [Term] id: OBI:0001170 name: reverse transcription polymerase chain reaction assay def: "An assay that determines the concentration of RNA in a sample in which an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR." [] is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0001171 name: half life datum (t 1/2) def: "The time it takes for 50% of a class of stochastic processes to occur." [] synonym: "t 1/2" EXACT [] is_a: IAO:0000416 ! time measurement datum [Term] id: OBI:0001172 name: dose response curve def: "A data item of paired values, one indicating the dose of a material, the other quantitating a measured effect at that dose. The dosing intervals are chosen so that effect values be interpolated by a plotting a curve." [] is_a: IAO:0000573 ! line graph [Term] id: OBI:0001173 name: service def: "A planned process in which a service provider performs a task (i.e. a planned process) for a service consumer." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0001174 name: passive immunization def: "The injection of immune effector material (antibodies, T cells or B cells) into an organism so that the organisms immune system gains its immune effector function to recognize specific antigens." [] synonym: "adoptive transfer" EXACT [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0001175 name: selective organism creation objective def: "an objective specification to generate a population or type of organism within species that have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms." [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0001176 name: Individual epitope immunization in vivo def: "An immunization in which an individual epitope is administered into a host organism." [] is_a: OBI:1110015 ! Immunization in vivo [Term] id: OBI:0001177 name: RNA sequencing assay def: "An assay that determines the sequence of an RNA molecule." [] is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001178 name: efficacy of epitope intervention experiment def: "An assay that tests if inducing an epitope specific immune response in an organism has an effect, such as the ability to prevent, treat or exacerbate diseases in the organism." [] synonym: "efficacy of in vivo intervention" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0001179 name: epitope protection from infectious challenge experiment def: "An epitope protection experiment in which the ability of the epitope to protect the host from an infection is assessed." [] synonym: "protection from infectious challenge" EXACT [] is_a: OBI:0001184 ! epitope protection experiment [Term] id: OBI:0001180 name: half maximal effective concentration (EC50) def: "half maximal effective concentration (EC50) is a scalar measurement datum corresponding to the concentration of a compound which induces a response halfway between the baseline and maximum after some specified exposure time." [] is_a: IAO:0000032 ! scalar measurement datum [Term] id: OBI:0001181 name: binding datum def: "A data item that states if two or more material entities have the disposition to form a complex, and if so, how strong that disposition is." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0001182 name: negative binding datum def: "A categorical binding datum that states that there is no significant disposition of two or more entities to form a complex." [] is_a: OBI:0003141 ! categorical binding datum [Term] id: OBI:0001183 name: epitope protection from tumor challenge experiment def: "An epitope protection experiment in which the ability of the epitope to protect the host from developing tumors is assessed." [] synonym: "protection from tumor challenge" EXACT [] is_a: OBI:0001184 ! epitope protection experiment [Term] id: OBI:0001184 name: epitope protection experiment def: "An efficacy of epitope intervention experiment that tests the efficacy of inducing an immune epitope response to prevent disease in a host." [] synonym: "protection from challenge" EXACT [] is_a: OBI:0001178 ! efficacy of epitope intervention experiment [Term] id: OBI:0001185 name: selectively maintained organism def: "An organism that is bred to have some uniform behavioral, morphological, physiological, or genetic characteristics with similarly bred organisms" [] synonym: "cultivar" EXACT [] synonym: "ecotype" EXACT [] synonym: "strain" EXACT [] is_a: OBI:0100026 ! organism [Term] id: OBI:0001186 name: epitope protection from infectious challenge experiment based on pathogen burden def: "An epitope protection from infectious challenge experiment in which the readout is a reduction in the presence of pathogens in the host compared to controls." [] synonym: "burden after infectious challenge" EXACT [] is_a: OBI:0001179 ! epitope protection from infectious challenge experiment [Term] id: OBI:0001187 name: infectious agent detection assay def: "An assay that measures the presence or amount of an infectious agent in an evaluant" [] is_a: OBI:0000070 ! assay [Term] id: OBI:0001188 name: epitope disease exacerbation experiment def: "An efficacy of epitope intervention experiment that tests the ability of inducing an epitope immune response to increase the severity of an existing disease in the host." [] synonym: "exacerbation assay" EXACT [] is_a: OBI:0001178 ! efficacy of epitope intervention experiment [Term] id: OBI:0001189 name: epitope protection experiment based on survival def: "An epitope protection experiment that determines the success of the epitope intervention based on increased survival of the host." [] synonym: "host survival after challenge" EXACT [] is_a: OBI:0001184 ! epitope protection experiment [Term] id: OBI:0001190 name: epitope treatment experiment def: "An epitope intervention experiment that tests the ability of inducing an epitope immune response to treat an existing disease in the host." [] synonym: "decreased disease symptoms after treatment" EXACT [] is_a: OBI:0001178 ! efficacy of epitope intervention experiment [Term] id: OBI:0001191 name: half maximal inhibitory concentration (IC50) def: "Half maximal inhibitory concentration (IC50) is a scalar measurement datum that measures the effectiveness of a compound to competitively inhibit a given process, and corresponds to the concentration of the compound at which it reaches half of its maximum inhibitory effect." [] is_a: IAO:0000032 ! scalar measurement datum [Term] id: OBI:0001192 name: epitope specific immune intervention def: "An administration in vivo to either actively or passively immunize an organism in order to induce a response against a specific immune epitope" [] is_a: OBI:0001174 ! passive immunization [Term] id: OBI:0001193 name: epitope specific cytokine production by T cells def: "A process of cytokine production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0001816 ! cytokine production [Term] id: OBI:0001194 name: ELISPOT assay measuring epitope specific transforming growth factor-beta production by T cells def: "An enzyme-linked immunospot assay that detects transforming growth factor-beta production by T cells." [] synonym: "TGFb release|ELISPOT" EXACT [] is_a: OBI:0001264 ! assay measuring epitope specific transforming growth factor-beta production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001195 name: operator variation design def: "A study design that assesses the operator performance and relation to data consistency and quality." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001196 name: cytometric bead array assay measuring epitope specific IP-10 production by T cells def: "A cytometric bead array assay that detects IP-10 production by T cells." [] synonym: "CXCL10/IP-10 release|cytometric bead array" EXACT [] is_a: OBI:0001308 ! assay measuring epitope specific IP-10 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001197 name: comparative genome hybridization by array design def: "A study design that detects genomic copy number variations using microarray technology." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001198 name: assay measuring epitope specific interleukin-27 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-27 production by T cells." [] synonym: "IL-27 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001199 name: in vivo design def: "A study design that is conducted entirely in a living organism, e.g. a compound treatment in a mouse model." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001200 name: genotyping by high throughput sequencing design def: "A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using high througput sequencing techniques." [] is_a: OBI:0001444 ! genotyping design [Term] id: OBI:0001201 name: epitope specific tolerance induction by T cells def: "A process of tolerance induction by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0002507 ! tolerance induction [Term] id: OBI:0001202 name: innate behavior design def: "A study design in which the innate behavior of the organism is examined, e.g. path finding in bees." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001203 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific transforming growth factor-beta production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects transforming growth factor-beta production by T cells." [] synonym: "TGFb release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001264 ! assay measuring epitope specific transforming growth factor-beta production by T cells [Term] id: OBI:0001204 name: SNP microarray def: "A DNA microarray used to detect polymorphisms in DNA samples" [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0001205 name: cell component comparison design def: "A study design that compares samples from different cell components." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001206 name: ELISPOT assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells def: "An enzyme-linked immunospot assay that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|ELISPOT" EXACT [] is_a: OBI:0001233 ! assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001207 name: epitope specific macrophage inflammatory protein-1 alpha production by T cells def: "A process of macrophage inflammatory protein-1 alpha production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0071608 ! macrophage inflammatory protein-1 alpha production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001208 name: epitope specific T cell activation def: "A process of T cell activation resulting from the recognition of a T cell epitope." [] is_a: GO:0042110 ! T cell activation [Term] id: OBI:0001209 name: assay measuring epitope specific interleukin-10 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001210 name: cytometric bead array assay measuring epitope specific transforming growth factor-beta production by T cells def: "A cytometric bead array assay that detects transforming growth factor-beta production by T cells" [] synonym: "TGFb release|cytometric bead array" EXACT [] is_a: OBI:0001264 ! assay measuring epitope specific transforming growth factor-beta production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001211 name: ex vivo design def: "A study design where all or part of an organism is removed and studied in vitro, e.g. part of a mouse is removed and cultured in vitro. A cell culture with an established cell line is an in vitro experiment." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001212 name: epitope specific type IV hypersensitivity by T cells def: "A process of type IV hypersensitivity by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0001806 ! type IV hypersensitivity [Term] id: OBI:0001214 name: normalization testing design def: "A study design that tests different normalization procedures." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001215 name: intracellular material detection assay measuring epitope specific perforin release def: "A flow cytometry assay that detects epitope specific perforin release by T cells." [] synonym: "perforin release|intracellular staining" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001497 ! assay measuring epitope specific perforin release by T cells [Term] id: OBI:0001216 name: cell culture analyte detection bioassay measuring epitope specific interleukin-2 production by T cells def: "A reporter cell line analyte detection bioassay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|bioassay" EXACT [] is_a: OBI:0000904 ! reporter cell line analyte detection bioassay is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells [Term] id: OBI:0001217 name: assay measuring epitope specific interleukin-22 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-22 production by T cells." [] synonym: "IL-22 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001218 name: assay measuring epitope specific interleukin-8 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-8 production by T cells." [] synonym: "IL-8 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001219 name: epitope specific chemokine (C-C motif) ligand 1 production by T cells def: "A process of chemokine (C-C motif) ligand 1 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0071610 ! chemokine (C-C motif) ligand 1 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001220 name: cell culture analyte detection bioassay measuring epitope specific interleukin-10 production by T cells def: "A reporter cell line analyte detection bioassay that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|bioassay" EXACT [] is_a: OBI:0000904 ! reporter cell line analyte detection bioassay is_a: OBI:0001209 ! assay measuring epitope specific interleukin-10 production by T cells [Term] id: OBI:0001221 name: ChIP-chip by SNP array assay def: "A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a SNP array to detect polymorphism specific DNA elements in the isolated chromatin" [] is_a: OBI:0001248 ! ChIP-chip assay [Term] id: OBI:0001222 name: ELISA measuring epitope specific RANTES production by T cells def: "An enzyme-linked immunosorbent assay that detects RANTES production by T cells." [] synonym: "CCL5/RANTES release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001232 ! assay measuring epitope specific RANTES production by T cells [Term] id: OBI:0001223 name: cytometric bead array assay measuring epitope specific interleukin-1 beta production by T cells def: "A cytometric bead array assay that detects interleukin-1 beta production by T cells." [] synonym: "IL-1b release|cytometric bead array" EXACT [] is_a: OBI:0001449 ! assay measuring epitope specific interleukin-1 beta production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001225 name: genetic population background information def: "a genetic characteristics information which is a part of genotype information that identifies the population of organisms" [] is_a: OBI:0001404 ! genetic characteristics information [Term] id: OBI:0001226 name: environmental history design def: "A study design in which some aspect of the organism's environmental history is studied, such as exposure to teratogen, radiation, climate etc." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001227 name: ELISPOT assay measuring epitope specific interleukin-6 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-6 production by T cells" [] synonym: "IL-6 release|ELISPOT" EXACT [] is_a: OBI:0001451 ! assay measuring epitope specific interleukin-6 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001228 name: in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response def: "A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response." [] synonym: "antibody help|in vivo assay" EXACT [] is_a: OBI:0001495 ! in vivo assay measuring epitope specific T cell helper activity [Term] id: OBI:0001229 name: plasmon resonance assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex def: "A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an epitope:MHC complex binding with a T cell receptor." [] synonym: "dissociation constant KD|surface plasmon resonance (SPR)|nM" EXACT [] is_a: OBI:0000923 ! surface plasmon resonance binding assay is_a: OBI:0002097 ! assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex [Term] id: OBI:0001230 name: assay measuring epitope specific interleukin-5 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001231 name: ELISA measuring epitope specific transforming growth factor-beta production by T cells def: "An enzyme-linked immunosorbent assay that detects transforming growth factor-beta production by T cells." [] synonym: "TGFb release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001264 ! assay measuring epitope specific transforming growth factor-beta production by T cells [Term] id: OBI:0001232 name: assay measuring epitope specific RANTES production by T cells def: "A T cell epitope specific cytokine production assay that detects RANTES production by T cells." [] synonym: "CCL5/RANTES release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001233 name: assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells def: "A T cell epitope specific cytokine production assay that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001234 name: epigenetic modification identification objective def: "A molecular feature identification objective that aims to detect epigenetic modifications, such as DNA methylation, histone modifications." [] is_a: OBI:0000131 ! molecular feature identification objective [Term] id: OBI:0001235 name: transcription profiling by tiling array assay def: "A transcription profiling by array assay that uses a tiling path array." [] is_a: OBI:0001463 ! transcription profiling by array assay [Term] id: OBI:0001236 name: ELISA measuring epitope specific interleukin-22 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-22 production by T cells." [] synonym: "IL-22 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001217 ! assay measuring epitope specific interleukin-22 production by T cells [Term] id: OBI:0001237 name: assay measuring epitope specific interleukin-21 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-21 production by T cells." [] synonym: "IL-21 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001238 name: ELISA measuring epitope specific interleukin-9 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-9 production by T cells." [] synonym: "IL-9 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001253 ! assay measuring interleukin-9 production by T cells [Term] id: OBI:0001239 name: transcription profiling by high throughput sequencing design def: "A study design in which sequencing technology (e.g. Solexa/454) is used to generate RNA sequence, analyse the transcibed regions of the genome, and/or to quantitate transcript abundance" [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001240 name: intracellular cytokine staining assay measuring epitope specific interleukin-6 production by T cells def: "A flow cytometry assay that detects interleukin-6 production by T cells." [] synonym: "IL-6 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001451 ! assay measuring epitope specific interleukin-6 production by T cells [Term] id: OBI:0001241 name: cell culture analyte detection bioassay measuring epitope specific interleukin-4 production by T cells def: "A reporter cell line analyte detection bioassay that detects interleukin-4 production by T cells." [] synonym: "IL-4 release|bioassay" EXACT [] is_a: OBI:0000904 ! reporter cell line analyte detection bioassay is_a: OBI:0001450 ! assay measuring epitope specific interleukin-4 production by T cells [Term] id: OBI:0001242 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor alpha production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor alpha production by T cells." [] synonym: "TNFa release|RNA/DNA detection" EXACT [] is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor alpha production by T cells is_a: OBI:0001788 ! detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001243 name: cytometric bead array assay measuring epitope specific monocyte chemotactic protein-1 production by T cells def: "A cytometric bead array assay that detects monocyte chemotactic protein-1 production by T cells." [] synonym: "CCL2/MCP-1 release|cytometric bead array" EXACT [] is_a: OBI:0001465 ! assay measuring epitope specific monocyte chemotactic protein-1 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001244 name: ELISA measuring epitope specific interleukin-23 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-23 production by T cells." [] synonym: "IL-23 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001363 ! assay measuring epitope specific interleukin-23 production by T cells [Term] id: OBI:0001245 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific perforin release def: "A detection of specific nucleic acids with complementary probes assay that detects epitope specific perforin release by T cells." [] synonym: "perforin release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001497 ! assay measuring epitope specific perforin release by T cells [Term] id: OBI:0001246 name: ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells def: "An enzyme-linked immunosorbent assay that detects tumor necrosis factor superfamily cytokine production by T cells." [] synonym: "TNF release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001247 name: genotyping by high throughput sequencing assay def: "A genotyping assay that uses a high througput sequencer" [] is_a: OBI:0000435 ! genotyping assay [Term] id: OBI:0001248 name: ChIP-chip assay def: "An assay in which chromatin is immunoprecipitated and subsequently analyzed using a DNA microarray to identify which parts of DNA are part of the isolated chromatin" [] synonym: "ChIP-on-chip assay" EXACT [] is_a: OBI:0001954 ! ChIP assay [Term] id: OBI:0001249 name: epitope specific T cell tolerance induction def: "A process of T cell tolerance induction resulting from the recognition of a T cell epitope." [] is_a: GO:0002517 ! T cell tolerance induction is_a: OBI:0001201 ! epitope specific tolerance induction by T cells [Term] id: OBI:0001250 name: obsolete intracellular material detection by flow cytometry assay of epitope specific cytotoxic T cell degranulation def: "An intracellular material detection by flow cytometry assay that measures epitope specific cytotoxic T cell degranulation" [] synonym: "T cell degranulation by intracellular staining" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: OBI:0000916 [Term] id: OBI:0001251 name: assay measuring epitope specific interleukin-13 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-13 production by T cells." [] synonym: "IL-13 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001252 name: array platform variation design def: "A study design in which the array platform is compared, e.g. Agilent versus Affymetrix." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001253 name: assay measuring interleukin-9 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-9 production by T cells." [] synonym: "IL-9 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001254 name: epitope specific interleukin-3 production by T cells def: "A process of interleukin-3 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0032632 ! interleukin-3 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001255 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-5 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001230 ! assay measuring epitope specific interleukin-5 production by T cells [Term] id: OBI:0001256 name: epitope specific lymphotoxin A production by T cells def: "A process of lymphotoxin A production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0032641 ! lymphotoxin A production is_a: OBI:0001351 ! epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001257 name: epitope specific interleukin-1 alpha production by T cells def: "A process of interleukin-1 alpha production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0032610 ! interleukin-1 alpha production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001258 name: ChIP-seq design def: "A study design which aims to identify protein and DNA interactions using a combination of chromatin immunoprecipitation and high throughput sequencing. Massively parallel sequence analyses are used in conjunction with whole-genome sequence databases to analyze the interaction pattern of any protein with DNA, or the pattern of any epigenetic chromatin modifications." [] is_a: OBI:0001425 ! protein binding site identification design [Term] id: OBI:0001259 name: translational bias design def: "A study design that characterizes the association of transcripts and translation machinery." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001260 name: ELISA measuring epitope specific interleukin-3 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001406 ! assay measuring epitope specific interleukin-3 production by T cells [Term] id: OBI:0001261 name: ELISA measuring epitope specific interleukin-1 alpha production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-1 alpha production by T cells." [] synonym: "IL-1a release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001388 ! assay measuring epitope specific interleukin-1 alpha production by T cells [Term] id: OBI:0001262 name: epitope specific interleukin-27 production by T cells def: "A process of interleukin-27 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0032631 ! interleukin-27 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001263 name: in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response def: "A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response." [] synonym: "T cell help|in vivo assay" EXACT [] is_a: OBI:0001495 ! in vivo assay measuring epitope specific T cell helper activity [Term] id: OBI:0001264 name: assay measuring epitope specific transforming growth factor-beta production by T cells def: "A T cell epitope specific cytokine production assay that detects transforming growth factor-beta production by T cells." [] synonym: "TGFb release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001265 name: FWER adjusted p-value def: "A quantitative confidence value resulting from a multiple testing error correction method which adjusts the p-value used as input to control for Type I error in the context of multiple pairwise tests" [] is_a: OBI:0000071 ! quantitative confidence value [Term] id: OBI:0001266 name: DNA methylation profiling by high throughput sequencing assay def: "A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using sequencing based technology" [] is_a: OBI:0000634 ! DNA methylation profiling assay [Term] id: OBI:0001267 name: epitope specific transforming growth factor-beta production by T cells def: "A process of transforming growth factor-beta production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0071604 ! transforming growth factor beta production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001268 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-12 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-12 production by T cells." [] synonym: "IL-12 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001391 ! assay measuring epitope specific interleukin-12 production by T cells [Term] id: OBI:0001269 name: assay measuring epitope specific cytotoxic T cell degranulation def: "A T cell epitope dependent biological activity assay that detects cytotoxic T cell degranulation." [] synonym: "degranulation|biological activity" EXACT [] is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:0001270 name: cell culture analyte detection bioassay measuring epitope specific transforming growth factor-beta production by T cells def: "A reporter cell line analyte detection bioassay that detects transforming growth factor-beta production by T cells." [] synonym: "TGFb release|bioassay" EXACT [] is_a: OBI:0000904 ! reporter cell line analyte detection bioassay is_a: OBI:0001264 ! assay measuring epitope specific transforming growth factor-beta production by T cells [Term] id: OBI:0001271 name: RNA-seq assay def: "An RNA sequencing assay that determines an RNA sequence by analyzing the transcibed regions of the genome and or to quantitate transcript abundance." [] synonym: "transcription profiling by high throughput sequencing" EXACT [] is_a: OBI:0001177 ! RNA sequencing assay [Term] id: OBI:0001272 name: ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells def: "An enzyme-linked immunospot assay that detects tumor necrosis factor superfamily cytokine production by T cells." [] synonym: "TNF release|ELISPOT" EXACT [] is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001273 name: cell culture analyte detection bioassay measuring epitope specific interleukin-5 production by T cells def: "A reporter cell line analyte detection bioassay that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|bioassay" EXACT [] is_a: OBI:0000904 ! reporter cell line analyte detection bioassay is_a: OBI:0001230 ! assay measuring epitope specific interleukin-5 production by T cells [Term] id: OBI:0001274 name: genotyping by array assay def: "A genotyping assay that uses an array" [] is_a: OBI:0000435 ! genotyping assay is_a: OBI:0001985 ! microarray assay [Term] id: OBI:0001275 name: epitope specific interleukin-16 production by T cells def: "A process of interleukin-16 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0032619 ! interleukin-16 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001276 name: assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells def: "A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 1 by T cells." [] synonym: "CCL1/TCA-3 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001277 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-2 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells [Term] id: OBI:0001278 name: DNA methylation profiling by array design def: "A study design in which the methylation state of DNA is determined and is compared between samples using array technology." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001279 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-22 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-22 production by T cells." [] synonym: "IL-22 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001217 ! assay measuring epitope specific interleukin-22 production by T cells [Term] id: OBI:0001280 name: assay measuring epitope specific interleukin-16 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001281 name: ELISA measuring epitope specific IP-10 production by T cells def: "An enzyme-linked immunosorbent assay that detects IP-10 production by T cells." [] synonym: "CXCL10/IP-10 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001308 ! assay measuring epitope specific IP-10 production by T cells [Term] id: OBI:0001282 name: translation profiling assay def: "An assay in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, which mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation." [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0001283 name: ELISA measuring epitope specific interleukin-15 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-15 production by T cells." [] synonym: "IL-15 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001292 ! assay measuring epitope specific interleukin-15 production by T cells [Term] id: OBI:0001284 name: cytometric bead array assay measuring epitope specific interleukin-12 production by T cells def: "A cytometric bead array assay that detects interleukin-12 production by T cells." [] synonym: "IL-12 release|cytometric bead array" EXACT [] is_a: OBI:0001391 ! assay measuring epitope specific interleukin-12 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001285 name: in vitro design def: "A study design that is done in a test tube or a culture dish, e.g. A bacterial invasion assay in an established cell culture." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001286 name: RNAi profiling by array design def: "A study design in which experiment double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001288 name: ELISA measuring epitope specific lymphotoxin A production by T cells def: "An enzyme-linked immunosorbent assay that detects lymphotoxin A production by T cells." [] synonym: "lymphotoxin A/TNFb release|ELISA" EXACT [] is_a: OBI:0001246 ! ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells is_a: OBI:0001327 ! assay measuring epitope specific lymphotoxin A production by T cells [Term] id: OBI:0001289 name: cytometric bead array assay measuring epitope specific interleukin-5 production by T cells def: "A cytometric bead array assay that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|cytometric bead array" EXACT [] is_a: OBI:0001230 ! assay measuring epitope specific interleukin-5 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001290 name: transcription profiling by array design def: "A study design that identifies forms and abundance of transcripts in the genome using microarray technology." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001291 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17 production by T cells." [] synonym: "IL-17 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:0001292 name: assay measuring epitope specific interleukin-15 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-15 production by T cells." [] synonym: "IL-15 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001293 name: disease state design def: "A study design in which the pathological condition of a part, organ, or system of an organism is studied. The etiology may be from infection, genetic defect, or environmental stress." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001294 name: wild type organism genotype information def: "a genotype information about an organism and includes information that there are no known modifications to the genetic background. Generally it is the genotype information of a representative individual from a class of organisms." [] is_a: OBI:0001305 ! genotype information [Term] id: OBI:0001295 name: assay measuring epitope specific interleukin-17 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-17 production by T cells." [] synonym: "IL-17 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001296 name: cytometric bead array assay measuring epitope specific interleukin-17 production by T cells def: "A cytometric bead array assay that detects interleukin-17 production by T cells." [] synonym: "IL-17 release|cytometric bead array" EXACT [] is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001297 name: cytometric bead array assay measuring epitope specific interleukin-10 production by T cells def: "A cytometric bead array assay that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|cytometric bead array" EXACT [] is_a: OBI:0001209 ! assay measuring epitope specific interleukin-10 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001298 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-21 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-21 production by T cells." [] synonym: "IL-21 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001237 ! assay measuring epitope specific interleukin-21 production by T cells [Term] id: OBI:0001299 name: intracellular cytokine staining assay measuring epitope specific interleukin-5 production by T cells def: "A flow cytometry assay that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001230 ! assay measuring epitope specific interleukin-5 production by T cells [Term] id: OBI:0001300 name: cytometric bead array assay measuring epitope specific interleukin-2 production by T cells def: "A cytometric bead array assay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|cytometric bead array" EXACT [] is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001301 name: cell culture analyte detection bioassay measuring epitope specific interleukin-16 production by T cells def: "A reporter cell line analyte detection bioassay that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|bioassay" EXACT [] is_a: OBI:0000904 ! reporter cell line analyte detection bioassay is_a: OBI:0001280 ! assay measuring epitope specific interleukin-16 production by T cells [Term] id: OBI:0001302 name: ELISA measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells def: "An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 alpha production by T cells." [] synonym: "CCL3/MIP-1a release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001333 ! assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells [Term] id: OBI:0001303 name: intracellular cytokine staining assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells def: "A flow cytometry assay that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001233 ! assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells [Term] id: OBI:0001304 name: RNAi profiling by array assay def: "An assay in which double stranded RNA is synthesized with a sequence complementary to a gene(s) of interest and introduced into a cell or organism, where it is recognized as exogenous genetic material and activates the RNAi pathway resulting in knockdown of the transcripts and providing a means to study downstream changes in gene expression." [] is_a: OBI:0001985 ! microarray assay [Term] id: OBI:0001305 name: genotype information def: "a genetic characteristics information that is about the genetic material of an organism and minimally includes information about the genetic background and can in addition contain information about specific alleles, genetic modifications, etc." [] is_a: OBI:0001404 ! genetic characteristics information [Term] id: OBI:0001306 name: RNA stability design def: "A study design that examines the stability and/or decay of RNA transcripts." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001307 name: tiling microarray def: "A DNA microarray which has short fragments of nucleic acid immobilized on a substrate. These are designed to cover the whole genome of the target species. Tiling arrays are used to determine genome binding in ChIP assays or to identify transcribed regions." [] synonym: "genome tiling array" EXACT [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0001308 name: assay measuring epitope specific IP-10 production by T cells def: "A T cell epitope specific cytokine production assay that detects IP-10 production by T cells." [] synonym: "CXCL10/IP-10 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001309 name: intracellular cytokine staining assay measuring epitope specific interleukin-13 production by T cells def: "A flow cytometry assay that detects interleukin-13 production by T cells." [] synonym: "IL-13 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001251 ! assay measuring epitope specific interleukin-13 production by T cells [Term] id: OBI:0001310 name: species comparison design def: "A study design that assays differences between distinct species." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001311 name: X-ray crystallography assay determining the 3D structure of a T cell epitope:MHC:TCR complex def: "A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a T cell epitope:MHC:TCR complex." [] synonym: "3D structure|x-ray crystallography|angstroms" EXACT [] is_a: OBI:0000912 ! X-ray crystallography 3D molecular structure determination assay is_a: OBI:0001999 ! 3D molecular structure determination assay of a T cell epitope:MHC:TCR complex [Term] id: OBI:0001313 name: transcription profiling by RT-PCR design def: "A study design which aims to examine the transcriptome of a biological sample by reverse transcription PCR (RT-PCR)." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001314 name: epitope specific T cell enhancement of B cell mediated immune response def: "A process of T cell enhancement of B cell mediated immune response resulting from the recognition of a T cell epitope." [] is_a: GO:0035399 ! helper T cell enhancement of B cell mediated immune response [Term] id: OBI:0001315 name: ELISA measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells def: "An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 1 production by T cells." [] synonym: "CCL1/TCA-3 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001276 ! assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells [Term] id: OBI:0001316 name: epitope specific interleukin-21 production by T cells def: "A process of interleukin-21 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0032625 ! interleukin-21 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001317 name: flow cytometry assay measuring cell-cell binding of a T cell epitope:MHC:TCR complex def: "A flow cytometry assay that measures the cell-cell binding of an epitope:MHC complex binding with a T cell receptor." [] synonym: "T cell- APC binding|binding assay" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:1110124 ! assay measuring qualitative binding of a T cell epitope:MHC:TCR complex [Term] id: OBI:0001318 name: proteomic profiling by array assay def: "An assay that detects proteins in a sample (quantified or otherwise analyzed), e.g. antibody profiling using an array based technology." [] is_a: OBI:0001985 ! microarray assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:0001319 name: cell culture analyte detection bioassay measuring epitope specific interferon-gamma production by T cells def: "A reporter cell line analyte detection bioassay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|bioassay" EXACT [] is_a: OBI:0000904 ! reporter cell line analyte detection bioassay is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells [Term] id: OBI:0001322 name: ELISPOT assay measuring epitope specific granzyme B release by T cells def: "An enzyme-linked immunospot assay that detects epitope specific granzyme B release by T cells." [] synonym: "granzyme B release|ELISPOT" EXACT [] is_a: OBI:0001436 ! assay measuring epitope specific granzyme B release by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001323 name: microRNA profiling by array design def: "A study design in which a microRNA array is used to analyse the microRNA component of the transcriptome." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001324 name: in vivo assay measuring T cell epitope specific tolerance induction def: "An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment." [] synonym: "tolerance|in vivo assay" EXACT [] is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity is_a: OBI:0001488 ! epitope tolerance induction experiment [Term] id: OBI:0001325 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific RANTES production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects RANTES production by T cells." [] synonym: "CCL5/RANTES release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001232 ! assay measuring epitope specific RANTES production by T cells [Term] id: OBI:0001326 name: cytometric bead array assay measuring epitope specific interleukin-4 production by T cells def: "A cytometric bead array assay that detects interleukin-4 production by T cells" [] synonym: "IL-4 release|cytometric bead array" EXACT [] is_a: OBI:0001450 ! assay measuring epitope specific interleukin-4 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001327 name: assay measuring epitope specific lymphotoxin A production by T cells def: "A T cell epitope specific cytokine production assay that detects lymphotoxin A production by T cells." [] synonym: "lymphotoxin A/TNFb release|biological activity" EXACT [] is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001328 name: organism development design def: "A study design that assays events associated with development. Development applies to organism(s) acquiring a mature state." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001329 name: family history design def: "A study design in which the family history such as traits, characteristics, susceptibility to disease is studied." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001330 name: ELISA measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells def: "An enzyme-linked immunosorbent assay that detects chemokine (C-X-C motif) ligand 9 production by T cells." [] synonym: "CXCL9/MIG release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001459 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells [Term] id: OBI:0001331 name: transcription profiling identification objective def: "A molecular feature identification objective that aims to characterize the abundance of transcripts" [] is_a: OBI:0000131 ! molecular feature identification objective [Term] id: OBI:0001332 name: DNA methylation profiling by array assay def: "A DNA methylation profiling assay in which the methylation state of DNA is determined and can be compared between samples using array technology" [] is_a: OBI:0000634 ! DNA methylation profiling assay [Term] id: OBI:0001333 name: assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells def: "A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 alpha production by T cells." [] synonym: "CCL3/MIP-1a release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001334 name: epitope specific granulocyte colony stimulating factor production by T cells def: "A process of granulocyte colony stimulating factor production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0071611 ! granulocyte colony-stimulating factor production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001335 name: microRNA profiling by array assay def: "An assay that analyses the microRNA component of the transcriptome using a microRNA array." [] is_a: OBI:0001926 ! microRNA profiling assay [Term] id: OBI:0001336 name: quality control testing design def: "A study design in which some aspects of the experiment is quality controlled for the purposes of quality assurance." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001337 name: clinical history design def: "A study design that the organism's clinical history of diagnosis, treatments, e.g. vaccinations, surgery etc. is studied." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001339 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-4 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-4 production by T cells." [] synonym: "IL-4 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001450 ! assay measuring epitope specific interleukin-4 production by T cells [Term] id: OBI:0001341 name: cell culture analyte detection bioassay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells def: "A reporter cell line analyte detection bioassay that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|bioassay" EXACT [] is_a: OBI:0000904 ! reporter cell line analyte detection bioassay is_a: OBI:0001233 ! assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells [Term] id: OBI:0001342 name: intracellular cytokine staining assay measuring epitope specific interleukin-21 production by T cells def: "A flow cytometry assay that detects interleukin-21 production by T cells." [] synonym: "IL-21 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001237 ! assay measuring epitope specific interleukin-21 production by T cells [Term] id: OBI:0001343 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific monocyte chemotactic protein-1 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects monocyte chemotactic protein-1 production by T cells." [] synonym: "CCL2/MCP-1 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001465 ! assay measuring epitope specific monocyte chemotactic protein-1 production by T cells [Term] id: OBI:0001344 name: ELISA measuring epitope specific monocyte chemotactic protein-1 production by T cells def: "An enzyme-linked immunosorbent assay that detects monocyte chemotactic protein-1 production by T cells." [] synonym: "CCL2/MCP-1 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001465 ! assay measuring epitope specific monocyte chemotactic protein-1 production by T cells [Term] id: OBI:0001345 name: assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 4 production by T cells." [] synonym: "CCL4/MIP-1b release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001346 name: ELISA measuring epitope specific interleukin-21 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-21 production by T cells." [] synonym: "IL-21 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001237 ! assay measuring epitope specific interleukin-21 production by T cells [Term] id: OBI:0001348 name: in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity def: "An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity." [] synonym: "type IV hypersensitivity (DTH)|in vivo skin test" EXACT [] is_a: OBI:0001178 ! efficacy of epitope intervention experiment is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity [Term] id: OBI:0001349 name: cytometric bead array assay measuring epitope specific interleukin-13 production by T cells def: "A cytometric bead array assay that detects interleukin-13 production by T cells." [] synonym: "IL-13 release|cytometric bead array" EXACT [] is_a: OBI:0001251 ! assay measuring epitope specific interleukin-13 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001350 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-gamma production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interferon-gamma production by T cells." [] synonym: "IFNg release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells [Term] id: OBI:0001351 name: epitope specific tumor necrosis factor superfamily cytokine production by T cells def: "A process of tumor necrosis factor superfamily cytokine production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0071706 ! tumor necrosis factor superfamily cytokine production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001352 name: allele information def: "a genetic alteration information that about one of two or more alternative forms of a gene or marker sequence and differing from other alleles at one or more mutational sites based on sequence. Polymorphisms are included in this definition." [] is_a: OBI:0001364 ! genetic alteration information [Term] id: OBI:0001353 name: cytometric bead array assay measuring epitope specific tumor necrosis factor alpha production by T cells def: "A cytometric bead array assay that detects tumor necrosis factor alpha production by T cells." [] synonym: "TNFa release|cytometric bead array" EXACT [] is_a: OBI:0001368 ! cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor alpha production by T cells [Term] id: OBI:0001354 name: ELISPOT assay measuring epitope specific interleukin-17 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-17 production by T cells." [] synonym: "IL-17 release|ELISPOT" EXACT [] is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001356 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interferon-beta production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interferon-beta production by T cells." [] synonym: "IFNb release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001390 ! assay measuring epitope specific interferon-beta production by T cells [Term] id: OBI:0001357 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001233 ! assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells [Term] id: OBI:0001358 name: post-transcriptional modification design def: "A study design in which a modification of the transcriptome, proteome (not genome) is made, for example RNAi, antibody targeting." [] is_a: OBI:0000115 ! intervention design [Term] id: OBI:0001359 name: ELISA measuring epitope specific interleukin-8 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-8 production by T cells." [] synonym: "IL-8 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001218 ! assay measuring epitope specific interleukin-8 production by T cells [Term] id: OBI:0001360 name: cytometric bead array assay measuring epitope specific interleukin-6 production by T cells def: "A cytometric bead array assay that detects interleukin-6 production by T cells." [] synonym: "IL-6 release|cytometric bead array" EXACT [] is_a: OBI:0001451 ! assay measuring epitope specific interleukin-6 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001361 name: transcription profiling by RT-PCR assay def: "A transcription profiling assay that uses reverse transcription PCR (RT-PCR)." [] is_a: OBI:0000424 ! transcription profiling assay is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0001362 name: epitope specific chemokine (C-C motif) ligand 4 production by T cells def: "A process of chemokine (C-C motif) ligand 4 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0071606 ! chemokine (C-C motif) ligand 4 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001363 name: assay measuring epitope specific interleukin-23 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-23 production by T cells." [] synonym: "IL-23 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001364 name: genetic alteration information def: "a genetic characteristics information that is about known changes or the lack thereof from the genetic background, including allele information, duplication, insertion, deletion, etc." [] is_a: OBI:0001404 ! genetic characteristics information [Term] id: OBI:0001365 name: cellular process design def: "A study design that aims to study the processes that are carried out at the cellular level, but are not necessarily restricted to a single cell. For example, cell communication occurs among more than one cell, but occurs at the cellular level." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001366 name: epitope specific RANTES production by T cells def: "A process of RANTES production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0071609 ! chemokine (C-C motif) ligand 5 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001367 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-10 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001209 ! assay measuring epitope specific interleukin-10 production by T cells [Term] id: OBI:0001368 name: cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells def: "A cytometric bead array assay that detects tumor necrosis factor superfamily cytokine production by T cells." [] synonym: "TNF release|cytometric bead array" EXACT [] is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001369 name: wild type allele information def: "an allele information that is about the allele found most frequently in natural populations, or in standard laboratory stocks for a given organism." [] is_a: OBI:0001352 ! allele information [Term] id: OBI:0001370 name: intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells def: "A flow cytometry assay that detects chemokine (C-C motif) ligand 4 production by T cells." [] synonym: "CCL4/MIP-1b release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001345 ! assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells [Term] id: OBI:0001371 name: epitope specific granzyme B production by T cells def: "A process of granzyme B production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0071613 ! granzyme B production [Term] id: OBI:0001373 name: epitope specific interleukin-8 production by T cells def: "A process of interleukin-8 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0032637 ! interleukin-8 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001374 name: injury design def: "A study design in which the response of an organism(s) to injury or damage is studied." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001376 name: intracellular cytokine staining assay measuring epitope specific interleukin-3 production by T cells def: "A flow cytometry assay that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001406 ! assay measuring epitope specific interleukin-3 production by T cells [Term] id: OBI:0001377 name: organism status comparison design def: "A study design that compares samples from live and dead organisms." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001378 name: ELISA measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells def: "An enzyme-linked immunosorbent assay that detects chemokine (C-C motif) ligand 4 production by T cells." [] synonym: "CCL4/MIP-1b release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001345 ! assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells [Term] id: OBI:0001379 name: cytometric bead array assay measuring epitope specific interferon-gamma production by T cells def: "A cytometric bead array assay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|cytometric bead array" EXACT [] is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001380 name: assay measuring epitope specific interleukin-18 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-18 production by T cells." [] synonym: "IL-18 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001381 name: epitope specific interleukin-23 production by T cells def: "A process of interleukin-23 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0032627 ! interleukin-23 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001382 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-27 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-27 production by T cells." [] synonym: "IL-27 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001198 ! assay measuring epitope specific interleukin-27 production by T cells [Term] id: OBI:0001383 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific IP-10 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects IP-10 production by T cells." [] synonym: "CXCL10/IP-10 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001308 ! assay measuring epitope specific IP-10 production by T cells [Term] id: OBI:0001384 name: cell culture analyte detection bioassay measuring epitope specific interleukin-3 production by T cells def: "A reporter cell line analyte detection bioassay that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|bioassay" EXACT [] is_a: OBI:0000904 ! reporter cell line analyte detection bioassay is_a: OBI:0001406 ! assay measuring epitope specific interleukin-3 production by T cells [Term] id: OBI:0001385 name: intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells def: "A flow cytometry assay that detects tumor necrosis factor superfamily cytokine production by T cells." [] synonym: "TNF release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001386 name: epitope specific monocyte chemotactic protein-1 production by T cells def: "A process of monocyte chemotactic protein-1 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0071605 ! monocyte chemotactic protein-1 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001387 name: genotyping by array design def: "A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs using microarray technology." [] is_a: OBI:0001444 ! genotyping design [Term] id: OBI:0001388 name: assay measuring epitope specific interleukin-1 alpha production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-1 alpha production by T cells." [] synonym: "IL-1a release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001389 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-6 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-6 production by T cells." [] synonym: "IL-6 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001451 ! assay measuring epitope specific interleukin-6 production by T cells [Term] id: OBI:0001390 name: assay measuring epitope specific interferon-beta production by T cells def: "A T cell epitope specific cytokine production assay that detects interferon-beta production by T cells." [] synonym: "IFNb release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001391 name: assay measuring epitope specific interleukin-12 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-12 production by T cells." [] synonym: "IL-12 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001392 name: in vivo assay measuring epitope specific T cell killing def: "An in vivo cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC." [] synonym: "cytotoxicity|in vivo assay" EXACT [] is_a: OBI:0000883 ! in vivo cell killing assay is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity is_a: OBI:1110130 ! assay measuring epitope specific T cell killing [Term] id: OBI:0001393 name: comparative genomic hybridization by array assay def: "An assay that measures changes in DNA sequence copy number using a microarray. For example the analysis of LOH in tumor cells vs a non diseased sample or the comparison of clinical isolated of disease causing bacteria." [] synonym: "array CGH" EXACT [] is_a: OBI:0000435 ! genotyping assay is_a: OBI:0001985 ! microarray assay [Term] id: OBI:0001394 name: epitope specific cytotoxic T cell degranulation def: "A process of cytotoxic T cell degranulation resulting from the recognition of a T cell epitope." [] is_a: GO:0043316 ! cytotoxic T cell degranulation [Term] id: OBI:0001395 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-23 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-23 production by T cells." [] synonym: "IL-23 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001363 ! assay measuring epitope specific interleukin-23 production by T cells [Term] id: OBI:0001396 name: stimulus or stress design def: "A study design in which the response of an organism(s) to the stress or stimulus is studied, e.g. osmotic stress, heat shock, radiation exposure, behavioral treatment etc." [] is_a: OBI:0000115 ! intervention design [Term] id: OBI:0001397 name: cytometric bead array assay measuring epitope specific granulocyte colony stimulating factor production by T cells def: "A cytometric bead array assay that detects granulocyte colony stimulating factor production by T cells." [] synonym: "G-CSF release|cytometric bead array" EXACT [] is_a: OBI:0001600 ! assay measuring epitope specific granulocyte colony stimulating factor production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001398 name: protein and DNA interaction identification objective def: "A sequence feature identification objective that aims to characterize the interactions between protein and DNA which includes identification of transcription factor binding sites." [] is_a: OBI:0000113 ! sequence feature identification objective [Term] id: OBI:0001399 name: epitope specific interleukin-22 production by T cells def: "A process of interleukin-22 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0032626 ! interleukin-22 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001400 name: assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells def: "A T cell epitope specific cytokine production assay that detects tumor necrosis factor superfamily cytokine production by T cells." [] synonym: "TNF release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001401 name: protocol optimization design def: "A study design where different protocols or protocol parameters are compared aims to find an optimized protocol" [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001402 name: promoter activity detection by reporter gene assay measuring epitope specific interleukin-2 production by T cells def: "A promoter activity detection by reporter gene assay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|reporter gene assay" EXACT [] is_a: OBI:0000913 ! promoter activity detection by reporter gene assay is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells [Term] id: OBI:0001403 name: ChIP-chip design def: "A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and DNA microarray (chip) assays." [] synonym: "ChIP-on-chip design" EXACT [] is_a: OBI:0001425 ! protein binding site identification design [Term] id: OBI:0001404 name: genetic characteristics information def: "a data item that is about genetic material including polymorphisms, disease alleles, and haplotypes." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0001405 name: cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells def: "A cytometric bead array assay that detects macrophage inflammatory protein-1 alpha production by T cells." [] synonym: "CCL3/MIP-1a release|cytometric bead array" EXACT [] is_a: OBI:0001333 ! assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001406 name: assay measuring epitope specific interleukin-3 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001407 name: assay measuring epitope specific T cell activation def: "A T cell epitope dependent biological activity assay that detects T cell activation." [] synonym: "activation|biological activity" EXACT [] is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:0001408 name: imprinting design def: "A study design where differences in genetic imprinting of maternally- and paternally-inherited chromosomes (e.g., due to in vivo differences in chemical modification and/or chromatin structure) are compared." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001409 name: cell cycle design def: "A study design that assays events that occur in relation to the cell cycle, which is the period between the formation of a cell, by division of its mother cell and the time when the cell itself divides to form two daughter cells." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001410 name: translation profiling design def: "A study design in which surface-bound, translationally competent ribosome complexes are used to generate a translation profile for mRNA, where mRNA may be a single molecular species, or a combination of species, including complex mixtures such as those found in the set of mRNAs isolated from a cell or tissue. One or more components of the surface-bound ribosome complex may be labeled at specific positions to permit analysis of multiple or single molecules for determination of ribosomal conformational changes and translation kinetics. Translation profiles are used as the basis for comparison of an mRNA or set of mRNA species. The translation profile can be used to determine such characteristics as kinetics of initiation, kinetic of elongation, identity of the polypeptide product, and the like. Analysis of translation profiles may be used to determine differential gene expression, optimization of mRNA sequences for expression, screening drug candidates for an effect on translation." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001411 name: cell type comparison design def: "A study design that compares cells of different type, for example different cell lines." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001412 name: cytometric bead array assay measuring epitope specific RANTES production by T cells def: "A cytometric bead array assay that detects RANTES production by T cells." [] synonym: "CCL5/RANTES release|cytometric bead array" EXACT [] is_a: OBI:0001232 ! assay measuring epitope specific RANTES production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001413 name: cell culture analyte detection bioassay measuring epitope specific interleukin-6 production by T cells def: "A reporter cell line analyte detection bioassay that detects interleukin-6 production by T cells." [] synonym: "IL-6 release|bioassay" EXACT [] is_a: OBI:0000904 ! reporter cell line analyte detection bioassay is_a: OBI:0001451 ! assay measuring epitope specific interleukin-6 production by T cells [Term] id: OBI:0001414 name: assay measuring epitope specific interferon-gamma production by T cells def: "A T cell epitope specific cytokine production assay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001415 name: epitope specific interleukin-9 production by T cells def: "A process of interleukin-9 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0032638 ! interleukin-9 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001416 name: assay measuring epitope specific tumor necrosis factor alpha production by T cells def: "An assay of epitope specific tumor necrosis factor alpha production by T cells that detects tumor necrosis factor production." [] synonym: "TNFa release|biological activity" EXACT [] is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001417 name: ChIP-chip by tiling array design def: "A study design which aims to identify protein binding sites in genomic DNA by a combination of chromatin immunoprecipitation and tiling microarray (chip) assays." [] is_a: OBI:0001403 ! ChIP-chip design [Term] id: OBI:0001418 name: dose response design def: "A study design that examines the relationship between the size of the administered dose and the extent of the response." [] is_a: OBI:0000951 ! compound treatment design [Term] id: OBI:0001419 name: ChIP-chip by tiling array assay def: "A ChIP-ChIP assay in which immunoprecipitated chromatin is run on a tiling array that covers stretches of DNA to to detect which elements in those stretches are present in the isolated chromatin" [] is_a: OBI:0001248 ! ChIP-chip assay [Term] id: OBI:0001420 name: epitope specific helper T cell enhancement of T cell mediated immune response def: "A process of helper T cell enhancement of T cell mediated immune response resulting from the recognition of a T cell epitope." [] is_a: GO:0035398 ! helper T cell enhancement of T cell mediated immune response [Term] id: OBI:0001421 name: epitope specific interferon-beta production by T cells def: "A process of interferon-beta production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0032608 ! interferon-beta production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001422 name: organism part comparison design def: "A study design that compares tissues, regions, organs within or between organisms" [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001423 name: intracellular material detection measuring epitope specific granzyme B release by T cells def: "A flow cytometry assay that detects epitope specific granzyme B release by T cells" [] synonym: "granzyme B release|intracellular staining" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001436 ! assay measuring epitope specific granzyme B release by T cells [Term] id: OBI:0001425 name: protein binding site identification design def: "A study design that investigates protein binding sites on nucleic acids." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001426 name: sex comparison design def: "A study design that assays differences associated with an organism's sex, gender or mating type." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001427 name: transcription profiling by tiling array design def: "A study design in which gene expression on a genome-wide basis is evaluated, without bias toward coding or noncoding regions, using tiling arrays containing oligonucleotides that are either overlapping or spaced at regular intervals." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001429 name: cell differentiation design def: "A study design that assays events associated with cell development or differentiation." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001430 name: transcription profiling design def: "A study design that identifies forms and abundance of transcripts in the genome." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001432 name: operon identification design def: "A study design that identifies locations and members of operons in a genome." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001433 name: radio immuno assay measuring epitope specific interferon-gamma production by T cells def: "A radio immuno assay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|radio immuno assay (RIA)" EXACT [] is_a: OBI:0000910 ! radio immuno assay is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells [Term] id: OBI:0001435 name: DNA methylation profiling by high throughput sequencing design def: "A study design in which the methylation state of DNA is determined and is compared between samples using high throughput sequencing technology." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001436 name: assay measuring epitope specific granzyme B release by T cells def: "A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme B release by T cells." [] synonym: "granzyme B release|biological activity" EXACT [] is_a: OBI:0001269 ! assay measuring epitope specific cytotoxic T cell degranulation [Term] id: OBI:0001437 name: intracellular cytokine staining assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells def: "A flow cytometry assay that detects chemokine (C-X-C motif) ligand 9 production by T cells." [] synonym: "CXCL9/MIG release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001459 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells [Term] id: OBI:0001438 name: ELISA measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells def: "An enzyme-linked immunosorbent assay that detects macrophage inflammatory protein-1 gamma production by T cells." [] synonym: "CCL9/MIP-1g release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001456 ! assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells [Term] id: OBI:0001439 name: epitope specific chemokine (C-X-C motif) ligand 9 production by T cells def: "A process of chemokine (C-X-C motif) ligand 9 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0035393 ! chemokine (C-X-C motif) ligand 9 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001440 name: all pairs design def: "A study design in which all specimens are compared to every other specimen." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001441 name: proteomic profiling by array design def: "A study design in which proteins in a sample are detected, quantified or otherwise analysed, through an array-based technology." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001442 name: q-value def: "A quantitative confidence value that measures the minimum false discovery rate that is incurred when calling that test significant. \nTo compute q-values, it is necessary to know the p-value produced by a test and possibly set a false discovery rate level." [] synonym: "FDR adjusted p-value" EXACT [] is_a: OBI:0000071 ! quantitative confidence value [Term] id: OBI:0001444 name: genotyping design def: "A study design that classifies an individual or group of individuals on the basis of alleles, haplotypes, SNPs." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001445 name: assay measuring epitope specific interleukin-2 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001446 name: epitope specific interleukin-15 production by T cells def: "A process of interleukin-15 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0032618 ! interleukin-15 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001447 name: epitope specific macrophage inflammatory protein-1 gamma production by T cells def: "A process of macrophage inflammatory protein-1 gamma production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0071607 ! macrophage inflammatory protein-1 gamma production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001448 name: individual genetic characteristics comparison design def: "A study design where genotype, haplotype, or other individual genetic characteristics are compared." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001449 name: assay measuring epitope specific interleukin-1 beta production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-1 beta production by T cells." [] synonym: "IL-1b release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001450 name: assay measuring epitope specific interleukin-4 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-4 production by T cells." [] synonym: "IL-4 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001451 name: assay measuring epitope specific interleukin-6 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-6 production by T cells." [] synonym: "IL-6 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001452 name: cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor alpha production by T cells def: "A reporter cell line analyte detection bioassay that detects tumor necrosis factor alpha production by T cells." [] synonym: "TNFa release|bioassay" EXACT [] is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor alpha production by T cells is_a: OBI:0003488 ! cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001453 name: intracellular cytokine staining assay measuring epitope specific lymphotoxin A production by T cells def: "A flow cytometry assay that detects lymphotoxin A production by T cells." [] synonym: "lymphotoxin A/TNFb release|ICS" EXACT [] is_a: OBI:0001327 ! assay measuring epitope specific lymphotoxin A production by T cells is_a: OBI:0001385 ! intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001454 name: pathogenicity design def: "A study design in which an infective agent such as a bacterium, virus, protozoan, fungus etc. infects a host organism(s) and the infective agent is assayed." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001455 name: ELISPOT assay measuring epitope specific interleukin-5 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|ELISPOT" EXACT [] is_a: OBI:0001230 ! assay measuring epitope specific interleukin-5 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001456 name: assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells def: "A T cell epitope specific cytokine production assay that detects macrophage inflammatory protein-1 gamma production by T cells." [] synonym: "CCL9/MIP-1g release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001457 name: cytometric bead array assay measuring epitope specific interleukin-8 production by T cells def: "A cytometric bead array assay that detects interleukin-8 production by T cells." [] synonym: "IL-8 release|cytometric bead array" EXACT [] is_a: OBI:0001218 ! assay measuring epitope specific interleukin-8 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001459 name: assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 9 production by T cells." [] synonym: "CXCL9/MIG release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001460 name: genetic modification design def: "A study design in which an organism(s) is studied that has had genetic material removed, rearranged, mutagenized or added, such as in a knock out." [] is_a: OBI:0000115 ! intervention design [Term] id: OBI:0001461 name: ELISA measuring epitope specific granzyme B release by T cells def: "An enzyme-linked immunosorbent assay that detects epitope specific granzyme B release by T cells." [] synonym: "granzyme B release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001436 ! assay measuring epitope specific granzyme B release by T cells [Term] id: OBI:0001462 name: epitope specific IP-10 production by T cells def: "A process of IP-10 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0071612 ! IP-10 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001463 name: transcription profiling by array assay def: "A transcription profiling assay that uses array technology." [] synonym: "RNA profiling by array assay" EXACT [] is_a: OBI:0000424 ! transcription profiling assay [Term] id: OBI:0001464 name: strain comparison design def: "A study design that assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001465 name: assay measuring epitope specific monocyte chemotactic protein-1 production by T cells def: "A T cell epitope specific cytokine production assay that detects monocyte chemotactic protein-1 production by T cells." [] synonym: "CCL2/MCP-1 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001466 name: intracellular cytokine staining assay measuring epitope specific interleukin-12 production by T cells def: "A flow cytometry assay that detects interleukin-12 production by T cells." [] synonym: "IL-12 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001391 ! assay measuring epitope specific interleukin-12 production by T cells [Term] id: OBI:0001467 name: in vivo assay measuring T cell epitope specific disease exacerbation def: "An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment." [] synonym: "disease exacerbation|in vivo assay" EXACT [] is_a: OBI:0001188 ! epitope disease exacerbation experiment is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity [Term] id: OBI:0001468 name: cell specimen def: "A specimen primarily composed of a cell or cells collected from a multicellular organism or a cell culture." [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0001469 name: monospecific T cell recognition assay measuring MHC ligand processing and presentation def: "A MHC ligand processing and presentation assay in which the presence of a specific ligand in an eluate is detected using the response of T cells that are known to be monospecific for that ligand as a readout." [] synonym: "ligand presentation|T cell recognition" EXACT [] is_a: OBI:1110125 ! assay measuring MHC ligand processing and presentation [Term] id: OBI:0001470 name: epitope specific interleukin-17F production by T cells def: "A process of interleukin-17F production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0097088 ! interleukin-17F production is_a: OBI:1110193 ! epitope specific IL-17 release by T cells [Term] id: OBI:0001471 name: T cell epitope specific immune intervention def: "An epitope specific immune intervention in which the induced response targets a T cell epitope" [] is_a: OBI:0001192 ! epitope specific immune intervention [Term] id: OBI:0001472 name: specimen with known storage state def: "A specimen for which it is known whether it has been subjected to storage of a specified type." [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0001473 name: in vivo assay measuring T cell epitope specific protection after tumor burden challenge def: "An in vivo assay measuring T cell epitope specific protection from tumor challenge using tumor burden." [] synonym: "tumor burden after challenge|in vivo assay" EXACT [] is_a: OBI:0003458 ! epitope protection from tumor challenge experiment based on burden is_a: OBI:0003461 ! in vivo assay measuring T cell epitope specific protection from tumor challenge [Term] id: OBI:0001474 name: lowess group transformation def: "A lowess transformation where a potentially different normalization curve is generated and used for two or more groups (delineated by some criteria); criteria could include blocks (e.g. print-tip groups) on an array, or the day on which mass spectrometry was performed." [] is_a: OBI:0001477 ! lowess transformation [Term] id: OBI:0001475 name: in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden def: "An in vivo assay measuring T cell epitope specific protection from pathogen challenge using pathogen burden." [] synonym: "pathogen burden after challenge|in vivo assay" EXACT [] is_a: OBI:0001186 ! epitope protection from infectious challenge experiment based on pathogen burden is_a: OBI:0003460 ! in vivo assay measuring T cell epitope specific protection from pathogen challenge [Term] id: OBI:0001476 name: phage display binding assay def: "A binding assay in which a collection of phages expressing a library of different peptides or protein fragnments is used to infect cells, followed by screening for cells that bind a protein of interest, and identifiying the sequence of infecting phages to determine a suitable binding partner." [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001477 name: lowess transformation def: "A data transformation of normalizing ratio data by using a locally weighted polynomial regression (typically after a log transformation). The regression can be performed on log ratios resulting from the relation of two data sets versus the average log intensity data from the same two data sets or it can be performed on raw or log transformed values from one data set versus values from another. The goal could be to remove intensity-dependent dye-specific effects from the set of pair wise ratios. This method can be applied globally, or limited by one or more specified criteria." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0001478 name: mass spectrometry assay measuring MHC ligand processing and presentation def: "A MHC ligand processing and presentation assay that uses a mass spectrometry assay to identify eluted ligands" [] synonym: "ligand presentation|mass spectrometry" EXACT [] is_a: OBI:1110125 ! assay measuring MHC ligand processing and presentation [Term] id: OBI:0001479 name: specimen from organism def: "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)." [] synonym: "tissue specimen" EXACT [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0001480 name: phage display library panning def: "Phage display library panning is a process in which a diverse collection of phages encoding peptides or proteins are screened and the ones encoding active peptides/proteins are selected in an iterative process similar to natural selection." [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0001481 name: lowess global transformation def: "A lowess transformation where the same normalization curve is used for all members of the data set; e.g. Features on an array, picked spots on a gel, or measured metabolites in a sample." [] is_a: OBI:0001477 ! lowess transformation [Term] id: OBI:0001482 name: intracellular cytokine staining assay measuring epitope specific transforming growth factor-beta production by T cells def: "A flow cytometry assay that detects transforming growth factor-beta production by T cells." [] synonym: "TGFb release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001264 ! assay measuring epitope specific transforming growth factor-beta production by T cells [Term] id: OBI:0001483 name: cell collecting def: "A planned process that collects cells from culture." [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0001484 name: assay measuring T cell epitope specific in vivo activity def: "A T cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment." [] synonym: "in vivo activity|biological activity" EXACT [] is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:0001485 name: purified MHC molecule preparation def: "A mixture containing MHC molecules that was purified to remove non-MHC molecular entities." [] is_a: OBI:0001633 ! purified material [Term] id: OBI:0001486 name: disposition to be bound by an MHC protein complex def: "Is the disposition borne by a material entity that is realized in a process of being bound in the antigen binding grove of an MHC protein complex." [] synonym: "MHC ligand disposition" EXACT [] is_a: BFO:0000016 ! disposition [Term] id: OBI:0001487 name: B cell epitope specific immune intervention def: "An epitope specific immune intervention in which the induced response targets a B cell epitope" [] is_a: OBI:0001192 ! epitope specific immune intervention [Term] id: OBI:0001488 name: epitope tolerance induction experiment def: "An efficacy of epitope intervention experiment that tests the ability of the intervention to decrease an existing immune response" [] synonym: "tolerance induction" EXACT [] is_a: OBI:0001178 ! efficacy of epitope intervention experiment [Term] id: OBI:0001489 name: mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from cellular MHC def: "A mass spectrometry of MHC ligands assay that identifies eluted ligands from cell bound MHC." [] synonym: "ligand presentation|cellular MHC/mass spectrometry" EXACT [] is_a: OBI:0001478 ! mass spectrometry assay measuring MHC ligand processing and presentation [Term] id: OBI:0001490 name: cytometric bead array measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells def: "A cytometric bead array assay that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|cytometric bead array" EXACT [] is_a: OBI:0001233 ! assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001491 name: binding assay using radioactivity detection def: "A binding assay that uses radioactivity detection as an indicator of binding." [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001492 name: in vivo assay measuring T cell epitope specific protection based on survival def: "An in vivo assay measuring T cell epitope specific protection from other challenge using survival." [] synonym: "survival from challenge|in vivo assay" EXACT [] is_a: OBI:0001189 ! epitope protection experiment based on survival is_a: OBI:0003462 ! in vivo assay measuring T cell epitope specific protection from other challenge [Term] id: OBI:0001493 name: cell bound MHC competitive binding assay of a MHC:ligand complex using T cell epitope recognition def: "A cell bound MHC binding assay that uses a T cell epitope recognition assay." [] synonym: "qualitative binding|cellular MHC/T cell inhibition" EXACT [] is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] id: OBI:0001494 name: linear amplification def: "An enzymatic amplification which amplifies nucleic acid sequence by making many copies off the same template." [] is_a: OBI:0600058 ! enzymatic amplification [Term] id: OBI:0001495 name: in vivo assay measuring epitope specific T cell helper activity def: "A T cell epitope dependent biological activity assay that detects the ability of epitope specific helper T cells to enhance either B cell or T cell adaptive immune response function." [] synonym: "helper response|in vivo assay" EXACT [] is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity [Term] id: OBI:0001496 name: intracellular cytokine staining assay measuring epitope specific interleukin-22 production by T cells def: "A flow cytometry assay that detects interleukin-22 production by T cells." [] synonym: "IL-22 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001217 ! assay measuring epitope specific interleukin-22 production by T cells [Term] id: OBI:0001497 name: assay measuring epitope specific perforin release by T cells def: "A T cell epitope specific cytotoxic T cell degranulation assay that detects perforin release by T cells." [] synonym: "perforin release|biological activity" EXACT [] is_a: OBI:0001269 ! assay measuring epitope specific cytotoxic T cell degranulation [Term] id: OBI:0001498 name: atmosphere def: "A growth environment pertaining to the atmospheric conditions that is used to culture or grow an organism." [] is_a: OBI:0000997 ! growth environment [Term] id: OBI:0001499 name: binding assay using fluorescence detection def: "A binding assay that uses fluorescence detection as an indicator of binding." [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001500 name: coelution assay measuring MHC ligand processing and presentation using T cell recognition of HPLC fractionated eluate compared to synthetic ligand def: "A MHC ligand processing and presentation assay in which an HPL chromatography is run to separate an input mixture of ligands eluted from MHC into fractions. These fractions are tested for recognition by T cells and compared to the recognition of a synthetic ligand that is presumed to be the recognized epitope. Identical HPLC fractionation and T cell recognition patterns confirm that the specific ligand was presented by MHC molecules." [] synonym: "ligand presentation|coelution" EXACT [] is_a: OBI:1110125 ! assay measuring MHC ligand processing and presentation [Term] id: OBI:0001501 name: fluorescence detection assay def: "An assay in which a material's fluorescence is determined." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0001502 name: epitope specific perforin production by T cells def: "The production of perforin, an immune mediator molecule involved in T cell degranulation, resulting from the recognition of a T cell epitope." [] is_a: GO:0035944 ! perforin production [Term] id: OBI:0001503 name: MHC protein complex binding to ligand def: "The process in which a ligand binds to an MHC molecule to form a stable complex." [] is_a: OBI:0001588 ! binding [Term] id: OBI:0001504 name: dissection def: "A planned process that separates and isolates tissues for surgical purposes, or for the analysis or study of their structures." [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0001505 name: purification def: "A planned process to separate a material entity into different compositions of which one or more have are purified fractions that contain higher concentration of a desired component, while others contain impurities and are not of interest" [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0001506 name: specimen with pre- or post-mortem status def: "A specimen that has been established to be taken from a live (pre-mortem) or dead (post-mortem) organism." [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0001507 name: in vivo assay measuring T cell epitope specific treatment of disease def: "An efficacy of T cell epitope intervention experiment that detects a decrease in disease." [] synonym: "decreased disease|in vivo assay" EXACT [] is_a: OBI:0001190 ! epitope treatment experiment is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity [Term] id: OBI:0001508 name: sampling time measurement datum def: "A time measurement datum when an observation is made or a sample is taken from a material as measured from some reference point." [] synonym: "time point" EXACT [] is_a: IAO:0000416 ! time measurement datum [Term] id: OBI:0001509 name: Edman degradation assay measuring MHC ligand processing and presentation def: "A MHC ligand processing and presentation assay that uses Edman degradation to identify the eluted ligands" [] synonym: "ligand presentation|Edman degradation" EXACT [] is_a: OBI:1110125 ! assay measuring MHC ligand processing and presentation [Term] id: OBI:0001510 name: mass spectrometry assay measuring MHC ligand processing and presentation of MHC ligands eluted from secreted MHC def: "A mass spectrometry of MHC ligands that identifies eluted ligands from secreted MHC." [] synonym: "ligand presentation|secreted MHC/mass spectrometry" EXACT [] is_a: OBI:0001478 ! mass spectrometry assay measuring MHC ligand processing and presentation [Term] id: OBI:0001511 name: disposition to be a product of antigen processing and presentation def: "A disposition of a material entity to be presented by MHC molecules on the cell surface as a result of antigen processing by an antigen presenting cell." [] is_a: BFO:0000016 ! disposition [Term] id: OBI:0001512 name: cytometric bead array assay measuring epitope specific interleukin-17A production by T cells def: "A cytometric bead array assay that detects interleukin-17A production by T cells." [] synonym: "IL-17A release|cytometric bead array" EXACT [] is_a: OBI:0001296 ! cytometric bead array assay measuring epitope specific interleukin-17 production by T cells is_a: OBI:0001773 ! assay measuring epitope specific interleukin-17A production by T cells [Term] id: OBI:0001513 name: radioactivity detection assay measuring competitive binding of a purified-MHC:ligand complex def: "A radioactivity detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "qualitative binding|purified MHC/competitive/radioactivity" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] id: OBI:0001514 name: minimal inhibitory concentration def: "A scalar measurement datum that indicates the lowest concentration at which a specific compound significantly inhibits a process from occurring compared to in the absence of the compound." [] is_a: IAO:0000032 ! scalar measurement datum [Term] id: OBI:0001515 name: material maintenance service def: "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." [] comment: Here we need to go back to the defintoin of storage process. It has object specification which is material maintenance. Not necessareley a material maintenance is needed in a storage process. is_a: OBI:0001528 ! material service [Term] id: OBI:0001516 name: radioactivity detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-lysate-MHC:ligand complex def: "A radioactivity detection assay that measures half maximal effective concentration (EC50) to detect the direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "half maximal effective concentration (EC50)|lysate MHC/direct/radioactivity|nM" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001991 ! assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex [Term] id: OBI:0001517 name: radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex def: "A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "half maximal inhibitory concentration (IC50)|cellular MHC/competitive/radioactivity|nM" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001992 ! assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex [Term] id: OBI:0001518 name: epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells def: "A process of tumor necrosis factor (ligand) superfamily member 11 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0072535 ! tumor necrosis factor (ligand) superfamily member 11 production is_a: OBI:0001351 ! epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001519 name: fluorescence detection assay measuring direct binding of a cell-lysate-MHC:ligand complex def: "A fluorescence detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "qualitative binding|lysate MHC/direct/fluorescence" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001579 ! assay measuring binding of a cell-lysate-MHC:ligand complex [Term] id: OBI:0001520 name: fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "half maximal inhibitory concentration (IC50)|cellular MHC/competitive/fluorescence|nM" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001992 ! assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex [Term] id: OBI:0001521 name: ELISA measuring epitope specific granulocyte colony stimulating factor production by T cells def: "An enzyme-linked immunosorbent assay that detects granulocyte colony stimulating factor production by T cells." [] synonym: "G-CSF release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001600 ! assay measuring epitope specific granulocyte colony stimulating factor production by T cells [Term] id: OBI:0001522 name: sequence assembly algorithm def: "An algorithm used to assemble individual sequence reads into larger contiguous sequences (contigs). Assembly details include but are not limited to assembler type (overlap-layout-consensus, deBruijn), assembler version, and any relevant quality control information such as per cent known genes/ESTs captured." [] synonym: "Assembly Algorithm" EXACT [] is_a: IAO:0000064 ! algorithm [Term] id: OBI:0001523 name: cytometric bead array assay measuring epitope specific interleukin-17F production by T cells def: "A cytometric bead array assay that detects interleukin-17F production by T cells." [] synonym: "IL-17F release|cytometric bead array" EXACT [] is_a: OBI:0001296 ! cytometric bead array assay measuring epitope specific interleukin-17 production by T cells is_a: OBI:0001772 ! assay measuring epitope specific interleukin-17F production by T cells [Term] id: OBI:0001524 name: fluorescence detection assay measuring equilibrium association constant [KA] to determine direct binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures equilibrium association constant (KA) to detect the direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "association constant KA|cellular MHC/direct/fluorescence|1/M" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001987 ! assay measuring the association constant [KA] of a MHC:ligand complex [Term] id: OBI:0001525 name: PDB file def: "A 3d structural organization datum capturing the results of X-ray crystallography or NMR experiment that is formatted as specified by the Protein Databank (http://www.wwpdb.org/docs.html). A PDB file can describe the structure of multiple molecules, each of which has a different chain identifier assigned." [] is_a: OBI:0001155 ! 3D structural organization datum [Term] id: OBI:0001526 name: epitope specific interleukin-17A production by T cells def: "A process of interleukin-17A production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0097087 ! interleukin-17A production is_a: OBI:1110193 ! epitope specific IL-17 release by T cells [Term] id: OBI:0001527 name: support service def: "A service in which the service provider assists the consumer in activities directly or indirectly associated with the production and analysis of experimental research data." [] is_a: OBI:0001173 ! service [Term] id: OBI:0001528 name: material service def: "A service which has a material entity as specified input and/or specified output." [] is_a: OBI:0001173 ! service [Term] id: OBI:0001529 name: data analysis service def: "A service in which a service consumer provides some input data and a service provider transforms, models, or interprets the input data and returns this generated data as output." [] is_a: OBI:0001530 ! data service [Term] id: OBI:0001530 name: data service def: "A service that has some information content entity as input and output." [] comment: Information content entity was used as specified input and output since it was more appropriate then data item or dataset. is_a: OBI:0001173 ! service [Term] id: OBI:0001531 name: fluorescence detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand." [] synonym: "half life|purified MHC/direct/fluorescence|min" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] id: OBI:0001532 name: cytometric bead array assay measuring epitope specific interleukin-9 production by T cells def: "A cytometric bead array assay that detects interleukin-9 production by T cells." [] synonym: "IL-9 release|cytometric bead array" EXACT [] is_a: OBI:0001253 ! assay measuring interleukin-9 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001533 name: data storage service def: "A storage service in which a service consumer provides data as input which a service provider stores and returns as output in its original form." [] is_a: OBI:0001530 ! data service [Term] id: OBI:0001534 name: fluorescence detection assay measuring competitive binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that detects loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "qualitative binding|purified MHC/competitive/fluorescence" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] id: OBI:0001535 name: epitope specific interleukin-7 production by T cells def: "A process of interleukin-7 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0032636 ! interleukin-7 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001536 name: equilibrium dissociation constant (KD) def: "A binding constant defined as the ratio of kon over koff (on-rate of binding divided by off-rate)" [] is_a: OBI:0001144 ! binding constant [Term] id: OBI:0001537 name: fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|purified MHC/competitive/fluorescence|nM" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] id: OBI:0001538 name: training service def: "A service in which the service provider offers educational materials or events, such as courses, workshops or graduate programs, to the service consumer." [] is_a: OBI:0001173 ! service [Term] id: OBI:0001539 name: fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|cellular MHC/competitive/fluorescence|nM" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] id: OBI:0001540 name: obsolete T cell recognition of eluted MHC ligand assay def: "An assay that identifies an MHC ligand using a T cell response assay as a readout" [] synonym: "T cell recognition" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: OBI:0001469 [Term] id: OBI:0001541 name: fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a purified-MHC:ligand complex def: "A fluorescence detection assay measuring binding on rate (kon) to detect direct binding of a purified-MHC:ligand complex." [] synonym: "on rate|purified MHC/direct/fluorescence|nM^-1s^-1" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001994 ! assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex [Term] id: OBI:0001542 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-13 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-13 production by T cells." [] synonym: "IL-13 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001251 ! assay measuring epitope specific interleukin-13 production by T cells [Term] id: OBI:0001543 name: fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine direct binding of a purified-MHC:ligand complex approximated by EC50 def: "A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect direct binding of a purified-MHC molecule with a ligand and provides EC50 values determined under assay conditions where the EC50 approximates a KD value." [] synonym: "dissociation constant KD (~EC50)|purified MHC/direct/fluorescence|nM" EXACT [] is_a: OBI:0001592 ! fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] id: OBI:0001544 name: radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-lysate-MHC:ligand complex def: "A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-lysate-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|lysate MHC/competitive/radioactivity|nM" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] id: OBI:0001545 name: intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells def: "A flow cytometry assay that detects macrophage inflammatory protein-1 alpha production by T cells." [] synonym: "CCL3/MIP-1a release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001333 ! assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells [Term] id: OBI:0001546 name: comparative phenotypic assessment def: "Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms to make a conclusion about a phenotypic difference" [] is_a: OBI:0000338 ! drawing a conclusion based on data is_a: OBI:0001834 ! drawing a conclusion [Term] id: OBI:0001547 name: material analysis service def: "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." [] is_a: OBI:0001528 ! material service [Term] id: OBI:0001548 name: equilibrium association constant (KA) def: "A binding constant defined as the ratio of koff over kon (off-rate of binding divided by on-rate)" [] is_a: OBI:0001144 ! binding constant [Term] id: OBI:0001549 name: radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a cell-bound-MHC:ligand complex def: "A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|cellular MHC/competitive/radioactivity|nM" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] id: OBI:0001550 name: assay measuring binding of a cell-bound-MHC:ligand complex def: "A qualitative binding assay that detects the binding of a cell-bound-MHC molecule with a ligand." [] synonym: "qualitative binding|cellular MHC" EXACT [] is_a: OBI:0002072 ! assay measuring qualitative binding of a MHC:ligand complex [Term] id: OBI:0001551 name: access service def: "A service in which a service consumer receives the right to use a resource (instrument, database, software, etc) that is owned or managed by a service provider. Ownership of the accessed resource remains with the service provider during and after provision of service." [] is_a: OBI:0001173 ! service [Term] id: OBI:0001552 name: intracellular cytokine staining assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells def: "A flow cytometry assay that detects tumor necrosis factor (ligand) superfamily member 11 production by T cells." [] synonym: "TNFSF11/RANKL release|ICS" EXACT [] is_a: OBI:0001385 ! intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells is_a: OBI:0001607 ! assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells [Term] id: OBI:0001553 name: assay measuring a binding constant of a MHC:ligand complex def: "A MHC:ligand binding assay that measures a binding constant." [] synonym: "binding constant|binding assay" EXACT [] is_a: OBI:0003145 ! assay measuring quantitative binding of a MHC:ligand complex [Term] id: OBI:0001554 name: rate measurement datum def: "A scalar measurement datum that represents the number of events occuring over a time interval" [] is_a: IAO:0000032 ! scalar measurement datum [Term] id: OBI:0001555 name: assay measuring binding of a purified-MHC:ligand complex def: "A qualitative binding assay that detects the binding of a purified-MHC molecule with a ligand." [] synonym: "qualitative binding|purified MHC" EXACT [] is_a: OBI:0002072 ! assay measuring qualitative binding of a MHC:ligand complex [Term] id: OBI:0001556 name: radioactivity detection assay measuring direct binding of a cell-lysate-MHC:ligand complex def: "A radioactivity detection assay that detects direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "qualitative binding|lysate MHC/direct/radioactivity" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001579 ! assay measuring binding of a cell-lysate-MHC:ligand complex [Term] id: OBI:0001557 name: material storage service def: "A storage service in which a service consumer provides some material as input which a service provider stores and returns as output." [] is_a: OBI:0001515 ! material maintenance service [Term] id: OBI:0001558 name: radioactivity detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex def: "A radioactivity detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "half life|cellular MHC/direct/radioactivity|min" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] id: OBI:0001559 name: fluorescence detection assay measuring half life to determine direct binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures half life to detect the direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "half life|cellular MHC/direct/fluorescence|min" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] id: OBI:0001560 name: obsolete cell lysate MHC binding constant determination assay def: "An assay that measures the affinity of a ligand to a MHC in a cell lysate preparation and that quantifies the affinity with a binding constant." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0001561 name: fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "half maximal effective concentration (EC50)|cellular MHC/direct/fluorescence|nM" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001991 ! assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex [Term] id: OBI:0001562 name: intracellular cytokine staining assay measuring epitope specific interleukin-17F production by T cells def: "A flow cytometry assay that detects interleukin-17F production by T cells." [] synonym: "IL-17F release|ICS" EXACT [] is_a: OBI:0001772 ! assay measuring epitope specific interleukin-17F production by T cells is_a: OBI:1110178 ! intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:0001563 name: material processing service def: "A service in which a service provider makes physical changes to a specified input material entity with the objective of producing a new material entity form input materials, or modifying the input material entity, and returning this as output to the service consumer." [] is_a: OBI:0001528 ! material service [Term] id: OBI:0001564 name: radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 def: "A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value." [] synonym: "dissociation constant KD (~IC50)|purified MHC/competitive/radioactivity|nM" EXACT [] is_a: OBI:0001568 ! radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex is_a: OBI:0001989 ! radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex [Term] id: OBI:0001565 name: radioactivity detection assay measuring half life to determine direct binding of a cell-lysate-MHC:ligand complex def: "A radioactivity detection assay that measures half life to detect the direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "half life|lysate MHC/direct/radioactivity|min" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] id: OBI:0001566 name: 50% dissociation of binding temperature (Tm) def: "A quantitative binding datum that specifies the temperature at which half of the binding partners are forming a complex and the other half are unbound." [] synonym: "melting temperature (Tm)" EXACT [] is_a: OBI:0003142 ! quantitative binding datum [Term] id: OBI:0001567 name: radioactivity detection assay measuring binding off rate [koff] to determine direct binding of a cell-lysate-MHC:ligand complex def: "A radioactivity detection assay that measures binding off rate [koff] to detect direct binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "off rate|lysate MHC/direct/radioactivity|1/s" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001993 ! assay measuring the off rate measurement [koff] of a MHC:ligand complex [Term] id: OBI:0001568 name: radioactivity detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex def: "A radioactivity detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "half maximal inhibitory concentration (IC50)|purified MHC/competitive/radioactivity|nM" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001992 ! assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex [Term] id: OBI:0001569 name: fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a purified-MHC molecule with a ligand." [] synonym: "off rate|purified MHC/direct/fluorescence|1/s" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001993 ! assay measuring the off rate measurement [koff] of a MHC:ligand complex [Term] id: OBI:0001570 name: assay measuring epitope specific vascular endothelial growth factor production by T cells def: "A T cell epitope specific cytokine production assay that detects vascular endothelial growth factor production by T cells." [] synonym: "VEGF release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001571 name: equilibrium dissociation constant (KD) approximated by IC50 def: "A measurement of an IC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, there is a single population of sites on the receptor that competitor and ligand are binding to, and the concentration of the receptor must be much less than the KD for the competitor and the ligand. In this case, according to Cheng and Prussoff, KD = IC50 / (1 + Lstot / KDs), in which Lstot is the total concentration of the labeled competitor and KDs is the KD value of that competitor." [] is_a: OBI:0001536 ! equilibrium dissociation constant (KD) is_a: OBI:0003144 ! IC50 binding datum [Term] id: OBI:0001572 name: obsolete cell bound MHC binding constant determination assay def: "An assay that measures the affinity of a ligand to MHC moleculs bound to the cell surface and that quantifies the affinity with a binding constant." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0001573 name: DNA sequence data def: "A sequence data item that is about the primary structure of DNA" [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0001574 name: obsolete cell lysate MHC competitive binding assay using radioactivity detection def: "competitive inhibition of binding assay measuring MHC ligand binding by radioactivity detection using MHC derived from a cell lysate" [] synonym: "cell lysate MHC competitive binding using radioactivity" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: OBI:0001544 [Term] id: OBI:0001575 name: assigning gene property based on phenotypic assessment def: "Interpreting data from assays that evaluate the qualities or dispositions inhering in an organism or organism part and comparing it to data from other organisms that have a defined genetic difference, and assigning a property to the product of the targeted gene as a result." [] is_a: OBI:0000338 ! drawing a conclusion based on data [Term] id: OBI:0001576 name: obsolete purified MHC binding constant determination assay def: "An assay that measures the affinity of a ligand to a purified MHC complex preparation and that quantifies the affinity with a binding constant." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0001577 name: cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-22 production by T cells def: "A cytometric bead array assay that detects interleukin-22 production by T cells." [] synonym: "IL-22 release|cytometric bead array" EXACT [] is_a: OBI:0001217 ! assay measuring epitope specific interleukin-22 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001578 name: ELISA measuring epitope specific vascular endothelial growth factor production by T cells def: "An enzyme-linked immunosorbent assay that detects vascular endothelial growth factor production by T cells." [] synonym: "VEGF release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001570 ! assay measuring epitope specific vascular endothelial growth factor production by T cells [Term] id: OBI:0001579 name: assay measuring binding of a cell-lysate-MHC:ligand complex def: "A qualitative binding assay that detects the binding of a cell-lysate-MHC molecule with a ligand." [] synonym: "qualitative binding|lysate MHC" EXACT [] is_a: OBI:0002072 ! assay measuring qualitative binding of a MHC:ligand complex [Term] id: OBI:0001580 name: material transport service def: "A service in which a service provider facilitates the transport of some material entity to a specified destination for the service consumer." [] is_a: OBI:0001528 ! material service [Term] id: OBI:0001581 name: equilibrium dissociation constant (KD) approximated by EC50 def: "A measurement of an EC50 value under specific assay conditions approximates KD, namely the binding reaction is at an equilibrium, and the concentration of the receptor must be much less than the KD for the ligand." [] is_a: OBI:0001536 ! equilibrium dissociation constant (KD) is_a: OBI:0003143 ! EC50 binding datum [Term] id: OBI:0001582 name: obsolete cell bound MHC direct binding assay def: "direct binding assay measuring MHC ligand binding using MHC derived from a cell" [] synonym: "cell bound MHC direct binding" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0001583 name: half life of binding datum def: "A half life datum of the time it takes for 50% of bound complexes in an ensemble to disassociate in absence of re-association." [] is_a: OBI:0001144 ! binding constant is_a: OBI:0001171 ! half life datum (t 1/2) [Term] id: OBI:0001584 name: phage display binding assay measuring binding of a purified-MHC:ligand complex def: "A phage display binding assay that detects direct binding of a purified-MHC molecule with a ligand." [] synonym: "qualitative binding|purified MHC/direct/phage display" EXACT [] is_a: OBI:0001476 ! phage display binding assay is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] id: OBI:0001585 name: cytometric bead array assay measuring epitope specific interleukin-7 production by T cells def: "A cytometric bead array assay that detects interleukin-7 production by T cells." [] synonym: "IL-7 release|cytometric bead array" EXACT [] is_a: OBI:0001587 ! assay measuring epitope specific interleukin-7 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001586 name: radioactivity detection assay measuring half life to determine direct binding of a purified-MHC:ligand complex def: "A radioactivity detection assay that measures half life to detect the direct binding of a purified-MHC molecule with a ligand." [] synonym: "half life|purified MHC/direct/radioactivity|min" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001990 ! assay measuring the half life of a MHC:ligand complex [Term] id: OBI:0001587 name: assay measuring epitope specific interleukin-7 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-7 production by T cells." [] synonym: "IL-7 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001588 name: binding def: "The process of material entities forming complexes." [] is_a: GO:0008150 ! biological_process [Term] id: OBI:0001589 name: intracellular cytokine staining assay measuring epitope specific interleukin-17A production by T cells def: "A flow cytometry assay that detects interleukin-17A production by T cells." [] synonym: "IL-17A release|ICS" EXACT [] is_a: OBI:0001773 ! assay measuring epitope specific interleukin-17A production by T cells is_a: OBI:1110178 ! intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:0001590 name: fluorescence detection assay measuring direct binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that detects direct binding of a purified-MHC molecule with a ligand." [] synonym: "qualitative binding|purified MHC/direct/fluorescence" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] id: OBI:0001591 name: direct binding assay def: "A binding assay that measures the formation or disassociation of a complex of 2 material entities directly without use of a competitve ligand." [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001592 name: fluorescence detection assay measuring half maximal effective concentration [EC50] to determine direct binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that measures half maximal effective concentration (EC50) to detect direct binding of a purified-MHC molecule with a ligand." [] synonym: "half maximal effective concentration (EC50)|purified MHC/direct/fluorescence|nM" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001991 ! assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex [Term] id: OBI:0001593 name: competitive inhibition of binding assay def: "A binding assay that detects the inhibition of binding between 2 material entities known to form a complex by the addition of a third material entity of interest. Inhibition of binding between the 2 materials reflects binding by the third material." [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001594 name: fluorescence detection assay measuring competitive binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "qualitative binding|cellular MHC/competitive/fluorescence" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] id: OBI:0001595 name: X-ray crystallography assay determining the 3D structure of a MHC:ligand complex def: "A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a MHC:ligand complex." [] synonym: "3D structure|x-ray crystallography|angstroms" EXACT [] is_a: OBI:0000912 ! X-ray crystallography 3D molecular structure determination assay is_a: OBI:0002050 ! 3D molecular structure determination assay of a MHC:ligand complex [Term] id: OBI:0001596 name: PDB file chain def: "A 3D structural organization datum that is part of a PDB file and has a specific chain identifier that identifies the entire information on a subset of the material entities." [] is_a: OBI:0001155 ! 3D structural organization datum [Term] id: OBI:0001597 name: cell bound MHC competitive binding assay measuring half maximal inhibitory concentration [IC50] of a MHC:ligand complex using T cell epitope recognition def: "A cell bound MHC ligand binding half maximal inhibitory concentration (IC50) determination assay that uses a T cell epitope recognition assay to measure ligand binding." [] synonym: "half maximal inhibitory concentration (IC50)|cellular MHC/T cell inhibition|nM" EXACT [] is_a: OBI:0001992 ! assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex [Term] id: OBI:0001598 name: data maintenance service def: "A maintenance service in which a service provider actively manages or maintains data or a database for the service consumer. Maintenance of the data is performed to maintain its integrity or enhance its quality or utility for the consumer, but new data is not generated as a result of the maintenance." [] is_a: OBI:0001530 ! data service [Term] id: OBI:0001599 name: radioactivity detection assay measuring competitive binding of a cell-bound-MHC:ligand complex def: "A radioactivity detection assay that detects loss of binding of a known reference ligand to cell-bound-MHC due to competition by the ligand under investigation." [] synonym: "qualitative binding|cellular MHC/competitive/radioactivity" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] id: OBI:0001600 name: assay measuring epitope specific granulocyte colony stimulating factor production by T cells def: "A T cell epitope specific cytokine production assay that detects granulocyte colony stimulating factor production by T cells." [] synonym: "G-CSF release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001601 name: cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-21 production by T cells def: "A cytometric bead array assay that detects interleukin-21 production by T cells." [] synonym: "IL-21 release|cytometric bead array" EXACT [] is_a: OBI:0001237 ! assay measuring epitope specific interleukin-21 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001602 name: radioactivity detection assay measuring direct binding of a cell-bound-MHC:ligand complex def: "A radioactivity detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "qualitative binding|cellular MHC/direct/radioactivity" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] id: OBI:0001603 name: binding off rate measurement datum (koff) def: "A rate measurement datum of how quickly bound complexes disassociate" [] is_a: OBI:0001144 ! binding constant is_a: OBI:0001554 ! rate measurement datum [Term] id: OBI:0001604 name: fluorescence detection assay measuring 50% dissociation of binding temperature [Tm] of a purified-MHC:ligand complex def: "A fluorescence detection assay that measures the 50% dissociation of binding temperature of a purified-MHC molecule with a ligand." [] synonym: "50% dissociation temperature|purified MHC/direct/fluorescence|°C" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0003145 ! assay measuring quantitative binding of a MHC:ligand complex [Term] id: OBI:0001605 name: binding on rate measurement datum (kon) def: "A rate measurement datum of how quickly bound complexes form" [] is_a: OBI:0001144 ! binding constant is_a: OBI:0001554 ! rate measurement datum [Term] id: OBI:0001606 name: fluorescence detection assay measuring direct binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that detects direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "qualitative binding|cellular MHC/direct/fluorescence" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001550 ! assay measuring binding of a cell-bound-MHC:ligand complex [Term] id: OBI:0001607 name: assay measuring epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells def: "An assay of epitope specific tumor necrosis factor (ligand) superfamily member 11 production by T cells that detects tumor necrosis factor production." [] synonym: "TNFSF11/RANKL release|biological activity" EXACT [] is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001608 name: radioactivity detection assay measuring direct binding of a purified-MHC:ligand complex def: "A radioactivity detection assay that detects direct binding of a purified-MHC molecule with a ligand." [] synonym: "qualitative binding|purified MHC/direct/radioactivity" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001555 ! assay measuring binding of a purified-MHC:ligand complex [Term] id: OBI:0001609 name: intracellular cytokine staining assay measuring epitope specific interleukin-8 production by T cells def: "A flow cytometry assay that detects interleukin-8 production by T cells." [] synonym: "IL-8 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001218 ! assay measuring epitope specific interleukin-8 production by T cells [Term] id: OBI:0001610 name: cytometric bead array assay measuring epitope specific intracellular cytokine staining (ICS) IL-23 production by T cells def: "A cytometric bead array assay that detects interleukin-23 production by T cells." [] synonym: "IL-23 release|cytometric bead array" EXACT [] is_a: OBI:0001363 ! assay measuring epitope specific interleukin-23 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001611 name: obsolete purified MHC direct binding assay def: "direct binding assay measuring MHC ligand binding using MHC derived from a purified MHC molecule preparation" [] synonym: "purified MHC direct binding" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0001612 name: epitope specific vascular endothelial growth factor production by T cells def: "A process of vascular endothelial growth factor production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0010573 ! vascular endothelial growth factor production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001613 name: fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex def: "A fluorescence detection assay that measures half maximal inhibitory concentration (IC50) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "half maximal inhibitory concentration (IC50)|purified MHC/competitive/fluorescence|nM" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001992 ! assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex [Term] id: OBI:0001614 name: GenBank ID def: "A CRID symbol uniquely indentifies the submitted GeneBank sequence record." [] synonym: "GenBank Record ID" EXACT [] is_a: IAO:0000577 ! centrally registered identifier symbol [Term] id: OBI:0001615 name: investigation description def: "A textual entity that describes an investigation." [] synonym: "project description" EXACT [] synonym: "study description" EXACT [] is_a: OBI:0001898 ! comment on investigation [Term] id: OBI:0001616 name: specimen identifier def: "A CRID symbol denotes a specimen and used to distinguish one specimen from another in an investigation." [] synonym: "Specimen ID" EXACT [] synonym: "specimen ID" EXACT [] is_a: IAO:0000577 ! centrally registered identifier symbol [Term] id: OBI:0001617 name: PubMed ID def: "A CRID symbol that is sufficient to look up a citation from the PubMed, a literature database of life sciences and biomedical information." [] synonym: "PMID" EXACT [] synonym: "Publication Citation" EXACT [] synonym: "PubMed Identifier" EXACT [] is_a: IAO:0000577 ! centrally registered identifier symbol [Term] id: OBI:0001618 name: average depth of sequence coverage def: "An average value of the depth of sequence coverage based both on external (e.g. Cot-based size estimates) and internal (average coverage in the assembly) measures of genome size." [] synonym: "Depth of Coverage - Average" EXACT [] is_a: OBI:0000679 ! average value [Term] id: OBI:0001619 name: specimen collection time measurement datum def: "A time measurement datum that is the measure of the time when the specimens are collected." [] synonym: "collection date" EXACT [] synonym: "Specimen Collection Date" EXACT [] is_a: IAO:0000416 ! time measurement datum [Term] id: OBI:0001620 name: latitude coordinate measurement datum def: "A measurement datum that is the measure of the latitude coordinate of a site." [] synonym: "latitude" EXACT [] synonym: "Specimen Collection Location - Latitude" EXACT [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0001621 name: longitude coordinate measurement datum def: "A measurement datum that is the measure of the longitude coordinate of a site." [] synonym: "longitude" EXACT [] synonym: "Specimen Collection Location - Longitude" EXACT [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0001622 name: investigation title def: "A textual entity that denotes an investigation." [] synonym: "project title" EXACT [] synonym: "study title" EXACT [] is_a: OBI:0001898 ! comment on investigation [Term] id: OBI:0001623 name: organism species detection objective def: "A biological feature identification objective to identify the organism species in a specimen." [] is_a: OBI:0000015 ! biological feature identification objective [Term] id: OBI:0001624 name: organism species detection assay def: "An organism detection assay that identifies the organism species in a specimen." [] synonym: "organism identification assay" EXACT [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0001625 name: sequence annotation algorithm def: "An algorithm used to identify sequence features (e.g. protein coding regions) in the assembled contig sequence. This may also include a description of any manual curation that may have generated or validated the annotation." [] synonym: "Annotation Algorithm" EXACT [] is_a: IAO:0000064 ! algorithm [Term] id: OBI:0001626 name: Bioinformatics Resource Center def: "An organization that is one of the Internet-based research centers established and funded by NIAID (the National Institute of Allergy and Infectious Diseases). The Bioinformatics Resource Centers (BRCs) were formed in response to the threats posed by emerging and re-emerging pathogens, particularly CDC Category A, B, and C pathogens, and their potential use in bioterrorism. The intention of NIAID in funding these bioinformatics centers is to assist researchers involved in the experimental characterization of such pathogens and the formation of drugs, vaccines, or diagnostic tools to combat them." [] synonym: "BRC" EXACT [] is_a: OBI:0000245 ! organization [Term] id: OBI:0001627 name: country name def: "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." [] synonym: "Specimen Collection Location - Country" EXACT [] is_a: IAO:0000300 ! textual entity [Term] id: OBI:0001628 name: investigation identifier def: "A CRID symbol used to identify an investigation." [] synonym: "project ID" EXACT [] is_a: IAO:0000577 ! centrally registered identifier symbol [Term] id: OBI:0001629 name: grant identifier def: "A CRID symbol used to identify a grant." [] synonym: "grant ID" EXACT [] is_a: IAO:0000577 ! centrally registered identifier symbol [Term] id: OBI:0001630 name: analytical chromatography def: "An analyte assay that uses a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials and thereby detect its presence in an input material." [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0001631 name: electron microscopy imaging assay def: "An imaging assay in which an electrons are used to probe the density, shape and composition of an input material which are detected in an electron microscope and utilized to produce an image of the material." [] is_a: OBI:0002119 ! microscopy assay [Term] id: OBI:0001632 name: immuno staining assay def: "A assay detecting a molecular label assay in which the label is attached to an antibody so that substances are marked based on the antibody's binding specificity." [] is_a: OBI:0600017 ! assay detecting a molecular label [Term] id: OBI:0001633 name: purified material def: "A material entity that is generated by a purification process in which an input material is separated to obtain a fraction with a higher concentration of a desired component" [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0001634 name: calorimetric binding assay def: "A binding assay in which the heat generated or absorbed during a binding event is measured, which allows determination of binding constants, reaction stoichiometry, enthalpy and entropy." [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001635 name: antibody binding detection by fluorescence quenching def: "A binding assay in which affinity is measured by detecting a change in fluorescence (usually quenching) that occurs upon binding of the antibody to the ligand. The fluorescent signal that is affected by binding is either from an exogenous fluorophore attached to the ligand, or is the intrisic fluorescence of aromatic (tryptophan) residues on the binding site of the antibody (no conjugated fluorophore necessary) or, less commonly, on the ligand binding region (epitope)." [] is_a: OBI:0001979 ! fluorescence quenching binding assay [Term] id: OBI:0001636 name: grant def: "A plan specification of organization A to give money to organization B so that B conducts investigations. Organization A has funder role and Organization B has research organization role." [] is_a: IAO:0000104 ! plan specification [Term] id: OBI:0001638 name: antigen inhibition assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex approximated by IC50 def: "A B cell epitope equilibrium dissociation constant (KD) assay that provides IC50 values determined under assay conditions where the IC50 approximates a KD value using a B cell epitope antigen inhibition of binding assay." [] synonym: "dissociation constant KD|inhibition by antigen (~ IC50)|nM" EXACT [] is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0001639 name: assay measuring epitope specific Ig-mediated histamine release def: "A B cell epitope specific activation of additional immune response assay that detects histamine release in vitro." [] synonym: "histamine release|biological activity" EXACT [] is_a: OBI:0001704 ! assay measuring epitope specific activation of additional immune response in vitro [Term] id: OBI:0001640 name: assay measuring epitope specific immunoglobulin-mediated antigen activation def: "A B cell epitope dependent biological activity determination assay that detects antigen activation." [] synonym: "antigen activation|biological activity" EXACT [] is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding [Term] id: OBI:0001641 name: assay measuring epitope specific complement-dependent cytotoxicity def: "A B cell epitope specific activation of additional immune response assay that detects complement-dependent cytotoxicity in vitro ." [] synonym: "complement-dependent cytotoxicity|biological activity" EXACT [] is_a: OBI:0001704 ! assay measuring epitope specific activation of additional immune response in vitro [Term] id: OBI:0001642 name: assay measuring epitope specific antibody-dependent cellular cytotoxicity def: "A B cell epitope specific activation of additional immune response assay that detects antibody-dependent cellular cytotoxicity in vitro." [] synonym: "antibody-dependent cellular cytotoxicity|biological activity" EXACT [] is_a: OBI:0001704 ! assay measuring epitope specific activation of additional immune response in vitro [Term] id: OBI:0001643 name: assay measuring epitope specific immunoglobulin-mediated neutralization def: "A B cell epitope dependent biological activity determination assay that detects neutralization of the antigen." [] synonym: "neutralization |biological activity" EXACT [] is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding [Term] id: OBI:0001644 name: assay measuring epitope specific opsonization def: "A B cell epitope specific activation of additional immune response assay that detects opsonization in vitro ." [] synonym: "opsonization|biological activity" EXACT [] is_a: OBI:0001704 ! assay measuring epitope specific activation of additional immune response in vitro [Term] id: OBI:0001645 name: calorimetry assay measuring binding of a B cell epitope:antibody complex def: "A calorimetric binding assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|calorimetry" EXACT [] is_a: OBI:0001634 ! calorimetric binding assay is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001646 name: electron microscopy assay determining the 3D structure of a B cell epitope:antibody complex def: "An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex" [] synonym: "3D structure|electron microscopy" EXACT [] is_a: OBI:0001721 ! 3D molecular structure determination assay of an antigen:antibody complex is_a: OBI:0003118 ! electron-microscopy 3D molecular structure determination assay [Term] id: OBI:0001647 name: NMR assay determining the 3D structure of a B cell epitope:antibody complex def: "A nuclear magnetic resonance 3D molecular structure determination assay that characterizes the 3-dimensional structure of a B cell epitope:antibody complex." [] synonym: "3D structure|nuclear magnetic resonance (NMR)" EXACT [] is_a: OBI:0000182 ! NMR 3D molecular structure determination assay is_a: OBI:0001721 ! 3D molecular structure determination assay of an antigen:antibody complex [Term] id: OBI:0001648 name: cross blocking assay measuring binding of a B cell epitope:antibody complex def: "A cross-blocking assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|cross blocking" EXACT [] is_a: OBI:0001699 ! antibody cross-blocking assay is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001649 name: RIA measuring binding of a B cell epitope:antibody complex def: "A radio immuno assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|radio immuno assay (RIA)" EXACT [] is_a: OBI:0000910 ! radio immuno assay is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001650 name: immunoblot assay measuring binding of a B cell epitope:antibody complex def: "An immunoblot assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|western blot" EXACT [] is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex is_a: OBI:0001978 ! immunoblot assay [Term] id: OBI:0001651 name: plasmon resonance assay measuring binding of a B cell epitope:antibody complex def: "A surface plasmon resonance binding assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|surface plasmon resonance (SPR)" EXACT [] is_a: OBI:0000923 ! surface plasmon resonance binding assay is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001652 name: immuno staining assay measuring binding of a B cell epitope:antibody complex def: "An immuno staining assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|immuno staining" EXACT [] is_a: OBI:0001632 ! immuno staining assay is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001653 name: immunoprecipitation assay measuring binding of a B cell epitope:antibody complex def: "An immunoprecipitation assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|immunoprecipitation" EXACT [] is_a: OBI:0001700 ! immunoprecipitation assay is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001654 name: mass spectrometry assay measuring binding of a B cell epitope:antibody complex def: "A mass spectrometry assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|mass spectrometry" EXACT [] is_a: OBI:0000470 ! mass spectrometry assay is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001655 name: phage display assay measuring binding of a B cell epitope:antibody complex def: "A phage display binding assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|phage display" EXACT [] is_a: OBI:0001476 ! phage display binding assay is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001656 name: electron microscopy assay measuring binding of a B cell epitope:antibody complex def: "An electron microscopy imaging assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|electron microscopy" EXACT [] is_a: OBI:0001631 ! electron microscopy imaging assay is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001657 name: ELISA measuring binding of a B cell epitope:antibody complex def: "An enzyme-linked immunosorbent assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001658 name: ELISPOT assay measuring binding of a B cell epitope:antibody complex def: "An enzyme-linked immunospot assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|ELISPOT" EXACT [] is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001659 name: flow cytometry assay measuring binding of a B cell epitope:antibody complex def: "A flow cytometry assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|flow cytometry" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001660 name: intracellular material detection assay measuring epitope specific granzyme A release by T cells def: "A flow cytometry assay that detects epitope specific granzyme A release by T cells." [] synonym: "granzyme A release|intracellular staining" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001809 ! assay measuring epitope specific granzyme A release by T cells [Term] id: OBI:0001661 name: chromatography assay measuring binding of a B cell epitope:antibody complex def: "An analytical chromatography assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|chromatography" EXACT [] is_a: OBI:0001630 ! analytical chromatography is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001662 name: NMR assay measuring binding of a B cell epitope:antibody complex def: "A B cell epitope qualitative binding to antibody assay that uses a nuclear magnetic resonance assay." [] synonym: "qualitative binding|nuclear magnetic resonance (NMR)" EXACT [] is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001663 name: ELISA measuring epitope specific granulysin release by T cells def: "An enzyme-linked immunosorbent assay that detects epitope specific granulysin release by T cells." [] synonym: "granulysin release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001810 ! assay measuring epitope specific granulysin release by T cells [Term] id: OBI:0001664 name: intracellular material detection assay measuring epitope specific granulysin release by T cells def: "A flow cytometry assay that detects epitope specific granulysin release by T cells." [] synonym: "granulysin release|intracellular staining" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001810 ! assay measuring epitope specific granulysin release by T cells [Term] id: OBI:0001665 name: fluorescence detection assay measuring binding off rate [koff] to determine direct binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures binding off rate [koff] to detect direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "off rate|cellular MHC/direct/fluorescence|1/s" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001993 ! assay measuring the off rate measurement [koff] of a MHC:ligand complex [Term] id: OBI:0001666 name: fluorescence detection assay measuring binding on rate [kon] to determine direct binding of a cell-bound-MHC:ligand complex def: "A fluorescence detection assay that measures binding on rate (kon) to detect direct binding of a cell-bound-MHC molecule with a ligand." [] synonym: "on rate|cellular MHC/direct/fluorescence|nM^-1s^-1" EXACT [] is_a: OBI:0001499 ! binding assay using fluorescence detection is_a: OBI:0001994 ! assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex [Term] id: OBI:0001667 name: fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex approximated by IC50 def: "A fluorescence detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation and provides IC50 values determined under assay conditions where the IC50 approximates a KD value." [] synonym: "dissociation constant KD (~IC50)|purified MHC/competitive/fluorescence|nM" EXACT [] is_a: OBI:0001537 ! fluorescence detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex is_a: OBI:0001613 ! fluorescence detection assay measuring half maximal inhibitory concentration [IC50] to determine competitive binding of a purified-MHC:ligand complex [Term] id: OBI:0001668 name: split-ubiquitin assay def: "A binding assay that screens membrane soluble proteins by fusion of two integral membrane proteins (bait and prey) to two different ubiquitin moieties. One moiety is also fused to a transcription factor (TF) that can be cleaved off by ubiquitin specific proteases. Upon bait and prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes." [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001669 name: far-western blot assay def: "An assay that measures protein-protein interactions by separating target proteins on an SDS-PAGE gel, transfering them to a solid substrate, hybridizing with a protein probe and visualizing bound proteins using a probe-directed antibody. This is a adaptation on the western blot assay." [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001670 name: RNA protection assay def: "An assay that determines the presence and estimates abundance of transcript species by first creating an homo or heteroduplex by adding a specific, complementary sequence to the sequence of interest and then exposing the mixture of ribonuclease, which will degrade only single stranded molecules. A detection step will reveal if the sample contained a sequence of interest." [] synonym: "RNAse protection assay" EXACT [] synonym: "RPA" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0001671 name: electrophoretic mobility shift assay def: "An assay that measures information about Protein-DNA or Protein-RNA interactions using gel electrophoresis and relying on the fact the molecular interactions will cause the heterodimer to be retarded on the gel when compared to controls corresponding to protein extract alone and protein extract + neutral nucleic acid." [] synonym: "band shift assay" EXACT [] synonym: "EMSA" EXACT [] synonym: "gel mobility shift assay" EXACT [] synonym: "gel retardation assay" EXACT [] synonym: "gel shift assay" EXACT [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001672 name: gene knock-down assay def: "An assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells." [] is_a: OBI:0003587 ! cell culture assay [Term] id: OBI:0001673 name: nano-cap analysis of gene expression assay def: "A transcription profiling assay that is performed using a very low amount (nanogram scale) of mRNA samples using Cap analysis gene expression (CAGE)." [] synonym: "nano-CAGE" EXACT [] is_a: OBI:0000424 ! transcription profiling assay [Term] id: OBI:0001674 name: cap analysis of gene expression assay def: "A transcription profiling assay which measures RNA transcript abundances in biological samples by extracting 5' ends of capped transcripts, RTPCR and sequence those. Copy numbers of CAGE tags provide a way of quantification and provide a measure of expression of the transcriptome" [] synonym: "CAGE" EXACT [] is_a: OBI:0000424 ! transcription profiling assay is_a: OBI:0002692 ! polymerase chain reaction assay is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001675 name: ELISA measuring epitope specific interleukin-17A production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-17A production by T cells." [] synonym: "IL-17A release|ELISA" EXACT [] is_a: OBI:0001773 ! assay measuring epitope specific interleukin-17A production by T cells is_a: OBI:1110162 ! ELISA measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:0001676 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-7 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-7 production by T cells." [] synonym: "IL-7 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001587 ! assay measuring epitope specific interleukin-7 production by T cells [Term] id: OBI:0001677 name: epitope specific granulysin production by T cells def: "A process of granulysin production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0036262 ! granulysin production [Term] id: OBI:0001678 name: epitope specific granzyme A production by T cells def: "A process of granzyme A production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0035746 ! granzyme A production [Term] id: OBI:0001679 name: yeast 2-hybrid assay def: "An assay that detects protein protein interactions and protein DNA interactions by testing for physical interactions (such as binding) between two proteins or a single protein and a DNA molecule, respectively. The premise behind the test is the activation of downstream reporter gene(s) by the binding of a transcription factor onto an upstream activating sequence (UAS). For two-hybrid screening, the transcription factor is split into two separate fragments, called the binding domain (BD) and activating domain (AD). The BD is the domain responsible for binding to the UAS and the AD is the domain responsible for the activation of transcription. The Y2H is thus a protein-fragment complementation assay." [] synonym: "Y2H" EXACT [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001680 name: Sos-recruitment assay def: "A binding assay that detects interacting proteins for a targeted domain where mammalian guanyl nucleotide exchange factor (GEF) Sos is recruited to the Saccharomyces cerevisiae plasma membrane harboring a temperature-sensitive Ras GEF, Cdc25-2, allowing growth at the nonpermissive temperature using the Sos recruitment system, a kind of yeast 2 hybrid system." [] synonym: "SRS" EXACT [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001681 name: yeast one-hybrid assay def: "An assay that determines protein DNA interactions using a single fusion protein in which the activating domain is linked directly to the binding domain." [] synonym: "Y1H" EXACT [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0001682 name: bacterial one-hybrid assay def: "An assay that identifies the sequence-specific target site of a DNA-binding domain. In this system, a given transcription factor (TF) is expressed as a fusion to a subunit of RNA polymerase. In parallel, a library of randomized oligonucleotides representing potential TF target sequences, is cloned into a separate vector containing the selectable genes HIS3 and URA3. If the DNA-binding domain (bait) binds a potential DNA target site (prey) in vivo, it will recruit RNA polymerase to the promoter and activate transcription of the reporter genes in that clone. The two reporter genes, HIS3 and URA3, allow for positive and negative selections, respectively. At the end of the process, positive clones are sequenced and examined with motif-finding tools in order to resolve the favoured DNA target sequence" [] synonym: "B1H" EXACT [] is_a: OBI:0001681 ! yeast one-hybrid assay [Term] id: OBI:0001683 name: chromosome organization assay by fluorescence in-situ hybridization def: "An in-situ hybridization assay that uses fluorescence to detect chromosomal integrity" [] is_a: OBI:0001686 ! in-situ hybridization assay [Term] id: OBI:0001684 name: methylation-specific polymerase chain reaction assay def: "An assay that uses initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA." [] synonym: "MSP" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0001685 name: amplification of intermethylated sites assay def: "An assay that estimates genome-wide DNA methylation and measures methylation of DNA sequences. AIMS is based on the differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers followed by restrained PCR amplification of methylated sequences." [] synonym: "AIMS assay" EXACT [] synonym: "intermethylated site amplification" EXACT [] is_a: OBI:0000634 ! DNA methylation profiling assay [Term] id: OBI:0001686 name: in-situ hybridization assay def: "An assay that localizes a specific DNA or RNA sequence within a portion or section of tissue using artificially induced nucleic hybridization." [] synonym: "in situ hybridization" EXACT [] synonym: "ISH" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0001687 name: contact representative role def: "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." [] is_a: BFO:0000023 ! role [Term] id: OBI:0001689 name: cytochalasin-induced inhibition of actin polymerization assay def: "An assay which uses compound cytochalasin (CHEBI: 23528) to block actin polymerization-dependent cell motility (GO:0070358) and actin filament polymerization (GO:0030041)." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0001690 name: molecular function identification objective def: "is an objective specification which aims to discover molecular function realized by a molecular entity" [] is_a: OBI:0000015 ! biological feature identification objective [Term] id: OBI:0001691 name: cellular structure feature identification objective def: "is an objective specification which aims to discover cellular structure properties" [] is_a: OBI:0000015 ! biological feature identification objective [Term] id: OBI:0001692 name: in vivo assay measuring B cell epitope specific protection from fertility def: "An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment based on reduction of fertility." [] synonym: "protection from fertility|in vivo assay" EXACT [] is_a: OBI:0001178 ! efficacy of epitope intervention experiment is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0001693 name: in vivo assay measuring B cell epitope specific tolerance induction def: "An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment." [] synonym: "tolerance|in vivo assay" EXACT [] is_a: OBI:0001488 ! epitope tolerance induction experiment is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0001694 name: in vivo assay measuring B cell epitope specific induction of hypersensitivity def: "An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions." [] synonym: "hypersensitivity|in vivo assay" EXACT [] is_a: OBI:0001178 ! efficacy of epitope intervention experiment is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0001695 name: assay measuring epitope specific immune complex formation def: "A B cell epitope specific activation of additional immune response assay that detects agglutination in vitro." [] synonym: "agglutination|biological activity" EXACT [] is_a: OBI:0001704 ! assay measuring epitope specific activation of additional immune response in vitro [Term] id: OBI:0001696 name: in vivo assay measuring B cell epitope specific protection based on survival def: "An in vivo assay measuring B cell epitope specific protection from other challenge using survival." [] synonym: "survival from challenge|in vivo assay" EXACT [] is_a: OBI:0001189 ! epitope protection experiment based on survival is_a: OBI:0003467 ! in vivo assay measuring B cell epitope specific protection from other challenge [Term] id: OBI:0001697 name: in vivo assay measuring B cell epitope specific treatment of disease def: "An efficacy of B cell epitope intervention experiment that detects a decrease in disease." [] synonym: "decreased disease|in vivo assay" EXACT [] is_a: OBI:0001190 ! epitope treatment experiment is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0001698 name: assay measuring B cell epitope specific in vivo activity def: "A B cell epitope dependent biological activity determination assay that uses an in vivo intervention experiment." [] synonym: "in vivo activity|biological activity" EXACT [] is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding [Term] id: OBI:0001699 name: antibody cross-blocking assay def: "A competitive inhibition of binding assay in which two antibodies that are known to bind the same antigen are tested for the ability of one antibody to inhibit binding of the other antibody to the antigen, thereby determining if they have overlapping binding sites." [] synonym: "antibody inhibition of antibody binding" EXACT [] is_a: OBI:0001593 ! competitive inhibition of binding assay [Term] id: OBI:0001700 name: immunoprecipitation assay def: "An analyte assay in which an input material is mixed with antibodies and bound antigen:antibody complexes are separated out using immunoprecipitation. Either the antibody has known specificy, and the antigen mixture is tested for the presence of a specific antigen, or the antigen solution is well defined and the antibody solution is tested for the presence of antigen specific antibodies." [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0001701 name: antigen inhibition assay measuring binding of a B cell epitope:antibody complex def: "A B cell epitope qualitative binding to antibody assay that measures the ability of an antigen to inhibit antibody binding to a known ligand." [] synonym: "qualitative binding|inhibition by antigen" EXACT [] is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001702 name: immunoglobulin binding to epitope def: "a process of an immunoglobulin complex binding to a material entity at the immunoglobulin complementarity determining region (CDR)." [] is_a: OBI:0001588 ! binding is_a: OBI:1110014 ! epitope binding by adaptive immune receptor [Term] id: OBI:0001703 name: assay measuring qualitative binding of a B cell epitope:antibody complex def: "An assay that detects the binding of an antigen with an antibody, and produces a qualitative measurement of the binding as an output." [] synonym: "qualitative binding|binding assay" EXACT [] is_a: OBI:1110127 ! assay measuring binding of a B cell epitope:antibody complex [Term] id: OBI:0001704 name: assay measuring epitope specific activation of additional immune response in vitro def: "A B cell epitope dependent biological activity determination assay that detects secondary in vitro activity." [] synonym: "secondary in vitro activity|biological activity" EXACT [] is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding [Term] id: OBI:0001705 name: assay measuring epitope specific antigen inhibition of antibody activity def: "A B cell epitope dependent biological activity determination assay that detects inhibition of the antibody's activity by the antigen." [] synonym: "antibody activity inhibition|biological activity" EXACT [] is_a: OBI:0001706 ! assay measuring biological activity resulting from B cell epitope:antibody binding [Term] id: OBI:0001706 name: assay measuring biological activity resulting from B cell epitope:antibody binding def: "A B cell epitope assay that measures the immune response process resulting from the binding of an antibody receptor to epitope or recognition of the epitope." [] synonym: "biological activity|any method" EXACT [] is_a: OBI:0003127 ! B cell epitope assay [Term] id: OBI:0001707 name: immunoglobulin mediated histamine release def: "The release of histamine by cells stimulated through their Fc receptors which are loaded with immunoglobulins." [] is_a: GO:0008150 ! biological_process [Term] id: OBI:0001708 name: assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex def: "A B cell epitope binding constant determination assay that measures the dissociation constant KD." [] synonym: "dissociation constant KD|binding assay|nM" EXACT [] is_a: OBI:0001709 ! assay measuring a binding constant of a B cell epitope:antibody complex [Term] id: OBI:0001709 name: assay measuring a binding constant of a B cell epitope:antibody complex def: "A B cell epitope recognition assay that quantitavely characterizes the binding of an antibody / BCR with a ligand by determining a binding constant." [] synonym: "binding constant|binding assay" EXACT [] is_a: OBI:0003146 ! assay measuring quantitative binding of an antigen:antibody complex [Term] id: OBI:0001710 name: in vivo assay measuring B cell epitope specific protection from challenge def: "An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment." [] synonym: "protection from challenge|in vivo assay" EXACT [] is_a: OBI:0001184 ! epitope protection experiment is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0001711 name: in vivo assay measuring B cell epitope specific disease exacerbation def: "An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment." [] synonym: "disease exacerbation|in vivo assay" EXACT [] is_a: OBI:0001188 ! epitope disease exacerbation experiment is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0001712 name: obsolete B cell epitope direct binding assay def: "A direct binding assay using a assay" [] synonym: "direct binding assay" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0001713 name: B cell epitope specific opsonization def: "opsonization resulting from antibody binding to epitope" [] is_a: GO:0008228 ! opsonization [Term] id: OBI:0001714 name: B cell epitope specific immunoglobulin-mediated neutralization def: "immunoglobulin-mediated neutralization resulting from antibody binding to epitope" [] is_a: GO:0097282 ! immunoglobulin-mediated neutralization [Term] id: OBI:0001715 name: obsolete B cell epitope competitive binding assay def: "A competitive inhibition of binding assay using a assay" [] synonym: "competitive binding assay" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0001716 name: B cell epitope specific complement-dependent cytotoxicity def: "complement-dependent cytotoxicity resulting from antibody binding to epitope" [] is_a: GO:0097278 ! complement-dependent cytotoxicity [Term] id: OBI:0001717 name: B cell epitope specific antibody-dependent cellular cytotoxicity def: "antibody-dependent cellular cytotoxicity resulting from antibody binding to epitope" [] is_a: GO:0001788 ! antibody-dependent cellular cytotoxicity [Term] id: OBI:0001718 name: assay measuring the on rate [kon] of a B cell epitope:antibody complex def: "A B cell epitope binding constant determination assay that measures the on rate." [] synonym: "on rate|binding assay|M^-1s^-1" EXACT [] is_a: OBI:0001709 ! assay measuring a binding constant of a B cell epitope:antibody complex [Term] id: OBI:0001719 name: assay measuring the association constant [KA] of a B cell epitope:antibody complex def: "A B cell epitope binding constant determination assay that measures the association constant KA." [] synonym: "association constant KA|binding assay|1/nM" EXACT [] is_a: OBI:0001709 ! assay measuring a binding constant of a B cell epitope:antibody complex [Term] id: OBI:0001720 name: B cell epitope specific immune complex formation def: "immune complex formation resulting from antibody binding to epitope" [] is_a: GO:0097281 ! immune complex formation is_a: OBI:0001702 ! immunoglobulin binding to epitope [Term] id: OBI:0001721 name: 3D molecular structure determination assay of an antigen:antibody complex def: "A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of an antigen:antobody complex." [] synonym: "3D structure|any method" EXACT [] is_a: OBI:0001145 ! 3D structure determination of bound molecular complex assay is_a: OBI:0003127 ! B cell epitope assay [Term] id: OBI:0001722 name: B cell epitope specific hypersensitivity def: "hypersensitivity resulting from antibody binding to epitope" [] is_a: GO:0002524 ! hypersensitivity [Term] id: OBI:0001723 name: assay measuring the off rate [koff] of a B cell epitope:antibody complex def: "A B cell epitope binding constant determination assay that measures the off rate." [] synonym: "off rate|binding assay|1/s" EXACT [] is_a: OBI:0001709 ! assay measuring a binding constant of a B cell epitope:antibody complex [Term] id: OBI:0001724 name: viral hemagglutination inhibition assay measuring binding of a B cell epitope:antibody complex def: "A viral hemagglutination inhibition assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding| hemagglutination inhibition" EXACT [] is_a: OBI:0000875 ! viral hemagglutination inhibition assay is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001725 name: B cell epitope specific histamine secretion mediated by immunoglobulin def: "histamine secretion mediated by immunoglobulin resulting from antibody binding to epitope" [] is_a: GO:0097280 ! histamine secretion mediated by immunoglobulin [Term] id: OBI:0001726 name: quenching assay measuring binding of a B cell epitope:antibody complex def: "A fluorescence quenching assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|quenching" EXACT [] is_a: OBI:0001635 ! antibody binding detection by fluorescence quenching is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex [Term] id: OBI:0001727 name: RIA measuring the dissociation constant [KD] of a B cell epitope:antibody complex def: "A radio immuno assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] synonym: "dissociation constant KD|radio immuno assay (RIA)|nM" EXACT [] is_a: OBI:0000910 ! radio immuno assay is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0001728 name: ELISA measuring the dissociation constant [KD] of a B cell epitope:antibody complex def: "An enzyme-linked immunosorbent assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] synonym: "dissociation constant KD|ELISA|nM" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0001729 name: quenching assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex def: "A fluorescence quenching assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] synonym: "dissociation constant KD|quenching|nM" EXACT [] is_a: OBI:0001635 ! antibody binding detection by fluorescence quenching is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0001730 name: surface plasmon resonance assay measuring the association constant [KA] of a B cell epitope:antibody complex def: "A surface plasmon resonance binding assay that measures the association constant [KA] of an antigen binding with an antibody." [] synonym: "association constant KA|surface plasmon resonance (SPR)|1/nM" EXACT [] is_a: OBI:0000923 ! surface plasmon resonance binding assay is_a: OBI:0001719 ! assay measuring the association constant [KA] of a B cell epitope:antibody complex [Term] id: OBI:0001731 name: surface plasmon resonance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex def: "A surface plasmon resonance binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] synonym: "dissociation constant KD|surface plasmon resonance (SPR)|nM" EXACT [] is_a: OBI:0000923 ! surface plasmon resonance binding assay is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0001732 name: quenching assay measuring the association constant [KA] of a B cell epitope:antibody complex def: "A fluorescence quenching assay that measures the association constant [KA] of an antigen binding with an antibody." [] synonym: "association constant KA|quenching|1/nM" EXACT [] is_a: OBI:0001635 ! antibody binding detection by fluorescence quenching is_a: OBI:0001719 ! assay measuring the association constant [KA] of a B cell epitope:antibody complex [Term] id: OBI:0001733 name: calorimetry assay measuring the association constant [KA] of a B cell epitope:antibody complex def: "A calorimetric binding assay that measures the association constant [KA] of an antigen binding with an antibody." [] synonym: "association constant KA|calorimetry|1/nM" EXACT [] is_a: OBI:0001634 ! calorimetric binding assay is_a: OBI:0001719 ! assay measuring the association constant [KA] of a B cell epitope:antibody complex [Term] id: OBI:0001734 name: calorimetry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex def: "A calorimetric binding assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] synonym: "dissociation constant KD|calorimetry|nM" EXACT [] is_a: OBI:0001634 ! calorimetric binding assay is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0001735 name: ELISA measuring the association constant [KA] of a B cell epitope:antibody complex def: "An enzyme-linked immunosorbent assay that measures the association constant [KA] of an antigen binding with an antibody." [] synonym: "association constant KA|ELISA|1/nM" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001719 ! assay measuring the association constant [KA] of a B cell epitope:antibody complex [Term] id: OBI:0001736 name: RIA measuring the association constant [KA] of a B cell epitope:antibody complex def: "A radio immuno assay that measures the association constant [KA] of an antigen binding with an antibody." [] synonym: "association constant KA|radio immuno assay (RIA)|1/nM" EXACT [] is_a: OBI:0000910 ! radio immuno assay is_a: OBI:0001719 ! assay measuring the association constant [KA] of a B cell epitope:antibody complex [Term] id: OBI:0001737 name: obsolete B cell epitope specific X-ray crystallography assay def: "A X-ray crystallography assay measuring epitope specfic antibody binding event in angstroms" [] synonym: "X-ray crystallography [Ã…]" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: OBI:0001738 [Term] id: OBI:0001738 name: X-ray crystallography assay determining the 3D structure of a B cell epitope:antibody complex def: "A X-ray crystallography 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a B cell epitope:antibody complex." [] synonym: "3D structure|x-ray crystallography|angstroms" EXACT [] is_a: OBI:0000912 ! X-ray crystallography 3D molecular structure determination assay is_a: OBI:0001721 ! 3D molecular structure determination assay of an antigen:antibody complex [Term] id: OBI:0001739 name: surface plasmon resonance assay measuring the off rate [koff] of a B cell epitope:antibody complex def: "A surface plasmon resonance binding assay that measures the off rate [koff] of an antigen binding with an antibody." [] synonym: "off rate|surface plasmon resonance (SPR)|1/s" EXACT [] is_a: OBI:0000923 ! surface plasmon resonance binding assay is_a: OBI:0001723 ! assay measuring the off rate [koff] of a B cell epitope:antibody complex [Term] id: OBI:0001740 name: quenching assay measuring the off rate [koff] of a B cell epitope:antibody complex def: "A fluorescence quenching assay that measures the off rate [koff] of an antigen binding with an antibody." [] synonym: "off rate|quenching|1/s" EXACT [] is_a: OBI:0001635 ! antibody binding detection by fluorescence quenching is_a: OBI:0001723 ! assay measuring the off rate [koff] of a B cell epitope:antibody complex [Term] id: OBI:0001741 name: surface plasmon resonance assay measuring the on rate [kon] of a B cell epitope:antibody complex def: "A surface plasmon resonance binding assay that measures the on rate [kon] of an antigen binding with an antibody." [] synonym: "on rate|surface plasmon resonance (SPR)|M^-1s^-1" EXACT [] is_a: OBI:0000923 ! surface plasmon resonance binding assay is_a: OBI:0001718 ! assay measuring the on rate [kon] of a B cell epitope:antibody complex [Term] id: OBI:0001742 name: quenching assay measuring the on rate [kon] of a B cell epitope:antibody complex def: "A fluorescence quenching assay that measures the on rate [kon] of an antigen binding with an antibody." [] synonym: "on rate|quenching|M^-1s^-1" EXACT [] is_a: OBI:0001635 ! antibody binding detection by fluorescence quenching is_a: OBI:0001718 ! assay measuring the on rate [kon] of a B cell epitope:antibody complex [Term] id: OBI:0001743 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 beta production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 beta production by T cells." [] synonym: "IL-1b release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001449 ! assay measuring epitope specific interleukin-1 beta production by T cells [Term] id: OBI:0001744 name: intracellular cytokine staining assay measuring epitope specific interleukin-1 alpha production by T cells def: "A flow cytometry assay that detects interleukin-1 alpha production by T cells." [] synonym: "IL-1a release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001388 ! assay measuring epitope specific interleukin-1 alpha production by T cells [Term] id: OBI:0001745 name: ELISPOT assay measuring epitope specific interleukin-1 alpha production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-1 alpha production by T cells." [] synonym: "IL-1a release|ELISPOT" EXACT [] is_a: OBI:0001388 ! assay measuring epitope specific interleukin-1 alpha production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001746 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-1 alpha production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-1 alpha production by T cells." [] synonym: "IL-1a release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001388 ! assay measuring epitope specific interleukin-1 alpha production by T cells [Term] id: OBI:0001747 name: cytometric bead array assay measuring epitope specific interleukin-1 alpha production by T cells def: "A cytometric bead array assay that detects interleukin-1 alpha production by T cells." [] synonym: "IL-1a release|cytometric bead array" EXACT [] is_a: OBI:0001388 ! assay measuring epitope specific interleukin-1 alpha production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001748 name: ELISPOT assay measuring epitope specific interferon-beta production by T cells def: "An enzyme-linked immunospot assay that detects interferon-beta production by T cells." [] synonym: "IFNb release|ELISPOT" EXACT [] is_a: OBI:0001390 ! assay measuring epitope specific interferon-beta production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001749 name: intracellular cytokine staining assay measuring epitope specific interferon-beta production by T cells def: "A flow cytometry assay that detects interferon-beta production by T cells." [] synonym: "IFNb release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001390 ! assay measuring epitope specific interferon-beta production by T cells [Term] id: OBI:0001750 name: intracellular cytokine staining assay measuring epitope specific granulocyte colony stimulating factor production by T cells def: "A flow cytometry assay that detects granulocyte colony stimulating factor production by T cells." [] synonym: "G-CSF release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001600 ! assay measuring epitope specific granulocyte colony stimulating factor production by T cells [Term] id: OBI:0001751 name: ELISA measuring epitope specific interferon-beta production by T cells def: "An enzyme-linked immunosorbent assay that detects interferon-beta production by T cells." [] synonym: "IFNb release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001390 ! assay measuring epitope specific interferon-beta production by T cells [Term] id: OBI:0001752 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific granulocyte colony stimulating factor production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects granulocyte colony stimulating factor production by T cells." [] synonym: "G-CSF release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001600 ! assay measuring epitope specific granulocyte colony stimulating factor production by T cells [Term] id: OBI:0001753 name: ELISPOT assay measuring epitope specific granulocyte colony stimulating factor production by T cells def: "An enzyme-linked immunospot assay that detects granulocyte colony stimulating factor production by T cells." [] synonym: "G-CSF release|ELISPOT" EXACT [] is_a: OBI:0001600 ! assay measuring epitope specific granulocyte colony stimulating factor production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001754 name: cytometric bead array assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells def: "A cytometric bead array assay that detects chemokine (C-X-C motif) ligand 9 production by T cells." [] synonym: "CXCL9/MIG release|cytometric bead array" EXACT [] is_a: OBI:0001459 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001755 name: selection criterion def: "A directive information entity which defines and states a principle of standard by which selection process may take place." [] synonym: "selection rule" EXACT [] is_a: IAO:0000033 ! directive information entity [Term] id: OBI:0001756 name: ELISPOT assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells def: "An enzyme-linked immunospot assay that detects chemokine (C-X-C motif) ligand 9 production by T cells." [] synonym: "CXCL9/MIG release|ELISPOT" EXACT [] is_a: OBI:0001459 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001757 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 9 production by T cells." [] synonym: "CXCL9/MIG release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001459 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 9 production by T cells [Term] id: OBI:0001758 name: ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells def: "An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 4 production by T cells." [] synonym: "CCL4/MIP-1b release|ELISPOT" EXACT [] is_a: OBI:0001345 ! assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001759 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 12 production by T cells." [] synonym: "CXCL12/SDF-1 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001776 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells [Term] id: OBI:0001760 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 13 production by T cells." [] synonym: "CXCL13/BLC release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001779 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells [Term] id: OBI:0001761 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-X-C motif) ligand 16 production by T cells." [] synonym: "CXCL16 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001778 ! assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells [Term] id: OBI:0001762 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 21 production by T cells." [] synonym: "CCL21/SLC release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001774 ! assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells [Term] id: OBI:0001763 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 22 production by T cells." [] synonym: "CCL22/MDC release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001777 ! assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells [Term] id: OBI:0001764 name: cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells def: "A cytometric bead array assay that detects chemokine (C-C motif) ligand 4 production by T cells." [] synonym: "CCL4/MIP-1b release|cytometric bead array" EXACT [] is_a: OBI:0001345 ! assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001765 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 4 production by T cells." [] synonym: "CCL4/MIP-1b release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001345 ! assay measuring epitope specific chemokine (C-C motif) ligand 4 production by T cells [Term] id: OBI:0001766 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific vascular endothelial growth factor production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects vascular endothelial growth factor production by T cells." [] synonym: "VEGF release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001570 ! assay measuring epitope specific vascular endothelial growth factor production by T cells [Term] id: OBI:0001767 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 19 production by T cells." [] synonym: "CCL19/MIP-3b release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001775 ! assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells [Term] id: OBI:0001768 name: intracellular cytokine staining assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells def: "A flow cytometry assay that detects chemokine (C-C motif) ligand 1 production by T cells." [] synonym: "CCL1/TCA-3 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001276 ! assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells [Term] id: OBI:0001769 name: specimen collector role def: "An Investigation agent role borne by a person or organization which \nis realized in a specimen collection process." [] is_a: OBI:0000202 ! investigation agent role [Term] id: OBI:0001770 name: intracellular cytokine staining assay measuring epitope specific vascular endothelial growth factor production by T cells def: "A flow cytometry assay that detects vascular endothelial growth factor production by T cells." [] synonym: "VEGF release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001570 ! assay measuring epitope specific vascular endothelial growth factor production by T cells [Term] id: OBI:0001771 name: ELISPOT assay measuring epitope specific vascular endothelial growth factor production by T cells def: "An enzyme-linked immunospot assay that detects vascular endothelial growth factor production by T cells." [] synonym: "VEGF release|ELISPOT" EXACT [] is_a: OBI:0001570 ! assay measuring epitope specific vascular endothelial growth factor production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001772 name: assay measuring epitope specific interleukin-17F production by T cells def: "An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17F production." [] synonym: "IL-17F release|biological activity" EXACT [] is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:0001773 name: assay measuring epitope specific interleukin-17A production by T cells def: "An assay of epitope specific interleukin-17 production by T cells that detects interleukin-17A production." [] synonym: "IL-17A release|biological activity" EXACT [] is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:0001774 name: assay measuring epitope specific chemokine (C-C motif) ligand 21 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 21 production by T cells." [] synonym: "CCL21/SLC release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001775 name: assay measuring epitope specific chemokine (C-C motif) ligand 19 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 19 production by T cells." [] synonym: "CCL19/MIP-3b release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001776 name: assay measuring epitope specific chemokine (C-X-C motif) ligand 12 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 12 production by T cells." [] synonym: "CXCL12/SDF-1 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001777 name: assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 22 production by T cells." [] synonym: "CCL22/MDC release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001778 name: assay measuring epitope specific chemokine (C-X-C motif) ligand 16 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 16 production by T cells." [] synonym: "CXCL16 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001779 name: assay measuring epitope specific chemokine (C-X-C motif) ligand 13 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-X-C motif) ligand 13 production by T cells." [] synonym: "CXCL13/BLC release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0001780 name: ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells def: "An enzyme-linked immunospot assay that detects macrophage inflammatory protein-1 alpha production by T cells." [] synonym: "CCL3/MIP-1a release|ELISPOT" EXACT [] is_a: OBI:0001333 ! assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001781 name: cytometric bead array assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells def: "A cytometric bead array assay that detects macrophage inflammatory protein-1 gamma production by T cells." [] synonym: "CCL9/MIP-1g release|cytometric bead array" EXACT [] is_a: OBI:0001456 ! assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001782 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 gamma production by T cells." [] synonym: "CCL9/MIP-1g release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001456 ! assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells [Term] id: OBI:0001783 name: intracellular cytokine staining assay measuring epitope specific monocyte chemotactic protein-1 production by T cells def: "A flow cytometry assay that detects monocyte chemotactic protein-1 production by T cells." [] synonym: "CCL2/MCP-1 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001465 ! assay measuring epitope specific monocyte chemotactic protein-1 production by T cells [Term] id: OBI:0001784 name: ELISPOT assay measuring epitope specific monocyte chemotactic protein-1 production by T cells def: "An enzyme-linked immunospot assay that detects monocyte chemotactic protein-1 production by T cells." [] synonym: "CCL2/MCP-1 release|ELISPOT" EXACT [] is_a: OBI:0001465 ! assay measuring epitope specific monocyte chemotactic protein-1 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001785 name: intracellular cytokine staining assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells def: "A flow cytometry assay that detects macrophage inflammatory protein-1 gamma production by T cells." [] synonym: "CCL9/MIP-1g release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001456 ! assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells [Term] id: OBI:0001786 name: ELISPOT assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells def: "An enzyme-linked immunospot assay that detects inflammatory protein-1 gamma production by T cells." [] synonym: "CCL9/MIP-1g release|ELISPOT" EXACT [] is_a: OBI:0001456 ! assay measuring epitope specific macrophage inflammatory protein-1 gamma production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001787 name: cytometric bead array assay measuring epitope specific vascular endothelial growth factor production by T cells def: "A cytometric bead array assay that detects vascular endothelial growth factor production by T cells." [] synonym: "VEGF release|cytometric bead array" EXACT [] is_a: OBI:0001570 ! assay measuring epitope specific vascular endothelial growth factor production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001788 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects tumor necrosis factor superfamily cytokine production by T cells." [] synonym: "TNF release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001789 name: intracellular cytokine staining assay measuring epitope specific RANTES production by T cells def: "A flow cytometry assay that detects RANTES production by T cells." [] synonym: "CCL5/RANTES release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001232 ! assay measuring epitope specific RANTES production by T cells [Term] id: OBI:0001790 name: ELISPOT assay measuring epitope specific RANTES production by T cells def: "An enzyme-linked immunospot assay that detects RANTES production by T cells." [] synonym: "CCL5/RANTES release|ELISPOT" EXACT [] is_a: OBI:0001232 ! assay measuring epitope specific RANTES production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001791 name: ELISPOT assay measuring epitope specific lymphotoxin A production by T cells def: "An enzyme-linked immunospot assay that detects lymphotoxin A production by T cells." [] synonym: "lymphotoxin A/TNFb release|ELISPOT" EXACT [] is_a: OBI:0001272 ! ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells is_a: OBI:0001327 ! assay measuring epitope specific lymphotoxin A production by T cells [Term] id: OBI:0001792 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects macrophage inflammatory protein-1 alpha production by T cells." [] synonym: "CCL3/MIP-1a release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001333 ! assay measuring epitope specific macrophage inflammatory protein-1 alpha production by T cells [Term] id: OBI:0001793 name: cytometric bead array assay measuring epitope specific lymphotoxin A production by T cells def: "A cytometric bead array assay that detects lymphotoxin A production by T cells." [] synonym: "lymphotoxin A/TNFb release|cytometric bead array" EXACT [] is_a: OBI:0001327 ! assay measuring epitope specific lymphotoxin A production by T cells is_a: OBI:0001368 ! cytometric bead array assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001794 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific lymphotoxin A production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects lymphotoxin A production by T cells." [] synonym: "lymphotoxin A/TNFb release|RNA/DNA detection" EXACT [] is_a: OBI:0001327 ! assay measuring epitope specific lymphotoxin A production by T cells is_a: OBI:0001788 ! detection of specific nucleic acids with complementary probes assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0001795 name: ELISPOT assay measuring epitope specific IP-10 production by T cells def: "An enzyme-linked immunospot assay that detects IP-10 production by T cells." [] synonym: "CXCL10/IP-10 release|ELISPOT" EXACT [] is_a: OBI:0001308 ! assay measuring epitope specific IP-10 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001796 name: intracellular cytokine staining assay measuring epitope specific IP-10 production by T cells def: "A flow cytometry assay that detects IP-10 production by T cells." [] synonym: "CXCL10/IP-10 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001308 ! assay measuring epitope specific IP-10 production by T cells [Term] id: OBI:0001797 name: ELISPOT assay measuring epitope specific interleukin-9 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-9 production by T cells." [] synonym: "IL-9 release|ELISPOT" EXACT [] is_a: OBI:0001253 ! assay measuring interleukin-9 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001798 name: intracellular cytokine staining assay measuring epitope specific interleukin-9 production by T cells def: "A flow cytometry assay that detects interleukin-9 production by T cells." [] synonym: "IL-9 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001253 ! assay measuring interleukin-9 production by T cells [Term] id: OBI:0001799 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-9 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-9 production by T cells." [] synonym: "IL-9 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001253 ! assay measuring interleukin-9 production by T cells [Term] id: OBI:0001800 name: ELISPOT assay measuring epitope specific interleukin-8 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-8 production by T cells." [] synonym: "IL-8 release|ELISPOT" EXACT [] is_a: OBI:0001218 ! assay measuring epitope specific interleukin-8 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001801 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-8 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-8 production by T cells." [] synonym: "IL-8 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001218 ! assay measuring epitope specific interleukin-8 production by T cells [Term] id: OBI:0001802 name: ELISPOT assay measuring epitope specific interleukin-3 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|ELISPOT" EXACT [] is_a: OBI:0001406 ! assay measuring epitope specific interleukin-3 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001803 name: ELISA measuring epitope specific interleukin-7 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-7 production by T cells." [] synonym: "IL-7 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001587 ! assay measuring epitope specific interleukin-7 production by T cells [Term] id: OBI:0001804 name: ELISPOT assay measuring epitope specific interleukin-7 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-7 production by T cells." [] synonym: "IL-7 release|ELISPOT" EXACT [] is_a: OBI:0001587 ! assay measuring epitope specific interleukin-7 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001805 name: intracellular cytokine staining assay measuring epitope specific interleukin-7 production by T cells def: "A flow cytometry assay that detects interleukin-7 production by T cells." [] synonym: "IL-7 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001587 ! assay measuring epitope specific interleukin-7 production by T cells [Term] id: OBI:0001806 name: intracellular cytokine staining assay measuring epitope specific interleukin-27 production by T cells def: "A flow cytometry assay that detects interleukin-27 production by T cells." [] synonym: "IL-27 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001198 ! assay measuring epitope specific interleukin-27 production by T cells [Term] id: OBI:0001807 name: cytometric bead array assay measuring epitope specific interleukin-3 production by T cells def: "A cytometric bead array assay that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|cytometric bead array" EXACT [] is_a: OBI:0001406 ! assay measuring epitope specific interleukin-3 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001808 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-3 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-3 production by T cells." [] synonym: "IL-3 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001406 ! assay measuring epitope specific interleukin-3 production by T cells [Term] id: OBI:0001809 name: assay measuring epitope specific granzyme A release by T cells def: "A T cell epitope specific cytotoxic T cell degranulation assay that detects granzyme A release by T cells." [] synonym: "granzyme A release|biological activity" EXACT [] is_a: OBI:0001269 ! assay measuring epitope specific cytotoxic T cell degranulation [Term] id: OBI:0001810 name: assay measuring epitope specific granulysin release by T cells def: "A T cell epitope specific cytotoxic T cell degranulation assay that detects granulysin release by T cells." [] synonym: "granulysin release|biological activity" EXACT [] is_a: OBI:0001269 ! assay measuring epitope specific cytotoxic T cell degranulation [Term] id: OBI:0001811 name: cytometric bead array assay measuring epitope specific interleukin-27 production by T cells def: "A cytometric bead array assay that detects interleukin-27 production by T cells." [] synonym: "IL-27 release|cytometric bead array" EXACT [] is_a: OBI:0001198 ! assay measuring epitope specific interleukin-27 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001812 name: intracellular cytokine staining assay measuring epitope specific interleukin-23 production by T cells def: "A flow cytometry assay that detects interleukin-23 production by T cells." [] synonym: "IL-23 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001363 ! assay measuring epitope specific interleukin-23 production by T cells [Term] id: OBI:0001813 name: ELISPOT assay measuring epitope specific interleukin-27 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-27 production by T cells." [] synonym: "IL-27 release|ELISPOT" EXACT [] is_a: OBI:0001198 ! assay measuring epitope specific interleukin-27 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001814 name: ELISA measuring epitope specific interleukin-27 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-27 production by T cells." [] synonym: "IL-27 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001198 ! assay measuring epitope specific interleukin-27 production by T cells [Term] id: OBI:0001815 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-18 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-18 production by T cells." [] synonym: "IL-18 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001380 ! assay measuring epitope specific interleukin-18 production by T cells [Term] id: OBI:0001816 name: epitope specific chemokine (C-X-C motif) ligand 13 production by T cells def: "A process of chemokine (C-X-C motif) ligand 13 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0097391 ! chemokine (C-X-C motif) ligand 13 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001817 name: ELISPOT assay measuring epitope specific interleukin-18 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-18 production by T cells." [] synonym: "IL-18 release|ELISPOT" EXACT [] is_a: OBI:0001380 ! assay measuring epitope specific interleukin-18 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001818 name: epitope specific chemokine (C-X-C motif) ligand 12 production by T cells def: "A process of chemokine (C-X-C motif) ligand 12 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0097390 ! chemokine (C-X-C motif) ligand 12 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001819 name: epitope specific chemokine (C-C motif) ligand 22 production by T cells def: "A process of chemokine (C-C motif) ligand 22 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0071924 ! chemokine (C-C motif) ligand 22 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001820 name: epitope specific chemokine (C-X-C motif) ligand 16 production by T cells def: "A process of chemokine (C-X-C motif) ligand 16 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0097392 ! chemokine (C-X-C motif) ligand 16 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001821 name: ELISPOT assay measuring epitope specific interleukin-22 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-22 production by T cells." [] synonym: "IL-22 release|ELISPOT" EXACT [] is_a: OBI:0001217 ! assay measuring epitope specific interleukin-22 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001822 name: ELISPOT assay measuring epitope specific interleukin-23 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-23 production by T cells." [] synonym: "IL-23 release|ELISPOT" EXACT [] is_a: OBI:0001363 ! assay measuring epitope specific interleukin-23 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001823 name: epitope specific chemokine (C-C motif) ligand 21 production by T cells def: "A process of chemokine (C-C motif) ligand 21 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0097389 ! chemokine (C-C motif) ligand 21 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001824 name: intracellular cytokine staining assay measuring epitope specific interleukin-18 production by T cells def: "A flow cytometry assay that detects interleukin-18 production by T cells." [] synonym: "IL-18 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001380 ! assay measuring epitope specific interleukin-18 production by T cells [Term] id: OBI:0001825 name: epitope specific chemokine (C-C motif) ligand 19 production by T cells def: "A process of chemokine (C-C motif) ligand 19 production by T cells resulting from the recognition of a T cell epitope." [] is_a: GO:0097388 ! chemokine (C-C motif) ligand 19 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0001826 name: ELISPOT assay measuring epitope specific interleukin-21 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-21 production by T cells." [] synonym: "IL-21 release|ELISPOT" EXACT [] is_a: OBI:0001237 ! assay measuring epitope specific interleukin-21 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001827 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 1 production by T cells." [] synonym: "CCL1/TCA-3 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001276 ! assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells [Term] id: OBI:0001828 name: cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells def: "A cytometric bead array assay that detects chemokine (C-C motif) ligand 1 production by T cells." [] synonym: "CCL1/TCA-3 release|cytometric bead array" EXACT [] is_a: OBI:0001276 ! assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001829 name: ELISPOT assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells def: "An enzyme-linked immunospot assay that detects chemokine (C-C motif) ligand 1 production by T cells." [] synonym: "CCL1/TCA-3 release|ELISPOT" EXACT [] is_a: OBI:0001276 ! assay measuring epitope specific chemokine (C-C motif) ligand 1 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001830 name: ELISPOT assay measuring epitope specific interleukin-17F production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-17F production by T cells." [] synonym: "IL-17F release|ELISPOT" EXACT [] is_a: OBI:0001354 ! ELISPOT assay measuring epitope specific interleukin-17 production by T cells is_a: OBI:0001772 ! assay measuring epitope specific interleukin-17F production by T cells [Term] id: OBI:0001831 name: ELISA measuring epitope specific interleukin-17F production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-17F production by T cells." [] synonym: "IL-17F release|ELISA" EXACT [] is_a: OBI:0001772 ! assay measuring epitope specific interleukin-17F production by T cells is_a: OBI:1110162 ! ELISA measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:0001832 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17F production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17F production by T cells." [] synonym: "IL-17F release|RNA/DNA detection" EXACT [] is_a: OBI:0001291 ! detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells is_a: OBI:0001772 ! assay measuring epitope specific interleukin-17F production by T cells [Term] id: OBI:0001833 name: ELISPOT assay measuring epitope specific interleukin-17A production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-17A production by T cells." [] synonym: "IL-17A release|ELISPOT" EXACT [] is_a: OBI:0001354 ! ELISPOT assay measuring epitope specific interleukin-17 production by T cells is_a: OBI:0001773 ! assay measuring epitope specific interleukin-17A production by T cells [Term] id: OBI:0001834 name: drawing a conclusion def: "A planned process in which new information is inferred from existing information." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0001835 name: cytometric bead array assay measuring epitope specific interleukin-18 production by T cells def: "A cytometric bead array assay that detects interleukin-18 production by T cells." [] synonym: "IL-18 release|cytometric bead array" EXACT [] is_a: OBI:0001380 ! assay measuring epitope specific interleukin-18 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0001836 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-16 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001280 ! assay measuring epitope specific interleukin-16 production by T cells [Term] id: OBI:0001837 name: ELISA measuring epitope specific interleukin-16 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001280 ! assay measuring epitope specific interleukin-16 production by T cells [Term] id: OBI:0001838 name: ELISPOT assay measuring epitope specific interleukin-16 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|ELISPOT" EXACT [] is_a: OBI:0001280 ! assay measuring epitope specific interleukin-16 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001839 name: intracellular cytokine staining assay measuring epitope specific interleukin-16 production by T cells def: "A flow cytometry assay that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001280 ! assay measuring epitope specific interleukin-16 production by T cells [Term] id: OBI:0001840 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17A production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-17A production by T cells." [] synonym: "IL-17A release|RNA/DNA detection" EXACT [] is_a: OBI:0001291 ! detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-17 production by T cells is_a: OBI:0001773 ! assay measuring epitope specific interleukin-17A production by T cells [Term] id: OBI:0001841 name: intracellular cytokine staining assay measuring epitope specific interleukin-1 beta production by T cells def: "A flow cytometry assay that detects interleukin-1 beta production by T cells." [] synonym: "IL-1b release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001449 ! assay measuring epitope specific interleukin-1 beta production by T cells [Term] id: OBI:0001842 name: ELISPOT assay measuring epitope specific interleukin-1 beta production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-1 beta production by T cells." [] synonym: "IL-1b release|ELISPOT" EXACT [] is_a: OBI:0001449 ! assay measuring epitope specific interleukin-1 beta production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001843 name: detection of specific nucleic acids with complementary probes measuring epitope specific interleukin-15 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-15 production by T cells." [] synonym: "IL-15 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001292 ! assay measuring epitope specific interleukin-15 production by T cells [Term] id: OBI:0001844 name: ELISPOT assay measuring epitope specific interleukin-12 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-12 production by T cells." [] synonym: "IL-12 release|ELISPOT" EXACT [] is_a: OBI:0001391 ! assay measuring epitope specific interleukin-12 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001845 name: intracellular cytokine staining assay measuring epitope specific interleukin-15 production by T cells def: "A flow cytometry assay that detects interleukin-15 production by T cells." [] synonym: "IL-15 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001292 ! assay measuring epitope specific interleukin-15 production by T cells [Term] id: OBI:0001846 name: ELISPOT assay measuring epitope specific interleukin-15 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-15 production by T cells." [] synonym: "IL-15 release|ELISPOT" EXACT [] is_a: OBI:0001292 ! assay measuring epitope specific interleukin-15 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0001848 name: chromatin interaction analysis by paired-end tag sequencing assay def: "An assay that incorporates chromatin immunoprecipitation (ChIP)-based enrichment, chromatin proximity ligation, Paired-End Tags, and high-throughput sequencing to determine de novo long-range chromatin interactions genome-wide." [] synonym: "ChIA-PET" EXACT [] synonym: "ChIA-PET assay" EXACT [] is_a: OBI:0002438 ! nuclear ligation assay is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001849 name: structural analysis by paired-end tag sequencing assay def: "An assay that incorporates Paired-End Tags and sequencing technology to determine structural variants." [] synonym: "DNA-PET" EXACT [] synonym: "DNA-PET assay" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0001850 name: transcript analysis by paired-end tag sequencing assay def: "A transcription profiling assay that determines transcripts, gene structures, and gene expressions using Paired-End Tags and sequencing technology." [] synonym: "RNA-PET" EXACT [] synonym: "RNA-PET assay" EXACT [] is_a: OBI:0000424 ! transcription profiling assay is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001851 name: transcription start site identification objective def: "A transcription profiling identification objective that aims to characterize the transcription start sites of genes." [] is_a: OBI:0001331 ! transcription profiling identification objective [Term] id: OBI:0001852 name: paired-end library preparation def: "A library preparation that results in the creation of a library of the 5' and 3' ends of DNA or cDNA fragments using adaptors and endonucleases. The preparation may or may not include cloning process." [] is_a: OBI:0000711 ! library preparation [Term] id: OBI:0001853 name: DNase I hypersensitive sites sequencing assay def: "An assay that identifies the location of regulatory regions, based on the genome-wide sequencing of regions super sensitive to cleavage by DNase I." [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0001854 name: protein and RNA interaction identification objective def: "A sequence feature identification objective that aims to characterize the interactions between protein and RNA." [] is_a: OBI:0000113 ! sequence feature identification objective [Term] id: OBI:0001857 name: RNP (ribonuclear particle) immunoprecipitation high- throughput sequencing assay def: "An analyte assay that combines immunoprecipitation of an RNA-binding protein and RNA-seq to identify mRNAs associated with selected RNA binding proteins (RBPs)." [] synonym: "RIP-seq" EXACT [] synonym: "RIP-seq assay" EXACT [] is_a: OBI:0000443 ! analyte assay is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001858 name: cross-linking immunoprecipitation high-throughput sequencing assay def: "An analyte assay that employs UV-crosslinking between RNA and a protein, followed by immunoprecipitation with antibodies for the protein, fragmentation, and high-throughput screening for RNA sequences that interact with a particular RNA-binding protein." [] synonym: "CLIP-seq" EXACT [] synonym: "CLIP-seq assay" EXACT [] synonym: "HITS-CLIP" EXACT [] is_a: OBI:0000443 ! analyte assay is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001859 name: formaldehyde-assisted isolation of regulatory elements assay def: "An assay to determine the sequences of those DNA regions in the genome associated with regulatory activity." [] synonym: "FAIRE-seq" EXACT [] synonym: "FAIRE-seq assay" EXACT [] is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001861 name: methylation-sensitive restriction enzyme sequencing assay def: "An assay that identifies unmethylated CpGs using methylation sensitive restriction enzymes to fragment DNA." [] synonym: "MRE-seq" EXACT [] synonym: "MRE-seq assay" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay is_a: OBI:0001266 ! DNA methylation profiling by high throughput sequencing assay [Term] id: OBI:0001862 name: reduced representation bisulfite sequencing assay def: "A bisulfite sequencing assay that identifies genomic methylation patterns using a bisulfite based protocol that enriches CG-rich parts of the genome." [] synonym: "reduced representation bisulfite-seq" EXACT [] synonym: "RRBS" EXACT [] synonym: "RRBS assay" EXACT [] is_a: OBI:0000748 ! bisulfite sequencing assay [Term] id: OBI:0001863 name: shotgun bisulfite-seq assay def: "A bisulfite sequencing assay that identifies methylated cytosines across the genome using high throughput sequencing." [] synonym: "Shotgun bisulfite sequencing" EXACT [] synonym: "WGBS" EXACT [] synonym: "WGSBS" EXACT [] synonym: "whole genome bisulfite sequencing" EXACT [] synonym: "whole-genome shotgun bisulfite sequencing" EXACT [] is_a: OBI:0000748 ! bisulfite sequencing assay [Term] id: OBI:0001864 name: RNA Annotation and Mapping of Promoters for the Analysis of Gene Expression assay def: "An transcription profiling assay that identifies transcription start sites (TSS), the quantification of their expression and the characterization of their transcripts using high throughput sequencing." [] synonym: "RAMPAGE" EXACT [] is_a: OBI:0000424 ! transcription profiling assay is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001865 name: assay array def: "A device made to be used in an analyte assay for immobilization of substances that bind the analyte at regular spatial positions on a surface." [] is_a: OBI:0000968 ! device [Term] id: OBI:0001866 name: secondary cultured cell def: "A cultured cell that has been passaged or derives from a cell that has been passaged in culture." [] comment: A secondary cultured cell has been passaged in culture or is a descendant of such a cell that is derived through propagation in culture. is_a: CL:0000010 ! cultured cell [Term] id: OBI:0001867 name: establishing cell line def: "a process whereby a new type of cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification, or selection of some defined subset)." [] is_a: OBI:0600036 ! establishing cell culture [Term] id: OBI:0001868 name: genetic material def: "A nucleic acid macromolecule that is part of a cell or virion and is inherited from an immediate ancestor, or incorporated in a manner that it has the disposition to be replicated and inherited by descendants." [] comment: Naturally occurring or experimentally incorporated nucleic acids that meet these criteria can qualify as genetic/genomic material.\n\nQualifying examples include: (1) inherited chromosomal DNA in germ cells, stem cells, fully differentiated cells, or cell line cells, or the DNA/RNA content of a virion; (2) natural replicons exchanged through horizontal gene transfer mechanisms such as bacterial conjugation, which are capable of replication and inheritance by progeny; (3) a chromosomally integrated gene targeting DNA construct transfected into a cell; or (4) a stable extra-chromosomal replicon delivered into cells, such as a plasmid in bacterial host with ori allowing indefinite propagation. \n\nNon-qualifying examples include a transiently transfected plasmid or siRNA oligo (as these are not able to be replicated and inherited by progeny cells). synonym: "genomic material" EXACT [] synonym: "hereditary genetic material" EXACT [] is_a: CHEBI:33696 ! nucleic acid [Term] id: OBI:0001869 name: Illumina BeadChip def: "An array that consists of 3-micron silica beads that self assemble in microwells on either of two materials: fiber optic bundles or planar silica slides." [] is_a: OBI:0001865 ! assay array [Term] id: OBI:0001870 name: Illumina methylation BeadChip def: "A BeadChip made for an analyte assay that generates information about DNA methylation." [] is_a: OBI:0001869 ! Illumina BeadChip [Term] id: OBI:0001871 name: LSRFortessa X-20 def: "A flow cytometer analyzer manifactured by Becton ans Dickinson. Can be configured with up to 5 lasers, 488nm, 532 or 561 nm, 640 nm, 405 nm, 355 nm for measuring up to 20 parameters simultaneously." [] is_a: OBI:0400008 ! flow cytometer analyzer [Term] id: OBI:0001872 name: sequence assembly process def: "A data transformation that assembles two or more individual sequence reads into contiguous sequences (i.e., contigs)." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0001873 name: number of errors def: "a data item that is the number of times that a given process failed, as an integer" [] is_a: IAO:0000027 ! data item is_a: OBI:0001933 ! value specification [Term] id: OBI:0001874 name: random access memory size def: "random access memory size is a scalar measurement datum which denotes the amount of physical memory know as random access memory present of a computer or required by a computational process or data transformation" [] is_a: IAO:0000032 ! scalar measurement datum [Term] id: OBI:0001875 name: cultured immune cell population def: "a cultured cell population comprised of a single type of immune system cell" [] synonym: "immune cell culture sample" EXACT [] is_a: OBI:0100060 ! cultured cell population [Term] id: OBI:0001876 name: cell culture def: "A material entity comprised of cultured cells and the media in which they are being propagated or stored." [] comment: A cell culture includes the cells in culture, as well as the media and all additives in which the cells are being grown or in which they are stored. is_a: OBI:0000047 ! processed material [Term] id: OBI:0001877 name: random access memory def: "Random-access memory (RAM) is a form of computer data storage. A random-access device allows stored data to be accessed directly in any random order. In contrast, other data storage media such as hard disks, CDs, DVDs and magnetic tape, as well as early primary memory types such as drum memory, read and write data only in a predetermined order, consecutively, because of mechanical design limitations. Therefore, the time to access a given data location varies significantly depending on its physical location" [] synonym: "RAM" EXACT [] is_a: IAO:0000178 ! material information bearer [Term] id: OBI:0001878 name: establishing primary cell culture def: "an establishing cell culture process whereby cells explanted directly from an organismal source or specimen, and placed in culture for maintenance or propagation as a primary cell culture" [] comment: Cells are originally plated at a certain concentration referred to as seeding density. Upon a first passage this primary culture becomes a secondary cell culture that can be propagated to become a stable and homogneous cell line. This class covers establishment of primary cultures from any native cell - 'in vivo' cells isolated from some multicellular organism, or 'in environment' unicellular organisms isolated from some natural environment. is_a: OBI:0600036 ! establishing cell culture [Term] id: OBI:0001879 name: reagent def: "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." [] comment: (copied from ReO)\nReagents 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.\n\nReagents 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.\n\nIn 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). is_a: OBI:0000047 ! processed material [Term] id: OBI:0001880 name: organization of specimen provider principal investigator def: "An organization that is the affiliation of the principal investigator providing the specimens for the investigation" [] synonym: "Sample Provider PI's Institution" EXACT [] is_a: OBI:0000245 ! organization [Term] id: OBI:0001881 name: organization of Bioinformatics Resource Center contact person def: "An organization that is the affiliation of the person who is contact representative of a Bioinformatics Resource Center" [] synonym: "Bioinformatics Resource Center Contact's Institution" EXACT [] is_a: OBI:0000245 ! organization [Term] id: OBI:0001882 name: target material in specimen specification def: "A plan specification which specifies the type of material that will be assayed in an investigation." [] synonym: "Target Material" EXACT [] is_a: IAO:0000104 ! plan specification [Term] id: OBI:0001883 name: Bioinformatics Resource Center contact person def: "A person who is the contact representative of a Bioinformatics Resource Center" [] synonym: "Bioinformatics Resource Center Contact Name" EXACT [] is_a: NCBITaxon:9606 ! Homo sapiens [Term] id: OBI:0001884 name: specimen-based scope of investigation specification def: "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." [] synonym: "Sample Scope" EXACT [] is_a: IAO:0000104 ! plan specification [Term] id: OBI:0001885 name: specimen repository organization def: "An organization that provides a service to store and distribute specimens" [] synonym: "Specimen Repository" EXACT [] is_a: OBI:0000245 ! organization [Term] id: OBI:0001887 name: email address of Bioinformatics Resource Center contact person def: "An email address of the person who is contact representative of a Bioinformatics Resource Center" [] synonym: "Bioinformatics Resource Center Contact's email" EXACT [] is_a: IAO:0000429 ! email address [Term] id: OBI:0001888 name: sequencing facility contact person def: "A person who is the contact representative at the sequencing facility" [] synonym: "Sequencing Facility Contact Name" EXACT [] is_a: NCBITaxon:9606 ! Homo sapiens [Term] id: OBI:0001889 name: specimen provider principal investigator def: "A person who is a principal investigator and provides the specimen" [] synonym: "Sample Provider Principal Investigator (PI) Name" EXACT [] is_a: NCBITaxon:9606 ! Homo sapiens [Term] id: OBI:0001890 name: email address of specimen collector def: "An email address of the person collecting the specimen" [] synonym: "Specimen Collector's email" EXACT [] is_a: IAO:0000429 ! email address [Term] id: OBI:0001891 name: sequencing facility organization def: "An organization that provides sequence determination service" [] synonym: "Sequencing Facility" EXACT [] is_a: OBI:0002198 ! molecular analysis facility organization [Term] id: OBI:0001892 name: specification of data to be generated in an investigation def: "An objective specification which indicates the type of data that will be generated and submitted to a database." [] synonym: "Project Objectives" EXACT [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0001893 name: organization of specimen collector def: "An organization that is the affiliation of the person collecting the specimen" [] synonym: "Specimen Collector's Institution" EXACT [] is_a: OBI:0000245 ! organization [Term] id: OBI:0001894 name: email address of sequencing facility contact person def: "An email address of the contact representative at the sequencing facility" [] synonym: "Sequencing Facility Contact's email" EXACT [] is_a: IAO:0000429 ! email address [Term] id: OBI:0001895 name: specimen collector def: "A person who collects the specimen" [] synonym: "Specimen Collector Name" EXACT [] is_a: NCBITaxon:9606 ! Homo sapiens [Term] id: OBI:0001896 name: investigation assay specification def: "A plan specification which indicates the assay type used to obtain data." [] synonym: "Project Method" EXACT [] is_a: IAO:0000104 ! plan specification [Term] id: OBI:0001897 name: organization of sequencing facility contact person def: "An organization that is the affiliation of the contact representative at the sequencing facility" [] synonym: "Sequencing Facility Contact's Institution" EXACT [] is_a: OBI:0000245 ! organization [Term] id: OBI:0001898 name: comment on investigation def: "A textual entity that is about any of the aspects of an investigation worth noting" [] synonym: "Comments" EXACT [] is_a: IAO:0000300 ! textual entity [Term] id: OBI:0001899 name: target capture specification def: "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." [] synonym: "Target Capture" EXACT [] is_a: IAO:0000104 ! plan specification [Term] id: OBI:0001900 name: specimen identifier assigned by specimen repository def: "A specimen identifier which is assigned by a specimen repository" [] synonym: "Specimen Repository Sample ID" EXACT [] is_a: OBI:0001616 ! specimen identifier [Term] id: OBI:0001901 name: specimen identifier assigned by sequencing facility def: "A specimen identifier which is assigned by a sequencing facility" [] synonym: "Sample ID - Sequencing Facility" EXACT [] is_a: OBI:0001616 ! specimen identifier [Term] id: OBI:0001902 name: sample preparation for sequencing assay def: "A sample preparation for assay that preparation of nucleic acids for a sequencing assay" [] synonym: "Nucleic Acid Preparation Method" EXACT [] is_a: OBI:0000073 ! sample preparation for assay [Term] id: OBI:0001903 name: email address of specimen provider principal investigator def: "An email address of the principal investigator providing the specimens for the investigation" [] synonym: "Sample Provider PI's email" EXACT [] is_a: IAO:0000429 ! email address [Term] id: OBI:0001904 name: sequencing service def: "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." [] is_a: OBI:0001547 ! material analysis service [Term] id: OBI:0001905 name: secondary cultured cell population def: "A cultured cell population that is derived through one or more passages in culture." [] comment: The concept of a 'secondary cultured cell population' covers cell lines as well as cultured cell populations more immediately derived from a primary culture which have yet to achieve adequate genetic stability and compositional homogeneity to be considered a cell line. The extent of the collection of cells in a 'secondary cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). Secondary cultured cell populations can be under active culture, stored in a quiescent state for future use, or applied experimentally. synonym: "secondary cell culture sample" EXACT [] is_a: OBI:0100060 ! cultured cell population [Term] id: OBI:0001906 name: cancer cell line def: "An immortal cell line derived from a transformed cell that was part of a malignant tumor." [] is_a: CLO:0009828 ! immortal cell line [Term] id: OBI:0001907 name: immortalizing cell line transformation def: "a genetic transformation of a cell line cell with transgenic constructs intended to confer the capability for indefinite propagation in culture" [] is_a: OBI:0600043 ! genetic transformation [Term] id: OBI:0001908 name: testable hypothesis def: "An information content entity that expresses an assertion that is intended to be tested." [] synonym: "hypothesis" EXACT [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0001909 name: conclusion based on data def: "An information content entity that is inferred from data." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0001910 name: primary cell culture def: "A cell culture comprised of primary cultured cells and the media in which they are being actively propaged or quiescently stored." [] is_a: OBI:0001876 ! cell culture [Term] id: OBI:0001911 name: cell line culture def: "A cell culture comprised of cell line cells and the media in which they are being actively propagated or quiescently stored." [] comment: A cell line culture includes the cells in culture, as well as the media and all additives/reagents in which the cells are being grown or in which they are stored. is_a: OBI:0001876 ! cell culture [Term] id: OBI:0001912 name: cell freezing medium def: "A processed material that serves as a liquid vehicle for freezing cells for long term quiescent stroage, which contains chemicls needed to sustain cell viability across freeze-thaw cycles." [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0001913 name: computation run time def: "computation run time is a time measurement datum which corresponds the time expressed in second, minute, hour necessary for a computer program to complete a process execution, for example genome assembly. It is an important metrics as it indicates the resource occupancy and computer program efficiency." [] synonym: "computation run time datum" EXACT [] is_a: IAO:0000416 ! time measurement datum [Term] id: OBI:0001914 name: multiplex ligation-mediated amplification def: "A polymerase chain reaction that amplifies multiple targets with a single primer pair mediated by hybridization of a primer with its target sequence using ligation." [] synonym: "LMA" EXACT [] synonym: "MLPA" EXACT [] synonym: "Multiplex ligation-dependent probe amplification" EXACT [] is_a: OBI:0000415 ! polymerase chain reaction [Term] id: OBI:0001915 name: DNA replication timing by array assay def: "An assay which quantifies the timing of DNA replication as a function of genome position using array technology." [] synonym: "Repli-chip" EXACT [] synonym: "Repli-chip assay" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0001916 name: DNA replication identification objective def: "A molecular feature identification objective that aims to examine charateristics of DNA replication, such as replication time." [] is_a: OBI:0000131 ! molecular feature identification objective [Term] id: OBI:0001917 name: chromosome conformation identification objective def: "A molecular feature identification objective that aims to determine spatial organization of chromatin." [] is_a: OBI:0000131 ! molecular feature identification objective [Term] id: OBI:0001918 name: RNA-binding protein immunoprecipitation array profiling assay def: "An assay that combines immunoprecipitation of an RNA-binding protein and array technology to identify mRNAs associated with selected RNA binding proteins (RBPs)." [] synonym: "RIP-chip" EXACT [] synonym: "RIP-chip assay" EXACT [] is_a: OBI:0001985 ! microarray assay [Term] id: OBI:0001919 name: Carbon-copy chromosome conformation capture assay def: "An assay that measures the organization of chromosomes at the genome-wide scale." [] synonym: "5C" EXACT [] synonym: "5C assay" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0001920 name: DNA replication timing by sequencing assay def: "An assay in which timing of DNA replication is quantified as a function of genome position based on genome-wide sequencing." [] synonym: "Repli-seq" EXACT [] synonym: "Repli-seq assay" EXACT [] is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001921 name: RNA-binding protein immunoprecipitation tiling array profiling assay def: "An RNA-binding protein immunoprecipitation array profiling assay that combines immunoprecipitation of an RNA-binding protein and RNA tiling array to identify mRNAs associated with selected RNA binding proteins (RBPs)." [] is_a: OBI:0001918 ! RNA-binding protein immunoprecipitation array profiling assay [Term] id: OBI:0001922 name: microRNA profiling by high throughput sequencing assay def: "A microRNA profiling assay that analyzes the microRNA component of the transcriptome using high throughput sequencing technology." [] synonym: "microRNA-seq" EXACT [] synonym: "microRNA-seq assay" EXACT [] synonym: "miRNA-HTS" EXACT [] synonym: "miRNA-seq" EXACT [] is_a: OBI:0001926 ! microRNA profiling assay [Term] id: OBI:0001923 name: protein sequencing by tandem mass spectrometry assay def: "A sequencing assay that detremines amino acid sequences of proteins using multiple rounds of mass spectrometry and molecule fragmentation." [] is_a: OBI:0000470 ! mass spectrometry assay is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001924 name: micrococcal nuclease digestion followed by high throughput sequencing assay def: "An assay that identifies nucleosome positioning by genome wide sequencing of regions sensitive to digestion by micrococal nuclease" [] synonym: "MNase-seq" EXACT [] synonym: "MNase-seq assay" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0001925 name: chromatin immunoprecipitation with exonuclease sequencing assay def: "A ChIP-seq assay which uses immunoprecipitation to isolate protein bound DNA followed by an exonuclease step to degrade DNA that is not protein bound to provide greater resolution of the DNA binding site" [] synonym: "ChIP-exo assay" EXACT [] is_a: OBI:0000716 ! ChIP-seq assay [Term] id: OBI:0001926 name: microRNA profiling assay def: "A transcription profiling assay that quantifies the microRNA species within a biological sample." [] synonym: "microRNA expression assay" EXACT [] synonym: "miRNA expression assay" EXACT [] is_a: OBI:0000424 ! transcription profiling assay [Term] id: OBI:0001928 name: selection def: "A planned process with the objective to create a group of entities by applying a predefined criteria to a larger group of entities." [] synonym: "selection process" EXACT [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0001929 name: mass value specification def: "A value specification that specifies the mass of some thing." [] is_a: OBI:0001931 ! scalar value specification [Term] id: OBI:0001930 name: categorical value specification def: "A value specification that is specifies one category out of a fixed number of nominal categories" [] is_a: OBI:0001933 ! value specification [Term] id: OBI:0001931 name: scalar value specification def: "A value specification that consists of two parts: a numeral and a unit label" [] is_a: OBI:0001933 ! value specification [Term] id: OBI:0001932 name: comparing prediction to measurement def: "A planned process in which predicted values for some thing are compared to measured values for that thing." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0001933 name: value specification def: "An information content entity that specifies a value within a classification scheme or on a quantitative scale." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0001934 name: predicted value def: "an information content entity that has been generated by a prediction process in which an estimate of a value of an entity is made which can be measured but without performing such a measurement. The value specification is intended to be close to the value a measurement process would produce modulo a prediction error." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0001935 name: predicted mass value def: "A predicted value where the prediction specifies the mass of some thing." [] is_a: OBI:0001934 ! predicted value [Term] id: OBI:0001936 name: molecular-labeled material def: "a material entity that is the specified output of an addition of molecular label process that aims to label some molecular target to allow for its detection in a detection of molecular label assay" [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0001939 name: genome coverage def: "A data item that is the total number of bases in reads, divided by genome size, assumed to be the reference size (for instance of 3.10 Gb for human and 2.73 Gb for mouse) and refers to the percentage of the genome that is contained in the assembly based on size estimates; these are usually based on cytological techniques. Genome coverage of 90–95% is generally considered to be good, as most genomes contain a considerable fraction of repetitive regions that are difficult to sequence. So it is not a cause for concern if the genome coverage of an assembly is a bit less than 100%." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0001940 name: N50 def: "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" [] synonym: "weighted median item size" EXACT [] is_a: IAO:0000032 ! scalar measurement datum [Term] id: OBI:0001941 name: contig N50 def: "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." [] is_a: OBI:0001940 ! N50 [Term] id: OBI:0001942 name: grant agency def: "An organization that provides funding support for projects such as investigations." [] synonym: "funding organization" EXACT [] is_a: OBI:0000245 ! organization [Term] id: OBI:0001943 name: software pipeline def: "A plan specification that specifies a chain encoded in software of processing elements (processes, threads, coroutines, etc.), arranged so that the output of each element is the input of the next. Usually some amount of buffering is provided between consecutive elements." [] is_a: IAO:0000104 ! plan specification [Term] id: OBI:0001944 name: sequence annotation def: "A planned process that identifies and reports sequence features (e.g. protein coding regions) in sequence data." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0001945 name: scaffold N50 def: "N50 statistic computed for the scaffold produced by the assembly process. The method for computing the value is similar to that of contig N50 but uses scaffold information instead of contig information" [] is_a: OBI:0001940 ! N50 [Term] id: OBI:0001946 name: forward PCR primer def: "A short oligonucleotide complementary to target DNA (5'->3' on plus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm." [] synonym: "5' primer" EXACT [] synonym: "forward primer" EXACT [] synonym: "sense primer" EXACT [] is_a: CHEBI:16991 ! deoxyribonucleic acid is_a: OBI:0001879 ! reagent [Term] id: OBI:0001947 name: sequence annotation provider def: "A person or organization reporting the feature annotation results from the analysis of a macromolecular sequence." [] synonym: "annotation provider" EXACT [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0001948 name: sequence assembly name def: "A textual entity that is used to denote a sequence assembly." [] synonym: "assembly name" EXACT [] is_a: IAO:0000300 ! textual entity [Term] id: OBI:0001949 name: sequence annotation reporting role def: "A reporting party role that is realized by a person or organization who reports the feature annotation results from the analysis of a macromolecular sequence." [] is_a: OBI:0000068 ! reporting party role [Term] id: OBI:0001951 name: reverse PCR primer def: "A short oligonucleotide complementary to target DNA (5'->3' on minus strand) that acts as the leader for DNA extension in a PCR reaction. The polymerase starts replication at the 3'-end of the primer, and copies the opposite strand. A primer is characterized by its 'melting temperature' (Tm) and pairs of primers should have similar Tm." [] synonym: "3' primer" EXACT [] synonym: "antisense primer" EXACT [] synonym: "reverse primer" EXACT [] is_a: CHEBI:16991 ! deoxyribonucleic acid is_a: OBI:0001879 ! reagent [Term] id: OBI:0001952 name: flash freezing def: "A freezing process by which material entities are quickly frozen by subjecting them to cryogenic temperatures, or in direct contact with Liquid nitrogen at -320.8F or -196°C." [] is_a: OBI:0001953 ! freezing [Term] id: OBI:0001953 name: freezing def: "A planned process with the objective to bring some material entity to a temperature below its freezing point." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0001954 name: ChIP assay def: "An assay in which portions of chromatin, the ordered and organized complex of DNA and its interaction partners that make up a chormosome, is extracted and purified by immunoprecipitation with antibodies or tags, and subsequently analyzed" [] synonym: "chromatin immunoprecipitation assay" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0001955 name: competitive binding reference ligand role def: "A positive reference substance role that inheres in a material entity that is known to bind to a target entity, and that is realized in a competitive binding assay that has as specified input the target entity, an evaluant and the positive reference substance, where the binding of the evaluant to the target is measured based on the evaluant's ability to compete with the positive reference substance for binding to the target." [] is_a: OBI:0000064 ! positive reference substance role [Term] id: OBI:0001956 name: assay using chromatin immunoprecipitation def: "An assay that produces data about protein-DNA interaction or DNA epigenetic modification using immunoprecipitation" [] is_a: OBI:0001700 ! immunoprecipitation assay [Term] id: OBI:0001957 name: hardware testing design def: "A study design that aims to compare different types of hardware for performance, reproducibility, accuracy and precision." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001958 name: systematic review study design def: "A study design for identifying in the literature prior studies of a pre-determined phenomenon or set of related phenomena according to certain criteria, extracting findings from these studies, and summarizing these findings and/or attempting to draw new conclusions from them which were not justified by any of the individual, prior studies. Many systematic reviews also assess the quality of the studies so reviewed." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001959 name: multiplexed nucleotide library sequencing def: "A planned process which consists in running a set of samples as a pool on a sequencing instrument, while retaining the ability to associate individual results to each of the individual input samples through the use of a ligated oligonucleotide (the \"multiplex identifier sequence\"). This oligonucleotide is introduced during the sequence library preparation, and is unique to and specific for all library fragments derived from each sample in a sample pool." [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0001960 name: taxonomic diversity assessment by targeted gene survey def: "An assay that dteremines taxonomic and community diversity information by sequencing specific genomic regions used as marker of identity or diversity." [] synonym: "environmental gene survey" EXACT [] synonym: "targeted gene survey" EXACT [] synonym: "targeted gene survey DNA barcoding" EXACT [] is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0001961 name: PCR program def: "a PCR program is a plan specification which is executed during a polymerase chain reaction (PCR) by a thermocycler instrument that will iterate through the changes in temperature and duration of each of the annealing, denaturation, elongation steps for as many times as specified by the program." [] is_a: IAO:0000104 ! plan specification [Term] id: OBI:0001962 name: target gene specification def: "is a directive information specifying a coding genomic region which is the focus of a planned process such as an assay, for instance in a environmental gene survey" [] synonym: "target gene" EXACT [] is_a: IAO:0000033 ! directive information entity [Term] id: OBI:0001963 name: target subfragment specification def: "is a directive information specifying a genomic region, possibly located in a coding genomic region, which is the focus of a planned process such as an assay, for instance in a environmental gene survey" [] synonym: "target subfragment" EXACT [] is_a: IAO:0000033 ! directive information entity [Term] id: OBI:0001964 name: decision-theoretic analysis objective def: "An objective specification which what includes a description of two or more alternative actions to take in a particular situation and a metric that enables comparisons of the two actions. The objective specified is achieved in a planned process which includes a data transformation, the output of which is an identification of the 'best' choice according to the metric." [] synonym: "decision analysis objective" EXACT [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0001965 name: decision analysis study design def: "a study design that has a decision analysis objective specification as part" [] is_a: OBI:0500000 ! study design [Term] id: OBI:0001966 name: sequence library data demultiplexing def: "is a data transformation which uses sequence alignment and 'multiplex identifier sequence' information to separate all reads belonging to a given single sample following the sequencing of a multiplexed library" [] is_a: OBI:0200187 ! sequence analysis data transformation [Term] id: OBI:0001967 name: multiplexing sequence identifier def: "A multiplexing sequence identifier is a nucleic acid sequence which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library" [] is_a: CHEBI:16991 ! deoxyribonucleic acid [Term] id: OBI:0001968 name: operational taxonomic unit matrix def: "Operational Taxonomic Unit matrix is a data item, organized as a table, where organismal taxonomic units, computed by sequence analysis and genetic distance calculation, are counted in a set of biological or environmental samples. The table is used to appraise biodiversity of a population or community of living organism." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0001969 name: biodiversity assessment objective def: "biodiversity assessment objective is an objective of a planned process aimed at producing data item whose interpretation should provide insight about variety of biological species found in a biological sample at macroscopic or microscopic level" [] is_a: OBI:0000015 ! biological feature identification objective [Term] id: OBI:0001970 name: multiplexed sequencing library def: "a multiplexed library is a material entity which is the output of a library preparation process that uses a ligation step to attach a unique multiplexing sequence identifier to a specific sample, then mixes several such tagged samples prior to the library amplification process proper. A multiplexed library allows the sequencing of several samples in one sequencing run." [] synonym: "DNA-barcoded sequencing library" EXACT [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0001971 name: Ion 316 Chip v2 def: "An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 316 chip is compatible with the Ion Torrent PGM and has a run time of: 3.0 hours for 200 bp reads with an output of 30-50 Mb, 4.9 hours for 400 bp reads with an output of 60 Mb-1 Gb." [] synonym: "Ion 316 Chip" EXACT [] synonym: "Ion PGM 316 Chip" EXACT [] synonym: "Ion PGM 316 Chip v2" EXACT [] is_a: OBI:0001973 ! ion semiconductor chip [Term] id: OBI:0001972 name: Ion 318 Chip v2 def: "An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 318 chip is compatible with the Ion Torrent PGM and has a run time of: 4.4 hours for 200 bp reads with an output of 60 Mb-1 Gb, 7.3 hours for 400 bp reads with an output of 1.2 Gb-2 Gb." [] synonym: "Ion 318 Chip" EXACT [] synonym: "Ion PGM 318 Chip" EXACT [] synonym: "Ion PGM 318 Chip v2" EXACT [] is_a: OBI:0001973 ! ion semiconductor chip [Term] id: OBI:0001973 name: ion semiconductor chip def: "An ion detector that is organized as an electronic circuit whose components, such as transistors and resistors, are etched or deposited on a single slice of semiconductor material to produce a chip. The specific chip detects ion charge induced when an ion passes by or hits a surface." [] synonym: "ion chip" EXACT [] synonym: "ion integrated circuit" EXACT [] synonym: "ion semiconductor" EXACT [] is_a: OBI:0000364 ! ion detector [Term] id: OBI:0001974 name: Ion 314 Chip v2 def: "An ion semiconductor chip manufactured by Life Technologies which detects polymerase-driven base incorporation to translate into digital form. The 314 chip is compatible with the Ion Torrent PGM and has a run time of: 2.3 hours for 200 bp reads with an output of 30-50 Mb, 3.7 hours for 400 bp reads with an output of 60-100 Mb." [] synonym: "Ion 314 Chip" EXACT [] synonym: "Ion PGM 314 Chip" EXACT [] synonym: "Ion PGM 314 Chip v2" EXACT [] is_a: OBI:0001973 ! ion semiconductor chip [Term] id: OBI:0001976 name: hydrogen/deuterium exchange footprinting assay def: "A footprinting assay that uses a chemical reaction whereby a covalently bonded hydrogen atom is replaced by a deuterium atom, or vice versa in order to gather information about the solvent accessibility of parts of a molecule and thus its tertiary structure." [] is_a: OBI:0002162 ! footprinting assay [Term] id: OBI:0001977 name: cytometry assay def: "An assay that counts and/or measures characteristics of cells." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0001978 name: immunoblot assay def: "An analyte assay that detects specific molecules in an input material by separating it using gel electrophoresis, transfering the separated molecules to a membrane, and staining them with_ antibodies specific to the analyte molecules." [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0001979 name: fluorescence quenching binding assay def: "A binding assay in which the proximity of two entities is monitored by measuring a fluorescent signal of one of the entities that gets reduced if the two entities are cliose to each other." [] is_a: OBI:0001499 ! binding assay using fluorescence detection [Term] id: OBI:0001980 name: in vivo intervention experiment def: "An assay in which the effect of a targeted process (the intervention) on an organism is tested." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0001981 name: disease exacerbation in vivo intervention experiment def: "An in vivo intervention experiment that tests the ability of the intervention to increase the severity of a disease in the host." [] is_a: OBI:0001980 ! in vivo intervention experiment [Term] id: OBI:0001982 name: protection from challenge in vivo intervention experiment def: "An in vivo intervention experiment that tests the ability of the intervention to prevent occurrence of a disease in a host." [] is_a: OBI:0001980 ! in vivo intervention experiment [Term] id: OBI:0001983 name: tolerance induction intervention experiment def: "An in vivo intervention experiment that tests the ability of the intervention to decrease an immune response." [] is_a: OBI:0001980 ! in vivo intervention experiment [Term] id: OBI:0001984 name: treatment intervention experiment def: "An in vivo intervention experiment in which the ability of the intervention to reduce or cure the effects of a disease are tested." [] is_a: OBI:0001980 ! in vivo intervention experiment [Term] id: OBI:0001985 name: microarray assay def: "An analyte assay where binding of the analyte to immobilized matrix is measured." [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0001986 name: immunohistochemistry def: "An immunostaining assay to detect and potentially localize antigens within the cells of a tissue section." [] is_a: OBI:0001632 ! immuno staining assay [Term] id: OBI:0001987 name: assay measuring the association constant [KA] of a MHC:ligand complex def: "A MHC binding constant determination assay measuring equilibrium association constant (KA)." [] synonym: "association constant KA|binding assay|1/M" EXACT [] is_a: OBI:0001553 ! assay measuring a binding constant of a MHC:ligand complex [Term] id: OBI:0001988 name: assay measuring the dissociation constant [KD] of a MHC:ligand complex def: "A MHC binding constant determination assay measuring equilibrium dissociation constant (KD)." [] synonym: "dissociation constant KD|binding assay|nM" EXACT [] is_a: OBI:0001553 ! assay measuring a binding constant of a MHC:ligand complex [Term] id: OBI:0001989 name: radioactivity detection assay measuring equilibrium dissociation constant [KD] to determine competitive binding of a purified-MHC:ligand complex def: "A radioactivity detection assay that measures equilibrium dissociation constant (KD) to detect the loss of binding of a known reference ligand to purified-MHC due to competition by the ligand under investigation." [] synonym: "dissociation constant KD|purified MHC/direct/radioactivity|nM" EXACT [] is_a: OBI:0001491 ! binding assay using radioactivity detection is_a: OBI:0001988 ! assay measuring the dissociation constant [KD] of a MHC:ligand complex [Term] id: OBI:0001990 name: assay measuring the half life of a MHC:ligand complex def: "A MHC binding constant determination assay measuring half life of binding." [] synonym: "half life|binding assay|min" EXACT [] is_a: OBI:0001553 ! assay measuring a binding constant of a MHC:ligand complex [Term] id: OBI:0001991 name: assay measuring the half maximal effective concentration [EC50] of a MHC:ligand complex def: "A MHC binding constant determination assay measuring half maximal effective concentration (EC50)." [] synonym: "half maximal effective concentration (EC50)|binding assay|nM" EXACT [] is_a: OBI:0003145 ! assay measuring quantitative binding of a MHC:ligand complex [Term] id: OBI:0001992 name: assay measuring the half maximal inhibitory concentration [IC50] of a MHC:ligand complex def: "A MHC binding constant determination assay measuring half maximal inhibitory concentration (IC50)." [] synonym: "half maximal inhibitory concentration (IC50)|binding assay|nM" EXACT [] is_a: OBI:0003145 ! assay measuring quantitative binding of a MHC:ligand complex [Term] id: OBI:0001993 name: assay measuring the off rate measurement [koff] of a MHC:ligand complex def: "A MHC binding constant determination assay measuring binding off rate measurement data item (koff)." [] synonym: "off rate|binding assay|1/s" EXACT [] is_a: OBI:0001553 ! assay measuring a binding constant of a MHC:ligand complex [Term] id: OBI:0001994 name: assay measuring the MHC ligand binding on rate [kon] of a MHC:ligand complex def: "A MHC binding constant determination assay measuring binding on rate (kon)." [] synonym: "on rate|binding assay|nM^-1s^-1" EXACT [] is_a: OBI:0001553 ! assay measuring a binding constant of a MHC:ligand complex [Term] id: OBI:0001995 name: chromatography assay measuring the association constant [KA] of a B cell epitope:antibody complex def: "An analytical chromatography assay that measures the association constant [KA] of an antigen binding with an antibody." [] synonym: "association constant KA|chromatography|1/nM" EXACT [] is_a: OBI:0001630 ! analytical chromatography is_a: OBI:0001719 ! assay measuring the association constant [KA] of a B cell epitope:antibody complex [Term] id: OBI:0001996 name: chromatography assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex def: "An analytical chromatography assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] synonym: "dissociation constant KD|chromatography|nM" EXACT [] is_a: OBI:0001630 ! analytical chromatography is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0001997 name: hydrogen/deuterium exchange footprinting assay measuring binding of a B cell epitope:antibody complex def: "A hydrogen/deuterium exchange footprinting assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|hydrogen/deuterium exchange footprinting assay" EXACT [] is_a: OBI:0001976 ! hydrogen/deuterium exchange footprinting assay is_a: OBI:0002449 ! footprinting assay measuring binding of a B cell epitope:antibody complex [Term] id: OBI:0001998 name: immunohistochemistry assay measuring binding of a B cell epitope:antibody complex def: "A immunohistochemistry assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|immunohistochemistry" EXACT [] is_a: OBI:0001652 ! immuno staining assay measuring binding of a B cell epitope:antibody complex is_a: OBI:0001986 ! immunohistochemistry [Term] id: OBI:0001999 name: 3D molecular structure determination assay of a T cell epitope:MHC:TCR complex def: "A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a T cell epitope:MHC:TCR complex." [] synonym: "3D structure|any method" EXACT [] is_a: OBI:0001145 ! 3D structure determination of bound molecular complex assay is_a: OBI:0003128 ! T cell epitope assay [Term] id: OBI:0002000 name: Genome Analyzer IIx def: "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." [] synonym: "Illumina GA IIx" EXACT [] synonym: "Illumina Genome Analyzer IIx" EXACT [] is_a: OBI:0000703 ! Illumina Genome Analyzer II [Term] id: OBI:0002001 name: Illumina HiSeq 2000 def: "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." [] synonym: "HiSeq 2000" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002002 name: Illumina HiSeq 2500 def: "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." [] synonym: "HiSeq 2500" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002003 name: MiSeq def: "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." [] synonym: "Illumina MiSeq" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002004 name: Methylation 450K BeadChip def: "A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 485,000 methylation sites per sample at single-nucleotide resolution." [] synonym: "Illumina Infinium Human Methylation 450K BeadChip" EXACT [] is_a: OBI:0001870 ! Illumina methylation BeadChip [Term] id: OBI:0002005 name: Methylation 27K BeadChip def: "A methylation BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array interrogates ~ 27,000 CpG sites per sample at single-nucleotide resolution." [] synonym: "Illumina Infinium Human Methylation 27K BeadChip" EXACT [] is_a: OBI:0001870 ! Illumina methylation BeadChip [Term] id: OBI:0002006 name: 1M-Duo Infinium HD BeadChip def: "A BeadChip which is manufactured by the Illumina corporation. Built upon BeadChip tehcnology, the array integrates ~ 1 million markers per sample for genotyping, and copy number variation (CNV) and Cytogenetic analysis." [] synonym: "Illumina Human 1M-Duo Infinium HD BeadChip" EXACT [] is_a: OBI:0001869 ! Illumina BeadChip [Term] id: OBI:0002007 name: SOLiD 3 Plus System def: "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." [] synonym: "Applied Biosystems SOLiD 3 Plus System" EXACT [] is_a: OBI:0000696 ! AB SOLiD System [Term] id: OBI:0002008 name: Mouse 385K Whole Genome CGH Tiling Array def: "A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 385,000 features." [] synonym: "Nimblegen Mouse 385K Whole Genome CGH Tiling Array" EXACT [] is_a: OBI:0001307 ! tiling microarray [Term] id: OBI:0002009 name: Mouse 3x720K Whole Genome CGH Tiling Array def: "A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for mouse DNA against 3x720,000 features." [] synonym: "Nimblegen Mouse 3x720K Whole Genome CGH Tiling Array" EXACT [] is_a: OBI:0001307 ! tiling microarray [Term] id: OBI:0002010 name: Human 3x720K Whole Genome CGH Tiling Array def: "A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 3x720,000 features." [] synonym: "Nimblegen Human 3x720K Whole Genome CGH Tiling Array" EXACT [] is_a: OBI:0001307 ! tiling microarray [Term] id: OBI:0002011 name: Human 2.1M Whole-Genome CGH Tiling Array v2.0 def: "A tiling array which is manufactured by the Nimblegen corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 2.1 million features." [] synonym: "Nimblegen Human 2.1M Whole-Genome CGH Tiling Array v2.0" EXACT [] is_a: OBI:0001307 ! tiling microarray [Term] id: OBI:0002012 name: PacBio RS II def: "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." [] synonym: "Pacific Biosciences RS II" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002013 name: nCounter Human miRNA Expression array def: "A human array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays." [] is_a: OBI:0001865 ! assay array [Term] id: OBI:0002014 name: DNA methylation profiling by ChIP-chip assay def: "An epigenetic modification assay that identifies sites of DNA methylation using ChIP-chip technologies." [] synonym: "DNA methylation ChIP-chip" EXACT [] is_a: OBI:0001248 ! ChIP-chip assay is_a: OBI:0002020 ! epigenetic modification assay [Term] id: OBI:0002015 name: transcription profiling by MPSS assay def: "A transcription profiling assay that uses Massive Parallel Signature Sequencing (MPSS)." [] synonym: "expression MPSS" EXACT [] is_a: OBI:0000424 ! transcription profiling assay [Term] id: OBI:0002016 name: histone modification identification by ChIP-chip assay def: "An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-chip techniques." [] synonym: "histone modification ChIP-chip" EXACT [] is_a: OBI:0001248 ! ChIP-chip assay is_a: OBI:0002020 ! epigenetic modification assay [Term] id: OBI:0002017 name: histone modification identification by ChIP-Seq assay def: "An epigenetic modification assay that identifies regions containing specific histones and their modifications using ChIP-Seq techniques." [] synonym: "histone modification ChIP-Seq" EXACT [] is_a: OBI:0000716 ! ChIP-seq assay is_a: OBI:0002020 ! epigenetic modification assay [Term] id: OBI:0002018 name: transcription factor binding site identification by ChIP-chip assay def: "A transcription factor binding site assay that utilizes ChIP-chip technology." [] synonym: "TF Binding ChIP-chip" EXACT [] is_a: OBI:0000291 ! transcription factor binding site assay is_a: OBI:0001248 ! ChIP-chip assay [Term] id: OBI:0002019 name: transcription factor binding site identification by ChIP-Seq assay def: "A transcription factor binding site assay that utilizes ChIP-seq technology." [] synonym: "TF Binding ChIP-Seq" EXACT [] is_a: OBI:0000291 ! transcription factor binding site assay is_a: OBI:0000716 ! ChIP-seq assay [Term] id: OBI:0002020 name: epigenetic modification assay def: "An assay that identifies epigenetic modifications including histone modifications, open chromatin, and DNA methylation." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002021 name: NextSeq 500 def: "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." [] synonym: "Illumina NextSeq 500" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002022 name: Illumina HiSeq 1000 def: "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." [] synonym: "HiSeq 1000" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002023 name: Human Genome U133 Plus 2.0 tiling array def: "A tiling array which is a comprehensive whole human genome expression array manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 47,000 transcripts and variants." [] synonym: "Affymetrix HT Human Genome U133 Plus 2 Array Plate Set" EXACT [] synonym: "HG-U133 Plus 2" EXACT [] synonym: "HG-U133 Plus 2 array" EXACT [] is_a: OBI:0001307 ! tiling microarray [Term] id: OBI:0002024 name: SOLiD 4 System def: "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." [] synonym: "Applied Biosystems SOLiD 4 System" EXACT [] synonym: "SOLiD 4" EXACT [] is_a: OBI:0000696 ! AB SOLiD System [Term] id: OBI:0002025 name: Human Exon 1.0 ST tilling array def: "A tiling microarray which is manufactured by the Affymetrix corporation. Built to analyze 3' DNA sequence copy number by comparative genomic hybridization for human DNA against 28,000 genes. It can be used for gene expression and alternative splicing assay" [] synonym: "Affymetrix Human Exon 1.0 St Array" EXACT [] synonym: "Human Exon 1.0" EXACT [] synonym: "Human Exon 1.0 ST Array" EXACT [] is_a: OBI:0001307 ! tiling microarray [Term] id: OBI:0002026 name: Human Genome U133 tiling array def: "A tiling array which is manufactured by the Affymetrix corporation. Built to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 39,000 transcripts and variants." [] synonym: "Affymetrix HT Human Genome U133 Array Plate Set" EXACT [] synonym: "HG-U133" EXACT [] synonym: "HG-U133 array" EXACT [] is_a: OBI:0001307 ! tiling microarray [Term] id: OBI:0002027 name: Genome Analyzer IIe def: "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." [] synonym: "Illumina GA IIe" EXACT [] synonym: "Illumina Genome Analyzer IIe" EXACT [] is_a: OBI:0000703 ! Illumina Genome Analyzer II [Term] id: OBI:0002028 name: SAGE ditag library preparation def: "A library preparation in which tags identifiying transcripts are created, ligated to form ditags, amplified, concatemerized and ligated into a vector to create a library." [] is_a: OBI:0000711 ! library preparation [Term] id: OBI:0002029 name: serial analysis of gene expression assay def: "A transcription profiling assay that quantifies RNA through creating short signature tags of the messages and ligating them into a larger molecule than was sequenced." [] synonym: "SAGE" EXACT [] is_a: OBI:0000424 ! transcription profiling assay [Term] id: OBI:0002030 name: genotyping by tiling array assay def: "A genotyping by array assay that uses tiling array technology." [] synonym: "DNA sequence variation detection by tiling array" EXACT [] is_a: OBI:0001274 ! genotyping by array assay [Term] id: OBI:0002031 name: genotyping by SNP array assay def: "A genotyping by array assay that uses SNP array technology." [] synonym: "DNA sequence variation detection by snp array" EXACT [] is_a: OBI:0001274 ! genotyping by array assay [Term] id: OBI:0002032 name: parallel analysis of RNA structure assay def: "A single-nucleotide-resolution nucleic acid structure mapping assay that performs simultaneous in vitro profiling of the secondary structure of thousands of RNA species at single nucleotide resolution using enzymatic probing based on deep sequencing fragments of RNAs that were treated with structure-specific enzymes" [] synonym: "PARS" EXACT [] is_a: OBI:0001014 ! single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing [Term] id: OBI:0002033 name: translation-associated transcript leader sequencing assay def: "An RNA-seq assay that combines TL-seq with polysome fractionation" [] synonym: "TATL-seq" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002034 name: transcript leader sequencing assay def: "An RNA-seq assay that combines enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing." [] synonym: "TL-seq" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002035 name: peptide mass fingerprinting assay def: "A mass spectrometry assay that measures the absolute mass of the cleaved peptides derived from an unknown protein of interest. These masses are then compared to values for known protein sequences to identify the unknown protein." [] synonym: "PMF" EXACT [] synonym: "protein fingerprinting" EXACT [] is_a: OBI:0000470 ! mass spectrometry assay [Term] id: OBI:0002036 name: array based nucleic acid structure mapping assay def: "An assay which aims to provide information about the in vivo organization/structure of nucleic acids using chemical or enzymatic probes using a microarray." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002037 name: micrococcal nuclease digestion followed by tiling array assay def: "An array based nucleic acid structure mapping assay that identifies nucleosome positions genome wide, by detection of regions protected by nucleosomes from digestion by micrococal nuclease using tiling array assays" [] is_a: OBI:0002036 ! array based nucleic acid structure mapping assay [Term] id: OBI:0002038 name: ribosomal profiling by sequencing assay def: "A RNA-seq assay that sequences only mRNA protected by the ribosome during translation." [] synonym: "Ribo-seq" EXACT [] synonym: "Ribo-seq assay" EXACT [] synonym: "ribosomal profiling" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002039 name: assay for transposase-accessible chromatin using sequencing def: "An assay to capture the location of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution by Tn5 transposase insertion." [] synonym: "ATAC-seq" EXACT [] synonym: "ATAC-seq assay" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002040 name: chromatin isolation by RNA purification sequencing assay def: "A detection of specific nucleic acids with complementary probes assay that measures regions of the genome which are bound by a specific RNA (or a by a ribonucleoprotein containing the RNA of interest) using high-throughput sequencing." [] synonym: "ChIRP-seq" EXACT [] synonym: "ChIRP-seq assay" EXACT [] synonym: "Chromatin Isolation by RNA purification" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes [Term] id: OBI:0002041 name: self-transcribing active regulatory region sequencing assay def: "An RNA-seq assay that identifies the sequences that act as transcriptional enhancers in a direct, quantitative, and genome-wide manner from sheared genomic DNA." [] synonym: "self-transcribing active regulatory region sequencing" EXACT [] synonym: "STARR-seq" EXACT [] synonym: "STARR-seq assay" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002042 name: carbon-copy chromosome conformation capture assay followed by sequencing assay def: "A carbon-copy chromosome conformation capture assay to analyze the organization of chromosomes in an unbiased, genome-wide manner using high throughput sequening following carbon-copy chromosome conformation capture." [] synonym: "Carbon-copy chromosome conformation capture assay followed by sequencing" EXACT [] synonym: "HiC" EXACT [] synonym: "HiC assay" EXACT [] is_a: OBI:0001919 ! Carbon-copy chromosome conformation capture assay [Term] id: OBI:0002043 name: individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay def: "A cross-linking immunoprecipitation high-throughput sequencing assay that identifies protein-RNA interactions using UV light to covalently bind proteins and RNA molecules, allowing for a very stringent purification of the linked protein-RNA complexes." [] synonym: "iCLIP" EXACT [] synonym: "iCLIP assay" EXACT [] synonym: "individual-nucleotide resolution cross-linking and immunoprecipitation" EXACT [] is_a: OBI:0001858 ! cross-linking immunoprecipitation high-throughput sequencing assay [Term] id: OBI:0002044 name: RNA Bind-n-Seq assay def: "An RNA-seq assay that comprehensively characterizes sequence and structural specificity of RNA binding proteins (RBPs)." [] synonym: "RBNS" EXACT [] synonym: "RNA Bind-n-Seq" EXACT [] synonym: "RNBS assay" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002045 name: polyA-site sequencing assay def: "A RNA-seq assay that quantitatively profiles RNA polyadenylation at the transcriptome level." [] synonym: "PAS-seq" EXACT [] synonym: "PAS-seq assay" EXACT [] synonym: "Poly(A)-site sequencing" EXACT [] synonym: "poly(A)-site sequencing assay" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002046 name: surface plasmon resonance sensor chip def: "A device that is used as a binding surface for ligand during a surface plasmon resonance assay, consisting of a glass plate to which a metal film is attached" [] synonym: "biosensor chip" EXACT [] synonym: "sensor chip" EXACT [] synonym: "SPR sensor chip" EXACT [] is_a: OBI:0000968 ! device [Term] id: OBI:0002047 name: enzyme-linked antibody def: "A processed material that is comprised of an antibody that is covalently linked to an enzyme through bioconjugation. The enzyme can be used as a detection method when the enzyme's reaction produces a detectable signal, for example a color change when the substrate is added." [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0002048 name: Illumina HiSeq 3000 def: "A DNA sequencer manufactured by Illumina corporation, with a single flow cell and a throughput of more than 200 Gb per day." [] synonym: "HiSeq 3000" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002049 name: Illumina HiSeq 4000 def: "A DNA sequencer manufactured by Illumina corporation, with two flow cell and a throughput of more than 400 Gb per day." [] synonym: "HiSeq 4000" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002050 name: 3D molecular structure determination assay of a MHC:ligand complex def: "A 3D structure determination of bound molecular complex assay that characterizes the 3-dimensional structure of a MHC:ligand complex." [] synonym: "3D structure|any method" EXACT [] is_a: OBI:0001145 ! 3D structure determination of bound molecular complex assay is_a: OBI:0002075 ! MHC ligand assay [Term] id: OBI:0002051 name: in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden def: "An in vivo assay measuring B cell epitope specific protection from pathogen challenge using pathogen burden." [] synonym: "pathogen burden after challenge|in vivo assay" EXACT [] is_a: OBI:0001186 ! epitope protection from infectious challenge experiment based on pathogen burden is_a: OBI:0003465 ! in vivo assay measuring B cell epitope specific protection from pathogen challenge [Term] id: OBI:0002052 name: in vivo assay measuring B cell epitope specific protection after tumor burden challenge def: "An in vivo assay measuring B cell epitope specific protection from tumor challenge using tumor burden." [] synonym: "tumor burden after challenge|in vivo assay" EXACT [] is_a: OBI:0003458 ! epitope protection from tumor challenge experiment based on burden is_a: OBI:0003466 ! in vivo assay measuring B cell epitope specific protection from tumor challenge [Term] id: OBI:0002053 name: microarray assay measuring binding of a B cell epitope:antibody complex def: "A microarray assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|microarray" EXACT [] is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex is_a: OBI:0001985 ! microarray assay [Term] id: OBI:0002054 name: NMR assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex def: "A B cell epitope equilibrium dissociation constant (KD) determination assay that uses a nuclear magnetic resonance assay." [] synonym: "dissociation constant KD|nuclear magnetic resonance (NMR)|nM" EXACT [] is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex [Term] id: OBI:0002055 name: assay measuring biological activity resulting from T cell epitope:MHC:TCR binding def: "A T cell epitope recognition assay that measures the immune response process resulting from the binding of a T cell receptor to epitope or the recongition of the epitope." [] synonym: "biological activity|any method" EXACT [] is_a: OBI:0003128 ! T cell epitope assay [Term] id: OBI:0002056 name: assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells def: "A T cell epitope specific cytokine production assay that detects production of chemokine (C-C motif) ligand 17 production by T cells." [] synonym: "CCL17/TARC release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0002057 name: assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells def: "A T cell epitope specific cytokine production assay that detects macrophage migration inhibitory factor (MIF) production by T cells." [] synonym: "MIF release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0002058 name: assay measuring epitope specific oncostatin M production by T cells def: "A T cell epitope specific cytokine production assay that detects oncostatin M production by T cells." [] synonym: "oncostatin M release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0002059 name: assay measuring a binding constant of a T cell epitope:MHC:TCR complex def: "A T cell epitope recognition assay that quantitavely characterizes the binding of a TCR with a ligand by determining a binding constant." [] synonym: "binding constant|binding assay" EXACT [] is_a: OBI:0003147 ! assay measuring quantitative binding of an epitope:MHC:TCR complex [Term] id: OBI:0002060 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects chemokine (C-C motif) ligand 17 production by T cells." [] synonym: "CCL17/TARC release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0002056 ! assay measuring epitope specific chemokine (C-C motif) ligand 17 production by T cells [Term] id: OBI:0002061 name: cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells def: "A cytometric bead array assay that detects chemokine (C-C motif) ligand 22 production by T cells." [] synonym: "CCL22/MDC release|cytometric bead array" EXACT [] is_a: OBI:0001777 ! assay measuring epitope specific chemokine (C-C motif) ligand 22 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002062 name: in vitro assay measuring epitope specific T cell killing def: "An in vitro cell killing assay that measures the killing of antigen presenting cells (APC) by T cells whose TCR recognizes an epitope presented by the APC." [] synonym: "cytotoxicity|in vitro assay" EXACT [] is_a: OBI:0000903 ! in vitro cell killing assay is_a: OBI:1110130 ! assay measuring epitope specific T cell killing [Term] id: OBI:0002063 name: cytometric bead array assay measuring epitope specific granzyme A release by T cells def: "A cytometric bead array assay that detects epitope specific granzyme A release by T cells." [] synonym: "granzyme A release|cytometric bead array" EXACT [] is_a: OBI:0001809 ! assay measuring epitope specific granzyme A release by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002064 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme A release by T cells def: "A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme A release by T cells." [] synonym: "granzyme A release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001809 ! assay measuring epitope specific granzyme A release by T cells [Term] id: OBI:0002065 name: cytometric bead array assay measuring epitope specific granzyme B release by T cells def: "A cytometric bead array assay that detects epitope specific granzyme B release by T cells." [] synonym: "granzyme B release|cytometric bead array" EXACT [] is_a: OBI:0001436 ! assay measuring epitope specific granzyme B release by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002066 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific granzyme B release by T cells def: "A detection of specific nucleic acids with complementary probes assay that detects epitope specific granzyme B release by T cells" [] synonym: "granzyme B release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0001436 ! assay measuring epitope specific granzyme B release by T cells [Term] id: OBI:0002067 name: cytometric bead array assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells def: "A cytometric bead array assay that detects macrophage migration inhibitory factor (MIF) production by T cells." [] synonym: "MIF release|cytometric bead array" EXACT [] is_a: OBI:0002057 ! assay measuring epitope specific macrophage migration inhibitory factor (MIF) production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002068 name: cytometric bead array assay measuring epitope specific oncostatin M production by T cells def: "A cytometric bead array assay that detects oncostatin M production by T cells." [] synonym: "oncostatin M release|cytometric bead array" EXACT [] is_a: OBI:0002058 ! assay measuring epitope specific oncostatin M production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002069 name: ELISPOT assay measuring epitope specific perforin release by T cells def: "An enzyme-linked immunospot assay that detects epitope specific perforin release by T cells." [] synonym: "perforin release|ELISPOT" EXACT [] is_a: OBI:0001497 ! assay measuring epitope specific perforin release by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:0002070 name: in vivo assay measuring epitope specific proliferation of T cells def: "A T cell epitope specific proliferation assay that is performed in vivo." [] synonym: "proliferation|in vivo assay" EXACT [] is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity is_a: OBI:1110131 ! assay measuring epitope specific proliferation of T cells [Term] id: OBI:0002071 name: in vitro assay measuring epitope specific proliferation of T cells def: "A T cell epitope specific proliferation assay that is performed on cells in vitro." [] synonym: "proliferation|in vitro assay" EXACT [] is_a: OBI:1110131 ! assay measuring epitope specific proliferation of T cells [Term] id: OBI:0002072 name: assay measuring qualitative binding of a MHC:ligand complex def: "An assay that detects the binding of a MHC molecule with a ligand, and produces a qualitative measurement of the binding as an output." [] synonym: "qualitative binding|binding assay" EXACT [] is_a: OBI:1110126 ! assay measuring binding of a MHC:ligand complex [Term] id: OBI:0002073 name: in vivo assay measuring T cell epitope specific protection from challenge def: "An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment." [] synonym: "protection from challenge|in vivo assay" EXACT [] is_a: OBI:0001184 ! epitope protection experiment is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity [Term] id: OBI:0002074 name: assay measuring T cell epitope specific suppression in vitro def: "T cell epitope dependent biological activity assay that detects suppression of an in vitro response." [] synonym: "suppression|in vitro assay" EXACT [] is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:0002075 name: MHC ligand assay def: "An immune epitope assay that characterizes the structrue of a MHC-ligand complex, or detects the processing and presentation of a ligand by an antigen presenting cell, or the binding of a ligand to an MHC molecule." [] synonym: "MHC ligand assay|any method" EXACT [] is_a: OBI:1110128 ! immune epitope assay [Term] id: OBI:0002076 name: collection of specimens def: "A material entity that has two or more specimens as its parts." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0002077 name: specimens derived from shared ancestor def: "A collection of specimens derived from one common specimen via one or more material processing process(es)." [] synonym: "specimen family" EXACT [] is_a: OBI:0002076 ! collection of specimens [Term] id: OBI:0002078 name: specimen set collection process def: "A specimen collection process that generates multiple specimens from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time." [] is_a: OBI:0000659 ! specimen collection process [Term] id: OBI:0002079 name: specimens collected in one encounter def: "A collection of specimens that is collected from one source (e.g. one organism) during a time period which for the purpose of the study can be considered to be taken at the same sampling time." [] synonym: "specimen set" EXACT [] is_a: OBI:0002076 ! collection of specimens [Term] id: OBI:0002080 name: human specimen set def: "A specimen set that is collected from one person during a time period which for the purpose of the study can be considered to be taken at the same sampling time." [] is_a: OBI:0002079 ! specimens collected in one encounter [Term] id: OBI:0002081 name: specimens collected longitudinally def: "A collection of specimens that was derived from the same source material entity at different time points in order to observe changes in that entity." [] is_a: OBI:0002076 ! collection of specimens [Term] id: OBI:0002082 name: reporter gene assay def: "An assay that detects expression of a reporter gene that was inserted under the control of a regulatory sequence of interest." [] synonym: "reporter gene detection assay" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002083 name: enhancer activity detection by reporter gene assay def: "A reporter gene assay that detects expression of a reporter gene that was inserted under the control of an enhancer of interest." [] synonym: "enhancer reporter gene assay" EXACT [] is_a: OBI:0002082 ! reporter gene assay [Term] id: OBI:0002084 name: transcription cofactor activity region identification by ChIP-Seq assay def: "A ChIP-seq assay that identifies regions of chromatin bound to a chromatin modifying protein, e.g. a histone acetyltransferase." [] synonym: "chromatin modifier binding site identification by ChIP-Seq assay" EXACT [] is_a: OBI:0000716 ! ChIP-seq assay [Term] id: OBI:0002085 name: transcript expression location detection by hybridization chain reaction assay def: "An in situ hybridization assay in which the location (e.g. anatomical/tissue) of a transcript is detected by a multiplexed fluorescent in situ hybridization, based on orthogonal amplification with hybridization chain reactions (HCR). RNA probes complementary to mRNA targets trigger chain reactions in which fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers." [] synonym: "transcript expression location detection by fluorescent HCR." EXACT [] is_a: OBI:0001686 ! in-situ hybridization assay [Term] id: OBI:0002086 name: Tet-assisted bisulfite sequencing assay def: "A bisulfite sequencing assay that identifies genomic methylation patterns by using a bisulfite based protocol with the Tet enzyme to differentiate 5-hydroxylmethylcytosine (5hmC) from 5-methylcytosine (5mC) through a step-wise oxidative demethylation of 5mC, converting it to 5-carboxylcytosine (5caC) while keeping 5hmC protected." [] synonym: "TAB-seq" EXACT [] synonym: "Tet-assisted bisulfite sequencing" EXACT [] is_a: OBI:0000748 ! bisulfite sequencing assay [Term] id: OBI:0002087 name: containing a specimen function def: "A contain function that involves physical contact with a specimen. This function is typically performed in such a way that the specimen is usable for an investigation or assay." [] is_a: OBI:0000370 ! contain function [Term] id: OBI:0002088 name: specimen container def: "A container with the function of containing a specimen." [] is_a: OBI:0000967 ! container [Term] id: OBI:0002089 name: physical store def: "A container with an environmental control function." [] is_a: OBI:0000967 ! container is_a: OBI:0001034 ! environmental control device [Term] id: OBI:0002090 name: rapid amplification of cDNA ends def: "A reverse transcribed polymerase chain reaction that is used to amplify a mRNA sequence between a defined internal site and the 5' or 3' end of the mRNA." [] synonym: "RACE" EXACT [] is_a: OBI:0000552 ! reverse transcribed polymerase chain reaction [Term] id: OBI:0002091 name: 5' rapid amplification of cDNA ends def: "A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 5' end of the mRNA." [] synonym: "5' RACE" EXACT [] is_a: OBI:0002090 ! rapid amplification of cDNA ends [Term] id: OBI:0002092 name: 3' rapid amplification of cDNA ends def: "A rapid amplication of cDNA ends to amplify a mRNA sequence between a defined internal site and the 3' end of the mRNA." [] synonym: "3' RACE" EXACT [] is_a: OBI:0002090 ! rapid amplification of cDNA ends [Term] id: OBI:0002093 name: 5' RNA ligase mediated rapid amplification of cDNA ends def: "A 5' rapid amplification pf cDNA ends that uses RNA ligase to add an RNA adapter oligonucleotide to intact 5' mRNA ends, allowing the amplification of cDNA only from full-length, capped mRNA." [] synonym: "5' RLM RACE" EXACT [] is_a: OBI:0002091 ! 5' rapid amplification of cDNA ends [Term] id: OBI:0002094 name: MethylC-Capture sequencing assay def: "A bisulfite sequencing assay in which a whole-genome sequencing library is prepared, bisulfite converted and amplified, followed by a capture enriching for targeted bisulfite-converted DNA fragments that are are subsequently identified by DNA sequencing." [] synonym: "Capture Methylome" EXACT [] synonym: "MCC-Seq" EXACT [] synonym: "MethylC-Capture Sequencing" EXACT [] is_a: OBI:0000748 ! bisulfite sequencing assay [Term] id: OBI:0002095 name: specimen family creation def: "A material processing that has as its input a specimen and as its output a collection of specimens." [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0002096 name: carboxyfluorescein succinimidyl ester staining assay measuring epitope specific proliferation of T cells def: "A CFSE assay that detects T cell epitope specific proliferation in vitro." [] synonym: "proliferation|CFSE" EXACT [] is_a: OBI:0002071 ! in vitro assay measuring epitope specific proliferation of T cells is_a: OBI:0002106 ! carboxyfluorescein succinimidyl ester staining assay [Term] id: OBI:0002097 name: assay measuring the dissociation constant [KD] of a T cell epitope:MHC:TCR complex def: "A T cell epitope binding constant determination assay that measures the dissociation constant KD." [] synonym: "dissociation constant KD|binding assay|nM" EXACT [] is_a: OBI:0002059 ! assay measuring a binding constant of a T cell epitope:MHC:TCR complex [Term] id: OBI:0002098 name: assay measuring the on rate [kon] of a T cell epitope:MHC:TCR complex def: "A T cell epitope binding constant determination assay that measures the on rate." [] synonym: "on rate|binding assay|M^-1s^-1" EXACT [] is_a: OBI:0002059 ! assay measuring a binding constant of a T cell epitope:MHC:TCR complex [Term] id: OBI:0002099 name: assay measuring the off rate [koff] of a T cell epitope:MHC:TCR complex def: "A T cell epitope binding constant determination assay that measures the off rate." [] synonym: "off rate|binding assay|1/s" EXACT [] is_a: OBI:0002059 ! assay measuring a binding constant of a T cell epitope:MHC:TCR complex [Term] id: OBI:0002100 name: assay measuring the association constant [KA] of a T cell epitope:MHC:TCR complex def: "A T cell epitope binding constant determination assay that measures the association constant KA." [] synonym: "association constant KA|binding assay|1/nM" EXACT [] is_a: OBI:0002059 ! assay measuring a binding constant of a T cell epitope:MHC:TCR complex [Term] id: OBI:0002101 name: small-angle scattering assay determining the 3D structure of a B cell epitope:antibody complex def: "A small-angle scattering 3D molecular structure determination assay that characterizes the 3-dimensional molecular structure of a B cell epitope:antibody complex" [] synonym: "3D structure|small-angle scattering assay" EXACT [] is_a: OBI:0001721 ! 3D molecular structure determination assay of an antigen:antibody complex is_a: OBI:0002108 ! small-angle scattering 3D molecular structure determination assay [Term] id: OBI:0002102 name: bio-layer interferometry assay measuring the on rate [kon] of a B cell epitope:antibody complex def: "A bio-layer interferometry assay that measures the on rate of an antigen with an antibody." [] synonym: "on rate|bio-layer interferometry assay|M^-1s^-1" EXACT [] is_a: OBI:0001718 ! assay measuring the on rate [kon] of a B cell epitope:antibody complex is_a: OBI:0002107 ! bio-layer interferometry assay [Term] id: OBI:0002103 name: bio-layer interferometry assay measuring the off rate [koff] of a B cell epitope:antibody complex def: "A bio-layer interferometry assay that measures the off rate of an antigen with an antibody." [] synonym: "off rate|bio-layer interferometry assay|1/s" EXACT [] is_a: OBI:0001723 ! assay measuring the off rate [koff] of a B cell epitope:antibody complex is_a: OBI:0002107 ! bio-layer interferometry assay [Term] id: OBI:0002104 name: bio-layer interferometry assay measuring binding of a B cell epitope:antibody complex def: "A bio-layer interferometry assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|bio-layer interferometry assay" EXACT [] is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex is_a: OBI:0002107 ! bio-layer interferometry assay [Term] id: OBI:0002105 name: bio-layer interferometry assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex def: "A bio-layer interferometry assay that measures the dissociation constant [KD] of an antigen with an antibody." [] synonym: "dissociation constant KD|bio-layer interferometry assay|nM" EXACT [] is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex is_a: OBI:0002107 ! bio-layer interferometry assay [Term] id: OBI:0002106 name: carboxyfluorescein succinimidyl ester staining assay def: "An assay using carboxyfluorescein succinimidyl ester staining." [] synonym: "CFSE assay" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002107 name: bio-layer interferometry assay def: "A binding assay that detects a shift in the interference pattern reflected from a layer of immobilized material on the biosensor tip to measure binding to- or dissociating from the material on the biosensor." [] synonym: "biolayer interferometry, BLI" EXACT [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0002108 name: small-angle scattering 3D molecular structure determination assay def: "A 3D molecular structure determination assay in which the scattering pattern of a neutron or x-ray beam targeted at a material entity is recorded at small angles relative to the incident beam to determine the size, shape and structure of the material entity examined." [] synonym: "SAXS" EXACT [] is_a: OBI:0003117 ! 3D molecular structure determination assay [Term] id: OBI:0002109 name: Human 6x630K CGH Whole Genome Tiling Array def: "A tiling array which is manufactured by the Nimblegen corporation to analyze DNA sequence copy number by comparative genomic hybridization for human DNA against 6x630,000 features." [] synonym: "NimbleGen Human 6x630K CGH Whole Genome Tiling Array" EXACT [] is_a: OBI:0001307 ! tiling microarray [Term] id: OBI:0002110 name: digital object identifier def: "A centrally registered identifier symbol used to uniquely identify objects given by International DOI Foundation. The DOI system is particularly used for electronic documents such as journal articles." [] synonym: "DOI" EXACT [] is_a: IAO:0000577 ! centrally registered identifier symbol [Term] id: OBI:0002111 name: enhanced cross-linking immunoprecipitation high-throughput sequencing assay def: "An iCLIP assay that is enhanced to robustly identify protein-RNA interactions with high efficiency through improvements in library preparation of RNA fragments." [] synonym: "eCLIP" EXACT [] is_a: OBI:0002043 ! individual-nucleotide resolution cross-linking and immunoprecipitation sequencing assay [Term] id: OBI:0002112 name: small RNA sequencing assay def: "An RNA-seq assay which is targeting small RNA (< 200 bp) sequences such as, but not exclusive to, miRNAs using, for example, small RNA library preparation kits." [] synonym: "short RNA-seq" EXACT [] synonym: "small RNA-seq" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002113 name: bromouridine labeling and sequencing assay def: "An RNA-seq assay to identify spans of nascent transcription in the genome through isolation of recent bromouridine (Bru) labelled RNAs." [] synonym: "Bru-seq" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002114 name: bromouridine pulse-chase and sequencing assay def: "An RNA-seq assay to identify RNA populations of specific ages through isolation of RNAs first labelled with bromouridine (Bru) followed by chasing in uridine for different periods of time." [] synonym: "BruChase-seq" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002115 name: cytometry time of flight assay def: "A cytometry assay in which the presence of molecules of interest on or in cells is indicated by binding of antibodies labeled with rare earth element tags which are detected by time-of-flight mass spectrometry." [] synonym: "CyTOF" EXACT [] synonym: "mass cytometry assay" EXACT [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0002116 name: high performance liquid chromotography assay def: "An analytical chromatography assay that utilizes a high performance liquid chromatography instrument for separation of compounts in a solution." [] synonym: "HPLC" EXACT [] is_a: OBI:0001630 ! analytical chromatography [Term] id: OBI:0002117 name: whole genome sequencing assay def: "A DNA sequencing assay that intends to provide information about the sequence of an entire genome of an organism." [] synonym: "WGS" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0002118 name: exome sequencing assay def: "A DNA sequencing assay that intends to provide information about the sequence of the protein coding components of a genome (exons)." [] synonym: "WES" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0002119 name: microscopy assay def: "An imaging assay that utilizes a microscope to magnify features of the visualized material of interest that are not visible to naked eye." [] is_a: OBI:0000185 ! imaging assay [Term] id: OBI:0002120 name: mixed lymphocyte reaction assay def: "A cytometry assay where lymphocytes from two individuals are co-cultured with the lymphocytes from one of the allogeneic individuals (Responders) being labeled (with 3H Thymidine or BrdU) and the proliferation of the labeled cells is measured, which is thought to reflect recognition of histocompatibility antigens on the unlabeled cells (stimulators)." [] synonym: "MLR" EXACT [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0002121 name: killer cell immunoglobulin-like receptor typing assay def: "A genotyping assay in which the alleles of genes encoding for killer cell immunoglobulin-like receptors are determined." [] synonym: "KIR typing" EXACT [] is_a: OBI:0000435 ! genotyping assay [Term] id: OBI:0002122 name: major histocompatibility typing assay def: "A genotyping assay in which the alleles of genes encoding for major histocompatibility complex molecules are determined." [] synonym: "MHC typing, HLA typing" EXACT [] is_a: OBI:0000435 ! genotyping assay [Term] id: OBI:0002123 name: IHC slide staining def: "A staining using labeled antibodies, i.e. the analytical part of immunohistochemistry. The staining is applied to fixed specimens on slides to identify biomarkers in tissues." [] is_a: OBI:0302887 ! staining [Term] id: OBI:0002124 name: H&E slide staining def: "A staining using hematoxylin and eosin. The staining is applied to fixed specimens on slides to observe the whole structure and morphology of cells in a tissue; nuclei are stained dark blue/purple while cytoplasm is stained pink." [] is_a: OBI:0302887 ! staining [Term] id: OBI:0002125 name: H&E-stained fixed tissue slide specimen def: "A fixed tissue slide specimen that is the output of H&E slide staining." [] is_a: OMIABIS:0000052 ! fixed tissue slide specimen [Term] id: OBI:0002126 name: IHC-stained fixed tissue slide specimen def: "A fixed tissue slide specimen that is the output of immunohistochemistry slide staining." [] synonym: "immunohistochemistry slide specimen" EXACT [] is_a: OMIABIS:0000052 ! fixed tissue slide specimen [Term] id: OBI:0002127 name: single cell specimen def: "A cell specimen that contains only one cell." [] is_a: OBI:0001468 ! cell specimen [Term] id: OBI:0002128 name: Illumina Genome Analyzer def: "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." [] synonym: "Illumina Genome Analyzer I" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002129 name: Illumina HiSeq X Ten def: "A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems." [] synonym: "HiSeq X Ten" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002130 name: Illumina Infinium Omni5Exome-4 Kit def: "An Illumina BeadChip which is an array that interrogates over 4.3 million whole-genome variants for genotyping and copy number variation." [] is_a: OBI:0001869 ! Illumina BeadChip [Term] id: OBI:0002131 name: Illumina Infinium MethylationEPIC v1.0 BeadChip def: "An Illumina methylation BeadChip which is an array that interrogates ~ 850,000 methylation sites per sample at single-nucleotide resolution." [] is_a: OBI:0001870 ! Illumina methylation BeadChip [Term] id: OBI:0002132 name: pulse stable isotope labeling by amino acids in cell culture def: "An assay that detects differences in protein abundance using samples that have been metabolically labeled in vivo with a stable non-radioactive heavy isotope containing amino acid for a short period of time. After diluting the pulsed cells into growth media without label, high resolution mass spectrometry-based proteomics is used to analyze the time-dependent decay and determine protein stability." [] synonym: "dynamic SILAC" EXACT [] synonym: "pulse SILAC" EXACT [] synonym: "pulsed SILAC" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002133 name: cytometric bead array assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells def: "A cytometric bead array assay that detects chemokine (C-C motif) ligand 20 production by T cells." [] synonym: "CCL20/MIP-3a release|cytometric bead array" EXACT [] is_a: OBI:0002134 ! assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002134 name: assay measuring epitope specific chemokine (C-C motif) ligand 20 production by T cells def: "A T cell epitope specific cytokine production assay that detects chemokine (C-C motif) ligand 20 production by T cells." [] synonym: "CCL20/MIP-3a release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0002136 name: RNA Integrity Number calculation def: "A data transformation using the RIN algorithm to generate a quality measure of RNA based on features from an electrophoretic trace." [] synonym: "RIN calculation" EXACT [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0002137 name: RNA Integrity Number value specification def: "A value specification that specifies the value of the RNA Integrity Number as a real value between 1 (most degraded) and 10 (most intact)." [] synonym: "RIN value specification" EXACT [] is_a: OBI:0001933 ! value specification [Term] id: OBI:0002138 name: temperature value specification def: "A value specification that specifies the temperature of some thing." [] is_a: OBI:0001933 ! value specification [Term] id: OBI:0002139 name: volume value specification def: "A value specification that specifies the volume of some thing." [] is_a: OBI:0001933 ! value specification [Term] id: OBI:0002140 name: temperature measurement assay def: "An assay to determine the temperature of an evaluant." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002141 name: volume measurement assay def: "An assay to determine the volume of an evaluant." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002142 name: Nanostring nCounter miRNA expression assay def: "A microRNA profiling assay using digital molecular barcoding technology to quantify target microRNA molecules without the need for amplification." [] synonym: "microRNA counts" EXACT [] is_a: OBI:0001926 ! microRNA profiling assay [Term] id: OBI:0002143 name: bromouride labeling and sequencing after UV exposure def: "An RNA-seq assay to identify transcription start sites and active enhancer elements through isolation of bromouridine (Bru) labelled RNAs after UV light exposure introduces transcription-blocking lesions." [] synonym: "BruUV-seq" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002144 name: extrachromosomal circular DNA sequencing assay def: "An assay which aims at identifying the endogenous population of extrachromosomal circular DNA originating from a subset of genomic loci and potentially having profound consequences on the regulatory and coding capabilities of these regions. The assay includes creation of a library out of the circular DNA molecules and subsequent sequencing using parallelized sequencing methods." [] synonym: "circulome-seq" EXACT [] synonym: "eccDNA-seq" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0002145 name: antigen specific antibodies assay def: "An analyte assay that measures the presence or amount of antibodies to a specified antigen." [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0002146 name: HIV antibody assay def: "An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) antigens." [] synonym: "HIV I/II Ab assay" EXACT [] is_a: OBI:0002145 ! antigen specific antibodies assay [Term] id: OBI:0002147 name: HIV group O antibody assay def: "An antigen specific antibodies assay that is meant to detect antibodies that bind to human immunodeficiency virus (HIV) group O antigens." [] synonym: "HIV I/II Plus O assay" EXACT [] is_a: OBI:0002145 ! antigen specific antibodies assay [Term] id: OBI:0002148 name: surface HBV antibody assay def: "An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) surface antigens." [] synonym: "HBsAb assay" EXACT [] is_a: OBI:0002145 ! antigen specific antibodies assay [Term] id: OBI:0002149 name: core HBV antibody assay def: "An antigen specific antibodies assay that is meant to detect antibodies that bind to hepatitis B virus (HBV) core antigens." [] synonym: "HBcAb assay" EXACT [] is_a: OBI:0002145 ! antigen specific antibodies assay [Term] id: OBI:0002150 name: core HBV IgM antibody assay def: "An antigen specific antibodies assay that is meant to detectimmunoglobulin M (IgM) antibodies that bind to hepatitis B virus (HBV) core antigens." [] synonym: "HBcAb-IgM assay" EXACT [] is_a: OBI:0002145 ! antigen specific antibodies assay [Term] id: OBI:0002151 name: HCV antibody assay def: "An antigen specific antibodies assay that is meant to detect antibodies that bind to Hepacivirus C (HCV) antigens." [] synonym: "HCV Ab assay" EXACT [] is_a: OBI:0002145 ! antigen specific antibodies assay [Term] id: OBI:0002152 name: EBV IgG antibody assay def: "An antigen specific antibodies assay that is meant to detect immunoglobulin G (IgG) antibodies that bind to Epstein-Barr virus (EBV) antigens." [] synonym: "EBV IgG Ab assay" EXACT [] is_a: OBI:0002145 ! antigen specific antibodies assay [Term] id: OBI:0002153 name: EBV IgM antibody assay def: "An antigen specific antibodies assay that is meant to detect immunoglobulin M (IgM) antibodies that bind to Epstein-Barr virus (EBV) antigens." [] synonym: "EBV IgM Ab assay" EXACT [] is_a: OBI:0002145 ! antigen specific antibodies assay [Term] id: OBI:0002154 name: CMV antibody assay def: "An antigen specific antibodies assay that is meant to detect antibodies that bind to cytomegalovirus (CMV) antigens." [] synonym: "CMV Ab assay" EXACT [] is_a: OBI:0002145 ! antigen specific antibodies assay [Term] id: OBI:0002155 name: venereal disease research laboratory test def: "An analyte assay that is meant to detect general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. VDRL tests require a microscope and can be done on cerebrospinal fluid as well as blood." [] synonym: "VDRL test" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0002156 name: rapid plasma reagin test def: "An analyte assay that is meant to detect with the aid of carbon or charcoal particles general antibodies that react with substances that are produced by cellular damage caused by Treponema pallidum indicating a syphilis infection. RPR tests can be done without a microscope." [] synonym: "RPR assay" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0002157 name: HBV surface antigen assay def: "An analyte assay that is meant to detect hepatitis B virus (HBV) surface antigens." [] synonym: "HBsAg assay" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0002158 name: HIV-1 nucleic acid testing def: "An analyte assay that is meant to detect human immunodeficiency virus (HIV-1) nucleic acids." [] synonym: "HIV-1 NAT" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0002159 name: HCV nucleic acid testing def: "An analyte assay that is meant to detect hepatitis C virus (HCV) nucleic acids." [] synonym: "HCV NAT" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0002160 name: multiplexed indexed T7 ChIP-seq assay def: "A ChIP-seq assay which leverages T7 promoter amplification to allow low sample input and chromatin barcoding and pool-and-split multiplexing for high-throughput, quantitative profiling of chromatin states." [] synonym: "Mint-ChIP" EXACT [] synonym: "Mint-ChIP-seq" EXACT [] is_a: OBI:0000716 ! ChIP-seq assay [Term] id: OBI:0002161 name: systematic evolution of ligands by exponential enrichment assay def: "A binding assay that identifies protein-binding sites on nucleic acids by selecting high-affinity target ligands from a randomized pool. The process is repeated in rounds, then the bound nucleic acids are separated from the unbound nucleic acids and amplified by PCR._" [] synonym: "SELEX" EXACT [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0002162 name: footprinting assay def: "An assay that measures ligand binding and conformational changes by the solvent accessibility of the backbone, bases, or side-chain structures of macromolecules through their sensitivity to chemical or enzymatic cleavage or modification reactions." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002163 name: DNAse footprinting assay def: "An enzymatic footprinting assay that determines protein-binding sites on DNA by identifying bound fragments that are protected from DNAse I-catalyzed hydrolysis" [] is_a: OBI:0002162 ! footprinting assay [Term] id: OBI:0002164 name: mammalian 2-hybrid assay def: "A binding assay that increases the expression of a reporter gene in mammalian cells by proteins of interest attached to two portions of the transcriptional activator, bringing those portions closer together." [] is_a: OBI:0001146 ! binding assay [Term] id: OBI:0002165 name: protein localization assay def: "An assay that determines the specific location of a protein. Subcellular localization is distinguished from tissue-based localization based on the type of microscopy applied." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002166 name: tissue-based protein localization assay def: "A protein localization assay that determines the specific location of a protein in a living tissue sample." [] is_a: OBI:0002165 ! protein localization assay [Term] id: OBI:0002167 name: subcellular protein localization assay def: "A protein localization assay that determines the specific subcellular location of a protein. The location is visualized through electron microscopy." [] is_a: OBI:0002165 ! protein localization assay [Term] id: OBI:0002168 name: subcellular protein immunohistochemistry assay def: "An immunohistochemistry assay that uses antibodies to display the specific subcellular location of proteins." [] is_a: OBI:0001986 ! immunohistochemistry [Term] id: OBI:0002169 name: ChIP-qPCR assay def: "A ChIP assay that uses quantitative PCR to determine levels of specific DNA in immunoprecipitated samples." [] is_a: OBI:0001954 ! ChIP assay is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0002170 name: genomic SELEX def: "A systematic evolution of ligands by exponential enrichment assay that starts with a library derived from genomic DNA instead of synthetically derived random DNA molecules." [] is_a: OBI:0002161 ! systematic evolution of ligands by exponential enrichment assay [Term] id: OBI:0002171 name: dot blot assay def: "An analyte assay that detects molecules in a mixture dotted on a membrane using DNA probes or antibodies." [] synonym: "dot blot analysis" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0002172 name: Northwestern blot assay def: "A direct binding assay that detects interactions of labeled RNA with immobilized protein on a membrane." [] synonym: "Northwestern analysis" EXACT [] synonym: "Northwestern assay" EXACT [] is_a: OBI:0001591 ! direct binding assay [Term] id: OBI:0002173 name: Southwestern blot assay def: "A direct binding assay that detects interactions of labeled DNA with immobilized protein on a membrane." [] is_a: OBI:0001591 ! direct binding assay [Term] id: OBI:0002174 name: immunocytochemistry def: "An immuno staining assay in which samples of intact cells are examined that have had most, if not all, of their surrounding extracellular matrix removed" [] is_a: OBI:0001632 ! immuno staining assay is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0002175 name: ATP bioluminescence assay def: "An analyte assay that detects ATP concentration through light intensity when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions, and molecular oxygen." [] synonym: "ATP quantitation assay" EXACT [] synonym: "cell viability ATP quantitation assay" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0002176 name: electrophysiology assay def: "An assay that measures the electrical properties of biological cells or tissues. Typically, this assay will generate measurements of voltage changes or electric current (or other associated variables such as impedence or capacitance)." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002177 name: patch clamp assay def: "An intracellular electrophysiology assay where a glass micropipette is sealed to the surface of the cell membrane as a recording electrode to study ion channel activity. The key distinction of this technique is the electrical resistance of the seal between the cell membrane and the pipette is of the order 10-100 gigaohms, permitting high-resolution current measurements over the cell membrane in several different standard configurations." [] is_a: OBI:0000447 ! intracellular electrophysiology recording assay [Term] id: OBI:0002178 name: whole-cell patch clamp assay def: "A patch-clamp assay where the electrode is left in place on the cell, as in cell-attached recordings, but the membrane patch has been perforated, providing access from the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell." [] is_a: OBI:0002177 ! patch clamp assay [Term] id: OBI:0002179 name: cell-attached patch clamp assay def: "A patch-clamp assay where the electrode is left in place on the cell, and the membrane patch has been left intact been perforated. This maintains the separation of the interior of the pipette to the intracellular space of the cell. Measurements made with this technique involve recording currents through multiple channels simultaneously, over the membrane of the entire cell." [] is_a: OBI:0002177 ! patch clamp assay [Term] id: OBI:0002180 name: inside-out patch clamp assay def: "A patch-clamp assay where a patch of the membrane is attached to the patch pipette, detached from the rest of the cell, and the cytosolic surface of the membrane is exposed to the external media, or bath. This provides the experimenter has access to the intracellular surface of the membrane via the bath and can manipulate the environment at the intracellular surface of single ion channels. For example, channels that are activated by intracellular ligands can then be studied through a range of ligand concentrations." [] is_a: OBI:0002177 ! patch clamp assay [Term] id: OBI:0002181 name: outside-out patch clamp assay def: "A patch-clamp assay where a patch of the membrane is attached to the patch pipette. In this configuration, the external surface of the cell membrane is exposed as the outside of the membrane patch relative to the patch electrode. An outside-out patch starts with a gigaohm seal in a whole-cell recording configuration. The electrode is slowly withdrawn from the cell, until a fragment of membrane bulges away from the cell, which detaches and reforms as a convex membrane on the end of the electrode, with the original external surface of the membrane facing outward from the electrode. This provides the experimenter with access to the extracellular surface of the membrane via the bath and can manipulate the environment at the extracellular surface of single ion channels." [] is_a: OBI:0002177 ! patch clamp assay [Term] id: OBI:0002182 name: voltage clamp assay def: "An cellular electrophysiology assay where the membrane potential of a cell is controlled by the experimentalist. This is accomplished through a feedback mechanism where any change in membrane potential is countered by permitting electrical current to flow into or out of the cell." [] is_a: OBI:0000447 ! intracellular electrophysiology recording assay [Term] id: OBI:0002183 name: two electrode voltage clamp assay def: "The two electrode voltage clamp (TEVC) method utilizes two low-resistance pipettes, one sensing voltage and the other injecting current. The microelectrodes are filled with conductive solution and inserted into the cell to artificially control membrane potential. The membrane acts as a dielectric as well as a resistor, while the fluids on either side of the membrane function as capacitors.[9] The microelectrodes compare the membrane potential against a command voltage, giving an accurate reproduction of the currents flowing across the membrane. Current readings can be used to analyze the electrical response of the cell to different applications. This technique is mainly used in the Oocyte preparation." [] synonym: "TEVC" EXACT [] is_a: OBI:0002182 ! voltage clamp assay [Term] id: OBI:0002184 name: cut open oocyte voltage clamp assay def: "The cut-open oocyte Vaseline gap (COVG) voltage-clamp technique is designed to solve weaknesses in the two elextrode voltage clamp by maximizing the benefits of the Xenopus oocyte expression system by improving on clamp speed, signal-to-noise ratio, and ability to effectively perfuse the oocyte. In this way, it was possible to combine the most popular transient expression system, and the associated benefits of molecular cloning and site-directed mutagenesis, with the superior voltage-clamp properties of cut-open cell techniques." [] synonym: "COVG" EXACT [] is_a: OBI:0002182 ! voltage clamp assay [Term] id: OBI:0002185 name: current clamp assay def: "The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in the voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in \"current clamp\" mode the membrane potential is free to vary, and the amplifier records whatever voltage the cell generates on its own or as a result of stimulation. This technique is used to study how a cell responds when electric current enters a cell; this is important for instance for understanding how neurons respond to neurotransmitters that act by opening membrane ion channels." [] is_a: OBI:0000447 ! intracellular electrophysiology recording assay [Term] id: OBI:0002186 name: electroencephalography def: "An extracellular electrophysiology assay where electrodes are mounted outside the brain (either on the surface of the scalp on onto the brain surface itself during surgery) to measure the electrical field over the external surface." [] synonym: "EEG" EXACT [] is_a: OBI:0000454 ! extracellular electrophysiology recording assay [Term] id: OBI:0002187 name: single-unit recording def: "An extracellular electrophysiology assay where a single microelectrode is placed in close proximity to a single neuron to measure voltage and current changes over time. This is the technicque used by Hubel and Wiesel to measure firing properties of primary visual cortex neurons in the 1950s in their original Nobel-prize winning study. A classic, old technique." [] is_a: OBI:0000454 ! extracellular electrophysiology recording assay is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0002188 name: multi-unit recording def: "An extracellular electrophysiology assay where a collection of microelectrodes (often in an 'array' configuration) is placed into neural tissue to measure the distribution of voltage and current changes for a population of cells over time." [] is_a: OBI:0000454 ! extracellular electrophysiology recording assay [Term] id: OBI:0002189 name: local field potential recording def: "An extracellular electrophysiology assay where a microelectrode is placed in the extracellular space of brain tissue to measure action potential and compared to an electrode either outside or inside that tissue." [] is_a: OBI:0000454 ! extracellular electrophysiology recording assay [Term] id: OBI:0002190 name: courier organization def: "An organization that delivers messages, packages, and mail." [] synonym: "courier" EXACT [] is_a: OBI:0000245 ! organization [Term] id: OBI:0002191 name: courier tracking number def: "A centrally registered identifier symbol assigned by a courier organization in order to track the delivery of an item." [] is_a: IAO:0000577 ! centrally registered identifier symbol [Term] id: OBI:0002192 name: Leica Peloris rapid tissue processor def: "An automatic tissue processor that is a dual retort tissue processor manufactured by the Leica company to provide fast, high quality tissue processing for histology laboratories." [] is_a: OBI:0001064 ! automatic tissue processor [Term] id: OBI:0002194 name: Microm Ergostar HM200 def: "A microtome that is manufactured by Microm and uses a vertical cutting stroke common to all rotary microtomes engaged by a horizontal sliding movement. An operating arm replaces the handwheel and is attached to both sides of the instrument for greater convenience to permit control of sectioning from the left or right." [] is_a: OBI:0400168 ! microtome [Term] id: OBI:0002195 name: microtome blade def: "A device that is the part of a microtome used to slice specimens to a desired thickness." [] is_a: OBI:0000968 ! device [Term] id: OBI:0002196 name: Sakura Low profile Accu-Edge microtome blade def: "A microtome blade that is manufactured by Feather and is disposable. The ultra-sharp blades section specimens without striations, distortion or chattering." [] is_a: OBI:0002195 ! microtome blade [Term] id: OBI:0002197 name: tissue section thickness def: "A length measurement datum that is the result of an assay measuring the thickness of a tissue section." [] is_a: IAO:0000408 ! length measurement datum [Term] id: OBI:0002198 name: molecular analysis facility organization def: "An organization that provides molecular analysis service." [] synonym: "MAF" EXACT [] is_a: OBI:0000245 ! organization [Term] id: OBI:0002199 name: reason for lack of data item def: "An information content entity that provides an explanation why a data item is not provided." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0002200 name: cannot be assessed determination def: "A reason for lack of data item that is the negative output of a determination if assay will provide reliable results." [] synonym: "cannot be assessed" EXACT [] is_a: OBI:0002199 ! reason for lack of data item [Term] id: OBI:0002201 name: determination if assay will provide reliable results def: "A planned process that is used to assess whether an assay will provide reliable results based on the conditions or qualities of the inputs, devices, and other participants of the assay." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0002202 name: GX def: "A cannot be assessed determination for histologic tumor grade." [] is_a: OBI:0002200 ! cannot be assessed determination [Term] id: OBI:0002203 name: pTX def: "A cannot be assessed determination for pathologic primary tumor staging." [] is_a: OBI:0002200 ! cannot be assessed determination [Term] id: OBI:0002204 name: pNX def: "A cannot be assessed determination of pathologic staging of lymph nodes." [] is_a: OBI:0002200 ! cannot be assessed determination [Term] id: OBI:0002205 name: histologic grade according to AJCC 7th edition def: "A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the American Joint Committee on Cancer (AJCC) 7th Edition grading system." [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002210 name: histologic grade according to the Fuhrman Nuclear Grading System def: "A categorical value specification that is a histologic grade assigned to a tumor slide specimen according to the Fuhrman Nuclear Grading System." [] synonym: "Histologic Grade (Fuhrman Nuclear Grading System)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002215 name: histologic grade for ovarian tumor def: "A categorical value specification that is a histologic grade assigned to a ovarian tumor." [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002216 name: histologic grade for ovarian tumor according to a two-tier grading system def: "A histologic grade for ovarian tumor that is from a two-tier histological classification of tumors." [] is_a: OBI:0002215 ! histologic grade for ovarian tumor [Term] id: OBI:0002219 name: histologic grade for ovarian tumor according to the World Health Organization def: "A histologic grade for ovarian tumor that is from a histological classification by the World Health Organization (WHO)." [] is_a: OBI:0002215 ! histologic grade for ovarian tumor [Term] id: OBI:0002224 name: pathologic primary tumor stage for colon and rectum according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] synonym: "pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002232 name: pathologic primary tumor stage for lung according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM American Joint Committee on Cancer (AJCC) version 7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] synonym: "pT: Pathologic spread lung primary tumor (AJCC 7th Edition)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002243 name: pathologic primary tumor stage for kidney according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] synonym: "pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002256 name: pathologic primary tumor stage for ovary according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of the primary tumor. TNM pathologic primary tumor findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] synonym: "pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002270 name: pathologic lymph node stage for colon and rectum according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of colorectal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." [] synonym: "pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002279 name: pathologic lymph node stage for lung according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." [] synonym: "pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002284 name: pathologic lymph node stage for kidney according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." [] synonym: "pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002287 name: pathologic lymph node stage for ovary according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to staging of regional lymph nodes." [] synonym: "pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002290 name: pathologic distant metastases stage for colon according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of colon cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] synonym: "M: colon distant metastases (AJCC 7th Edition)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002298 name: pathologic distant metastases stage for lung according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of lung cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] synonym: "M: lung distant metastases (AJCC 7th Edition)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002306 name: pathologic distant metastases stage for kidney according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of renal cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] synonym: "M: kidney distant Metastases (AJCC 7th Edition)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002310 name: pathologic distant metastases stage for ovary according to AJCC 7th edition def: "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the TNM AJCC v7 classification system as they pertain to distant metastases. TNM pathologic distant metastasis findings are based on clinical findings supplemented by histopathologic examination of one or more tissue specimens acquired during surgery." [] synonym: "M: ovarian distant metastases (AJCC 7th Edition)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002314 name: clinical tumor stage group according to AJCC 7th edition def: "A categorical value specification that is an assessment of the stage of a cancer according to the American Joint Committee on Cancer (AJCC) v7 staging systems." [] synonym: "Clinical tumor stage group (AJCC 7th Edition)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002326 name: International Federation of Gynecology and Obstetrics cervical cancer stage value specification def: "A categorical value specification that is an assessment of the stage of a gynecologic cancer according to the International Federation of Gynecology and Obstetrics (FIGO) staging systems." [] synonym: "Clinical FIGO stage" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002341 name: International Federation of Gynecology and Obstetrics ovarian cancer stage value specification def: "A categorical value specification that is a pathologic finding about one or more characteristics of ovarian cancer following the rules of the FIGO classification system." [] synonym: "Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002356 name: performance status value specification def: "A categorical value specification that is an assessment of a participant's performance status (general well-being and activities of daily life)." [] synonym: "Performance Status Scale" EXACT [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002357 name: Eastern Cooperative Oncology Group score value specification def: "A performance status value specification designed by the Eastern Cooperative Oncology Group to assess disease progression and its affect on the daily living abilities of the patient." [] synonym: "ECOG score" EXACT [] is_a: OBI:0002356 ! performance status value specification [Term] id: OBI:0002363 name: Karnofsky score vaue specification def: "A performance status value specification designed for classifying patients 16 years of age or older by their functional impairment." [] synonym: "Karnofsky Score" EXACT [] is_a: OBI:0002356 ! performance status value specification [Term] id: OBI:0002368 name: clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer." [] is_a: OGMS:0000015 ! clinical history [Term] id: OBI:0002369 name: clinical history devoid of cancer def: "A clinical history in which there was no diagnosis of cancer." [] synonym: "clinical history of no cancer" EXACT [] is_a: OGMS:0000015 ! clinical history [Term] id: OBI:0002370 name: unknown clinical history of cancer def: "A clinical history in which it is not known whether there was a diagnosis of cancer." [] is_a: OGMS:0000015 ! clinical history [Term] id: OBI:0002371 name: diagnosis of cancer def: "A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has cancer." [] synonym: "cancer diagnosis" EXACT [] is_a: OGMS:0000073 ! diagnosis [Term] id: OBI:0002372 name: family clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer in a blood relative." [] synonym: "family history of cancer" EXACT [] is_a: OGMS:0000015 ! clinical history [Term] id: OBI:0002373 name: aunt clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer in the female sibling of a parent." [] is_a: OBI:0002372 ! family clinical history of cancer [Term] id: OBI:0002374 name: brother clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer in a male sibling." [] is_a: OBI:0002372 ! family clinical history of cancer [Term] id: OBI:0002375 name: daughter clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer in a person's female child." [] is_a: OBI:0002372 ! family clinical history of cancer [Term] id: OBI:0002376 name: father clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer in a male parent." [] is_a: OBI:0002372 ! family clinical history of cancer [Term] id: OBI:0002377 name: mother clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer in a female parent." [] is_a: OBI:0002372 ! family clinical history of cancer [Term] id: OBI:0002378 name: sister clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer in a female sibling." [] is_a: OBI:0002372 ! family clinical history of cancer [Term] id: OBI:0002379 name: son clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer in a person's male child." [] is_a: OBI:0002372 ! family clinical history of cancer [Term] id: OBI:0002380 name: uncle clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer in a male sibling of a parent." [] is_a: OBI:0002372 ! family clinical history of cancer [Term] id: OBI:0002381 name: grandmother clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer in a female parent of a parent." [] is_a: OBI:0002372 ! family clinical history of cancer [Term] id: OBI:0002382 name: grandfather clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer in a male parent of a parent." [] is_a: OBI:0002372 ! family clinical history of cancer [Term] id: OBI:0002383 name: nephew clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer in a male child of a sibling." [] is_a: OBI:0002372 ! family clinical history of cancer [Term] id: OBI:0002384 name: niece clinical history of cancer def: "A clinical history in which there is a diagnosis of cancer in a female child of a sibling." [] is_a: OBI:0002372 ! family clinical history of cancer [Term] id: OBI:0002385 name: diagnosis of infectious disease def: "A diagnosis that is an assertion that a patient who is the subject of a diagnostic process has an infectious disease." [] is_a: OGMS:0000073 ! diagnosis [Term] id: OBI:0002386 name: diagnosis of hepatitis B def: "A diagnosis of infectious disease caused by the hepatitis B virus." [] is_a: OBI:0002385 ! diagnosis of infectious disease [Term] id: OBI:0002387 name: diagnosis of hepatitis C def: "A diagnosis of infectious disease caused by the hepatitis C virus." [] is_a: OBI:0002385 ! diagnosis of infectious disease [Term] id: OBI:0002388 name: diagnosis of HIV def: "A diagnosis of infectious disease caused by the human immunodeficiency virus (1 or 2)." [] is_a: OBI:0002385 ! diagnosis of infectious disease [Term] id: OBI:0002389 name: clinical history of repeated HIV assays def: "A clinical history in which there is repeated reactive screening assays for human immunodeficiency virus (1 or 2) antibodies regardless of the results of supplemental assays." [] is_a: OGMS:0000015 ! clinical history [Term] id: OBI:0002390 name: exposure to second hand smoke def: "A clinical history in which there has been second hand exposure to tobacco smoking." [] is_a: OGMS:0000015 ! clinical history [Term] id: OBI:0002391 name: exposure to second hand smoke in household during childhood def: "An exposure to second hand smoke that occurred in the (patient's) household when the person was a child." [] is_a: OBI:0002390 ! exposure to second hand smoke [Term] id: OBI:0002392 name: exposure to second hand smoke in current household def: "An exposure to second hand smoke in person's current household." [] is_a: OBI:0002390 ! exposure to second hand smoke [Term] id: OBI:0002393 name: pregnancy history def: "A clinical history in which a female has had a pregnancy." [] is_a: OGMS:0000015 ! clinical history [Term] id: OBI:0002394 name: number of pregnancies def: "A measurement datum of the total number of pregnancies a woman has had." [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0002395 name: number of live births def: "A measurement datum of the total number of live births a female has had." [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0002396 name: age when gave birth to first child def: "An age measurement datum performed on a female when her first biological child was born." [] is_a: OBI:0001167 ! age measurement datum [Term] id: OBI:0002397 name: gynecologic surgery history def: "A clinical history in which a woman has had gynecologic surgery in the past." [] is_a: OGMS:0000015 ! clinical history [Term] id: OBI:0002398 name: hysterectomy history def: "A gynecologic surgery history in which a woman has had a hysterectomy." [] is_a: OBI:0002397 ! gynecologic surgery history [Term] id: OBI:0002399 name: unilateral oophorectomy history def: "A gynecologic surgery history in which a woman has had a unilateral oophorectomy." [] is_a: OBI:0002397 ! gynecologic surgery history [Term] id: OBI:0002400 name: neither hysterectomy nor oophorectomy history def: "A gynecologic surgery history in which a woman has not had either a hysterectomy or an oophorectomy." [] is_a: OBI:0002397 ! gynecologic surgery history [Term] id: OBI:0002401 name: hormonal birth control use history def: "An information content entity that indicates whether a woman has ever used oral contraceptives in order to block ovulation and prevent the occurrence of pregnancy." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0002402 name: hormonal birth control former use history def: "A hormonal birth control use history that indicates an individual has previously been a hormonal birth control user but is not a current user." [] is_a: OBI:0002401 ! hormonal birth control use history [Term] id: OBI:0002403 name: hormonal birth control current use history def: "A hormonal birth control use history that indicates an individual is currently a hormonal birth control user." [] is_a: OBI:0002401 ! hormonal birth control use history [Term] id: OBI:0002404 name: no hormonal birth control use history def: "A hormonal birth control use history that indicates an individual has not ever been a hormonal birth control user." [] is_a: OBI:0002401 ! hormonal birth control use history [Term] id: OBI:0002405 name: hormonal replacement therapy history def: "A clinical history in which an individual has had hormonal replacement therapy in the past." [] is_a: OGMS:0000015 ! clinical history [Term] id: OBI:0002406 name: delivery form for hormonal replacement therapy def: "A processed material used for delivery of hormones in hormone replacement therapy." [] synonym: "form of hormone replacement therapy" EXACT [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0002407 name: pill delivery form for hormonal replacement therapy def: "A delivery form for hormonal replacement therapy that is a pill for oral administration." [] is_a: OBI:0002406 ! delivery form for hormonal replacement therapy [Term] id: OBI:0002408 name: patch delivery form for hormonal replacement therapy def: "A delivery form for hormonal replacement therapy that is a patch for transdermal administration." [] is_a: OBI:0002406 ! delivery form for hormonal replacement therapy [Term] id: OBI:0002409 name: cream delivery form for hormonal replacement therapy def: "A delivery form for hormonal replacement therapy that is a cream for transdermal administration." [] is_a: OBI:0002406 ! delivery form for hormonal replacement therapy [Term] id: OBI:0002410 name: menopausal status def: "An information content entity that indicates the state of a female's cessation of menstruation." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0002411 name: indeterminate menopausal status def: "A menopausal status that is neither pre- nor post-menopausal." [] is_a: OBI:0002410 ! menopausal status [Term] id: OBI:0002412 name: premenopausal status def: "A menopausal status indicating that less than 6 months has passed since the last menstrual period and there has not been prior bilateral oophorectomy and not on estrogen replacement." [] is_a: OBI:0002410 ! menopausal status [Term] id: OBI:0002413 name: perimenopausal status def: "A menopausal status indicating that it has been 6-12 months since last menstrual period." [] is_a: OBI:0002410 ! menopausal status [Term] id: OBI:0002414 name: postmenopausal status def: "A menopausal status indicating that it has been more than 12 months since the last menstrual period with no prior hysterectomy or that there has been a prior bilateral oophorectomy." [] is_a: OBI:0002410 ! menopausal status [Term] id: OBI:0002415 name: exposure to environmental and workplace carcinogens history def: "An information content entity that indicates the exposure of an individual to carcinogens in the workplace or environment." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0002416 name: exposure to arsenic history def: "An exposure to environmental and workplace carcinogens history where the carcinogen is arsenic." [] is_a: OBI:0002415 ! exposure to environmental and workplace carcinogens history [Term] id: OBI:0002417 name: exposure to asbestos history def: "An exposure to environmental and workplace carcinogens history where the carcinogen is asbestos." [] is_a: OBI:0002415 ! exposure to environmental and workplace carcinogens history [Term] id: OBI:0002418 name: exposure to diesel exhaust history def: "An exposure to environmental and workplace carcinogens history where the carcinogen is diesel exhaust." [] is_a: OBI:0002415 ! exposure to environmental and workplace carcinogens history [Term] id: OBI:0002419 name: exposure to chromium history def: "An exposure to environmental and workplace carcinogens history where the carcinogen is chromium." [] is_a: OBI:0002415 ! exposure to environmental and workplace carcinogens history [Term] id: OBI:0002420 name: exposure to silica history def: "An exposure to environmental and workplace carcinogens history where the carcinogen is silica." [] is_a: OBI:0002415 ! exposure to environmental and workplace carcinogens history [Term] id: OBI:0002421 name: indicator of whether an inclusion criterion was met def: "An information content entity that indicates whether or not an entity has met a specific requirement in order to take part in a given process." [] synonym: "eligibility criterion met" EXACT [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0002422 name: indicator of whether all inclusion criteria were met def: "An information content entity that indicates whether or not an entity has met all specific requirements in order to take part in a given process." [] synonym: "all eligibility criteria met" EXACT [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0002423 name: age of majority inclusion criterion def: "An inclusion criterion that uses the age of majority for a state or institution, where one is generally considered to be an adult, which if met, makes an individual suitable for a given task or participation in a given process." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002424 name: chemotherapy treatment exclusion criterion def: "An exclusion criterion that defines whether chemotherapy was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process" [] is_a: OBI:0500028 ! exclusion criterion [Term] id: OBI:0002425 name: radiation treatment exclusion criteria def: "An exclusion criterion that defines whether radiation was received or is being received for a previous or current cancer, which when met, makes an individual unsuitable for a given task or participation in a given process" [] is_a: OBI:0500028 ! exclusion criterion [Term] id: OBI:0002426 name: chemotherapy treatment within the recent past exclusion criterion def: "An exclusion criterion that defines whether chemotherapy was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process." [] is_a: OBI:0500028 ! exclusion criterion [Term] id: OBI:0002427 name: radiation treatment within the recent past exclusion criterion def: "An exclusion criterion that defines whether radiation was received within a certain timeframe, which when met, makes an individual unsuitable for a given task or participation in a given process." [] is_a: OBI:0500028 ! exclusion criterion [Term] id: OBI:0002428 name: BMI range inclusion criterion def: "An inclusion criterion that defines and states a Body Mass Index range, which if met, makes an individual suitable for a given task or participation in a given process." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002429 name: blood transfusion exclusion criterion def: "An exclusion criterion that is defined by whether the specimen donor received a whole blood transfusion within a specified time frame prior to death, which if met, makes a specimen donor unsuitable for a given task or participation in a given process." [] is_a: OBI:0500028 ! exclusion criterion [Term] id: OBI:0002430 name: history of metastatic cancer exclusion criterion def: "An exclusion criterion defined as whether an individual has ever been diagnosed with metastatic cancer (cancer that spread beyond the initial site such as to other organs like brain bone or liver), which if met, makes the individual unsuitable for a given task or participation in a given process." [] is_a: OBI:0500028 ! exclusion criterion [Term] id: OBI:0002431 name: intravenous drug use exclusion criterion def: "An exclusion criterion defined as when an individual has a history of intravenous drug abuse for a specific timeframe, which if met, makes the individual unsuitable for a given task or participation in a given process." [] is_a: OBI:0500028 ! exclusion criterion [Term] id: OBI:0002432 name: history of sex with someone with a history of blood borne infection exclusion criterion def: "An exclusion criterion defined as whether an individual has a history of sex with someone who has been diagnosed or at risk for a blood borne infections disease in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process." [] is_a: OBI:0500028 ! exclusion criterion [Term] id: OBI:0002433 name: history of sex with someone with a history of intravenous drugs exclusion criterion def: "An exclusion criterion defined as whether an individual has a history of sex with someone who has used intravenous drugs in a specified time frame, which if met, makes the individual unsuitable for a given task or participation in a given process." [] is_a: OBI:0500028 ! exclusion criterion [Term] id: OBI:0002434 name: HIV exclusion criterion def: "An exclusion criterion defined as whether an individual has a history of repeatedly reactive screening assays for HIV-1 or HIV-2 antibody regardless of the results of supplemental assays, which if met, makes the individual unsuitable for a given task or participation in a given process." [] is_a: OBI:0500028 ! exclusion criterion [Term] id: OBI:0002435 name: exposure to blood borne infectious disease exclusion criterion def: "An exclusion criterion defined as whether an individual has been exposed to a blood borne infections disease through needle sticks and/or contact with non-intact skin and/or contact with open wounds and/or contact with mucous membranes, which if met, makes the individual unsuitable for a given task or participation in a given process." [] is_a: OBI:0500028 ! exclusion criterion [Term] id: OBI:0002436 name: RNA interactome capture def: "An assay that identifies RNA binding proteins by cross-linking RNA and proteins with UV light, then purifying the bound complexes by oligo(dT) capture. Finally, the complexes are analyzed by mass spectrometry." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002437 name: widefield microscopy assay def: "A fluorescence microscopy technique where the specimen under investigation is fully bathed in light, as opposed to confocal microscopy in which only a small portion of the specimen is illuminated." [] synonym: "WFM" EXACT [] is_a: CHMO:0000087 ! fluorescence microscopy assay [Term] id: OBI:0002438 name: nuclear ligation assay def: "An assay that detects the proximity of chromosomal DNA through the use of a ligation reaction in isolated nuclei." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002439 name: chromosome conformation capture assay def: "A nuclear ligation assay that detects chromosomal interactions between any two genomic loci. Chromatin segments are cross-linked, cut by restriction enzymes, ligated, and finally analyzed by PCR." [] synonym: "3C assay" EXACT [] is_a: OBI:0002438 ! nuclear ligation assay [Term] id: OBI:0002440 name: Hi-C assay def: "A chromosome conformation capture assay that detects genome-wide chromosomal interactions. High-throughput techniques are used to sequence the ligated fragments after cross-linking and cutting with restriction enzymes." [] is_a: OBI:0002439 ! chromosome conformation capture assay [Term] id: OBI:0002441 name: physical examination of an organism def: "An assay that produces a description of the qualities of an organism that has not been transformed, through observation and physical, non-invasive techniques." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002442 name: hydroxyl-radical footprinting assay def: "A footprinting assay that uses the reaction of hydroxyl radicals with side-chain sites in molecules (proteins, DNA, etc)_ with the resultant mass shift demonstrating the site of modification, used to_ to asses the accessibility of that site." [] is_a: OBI:0002162 ! footprinting assay [Term] id: OBI:0002443 name: methidiumpropyl-EDTA-iron(II) footprinting assay def: "A footprinting assay that determines protein-binding sites on DNA by partial cleavage of ligand-protected DNA restriction fragments with methidium-propyl-EDTA (MPE). MPE-Fe(II) in the presence of oxygen efficiently catalyzes the non-specific clevage of DNA." [] synonym: "MPE-Fe(II) footprinting" EXACT [] is_a: OBI:0002162 ! footprinting assay [Term] id: OBI:0002444 name: measurand role def: "A role borne by a material entity and realized in an assay which achieves the objective to measure the magnitude/concentration/amount of the measurand in the entity bearing evaluant role." [] is_a: BFO:0000023 ! role [Term] id: OBI:0002445 name: transcription start site mapping by primer extension assay def: "A transcription profiling assay in which the transcription start site for a gene is determined by identifying the 5' end of mRNA. A radio-labeled primer is annealed to a complementary mRNA sequence near the 3' end, then cDNA is synthesized until the 5' end is reached." [] is_a: OBI:0000424 ! transcription profiling assay [Term] id: OBI:0002446 name: proteomic profiling design def: "A study design in which proteins in a sample are detected, quantified or otherwise analysed." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0002447 name: suppression subtractive hybridization def: "An artificially induced nucleic acid hybridization that is performed to compare gene expression in different cell or tissue types based on normalization and suppression, which creates a subtracted cDNA or genomic DNA library." [] synonym: "SSH" EXACT [] synonym: "subtractive hybridization" EXACT [] is_a: OBI:0000253 ! artificially induced nucleic acid hybridization [Term] id: OBI:0002448 name: differential screening hybridization def: "An artificially induced nucleic acid hybridization that is performed to identify differentially expressed genes through hybridization of cDNA probes." [] synonym: "differential screening" EXACT [] synonym: "DSH" EXACT [] is_a: OBI:0000253 ! artificially induced nucleic acid hybridization [Term] id: OBI:0002449 name: footprinting assay measuring binding of a B cell epitope:antibody complex def: "A footprinting assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|footprinting assay" EXACT [] is_a: OBI:0001703 ! assay measuring qualitative binding of a B cell epitope:antibody complex is_a: OBI:0002162 ! footprinting assay [Term] id: OBI:0002450 name: hydroxyl-radical footprinting assay measuring binding of a B cell epitope:antibody complex def: "A hydroxyl-radical footprinting assay that detects the binding of an antigen with an antibody." [] synonym: "qualitative binding|hydroxyl-radical footprinting assay" EXACT [] is_a: OBI:0002442 ! hydroxyl-radical footprinting assay is_a: OBI:0002449 ! footprinting assay measuring binding of a B cell epitope:antibody complex [Term] id: OBI:0002451 name: ELISA measuring epitope specific interferon-alpha production by T cells def: "An enzyme-linked immunosorbent assay that detects interferon-alpha production by T cells." [] synonym: "IFNa release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0002452 ! assay measuring epitope specific interferon-alpha production by T cells [Term] id: OBI:0002452 name: assay measuring epitope specific interferon-alpha production by T cells def: "A T cell epitope specific cytokine production assay that detects interferon-alpha production by T cells." [] synonym: "IFNa release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0002453 name: health status inclusion criterion def: "An inclusion criterion that defines and states one or more clinically significant bodily components, dispositions, and/or bodily processes of an entity that are inferred from relevant clinical findings or self-reported, which, if met, makes the entity suitable for a given task or participation in a given process." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002454 name: clinically relevant lifestyle inclusion criterion def: "An inclusion criterion that defines and states one or more clinically relevant planned processes that a human being actively participates in , which, if met, makes the human being suitable for a given task or participation in a given process." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002455 name: clinically relevant exposure inclusion criterion def: "An inclusion criterion that defines and states one or more clinically relevant histories of exposure of an entity, which, if met, makes the entity suitable for a given task or participation in a given process." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002456 name: gravidity inclusion criterion def: "An inclusion criterion that defines and states one or more gravidity statuses of an organism, which, if met, makes the entity suitable for a given task or participation in a given process." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002457 name: precision nuclear run-on sequencing assay def: "An RNA-seq assay that maps the genome-wide distribution of transcriptionally-engaged Pol II at base-pair resolution by using biotin-labeled ribonucleotide triphosphate analogs (biotin-NTP) for nuclear run-on reactions, allowing the efficient affinity purification of nascent RNAs for high throughput sequencing from their 3' ends." [] synonym: "precision nuclear run-on and sequencing assay" EXACT [] synonym: "PRO-Seq" EXACT [] is_a: OBI:0001271 ! RNA-seq assay is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0002458 name: chromosome conformation capture-on-chip assay def: "A nuclear ligation assay which uses cross-linking of proteins to proteins and DNA, followed by two rounds of digestion and ligation, inverse PCR, and characterization by microarray or DNA sequencing. This enables unbiased genome-wide screens for DNA contacts made by single genomic sites of interest." [] synonym: "4C assay" EXACT [] synonym: "circularized chromosome conformation capture assay" EXACT [] is_a: OBI:0002438 ! nuclear ligation assay is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0002459 name: genotype phasing by Hi-C assay def: "A genotyping assay in which carbon-copy chromosome conformation is used to detect polymorphism in DNA samples." [] synonym: "haplotype reconstruction by Hi-C assay" EXACT [] is_a: OBI:0000435 ! genotyping assay [Term] id: OBI:0002460 name: defined population inclusion criterion def: "An inclusion criterion that is based on fitting within the defined characteristics of a population based study design." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002461 name: BCL format def: "A data format specification that is a binary file containing base calling data. These files are created by sequencing machines during the act of sequencing, and contain data about each of the nucleotide clusters on a sequencing flow cell." [] is_a: IAO:0000098 ! data format specification [Term] id: OBI:0002462 name: ERCC RNA spike-in def: "A processed material developed by the External RNA Controls Consortium (ERCC) that consists of 92 transcripts, derived and traceable from NIST-certified DNA plasmids." [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0002463 name: SIRV RNA spike-in def: "A processed material that consists of transcript isoforms of 7 spike-in RNA variant (SIRV) genes and possibly the 92 External RNA Controls Consortium (ERCC) RNA spike-in genes." [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0002464 name: SRS identifier def: "An accession number that applies to a database record for an individual sample object in an NCBI Sequence Read Archive (SRA) submission. These records are imported from the NCBI BioSample database." [] synonym: "SRA sample accession number" EXACT [] is_a: IAO:0000577 ! centrally registered identifier symbol [Term] id: OBI:0002465 name: age since culture seeding measurement datum def: "An age measurement datum that is the result of the measurement of the age of a cell since cultured (the process of seeding cells onto a culture dish)." [] synonym: "age of culture" EXACT [] is_a: OBI:0001167 ! age measurement datum [Term] id: OBI:0002466 name: alignment counting algorithm def: "An algorithm used to assign aligned sequence reads, resulting from a reference genome transcriptome alignment algorithm, to sequence features (e.g. genes or transcripts)." [] is_a: IAO:0000064 ! algorithm [Term] id: OBI:0002467 name: alignment counting application def: "A software application that implements an alignment counting algorithm, used to count the overlap of aligned sequencing reads with genes." [] is_a: IAO:0000594 ! software application [Term] id: OBI:0002468 name: base calling algorithm def: "An algorithm that assigns nucleotides to temporal or spatial peaks generated by a detector, such as peaks of light intensities generated by a DNA sequencer" [] is_a: IAO:0000064 ! algorithm [Term] id: OBI:0002469 name: base calling application def: "A base-calling application that implments a base-calling algorithm to convert BCL (binary base call) files, (e.g., those generated by Illumina sequencing systems) to standard FASTQ file formats for downstream analysis." [] is_a: IAO:0000594 ! software application [Term] id: OBI:0002470 name: bcl2fastq software application def: "A base calling application that implments a base calling algorithm to convert BCL (binary base call) files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis." [] is_a: OBI:0002469 ! base calling application [Term] id: OBI:0002471 name: date process started def: "A data item that is the date when a process was initiated." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0002472 name: dbGaP study identifier def: "A central registered identifier symbol that denotes a specific study in dbGaP." [] synonym: "dbGaP accession number" EXACT [] is_a: IAO:0000577 ! centrally registered identifier symbol [Term] id: OBI:0002473 name: material amplification role def: "A worker role played by the person who runs the enzymatic amplifying process." [] is_a: OBI:0000116 ! worker role [Term] id: OBI:0002474 name: material sequencing library preparation role def: "A worker role played by the person who performs the library preparation process to generate a sequencing library for a sample to be sequenced." [] is_a: OBI:0000116 ! worker role [Term] id: OBI:0002475 name: number of PCR cycles during library construction def: "A data item that is the number of PCR cycles used during the construction of a sequencing library." [] synonym: "library construction PCR cycles" EXACT [] is_a: IAO:0000027 ! data item [Term] id: OBI:0002476 name: number of rounds of amplification def: "A data item that is the number of times an amplification reaction happened." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0002477 name: reference genome role def: "A reference substance role that is played by a reference genome when used during sequence alignment." [] is_a: OBI:0000025 ! reference substance role [Term] id: OBI:0002478 name: reference genome-transcriptome alignment algorithm def: "An algorithm that attempts to align a nucleic acid sequence to a reference genome and transcriptome." [] is_a: IAO:0000064 ! algorithm [Term] id: OBI:0002479 name: sequence read length measurement datum def: "A measurement datum that is the result of the measurement of the number of bases in a DNA or RNA sequence." [] synonym: "read length, read length measurement datum" EXACT [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0002480 name: sequencing library input quantity measurement datum def: "A scalar measurement datum that indicates the amount of sequencing library used as input for a sequencer." [] synonym: "library input amount" EXACT [] is_a: IAO:0000032 ! scalar measurement datum [Term] id: OBI:0002481 name: single-end library def: "A cDNA library that is a collection of short tags from only one end of DNA fragments." [] is_a: OBI:0002754 ! cDNA library [Term] id: OBI:0002482 name: specimen harvest quantity def: "A scalar measurement datum that indicates the amount of specimen collected." [] synonym: "harvest quantity" EXACT [] is_a: IAO:0000109 ! measurement datum [Term] id: OBI:0002483 name: spike-in dilution factor def: "A data item that indicates the dilution of spike-in added to a specimen." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0002484 name: star algorithm def: "A reference genome transcriptome alignment algorithm that is a standalone RNA-seq alignment algorithm that uses uncompressed suffix arrays and a mapping algorithm similar to those used in large-scale genome alignment tools to align RNA-seq reads to a genomic reference." [] is_a: OBI:0002478 ! reference genome-transcriptome alignment algorithm [Term] id: OBI:0002485 name: transcript analysis by single-end sequencing assay def: "A sequencing assay that incorporates single-end reads and sequencing technology to determine transcripts, gene structures, and gene expressions." [] synonym: "transcript analysis by single-end sequencing" EXACT [] is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0002486 name: verse algorithm def: "An alignment counting algorithm that assigns gene features to genomic alignments using a hierarchical assignment scheme, which allows simultaneous quantification of multiple feature types or annotation levels without repeatedly assigning reads." [] is_a: OBI:0002466 ! alignment counting algorithm [Term] id: OBI:0002487 name: microraft def: "A material separation device also commerically known as Isoraft, that is used to isolate single cells." [] is_a: OBI:0000932 ! material separation device [Term] id: OBI:0002488 name: pipette def: "A device that is a laboratory tool commonly used in chemistry, biology and medicine to transport a measured volume of liquid, often as a media dispenser." [] is_a: OBI:0000968 ! device [Term] id: OBI:0002489 name: differential medium assay def: "An organism detection assay that uses a differential medium to achieve its objective." [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0002490 name: medication time value specification def: "A scalar value specification that specifies the point in time that a human participant under investigation self-administers a medication material" [] synonym: "medication timepoint" EXACT [] is_a: OBI:0001931 ! scalar value specification [Term] id: OBI:0002491 name: medication dose value specification def: "A scalar value specification that specifies the value of the quantity of a material entity administered to an organism as a treatment" [] synonym: "medication dose" EXACT [] is_a: OBI:0001931 ! scalar value specification [Term] id: OBI:0002492 name: case role in case-control study def: "A role that is borne by a case-control study design participant under investigation that is associated with the outcome mentioned in the study design." [] is_a: OBI:0000097 ! participant under investigation role [Term] id: OBI:0002493 name: control role in case-control study def: "A role that is borne by a case-control study design participant under investigation that is not associated with the outcome mentioned in the study design." [] is_a: OBI:0000097 ! participant under investigation role [Term] id: OBI:0002500 name: amniotic fluid specimen def: "A specimen that is derived from amniotic fluid." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002501 name: bile specimen def: "A specimen that is derived from bile." [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:0002502 name: cerebrospinal fluid specimen def: "A specimen that is derived from cerbrospinal fluid." [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:0002503 name: feces specimen def: "A specimen that is derived from feces." [] synonym: "stool specimen" EXACT [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002504 name: digestive system fluid or secretion specimen def: "A specimen that is derived from digestive system fluid or secretion." [] synonym: "gastric fluid specimen" EXACT [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002505 name: milk specimen def: "A specimen that is derived from milk." [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:0002506 name: pericardial fluid specimen def: "A specimen that is derived from pericardial fluid." [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:0002507 name: saliva specimen def: "A specimen that is derived from saliva." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002508 name: sputum specimen def: "A specimen that is derived from sputum." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002509 name: sweat specimen def: "A specimen that is derived from sweat." [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:0002510 name: synovial fluid specimen def: "A specimen that is derived from synovial fluid." [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:0002511 name: vitreous humor specimen def: "A specimen that is derived from vireous humor." [] synonym: "vitreous fluid specimen" EXACT [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002512 name: bone marrow specimen def: "A specimen that is derived from bone marrow." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002513 name: placenta specimen def: "A specimen that is derived from placenta." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002514 name: peritoneal fluid specimen def: "A specimen that is derived from peritoneal fluid." [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:0002515 name: pleural fluid specimen def: "A specimen that is derived from pleural fluid." [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:0002516 name: brain specimen def: "A specimen that is derived from brain." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002517 name: hair specimen def: "A specimen that is derived from hair." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002518 name: prostate gland specimen def: "A specimen that is derived from prostate gland." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002519 name: skeletal muscle tissue specimen def: "A specimen that is derived from skeletal muscle." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002520 name: heart specimen def: "A specimen that is derived from heart." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002521 name: renal medulla specimen def: "A specimen that is derived from renal medulla." [] synonym: "kidney medulla specimen" EXACT [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002522 name: adrenal gland specimen def: "A specimen that is derived from adrenal gland." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002523 name: breast specimen def: "A specimen that is derived from breast." [] synonym: "mammary tissue specimen" EXACT [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002524 name: urinary bladder specimen def: "A specimen that is derived from urinary bladder." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002525 name: tibial artery specimen def: "A specimen that is derived from tibial artery." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002526 name: skin of body specimen def: "A specimen that is derived from skin." [] synonym: "skin specimen" EXACT [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002527 name: pancreas specimen def: "A specimen that is derived from pancreas." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002528 name: stomach specimen def: "A specimen that is derived from stomach." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002529 name: pituitary gland specimen def: "A specimen that is derived from pituitary gland." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002530 name: adipose tissue specimen def: "A specimen that is derived from adipose tissue." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002531 name: cortex of kidney specimen def: "A specimen that is derived from cortex of kidney." [] synonym: "kidney cortex specimen" EXACT [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002532 name: esophagus mucosa specimen def: "A specimen that is derived from esophagus mucosa." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002533 name: colon specimen def: "A specimen that is derived from colon." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002534 name: lung specimen def: "A specimen that is derived from lung." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002535 name: esophagus muscularis mucosa specimen def: "A specimen that is derived from esophagus muscularis mucosa." [] synonym: "esophagus muscularis specimen" EXACT [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002536 name: cerebral cortex specimen def: "A specimen that is derived from cerebral cortex." [] synonym: "brain cortex specimen" EXACT [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002537 name: thyroid gland specimen def: "A specimen that is derived from thyroid gland." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002538 name: cerebellum specimen def: "A specimen that is derived from cerebellum." [] synonym: "brain cerebellum specimen" EXACT [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002539 name: tibial nerve specimen def: "A specimen that is derived from tibial nerve." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002540 name: coronary artery specimen def: "A specimen that is derived from coronary artery." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002541 name: spleen specimen def: "A specimen that is derived from spleen." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002542 name: aorta specimen def: "A specimen that is derived from aorta." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002543 name: atrial appendage specimen def: "A specimen that is derived from the atrium auricular region." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002544 name: esophagogastric junction specimen def: "A specimen that is derived from the esophagogastric junction." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002545 name: ileum specimen def: "A specimen that is derived from ileum." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002546 name: liver specimen def: "A specimen that is derived from liver." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002547 name: minor salivary gland specimen def: "A specimen that is derived from minor salivary gland." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002548 name: omentum specimen def: "A specimen that is derived from omentum." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002549 name: ovary specimen def: "A specimen that is derived from female gonad." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002550 name: sigmoid colon specimen def: "A specimen that is derived from sigmoid colon." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002551 name: suprapubic skin specimen def: "A specimen that is derived from suprapubic skin." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002552 name: testis specimen def: "A specimen that is derived from testis." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002553 name: uterus specimen def: "A specimen that is derived from uterus." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002554 name: vagina specimen def: "A specimen that is derived from vagina." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002555 name: age group inclusion criterion def: "An inclusion criterion that defines and states an age bracket which, if met, makes an entity suitable for a given task or participation in a given process." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002556 name: minimum age value specification def: "A value specifcation that specifies the youngest age when specifying an age range." [] is_a: OBI:0001933 ! value specification [Term] id: OBI:0002557 name: maximum age value specification def: "A value specifcation that specifies the oldest age when specifying an age range." [] is_a: OBI:0001933 ! value specification [Term] id: OBI:0002558 name: use of medication inclusion criterion def: "An inclusion criterion that defines and states a a set of medications, which, if used by an entity, makes that entity suitable for a given task or participation in a given process." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002559 name: hospital patient inclusion criterion def: "An inclusion criterion defines that a human being has to be a hospital patient to be suitable for a given task or participation in a given process." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002560 name: family status inclusion criterion def: "An inclusion criterion that defines and states one or more family statuses, which, if met, makes a human being suitable for a given task or participation in a given process." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002561 name: sex inclusion criterion def: "An inclusion criterion that defines and states one or more sexes which, if met, makes an entity suitable for a given task or participation in a given process." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002562 name: country of residence inclusion criteria def: "An inclusion criterion that defines and states one or more countries of residence which, if met, makes a human being suitable for a given task or participation in a given process." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002563 name: ethnicity inclusion criterion def: "An inclusion criteria that defines and states one or more ethnicities which, if met, makes an entity suitable for a given task or participation in a given process." [] is_a: OBI:0500027 ! inclusion criterion [Term] id: OBI:0002564 name: histopathology assay def: "A histological assay that is intended to check for the presence or level of a specific disease." [] is_a: OBI:0600020 ! histological assay [Term] id: OBI:0002565 name: adapter-sequence trimming def: "A data transformation in which adapter sequences at the end of a molecular sequence are cut (removed)." [] is_a: OBI:0002585 ! sequence trimming [Term] id: OBI:0002566 name: file merge def: "A data transformation in which data contained in 2 or more files are merged into a single file." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0002567 name: sequence alignment def: "A data transformation in which one or more sequences (reads) are positioned on a reference sequence template (often a reference set of genes), according to the genetic base-pairing paradigm." [] is_a: OBI:0200187 ! sequence analysis data transformation [Term] id: OBI:0002568 name: sequence data feature count tabulation def: "The counting of features (typically, genes) within aligned sequence data, and organization of these counts into one or more tables." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200187 ! sequence analysis data transformation [Term] id: OBI:0002569 name: trimmed sequence data def: "The results of a data transformation of sequence data in which (e.g., low quality) read bases are removed, to achieve some specific objective." [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002570 name: nCounter Mouse miRNA Expression array def: "A mouse array which is manufacutred by NanoString Technologies. Built upon color-coded molecular barcodes technology, the array profiles miRNA with increased specificity and sensitivty than microarrays." [] is_a: OBI:0001865 ! assay array [Term] id: OBI:0002571 name: polyA-selected RNA sequencing assay def: "An RNA-seq assay to study transcriptomes through the enrichment of polyadenylated transcripts or removal of ribosomal RNA prior to high-throughput sequencing." [] synonym: "mRNA-seq" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002572 name: polyA-depleted RNA sequencing assay def: "An RNA-seq assay to study non-polyadenylated transcripts, such as, but not exclusive to unspliced and circular isoforms, through the depletion of polyadenylated transcripts prior to high-throughput sequencing." [] synonym: "polyA-depleted RNA-seq" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002573 name: polyA depleted RNA extract def: "A RNA extract that is the output of an extraction process in which RNA molecules lacking poly A tails at thier 3' ends are purified." [] is_a: OBI:0000880 ! RNA extract [Term] id: OBI:0002574 name: RNA extraction with polyA depletion def: "A RNA extraction process in which only RNAs lacking a polyA tail are retained" [] is_a: OBI:0666666 ! RNA extraction [Term] id: OBI:0002575 name: isoform sequencing def: "A method for sequencing isoforms by enriching a cDNA library for full-length reads spanning entire transcript isoforms." [] synonym: "ISO-seq" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002578 name: adapter sequence data def: "Nucleotide sequences of molecules that are ligated to assay samples prior to sequencing of these samples; these sequences are provided by assay kit manufacturers and typically used to combine sequencing of multiple samples in one assay run." [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002579 name: adapter-trimmed sequence data def: "The results of a data transformation of sequence data in which reference subsequences corresponding to ligated library adapters are removed." [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002580 name: aligned sequence data def: "The results of a sequence alignment." [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002581 name: merged aligned sequence data def: "The results of a data transformation of sequence data in which files containing aligned sequence data are merged together" [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002582 name: sequence library feature count data def: "The results of a sequence data feature count tabulation." [] is_a: IAO:0000100 ! data set [Term] id: OBI:0002583 name: DNA methylation profiling data def: "The results of a DNA methylation profiling assay" [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002584 name: differential expression analysis data def: "The results of a differential expression analysis." [] is_a: IAO:0000100 ! data set [Term] id: OBI:0002585 name: sequence trimming def: "A data transformation in which subsequences of a molecular sequence are cut (removed)." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0002586 name: digital acquisition card def: "The digital acquisition card acts as the interface between the computer and a measurement device via the computer bus. It converts the signal generated by a measurement device (output from device) to a digital signal via an analog-to-digital converter, ADC. It also converts a digital signal to an analog signal via a digital-to-analog converter, DAC. This analog signal (e.g., stimulus) is fed to a measurement device (input to device)." [] synonym: "DAQ device" EXACT [] synonym: "digital acquisition and digital generation card" EXACT [] is_a: OBI:0000968 ! device [Term] id: OBI:0002587 name: machine learning def: "A planned process with the objective to give a computer the ability to use patterns in data to progressively improve its performance on a specific task, achieved by using statistical techniques instead of explicitly programming the ability." [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0002588 name: supervised machine learning def: "A machine learning process using a function that maps an input to an output based on example input-output pairs. It infers a function from labeled training data consisting of a set of training examples." [] is_a: OBI:0002587 ! machine learning [Term] id: OBI:0002589 name: unsupervised machine learning def: "A machine learning process that infers a function describing the structure of \"unlabeled\" data (i.e. data that has not been classified or categorized)." [] is_a: OBI:0002587 ! machine learning [Term] id: OBI:0002590 name: molecular interaction identification design def: "A study design that investigates the features of interaction between molecules." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0002591 name: colocalization identification design def: "A molecular interaction identification design that investigates the co-occurence and correlation of two or more molecules." [] is_a: OBI:0002590 ! molecular interaction identification design [Term] id: OBI:0002592 name: genetic interaction identification design def: "A molecular interaction identification design that investigates a phenotype that is the result of two or more genetic perturbations, and is not explained by the individual genetic perturbations alone." [] is_a: OBI:0002590 ! molecular interaction identification design [Term] id: OBI:0002593 name: functional association identification design def: "A molecular interaction identification design that investigates a relationship that is the result of intermediate steps between two or more molecules that are not necessarily in direct contact with each other." [] is_a: OBI:0002590 ! molecular interaction identification design [Term] id: OBI:0002594 name: direct interaction identification design def: "A molecular interaction identification design that investigates the influence of molecules, which are in direct contact, on one another." [] synonym: "molecular binding identification design" EXACT [] is_a: OBI:0002590 ! molecular interaction identification design [Term] id: OBI:0002595 name: enzymatic reaction identification design def: "A direct interaction identification design that investigations a biological reaction on a molecule which has been triggered by an enzyme." [] is_a: OBI:0002594 ! direct interaction identification design [Term] id: OBI:0002596 name: self interaction identification design def: "A molecular interaction identification design that investigates intra-molecular interactions between two or more regions of a single molecule." [] is_a: OBI:0002590 ! molecular interaction identification design [Term] id: OBI:0002597 name: chromosome conformation capture sequencing assay def: "A chromosome conformation capture-on-chip assay quantitates the products with multiplexed high-throughput sequencing." [] synonym: "3C-seq assay" EXACT [] is_a: OBI:0002458 ! chromosome conformation capture-on-chip assay is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0002598 name: inverse polymerase chain reaction def: "A polymerase chain reaction which amplifies DNA with only one known sequence from which primers may be designed. A series of restriction digestions and ligations result in a looped DNA fragment which can be primed for PCR." [] synonym: "inverse PCR" EXACT [] is_a: OBI:0000415 ! polymerase chain reaction [Term] id: OBI:0002599 name: swab specimen def: "A specimen that is stored on a swab as the output of a collecting specimen with swab process." [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0002600 name: collecting specimen with swab def: "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)." [] is_a: OBI:0000659 ! specimen collection process [Term] id: OBI:0002601 name: demultiplexed sequence data def: "Sequence data in which an identifier subsequence has been used to categorize each reads by source." [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002602 name: multiplexed sequence data def: "Sequence data from a sequence library generated from at least two different sources, where each read in the sequence data includes base calls from a multiplex identifier sequence that can be used to trace the source of the read to its source." [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002603 name: areolar swab specimen def: "A specimen that is collected with a swab from the surface of an areola of a breast." [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002604 name: breast swab specimen def: "A specimen that is collected with a swab from the surface of a breast." [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002605 name: cheek swab specimen def: "A specimen that is collected with a swab from the cheek portion of the inside surface of a mouth." [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002606 name: nasopharyngeal swab specimen def: "A specimen that is collected with a swab from the surface of a nasopharynx." [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002607 name: oral swab specimen def: "A specimen that is collected with a swab from the inside surface of a mouth." [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002608 name: oropharyngeal swab specimen def: "A specimen that is collected with a swab from the surface of a oropharynx." [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002609 name: rectal swab specimen def: "A specimen that is collected with a swab from the surface of a rectum." [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002610 name: tongue swab specimen def: "A specimen that is collected with a swab from the surface of a tongue." [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002611 name: vagina swab specimen def: "A specimen that is collected with a swab from the surface of a vagina." [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002612 name: fecal swab specimen def: "A specimen that is collected with a swab from the surface of a feces." [] synonym: "stool swab specimen" EXACT [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002613 name: environmental swab specimen def: "A specimen that is collected with a swab from the surface of an environmenal material." [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002614 name: birth cohort study design def: "A cohort study design for which the subjects are followed from the time of birth usually including information about gestation and follow up." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0002615 name: disease specific study design def: "A study design for which material and information is collected from subjects that have already developed a particular disease." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0002616 name: genealogical record def: "A document about the family relationships of persons related as members of a domestic group linked through descent from a common ancestor, marriage, or adoption." [] is_a: IAO:0000310 ! document [Term] id: OBI:0002617 name: national registry def: "An information content entity that contains information about a nationwide group of individuals." [] is_a: IAO:0000030 ! information content entity [Term] id: OBI:0002618 name: national biomedical registry def: "A national registry that contains information about individuals that was accumulated for a biomedical purpose, such as diagnoses, treatments, or outcomes." [] is_a: OBI:0002617 ! national registry [Term] id: OBI:0002619 name: site-directed mutagenesis def: "An induced mutation in which a specific base change is programmed into the sequence of a synthetic primer." [] is_a: OBI:0001154 ! induced mutagenesis [Term] id: OBI:0002620 name: random mutagenesis def: "An induced mutation that produces a random mutation, either by introducing the organism to mutagens, or through a process such as error-prone PCR." [] is_a: OBI:0001154 ! induced mutagenesis [Term] id: OBI:0002621 name: reconstitution assay def: "An assay in which a cellular process is replicated from the bottom-up using isolated components in order to observe how the components work together." [] synonym: "reconstitution experiment" EXACT [] is_a: OBI:0000070 ! assay is_a: OBI:0000471 ! study design execution [Term] id: OBI:0002622 name: in vitro transcription reconstitution assay def: "A reconstitution assay in which RNA synthesis is investigated using RNA polymerase II transcription systems replicated in vitro from their base components." [] is_a: OBI:0002621 ! reconstitution assay [Term] id: OBI:0002623 name: whole metagenome sequencing assay def: "A DNA sequencing assay that intends to provide information on the DNA sequences of multiple genomes (a metagenome) from different organisms present in the same input sample." [] synonym: "WMS" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0002624 name: case-control study design def: "A study design that entails the creation of two types of roles, such that each participant under investigation bears one or the other. What distinguishes the two types of roles is an 'outcome', which is associated with participants that have the case role but not associated with participants that have the control role. A case-control study examines the hypothesis that the presence of the outcome in case participants is associated with an 'exposure' that is not associated with control participants." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0002625 name: gene knockdown def: "A genetic transformation which reduces the expression of a specific gene or genes in an organism." [] synonym: "gene knock-down" EXACT [] is_a: OBI:0600043 ! genetic transformation [Term] id: OBI:0002626 name: RNAi gene knockdown def: "A gene knockdown that silences genes through artificially-induced RNA interference. This is accomplished by introducing small double-stranded interfering RNA complementary to the target mRNA to be silenced, which is then cleaved by a ribonuclease." [] synonym: "RNA interference gene knockdown" EXACT [] is_a: OBI:0002625 ! gene knockdown [Term] id: OBI:0002627 name: ribosomal RNA-depleted RNA extract def: "An extract of RNA which is produced through rRNA (ribosomal RNA) depletion (the removal of highly abundant rRNA species)." [] is_a: OBI:0000880 ! RNA extract [Term] id: OBI:0002628 name: RNAi knockdown assay def: "A gene knockdown assay in which RNAi gene knockdown is used to disrupt gene transcripts." [] synonym: "RNA interference knockdown assay" EXACT [] synonym: "RNAi gene knockdown assay" EXACT [] is_a: OBI:0001672 ! gene knock-down assay [Term] id: OBI:0002629 name: direct RNA sequencing assay def: "An assay to study transcription through direct RNA sequence determination, without prior conversion of RNA molecules to cDNA." [] synonym: "direct RNA-seq" EXACT [] synonym: "DRS" EXACT [] is_a: OBI:0001177 ! RNA sequencing assay [Term] id: OBI:0002630 name: Illumina NovaSeq 6000 def: "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." [] synonym: "NovaSeq 6000" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002631 name: single-cell RNA sequencing assay def: "An RNA sequencing assay that uses RNA extracts as input that can be traced to a single cell of origin." [] synonym: "scRNA-seq" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002632 name: PacBio Sequel def: "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" [] synonym: "Pacific BioSciences Sequel" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002633 name: PacBio Sequel II def: "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." [] synonym: "Pacific BioSciences Sequel II" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002634 name: in vivo assay measuring B cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific antibodies or B cells def: "An efficacy of B cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specific antibodies or B cells." [] synonym: "disease exacerbation after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001711 ! in vivo assay measuring B cell epitope specific disease exacerbation is_a: OBI:0002677 ! in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0002635 name: in vivo assay measuring T cell epitope specific disease reduction resulting from the adoptive transfer of epitope specific T cells def: "An efficacy of T cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specfic T cells." [] synonym: "decreased disease after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001507 ! in vivo assay measuring T cell epitope specific treatment of disease is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells [Term] id: OBI:0002636 name: in vivo assay measuring B cell epitope specific disease reduction resulting from adoptive transfer of epitope specific antibodies or B cells def: "An efficacy of B cell epitope intervention experiment that detects a decrease in disease after adoptive transfer of epitope specific antibodies or B cells." [] synonym: "decreased disease after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001697 ! in vivo assay measuring B cell epitope specific treatment of disease is_a: OBI:0002677 ! in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0002637 name: in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells def: "An efficacy of T cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specfic T cells." [] synonym: "protection from challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0002073 ! in vivo assay measuring T cell epitope specific protection from challenge is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells [Term] id: OBI:0002638 name: in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells def: "An efficacy of B cell epitope intervention experiment that uses a epitope protection experiment after adoptive transfer of epitope specific antibodies or B cells." [] synonym: "protection from challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001710 ! in vivo assay measuring B cell epitope specific protection from challenge is_a: OBI:0002677 ! in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0002639 name: in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on pathogen burden def: "An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden." [] synonym: "pathogen burden after challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001475 ! in vivo assay measuring T cell epitope specific protection from infectious challenge based on pathogen burden is_a: OBI:0003470 ! in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells [Term] id: OBI:0002640 name: in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on pathogen burden def: "An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using pathogen burden." [] synonym: "pathogen burden after challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0002051 ! in vivo assay measuring B cell epitope specific protection from infectious challenge based on pathogen burden is_a: OBI:0003475 ! in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0002641 name: in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells based on survival def: "An in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells using survival." [] synonym: "survival from other challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001492 ! in vivo assay measuring T cell epitope specific protection based on survival is_a: OBI:0003474 ! in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells [Term] id: OBI:0002642 name: in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival def: "An in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival." [] synonym: "survival from other challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001696 ! in vivo assay measuring B cell epitope specific protection based on survival is_a: OBI:0003479 ! in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0002643 name: in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells based on tumor burden def: "An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using tumor burden." [] synonym: "tumor burden after challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001473 ! in vivo assay measuring T cell epitope specific protection after tumor burden challenge is_a: OBI:0003472 ! in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells [Term] id: OBI:0002644 name: in vivo assay measuring B cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on tumor burden def: "An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using tumor burden." [] synonym: "tumor burden after challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0002052 ! in vivo assay measuring B cell epitope specific protection after tumor burden challenge is_a: OBI:0003477 ! in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0002645 name: in vivo assay measuring T cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific T cells def: "An efficacy of T cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specfic T cells." [] synonym: "tolerance after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001324 ! in vivo assay measuring T cell epitope specific tolerance induction is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells [Term] id: OBI:0002646 name: in vivo assay measuring B cell epitope specific tolerance induction resulting from the adoptive transfer of epitope specific antibodies or B cells def: "An efficacy of B cell epitope intervention experiment that uses a tolerance induction intervention experiment after adoptive transfer of epitope specific antibodies or B cells." [] synonym: "tolerance after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001693 ! in vivo assay measuring B cell epitope specific tolerance induction is_a: OBI:0002677 ! in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0002647 name: Giemsa stain assay def: "An assay that uses a Giemsa stain to characterize cells." [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0002648 name: individual organism specimen def: "A specimen composed of an individual organism to be studied in an investigation." [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0002649 name: blood microbiology assay def: "An organism detection assay that detects microorganisms in a blood specimen." [] is_a: OBI:0003040 ! blood assay is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0002650 name: biopsy def: "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." [] is_a: OBI:0600005 ! collecting specimen from organism [Term] id: OBI:0002651 name: image guided biopsy def: "A biopsy which uses an imaging procedure to guide a needle biopsy." [] synonym: "image guided needle biopsy" EXACT [] synonym: "image-guided biopsy" EXACT [] synonym: "imaging guided biopsy" EXACT [] is_a: OBI:0002654 ! needle biopsy [Term] id: OBI:0002652 name: computed tomography assisted biopsy def: "A needle biopsy guided by real-time computed tomography (CT) scan images." [] synonym: "Computed Tomography Assisted Biopsy" EXACT [] synonym: "Computed Tomography-Guided Needle Biopsy" EXACT [] synonym: "CT Assisted Biopsy" EXACT [] synonym: "CT Guided Biopsy" EXACT [] is_a: OBI:0002651 ! image guided biopsy [Term] id: OBI:0002653 name: ultrasound-guided needle biopsy def: "A needle biopsy guided by ultrasound visualization." [] is_a: OBI:0002651 ! image guided biopsy [Term] id: OBI:0002654 name: needle biopsy def: "A biopsy that uses a hollow needle to extract cells." [] is_a: OBI:0002650 ! biopsy [Term] id: OBI:0002655 name: fine needle aspiration biopsy def: "A biopsy that uses a thin needle to extract cells." [] synonym: "FNA" EXACT [] synonym: "FNAB" EXACT [] is_a: OBI:0002654 ! needle biopsy [Term] id: OBI:0002656 name: core needle biopsy def: "A biopsy that uses a hollow tube to collect a core of tissue." [] synonym: "CNB" EXACT [] is_a: OBI:0002654 ! needle biopsy [Term] id: OBI:0002657 name: surgical biopsy def: "A biopsy involving a surgical incision into an organism to access the biopsy material." [] synonym: "excisional biopsy" EXACT [] synonym: "open biopsy" EXACT [] is_a: OBI:0002650 ! biopsy [Term] id: OBI:0002660 name: abdominal wall fat pad biopsy def: "A biopsy involving the collection of a small part of the abdominal wall fat pad." [] synonym: "abdominal wall biopsy" EXACT [] synonym: "fat biopsy" EXACT [] is_a: OBI:0002650 ! biopsy [Term] id: OBI:0002661 name: tail biopsy def: "A biopsy involving the collection of the tip of a mamallian tail." [] synonym: "snip" EXACT [] is_a: OBI:0002650 ! biopsy [Term] id: OBI:0002662 name: bone marrow biopsy def: "A biopsy where a small amount of bone and a small amount of fluid and bone marrow are collected." [] is_a: OBI:0002650 ! biopsy [Term] id: OBI:0002663 name: skinpunch biopsy def: "A biopsy that involves the collection of a cylinder of skin (including epidermis, dermis and superficial fat) using a punch tool." [] synonym: "punch biopsy; skin biopsy" EXACT [] is_a: OBI:0002650 ! biopsy [Term] id: OBI:0002664 name: cytometric bead array assay measuring epitope specific interleukin-15 production by T cells def: "A cytometric bead array assay that detects interleukin-15 production by T cells." [] synonym: "IL-15 release|cytometric bead array" EXACT [] is_a: OBI:0001292 ! assay measuring epitope specific interleukin-15 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002665 name: cytometric bead array assay measuring epitope specific interleukin-16 production by T cells def: "A cytometric bead array assay that detects interleukin-16 production by T cells." [] synonym: "IL-16 release|cytometric bead array" EXACT [] is_a: OBI:0001280 ! assay measuring epitope specific interleukin-16 production by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0002666 name: in vivo assay measuring B cell epitope specific induction of hypersensitivity resulting from the adoptive transfer of epitope specific antibodies or B cells def: "An efficacy of B cell epitope intervention experiment that detects a hypersensitivity response by monitoring skin reactions after adoptive transfer of epitope specific antibodies or B cells." [] synonym: "hypersensitivity after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001694 ! in vivo assay measuring B cell epitope specific induction of hypersensitivity is_a: OBI:0002677 ! in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0002667 name: in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity resulting from the adoptive transfer of epitope specific T cells def: "An efficacy of T cell epitope intervention experiment that detects epitope specific type IV hypersensitivity after adoptive transfer of epitope specfic T cells." [] synonym: "type IV hypersensitivity (DTH) after adoptive transfer|in vivo skin test" EXACT [] is_a: OBI:0001348 ! in vivo skin test assay measuring T cell epitope specific type IV hypersensitivity is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells [Term] id: OBI:0002668 name: in vivo assay measuring epitope specific proliferation of T cells resulting from the adoptive transfer of epitope specific T cells def: "A T cell epitope specific proliferation assay that is performed in vivo after adoptive transfer of epitope specfic T cells." [] synonym: "proliferation after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0002070 ! in vivo assay measuring epitope specific proliferation of T cells is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells [Term] id: OBI:0002669 name: assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response resulting from the adoptive transfer of epitope specific T cells def: "A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance an antibody response after adoptive transfer of epitope specfic T cells." [] synonym: "antibody help after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001228 ! in vivo assay measuring epitope specific helper T cell enhancement of a B cell mediated immune response is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells [Term] id: OBI:0002670 name: assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response resulting from the adoptive transfer of epitope specific T cells def: "A T cell epitope specific helper activity assay that detects the ability of a T cell epitope to enhance a T cell response after adoptive transfer of epitope specfic T cells." [] synonym: "T cell help after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001263 ! in vivo assay measuring epitope specific helper T cell enhancement of a T cell mediated immune response is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells [Term] id: OBI:0002671 name: in vivo assay measuring epitope specific T cell killing resulting from the adoptive transfer of epitope specific T cells def: "An in vivo cell killing assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC after adoptive transfer of epitope specific T cells." [] synonym: "cytotoxicity after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001392 ! in vivo assay measuring epitope specific T cell killing is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells [Term] id: OBI:0002672 name: ELISA measuring epitope specific perforin release by T cells def: "An enzyme-linked immunosorbent assay that detects epitope specific perforin release by T cells." [] synonym: "perforin release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001497 ! assay measuring epitope specific perforin release by T cells [Term] id: OBI:0002673 name: enrichment culture medium def: "A culture medium that is designed to favor the growth of a particular microorganism or cells over others, enriching a sample for the microorganism or cells of interest." [] synonym: "isolation medium" EXACT [] is_a: OBI:0000079 ! culture medium [Term] id: OBI:0002674 name: case series design def: "A study design that samples only subjects who have experienced a particular event (outcome or exposure). Such a design, in contrast to a cohort study, does not permit calculation of absolute risk as non-case subjects are not included." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0002675 name: massively parallel reporter assay def: "An assay in which multiplexing the construction and interrogation of larger libraries of reporter constructs allows measurement of the transcriptional regulatory activities of thousands to hundreds of thousands of DNA sequences." [] synonym: "MPRA" EXACT [] is_a: OBI:0002082 ! reporter gene assay [Term] id: OBI:0002676 name: in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells def: "An efficacy of T cell epitope intervention experiment that is performed after adoptive transfer of epitope specfic T cells." [] synonym: "in vivo response after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001484 ! assay measuring T cell epitope specific in vivo activity [Term] id: OBI:0002677 name: in vivo assay measuring a B cell epitope specific response after adoptive transfer of epitope specific antibodies or B cells def: "An efficacy of B cell epitope intervention experiment that is performed after adoptive transfer of epitope specific antibodies or B cells." [] synonym: "in vivo response after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001698 ! assay measuring B cell epitope specific in vivo activity [Term] id: OBI:0002678 name: in vivo assay measuring T cell epitope specific disease exacerbation resulting from the adoptive transfer of epitope specific T cells def: "An efficacy of T cell epitope intervention experiment that uses a disease exacerbation in vivo intervention experiment after adoptive transfer of epitope specfic T cells." [] synonym: "disease exacerbation after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001467 ! in vivo assay measuring T cell epitope specific disease exacerbation is_a: OBI:0002676 ! in vivo assay measuring a T cell epitope specific response after adoptive transfer of epitope specific T cells [Term] id: OBI:0002679 name: vacuum-assisted biopsy needle def: "A core biopsy needle integrated with a vacuum system which facilitates the collection of specimen material." [] is_a: OBI:0000436 ! needle [Term] id: OBI:0002680 name: pseudovirus entry assay def: "An assay that measures the entry in target cells of reporter viral particles that express an envelope protein of a different virus of interest." [] synonym: "pseudotype cell entry" EXACT [] synonym: "pseudotype entry" EXACT [] synonym: "pseudotyped particle cell entry assay" EXACT [] synonym: "pseudovirus cell entry" EXACT [] is_a: OBI:0001187 ! infectious agent detection assay [Term] id: OBI:0002681 name: glass bottle def: "A container with a narrow neck that is made of glass." [] is_a: OBI:0000967 ! container [Term] id: OBI:0002682 name: glass bottle coated with insecticides def: "A glass bottle that coated with material designed to control insects." [] is_a: OBI:0002681 ! glass bottle [Term] id: OBI:0002683 name: short interspersed nuclear elements polymerase chain reaction def: "A polymerase chain reaction that amplifies short interspersed nuclear elements (SINEs)." [] synonym: "short interspersed elements PCR" EXACT [] is_a: OBI:0000415 ! polymerase chain reaction [Term] id: OBI:0002684 name: nested polymerase chain reaction def: "A polymerase chain reaction with modification intended to reduce non-specific binding in products due to the amplification of unexpected primer binding sites. The nested polymerase chain reaction (PCR) involves the use of two primer sets and two successive PCR reactions. The first set of primers are designed to anneal to sequences upstream from the second set of primers and are used in an initial PCR reaction." [] synonym: "nested PCR" EXACT [] synonym: "nested-PCR" EXACT [] is_a: OBI:0000415 ! polymerase chain reaction [Term] id: OBI:0002685 name: immunoelectrophoresis def: "An electrophoresis that separates and characterize proteins based on reaction with antibodies." [] synonym: "IEP" EXACT [] is_a: OBI:0600053 ! electrophoresis [Term] id: OBI:0002686 name: counter current immunoelectrophoresis def: "An electrophoresis in which antigen and antibody move in opposite directions and form precipitates in the area between the cells where they meet in concentrations of optimal proportions." [] is_a: OBI:0600053 ! electrophoresis [Term] id: OBI:0002687 name: ligase detection reaction def: "A linear amplification that uses a thermostable ligase to amplify a piece of DNA. Because the enzyme retains activity after multiple thermal cycles, the ligations may be repeated to linearly increase product." [] synonym: "LDR" EXACT [] is_a: OBI:0001494 ! linear amplification [Term] id: OBI:0002688 name: loop-mediated isothermal amplification def: "An enzymatic amplification in which a piece of DNA is amplified at a constant temperature of 60 - 65 degree C using either two or three sets of primers and a polymerase with high strand displacement activity in addition to a replication activity. This amplification does not need thermal cyclers and may be a low cost alternative to PCR." [] synonym: "LAMP" EXACT [] is_a: OBI:0600058 ! enzymatic amplification [Term] id: OBI:0002689 name: detection of pathogenic organisms objective def: "An organism feature identification objective that aims to detect whether an organism contains pathogenic organisms." [] is_a: OBI:0000268 ! organism feature identification objective [Term] id: OBI:0002690 name: insecticide resistance detection objective def: "An organism feature identification objective that aims to detect insecticide resistance of an insect." [] is_a: OBI:0000268 ! organism feature identification objective [Term] id: OBI:0002691 name: arthropod meal of blood specimen def: "A specimen of the blood ingested by an arthropod." [] synonym: "blood meal" EXACT [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0002692 name: polymerase chain reaction assay def: "An assay that uses polymerase chain reaction technique to amplify DNA." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002693 name: restriction fragment length polymorphism assay def: "An assay that uses digestion of DNA with specific restriction enzymes followed by gel electropheresis to detect differences in the sizes of the generated fragments that are due to genetic differences (polymorphisms) in homologous sequences." [] synonym: "restriction fragment length polymorphism" EXACT [] synonym: "restriction fragment length polymorphism analysis" EXACT [] synonym: "RFLP" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002694 name: DNA fingerprinting assay def: "An assay to identify a specific individual organism from a DNA specimen by looking at unique patterns in their DNA." [] synonym: "DNA finger printing" EXACT [] synonym: "DNA fingerprint" EXACT [] synonym: "DNA fingerprinting" EXACT [] synonym: "DNA profiling" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002695 name: insecticide resistance assay def: "An assay that aims to detect the presence and/or frequency of resistance to insecticides in an organism or organism population." [] synonym: "resistance identification/monitoring" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002696 name: insecticide resistance by monitoring known mutations assay def: "An insecticide resistance assay that detects, in a population, presence and frequency of mutant alleles for previously characterized mutations with insecticide resistance phenotypes." [] synonym: "monitoring known mutations" EXACT [] is_a: OBI:0002695 ! insecticide resistance assay [Term] id: OBI:0002697 name: insecticide resistance by detecting enzyme activity assay def: "An insecticide resistance assay that is based on determination the catalytic activity of an enzyme associated with insecticide resistance phenotypes." [] synonym: "metabolic resistance assay" EXACT [] is_a: OBI:0002695 ! insecticide resistance assay [Term] id: OBI:0002698 name: insecticide resistance bioassay def: "An insecticide resistance assay that is typically conducted to measure the effects of a substance on a living organism." [] synonym: "bioassay" EXACT [] is_a: OBI:0002695 ! insecticide resistance assay [Term] id: OBI:0002699 name: insecticide resistance by detecting alpha esterase activity assay def: "An insecticide resistance by detecting enzyme activity assay that measures activity of alpha esterase." [] synonym: "alpha esterase activity assay" EXACT [] is_a: OBI:0002697 ! insecticide resistance by detecting enzyme activity assay [Term] id: OBI:0002700 name: insecticide resistance by detecting beta esterase activity assay def: "An insecticide resistance by detecting enzyme activity assay that measures activity of beta esterase." [] synonym: "beta esterase activity assay" EXACT [] is_a: OBI:0002697 ! insecticide resistance by detecting enzyme activity assay [Term] id: OBI:0002701 name: insecticide resistance by detecting acetylcholinesterase activity assay def: "An insecticide resistance by detecting enzyme activity assay that measures activity of acetylcholinesterase." [] synonym: "acetylcholinesterase assay" EXACT [] synonym: "AChE activity assay" EXACT [] synonym: "AChE assay" EXACT [] is_a: OBI:0002697 ! insecticide resistance by detecting enzyme activity assay [Term] id: OBI:0002702 name: insecticide resistance by detecting glutathione S-transferase activity assay def: "An insecticide resistance by detecting enzyme activity assay that measures activity of glutathione S-transferase (GST)." [] synonym: "GST related assay" EXACT [] is_a: OBI:0002697 ! insecticide resistance by detecting enzyme activity assay [Term] id: OBI:0002703 name: insecticide resistance by detecting carboxylic ester hydrolase activity assay def: "An insecticide resistance by detecting enzyme activity assay that measures activity of carboxylic ester hydrolase using p-nitrophenyl acetate as a substrate." [] synonym: "pNPA assay" EXACT [] is_a: OBI:0002697 ! insecticide resistance by detecting enzyme activity assay [Term] id: OBI:0002704 name: insecticide resistance by detecting mixed-function oxidase assay def: "An insecticide resistance by detecting enzyme activity assay that measures whether mixed-function oxidase activity present." [] synonym: "mixed-function oxidase assay" EXACT [] is_a: OBI:0002697 ! insecticide resistance by detecting enzyme activity assay [Term] id: OBI:0002705 name: direct insecticide resistance bioassay def: "An insecticide resistance bioassay without the use of any synergist." [] synonym: "direct bioassay" EXACT [] is_a: OBI:0002698 ! insecticide resistance bioassay [Term] id: OBI:0002706 name: topical application insecticide resistance bioassay def: "An insecticide resistance bioassay by adding insecticide directly to the thorax of the insect." [] synonym: "topical application assay" EXACT [] is_a: OBI:0002698 ! insecticide resistance bioassay [Term] id: OBI:0002707 name: direct insecticide resistance diagnostic assay def: "A direct insecticide resistance assay that at preset insecticide dosage scoring mortality to determine resistance of a population." [] synonym: "diagnostic test" EXACT [] is_a: OBI:0002705 ! direct insecticide resistance bioassay [Term] id: OBI:0002708 name: insecticide resistance dose response assay def: "A direct insecticide resistance assay in which an insect population is exposed to a range of insecticide dosage scoring mortality to determine resistance." [] synonym: "dose response test" EXACT [] is_a: OBI:0002705 ! direct insecticide resistance bioassay [Term] id: OBI:0002709 name: insecticide resistance time response assay def: "A direct insecticide resistance assay to determine resistance as a consequence of the time of exposure to insecticide." [] synonym: "time response test" EXACT [] is_a: OBI:0002705 ! direct insecticide resistance bioassay [Term] id: OBI:0002710 name: Centre for Disease Control and Prevention bottle bioassay def: "A direct insecticide resistance diagnostic assay performs in a glass bottle coated with insecticides for detecting resistance to insecticides in vector populations." [] synonym: "CDC bottle bioassay" EXACT [] is_a: OBI:0002707 ! direct insecticide resistance diagnostic assay [Term] id: OBI:0002711 name: WHO cone kit diagnostic assay def: "A direct insecticide resistance diagnostic assay uses WHO cone kit." [] synonym: "cone DT" EXACT [] is_a: OBI:0002707 ! direct insecticide resistance diagnostic assay [Term] id: OBI:0002712 name: WHO paper kit diagnostic assay def: "A direct insecticide resistance diagnostic assay uses WHO paper kit." [] synonym: "WHO paper kit DT" EXACT [] is_a: OBI:0002707 ! direct insecticide resistance diagnostic assay [Term] id: OBI:0002713 name: WHO larvicide diagnostic assay def: "A direct insecticide resistance diagnostic assay tests survival of larvae in a medium supplemented with insecticide." [] synonym: "WHO larvicide DT" EXACT [] is_a: OBI:0002707 ! direct insecticide resistance diagnostic assay [Term] id: OBI:0002714 name: insecticide resistance dose response by bottle assay def: "An insecticide resistance dose response assay that performs in a glass bottle coated with insecticides." [] synonym: "bottle bioassay DR test" EXACT [] is_a: OBI:0002708 ! insecticide resistance dose response assay [Term] id: OBI:0002715 name: insecticide resistance dose response by survival of larvae assay def: "An insecticide resistance dose response assay that tests survival of larvae in a medium supplemented with insecticide." [] synonym: "WHO larvicide DR test" EXACT [] is_a: OBI:0002708 ! insecticide resistance dose response assay [Term] id: OBI:0002716 name: insecticide resistance dose response by WHO paper kit assay def: "An insecticide resistance dose response assay using WHO paper kit." [] synonym: "WHO paper kit DR test" EXACT [] is_a: OBI:0002708 ! insecticide resistance dose response assay [Term] id: OBI:0002717 name: insecticide resistance time response by bottle assay def: "An insecticide resistance time response assay that is performed in a glass bottle coated with insecticides, with the presence of a synergist." [] synonym: "bottle bioassay TR test" EXACT [] is_a: OBI:0002709 ! insecticide resistance time response assay [Term] id: OBI:0002718 name: insecticide resistance time response by WHO paper kit assay def: "An insecticide resistance time response assay using WHO paper kit, with the presence of a synergist." [] synonym: "WHO paper kit TR test" EXACT [] is_a: OBI:0002709 ! insecticide resistance time response assay [Term] id: OBI:0002719 name: insecticide resistance by amplification refractory mutation system assay def: "An insecticide resistance by monitoring known mutations assay that detects any mutation involving single base changes or small deletions using amplification refractory mutation system (ARMS). The ARMS is based on the use of sequence-specific PCR primers that allow amplification of test DNA only when the target allele is contained within the sample. Following an ARMS reaction the presence or absence of a PCR product is diagnostic for the presence or absence of the target allele. It can be used to analyze human genomic DNA for one or more mutations." [] synonym: "Amplification Refractory Mutation System" EXACT [] synonym: "ARMS" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay [Term] id: OBI:0002720 name: insecticide resistance by primer introduced restriction analysis PCR assay def: "An insecticide resistance by monitoring known mutations assay that detects Single Nucleotide Polymorphisms (SNPs) using PCR technique and mismatched primers that is close to the mutation of interest and digested the PCR productions using restriction enzymes." [] synonym: "PIRA-PCR" EXACT [] synonym: "polymerase chain reaction-primer-introduced restriction analysis" EXACT [] synonym: "Primer Introduced Restriction Analysis PCR" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay [Term] id: OBI:0002721 name: insecticide resistance by nested polymerase chain reaction assay def: "An insecticide resistance by monitoring known mutations assay that detects gene mutation based on nested polymerase chain reaction technique." [] synonym: "gene mutation detection by nested PCR" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay [Term] id: OBI:0002722 name: insecticide resistance by ligase detection reaction assay def: "An insecticide resistance assay that is based on monitoring known mutations using ligase detection reaction exquisitely discriminate between a mismatched and complementary DNA helix." [] is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay [Term] id: OBI:0002723 name: insecticide resistance by ligase detection reaction-fluorescent microsphere assay def: "An insecticide resistance by ligase detection reaction assay that uses fluorescently labeled conserved probes in ligase detection reaction." [] synonym: "gene mutation detection by LDR-FMA" EXACT [] synonym: "ligase detection reaction-fluorescent microsphere assay" EXACT [] is_a: OBI:0002722 ! insecticide resistance by ligase detection reaction assay [Term] id: OBI:0002724 name: insecticide resistance by PCR amplification of specific alleles assay def: "An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of specific alleles to detect polymorphic or mutant alleles." [] synonym: "allele-specific amplification and amplification refractory mutation system" EXACT [] synonym: "PASA" EXACT [] synonym: "PCR amplification of specific alleles" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay [Term] id: OBI:0002725 name: insecticide resistance by fluorogenic PCR assay def: "An insecticide resistance assay that is based on monitoring known mutations by PCR technique that uses target specific probes labeled with fluorogenic chromophores to detect gene mutation." [] is_a: OBI:0002692 ! polymerase chain reaction assay is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay [Term] id: OBI:0002726 name: insecticide resistance by PCR-RFLP assay def: "An insecticide resistance by monitoring known mutations assay based on restriction fragment length polymorphism assay." [] synonym: "PCR-RFLP" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay [Term] id: OBI:0002727 name: insecticide resistance by short interspersed elements PCR assay def: "An insecticide resistance assay that is based on monitoring known mutations by PCR amplification of short interspersed elements (SINEs)." [] synonym: "Short Interspersed Elements PCR" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay is_a: OBI:0002696 ! insecticide resistance by monitoring known mutations assay [Term] id: OBI:0002728 name: pathogen detection assay def: "An organism detection assay that detects pathogens." [] synonym: "pathogen detection method" EXACT [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0002729 name: VectorTest assay def: "A pathogen detection assay that identifies the presence or absence of specific peptide epitopes of circumsporozoite (CS) protein of the most important Plasmodium falciparum and two strains (variants 210 and 247) of the more widespread Plasmodium vivax using a dipstick wicking test strip." [] synonym: "VectorTest" EXACT [] is_a: OBI:0002728 ! pathogen detection assay [Term] id: OBI:0002730 name: pathogen detection by Rapid Analyte Measurement Platform assay def: "A pathogen detection assay that is based on Rapid Analyte Measurement Platform (RAMP) technology to quantify immunologically active substances." [] synonym: "Rapid Analyte Measurement Platform" EXACT [] is_a: OBI:0002728 ! pathogen detection assay [Term] id: OBI:0002731 name: pathogen detection by loop-mediated isothermal amplification assay def: "A pathogen detection assay that is based on loop-mediated isothermal amplification." [] synonym: "Loop-mediated isothermal amplification" EXACT [] is_a: OBI:0002728 ! pathogen detection assay [Term] id: OBI:0002732 name: blood meal assay def: "An assay that analyzes the specimen taken from blood meal fed organism, such as insect." [] synonym: "blood meal analysis" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002733 name: blood meal by counter current immunoelectrophoresis assay def: "A blood meal assay that uses a counter current immunoelectrophoresis technique." [] synonym: "CIE" EXACT [] synonym: "countercurrent immunoelectrophoresis" EXACT [] is_a: OBI:0002732 ! blood meal assay [Term] id: OBI:0002734 name: DNA based blood meal finger printing assay def: "A DNA fingerprinting assay that uses DNA extracted from blood meal fed organism, such as insect." [] synonym: "DNA based blood meal finger printing" EXACT [] is_a: OBI:0002694 ! DNA fingerprinting assay is_a: OBI:0002732 ! blood meal assay [Term] id: OBI:0002735 name: organism detection by size assay def: "An organism detection assay that is based on the size of organism." [] synonym: "by size" EXACT [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0002736 name: organism detection by cross mating assay def: "An organism detection assay that is based on genetic crossings between specimens collected in the field to determine whether fertile progeny is produced." [] synonym: "cross mating experiment" EXACT [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0002737 name: organism detection by cytological chromosome examination assay def: "An organism detection assay that is based on analysis of polytene chromosomes through cytological examination of the banding pattern of the species." [] synonym: "cytological chromosome examination" EXACT [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0002738 name: organism detection by isoenzyme electrophoresis assay def: "An organism detection assay that is based on electrophoresis to determine the isozymes that are present in a specific population to determine the species." [] synonym: "isoenzyme electrophoresis" EXACT [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0002739 name: organism detection by morphological examination assay def: "An organism detection assay that is based on examination of morphology and the use of specific taxonomic keys to determine the species of the specimen." [] synonym: "morphological examination" EXACT [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0002740 name: organism detection by PCR assay def: "An organism detection assay that is based on PCR." [] synonym: "PCR-based species identification" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0002741 name: organism detection by specific DNA hybridization assay def: "An organism detection assay that is based on DNA hybrdization." [] synonym: "species specific DNA hybridization" EXACT [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0002742 name: organism detection by salinity tolerance assay def: "An organism detection assay of mosquito species that is on the basis of mosquito survival depending on the salt concentration in the water used to lay their eggs to differentiate between morphologically very similar species." [] synonym: "salinity tolerance tests" EXACT [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0002743 name: molecular label role def: "A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay." [] synonym: "molecular tracer role" EXACT [] is_a: OBI:0000086 ! reagent role [Term] id: OBI:0002744 name: molecular label def: "A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay" [] synonym: "molecular tracer" EXACT [] is_a: CHEBI:23367 ! molecular entity is_a: OBI:0001879 ! reagent [Term] id: OBI:0002745 name: vacuum-assisted biopsy def: "A biopsy performed with a needle augmented with a vacuum device." [] synonym: "VAB" EXACT [] is_a: OBI:0002654 ! needle biopsy [Term] id: OBI:0002746 name: induced sputum specimen def: "A sputum specimen that is collected from an organism following its inhalation of a nebulized salt solution." [] is_a: OBI:0002508 ! sputum specimen [Term] id: OBI:0002747 name: passage process def: "A material processing that consists of first growing an organism in an environmental system and then removing the organism to be grown in another environmental system, a process which may be repeated with the objective of altering the organism or increasing its number." [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0002748 name: passage history record def: "A data item that is about the sequence of environmental systems in each of which is grown an organism in a passage process." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0002750 name: Oxford Nanopore MinION def: "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." [] synonym: "ONT MinION, MinION" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002751 name: Oxford Nanopore GridION Mk1 def: "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." [] synonym: "Oxford Nanopore GridION X5, GridION Mk1" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002752 name: Oxford Nanopore PromethION def: "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." [] synonym: "PromethION" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0002753 name: PRO-cap def: "Precision nuclear run-on and sequencing to detect Pol II initiation sites" [] synonym: "PRO-CAP" EXACT [] is_a: OBI:0001177 ! RNA sequencing assay is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0002754 name: cDNA library def: "A collection of DNA molecules with sequences complementary to a specified set of mRNA molecules and commonly developed by enzymatic reverse transcription." [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0002756 name: ordinal value specification def: "A categorical value specification in which the available categories were created with an explicit order." [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0002759 name: ribosomal RNA-depleted RNA sequencing assay def: "An RNA-seq assay in which highly abundant ribosomal RNAs are removed from total RNA before sequencing, resulting in more efficient transcript/gene detection." [] synonym: "rRNA-deleted RNA sequencing assay" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002760 name: metatranscriptome sequencing assay def: "An RNA-seq assay that determines the RNA sequence of microbial transcripts from a microbioal community of mixed species from a given microbiome." [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0002761 name: lipid profiling assay def: "An analyte assay assay that detects and identifies lipids resulting from biochemical and cellular metabolism." [] synonym: "lipidomic assay" EXACT [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0002762 name: single-nucleus ATAC-seq def: "An ATAC-seq assay in which single nuclei are isolated from frozen tissue samples, through a protocol designed to maximally preserve nucleus integrity during sample processing and optimize transposase-mediated fragmentation of chromatin in individual nuclei." [] synonym: "snATAC-seq" EXACT [] is_a: OBI:0002039 ! assay for transposase-accessible chromatin using sequencing [Term] id: OBI:0002763 name: 16s ribosomal gene sequencing assay def: "An amplicon sequencing assay in which the amplicon is derived from universal primers used to amplify the 16S ribosomal RNA gene from isolate bacterial genomic DNA or metagenomic DNA from a microbioal community. Resulting sequences are compared to reference 16S sequence databases to identify or classify bacteria present within a given sample." [] synonym: "16S rRNA sequencing assay" EXACT [] is_a: OBI:0001960 ! taxonomic diversity assessment by targeted gene survey is_a: OBI:0002767 ! amplicon sequencing assay [Term] id: OBI:0002764 name: single-cell ATAC-seq def: "An ATAC assay designed to robustly map the accessible genome of individual cells, using sequencing integrated into a programmable microfluidics platform, in order to provide insights into cell-to-cell variation in accessibility profiles." [] synonym: "scATAC-seq" EXACT [] is_a: OBI:0002039 ! assay for transposase-accessible chromatin using sequencing [Term] id: OBI:0002765 name: microbiome protein expression profiling assay def: "A protein expression profiling assay of microbial proteins extracted from a microbioal community of mixed species from a given microbiome." [] synonym: "metaproteomic assay" EXACT [] is_a: OBI:0000615 ! protein expression profiling assay [Term] id: OBI:0002766 name: cytokine assay def: "An analyte assay to study presence, concentration, or amount of cytokines." [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0002767 name: amplicon sequencing assay def: "A sequencing assay in which a DNA or RNA input molecule is amplified by PCR and the product sequenced." [] is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0002768 name: whole virome sequencing assay def: "A whole metagenome sequencing assay that intends to provide information on multiple genome sequences from different viruses present in the same input sample." [] is_a: OBI:0002623 ! whole metagenome sequencing assay [Term] id: OBI:0002769 name: karyotype information def: "A genetic characteristics information that is about the number and appearance of chromosomes in the nucleus of an eukaryotic cell." [] is_a: OBI:0001404 ! genetic characteristics information [Term] id: OBI:0002770 name: partial karyotype information def: "A karyotype information that is about the structural variation of partial genome rather than whole genome." [] is_a: OBI:0002769 ! karyotype information [Term] id: OBI:0002771 name: full karyotype information def: "A karyotype information that is about the structural variation of the whole genome." [] is_a: OBI:0002769 ! karyotype information [Term] id: OBI:0002772 name: presence or over-threshold value specification def: "An ordinal value specification that indicates that either \na) an analyte or mesaurand is present in an evaluant, or \nb) that the amount of analyte/measurand detected is over some predetermined threshold." [] comment: bump is_a: OBI:0002756 ! ordinal value specification [Term] id: OBI:0002773 name: single-value binding of antibody with reporter to antigen assay def: "An assay that detects the linking of antigens and antibodies via special signaling mechanisms, such as EIA, ELISA, chemiluminescence, etc. that produces one measure (quantitative or qualitative) of the analyte of interest" [] synonym: "IA" EXACT [] synonym: "immunoassay" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002774 name: platelet-poor plasma specimen def: "A blood plasma specimen that is the output of some platelet-poor plasma preparation and is the portion of plasma that contains fewer than 10,000 platelets per microliter." [] is_a: OBI:0100016 ! blood plasma specimen [Term] id: OBI:0002775 name: platelet-poor plasma preparation process def: "A material component separation process in which (1) whole blood is first centrifuged to separate red blood cells from blood plasma, which forms the supernatant, and (2) the blood plasma is then centrifuged to separate platelets from the plasm." [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0002776 name: cytometry analysis by automated gating def: "A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by an algorithm in order to quantify the frequency of different cell populations of interest." [] is_a: OBI:0200077 ! gating [Term] id: OBI:0002777 name: cytometry analysis by manual gating def: "A gating in which the output of a flow- or mass- cytometry experiment is separated into gates that were set by a human operator in order to quantify the frequency of different cell populations of interest." [] is_a: OBI:0200077 ! gating [Term] id: OBI:0002778 name: tracheal aspirate specimen def: "A specimen that is collected with a suctioning tube from the trachea." [] synonym: "tracheal wash specimen" EXACT [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0002779 name: mid-turbinate nasal swab specimen def: "A specimen that is collected with a mid-turbinate nasal swab from the turbinate area of the nasal cavity." [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002780 name: nasal aspirate specimen def: "A specimen that is collected with a suctioning tube from the nasal cavity." [] synonym: "nasal wash specimen|nasopharyngeal aspirate" EXACT [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0002781 name: lower respiratory tract aspirate specimen def: "A specimen that is collected with a suctioning tube from the lower respiratory tract." [] synonym: "lower respiratory tract wash specimen" EXACT [] is_a: OBI:0002783 ! lower respiratory tract specimen [Term] id: OBI:0002782 name: upper respiratory specimen def: "A specimen that is derived from the upper respiratory tract" [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002783 name: lower respiratory tract specimen def: "A specimen that is derived from the lower respiratory tract." [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0002784 name: anterior nasal swab specimen def: "A specimen that is derived from the anterior nasal wall" [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:0002785 name: aspiration specimen collection def: "Procedure using suction, usually with a thin needle and syringe, to remove bodily fluid or tissue." [] synonym: "aspiration procedure" EXACT [] is_a: OBI:0000659 ! specimen collection process [Term] id: OBI:0002786 name: personal protective device def: "A device which is a wearable garment designed to protect the wearer's body from injury or infection." [] synonym: "personal protective equipment" EXACT [] synonym: "PPE" EXACT [] is_a: OBI:0000968 ! device [Term] id: OBI:0002787 name: face mask def: "A personal protective device worn over the nose and mouth as a respiratory filter to inhibit the flow of particles." [] synonym: "face covering" EXACT [] synonym: "respirator" EXACT [] is_a: OBI:0002786 ! personal protective device [Term] id: OBI:0002788 name: non-medical mask def: "A face mask not manufactured according to medical equipment standards." [] synonym: "cloth mask" EXACT [] is_a: OBI:0002787 ! face mask [Term] id: OBI:0002789 name: medical mask def: "A face mask manufactured according to a recognized medical equipment standard." [] synonym: "surgical mask" EXACT [] is_a: OBI:0002787 ! face mask [Term] id: OBI:0002790 name: N95 respirator def: "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." [] synonym: "N95" EXACT [] synonym: "N95 face mask" EXACT [] synonym: "N95 facemask" EXACT [] synonym: "N95 respirator mask" EXACT [] is_a: OBI:0002787 ! face mask [Term] id: OBI:0002791 name: face shield def: "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." [] synonym: "faceshield" EXACT [] synonym: "splash shield" EXACT [] is_a: OBI:0002786 ! personal protective device [Term] id: OBI:0002792 name: patient gown def: "A personal protective clothing item which is a gown designed for use by a patient to facilitate caregiving by medical staff." [] synonym: "hospital gown" EXACT [] is_a: OBI:0002800 ! personal protective clothing item [Term] id: OBI:0002793 name: scrubs def: "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." [] synonym: "scrub clothing item" EXACT [] is_a: OBI:0002800 ! personal protective clothing item [Term] id: OBI:0002794 name: reusable patient gown def: "A patient gown intended to be reused after being laundered." [] is_a: OBI:0002792 ! patient gown [Term] id: OBI:0002795 name: disposable patient gown def: "A patient gown intended for a single period of continuous use and then disposed of." [] is_a: OBI:0002792 ! patient gown [Term] id: OBI:0002796 name: medical gown def: "A personal protective clothing item which is a gown worn by a medical professional in order to provide a barrier between patient and professional." [] synonym: "hospital gown" EXACT [] is_a: OBI:0002800 ! personal protective clothing item [Term] id: OBI:0002797 name: apron def: "A garment which is worn over other clothing and covers mainly the front of the body." [] is_a: OBI:0000968 ! device [Term] id: OBI:0002798 name: surgical gown def: "A medical gown which is subjected to a sterilization process and which is intended to be worn by a medical professional during surgical procedures." [] is_a: OBI:0002796 ! medical gown [Term] id: OBI:0002799 name: personal protective glove def: "A personal protective device which is a glove." [] is_a: OBI:0002800 ! personal protective clothing item [Term] id: OBI:0002800 name: personal protective clothing item def: "A personal protective device which consists of a garment that serves in place of or in addition to regular body clothing." [] is_a: OBI:0002786 ! personal protective device [Term] id: OBI:0002802 name: laboratory coat def: "A personal protective clothing item which is an overcoat worn by medical or laboratory professionals." [] synonym: "white coat" EXACT [] is_a: OBI:0002800 ! personal protective clothing item [Term] id: OBI:0002803 name: medical glove def: "A personal protective glove which is disposable and is used during medical examinations and procedures to help prevent cross-contamination between caregivers and patients." [] is_a: OBI:0002799 ! personal protective glove [Term] id: OBI:0002804 name: nitrile glove def: "A personal protective glove which is made out of nitrile rubber." [] is_a: OBI:0002799 ! personal protective glove [Term] id: OBI:0002805 name: transparent droplet barrier def: "A device which is a transparent constructed barrier, usually made out of acrylic (Plexiglass) or polycarbonate plastic, installed in facilities to intercept respiratory droplets, encourage physical distancing requirements." [] synonym: "transparent partition" EXACT [] is_a: OBI:0000968 ! device [Term] id: OBI:0002806 name: footwear cover def: "A personal protective device which is an impermiable material which covers a shoe or boot in order to prevent spread of specific environmental contaminants." [] synonym: "boot cover" EXACT [] synonym: "shoe cover" EXACT [] is_a: OBI:0002800 ! personal protective clothing item [Term] id: OBI:0002807 name: disposable footwear cover def: "A footwear cover which is designed for a single period of continuous use and then disposed of." [] is_a: OBI:0002806 ! footwear cover [Term] id: OBI:0002808 name: reusable footwear cover def: "A footwear cover which is designed for repeated use." [] is_a: OBI:0002806 ! footwear cover [Term] id: OBI:0002809 name: surgical N95 respirator def: "A N95 respirator which has been approved by the FDA as a surgical mask." [] synonym: "healthcare respirator" EXACT [] synonym: "medical respirator" EXACT [] synonym: "surgical N95" EXACT [] synonym: "surgical N95 respirator" EXACT [] is_a: OBI:0002790 ! N95 respirator [Term] id: OBI:0002810 name: protective coverall def: "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." [] is_a: OBI:0002800 ! personal protective clothing item [Term] id: OBI:0002811 name: protective sleeve def: "A personal protective clothing item which is a protective cover worn over the arm." [] is_a: OBI:0002800 ! personal protective clothing item [Term] id: OBI:0002812 name: protective apron def: "A personal protective clothing item which is an apron." [] is_a: OBI:0002800 ! personal protective clothing item [Term] id: OBI:0002813 name: medical cap def: "A personal protective device which is worn on the head that helps prevent transmission of contaminants contained in hair and scalp." [] synonym: "bouffant cap" EXACT [] synonym: "bouffant hat" EXACT [] synonym: "medical bonnet" EXACT [] synonym: "scrub cap" EXACT [] synonym: "surgical hat" EXACT [] is_a: OBI:0002800 ! personal protective clothing item [Term] id: OBI:0002814 name: specimen collection device def: "A device used to collect a specimen." [] is_a: OBI:0000968 ! device [Term] id: OBI:0002816 name: chromatography vial def: "A vial with cap and container material suited to optical, sanitary and handling requirements of chromatography." [] is_a: OBI:0000601 ! chromatography consumable [Term] id: OBI:0002819 name: specimen pad def: "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." [] synonym: "absorbant pad" EXACT [] synonym: "polysponge" EXACT [] synonym: "sample pad" EXACT [] synonym: "sampling sponge" EXACT [] synonym: "specimen sponge" EXACT [] synonym: "surface wipe" EXACT [] synonym: "swab" EXACT [] is_a: OBI:0002814 ! specimen collection device [Term] id: OBI:0002820 name: specimen collection swab stick def: "A specimen collection device which is a specimen pad attached to a long handle used to collect specimen material." [] synonym: "polyprobe" EXACT [] synonym: "sponge probe" EXACT [] synonym: "sponge stick" EXACT [] synonym: "sponge-stick" EXACT [] is_a: OBI:0002814 ! specimen collection device [Term] id: OBI:0002821 name: cotton swab def: "A device which is a cotton pad mounted on one or both ends of a stick." [] synonym: "Q-tip" EXACT [] synonym: "swab-sampler" EXACT [] is_a: OBI:0000968 ! device [Term] id: OBI:0002822 name: drag swab def: "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" [] is_a: OBI:0002814 ! specimen collection device [Term] id: OBI:0002823 name: pre-moistened swab stick def: "A specimen collection swab stick that is pre-moistened with liquid prior to sampling." [] is_a: OBI:0002820 ! specimen collection swab stick [Term] id: OBI:0002824 name: surface wipe def: "A sample collection device consisting of a thin, less absorbent sheet, used to collect material from surfaces." [] is_a: OBI:0002814 ! specimen collection device [Term] id: OBI:0002830 name: catheter def: "A device which is a flexible tube inserted into a body and which enables transfer of fluids into or out of a body." [] is_a: OBI:0000968 ! device [Term] id: OBI:0002897 name: surveillance process def: "An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity." [] is_a: OBI:0000066 ! investigation [Term] id: OBI:0002898 name: cluster study group role def: "A study group role that is the result of the allocation of a cluster of study-defined groupings of people in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol." [] synonym: "cluster study arm" EXACT [] is_a: OBI:0000174 ! study group role [Term] id: OBI:0002899 name: compound study group role def: "A study group role that is the result of the allocation of a compound of geographically-proximate households with a shared component in a clinical trial to receive a specific intervention/treatment, or no intervention, according to the trial's protocol." [] synonym: "compound study arm" EXACT [] is_a: OBI:0000174 ! study group role [Term] id: OBI:0002900 name: ultraviolet light source def: "A light source that provides ultraviolet (UV) light for use in a distant area using a delivery system." [] synonym: "UV light source" EXACT [] is_a: OBI:0400065 ! light source [Term] id: OBI:0002901 name: visible light source def: "A light source that provides visible light for use in a distant area using a delivery system." [] is_a: OBI:0400065 ! light source [Term] id: OBI:0002902 name: solar light source def: "A light source that light is produced from solar energy." [] is_a: OBI:0400065 ! light source [Term] id: OBI:0002904 name: adult arthropod specimen collection process def: "A live arthropod specimen collection process in which the arthropods are in the adult stage." [] synonym: "collection of adults" EXACT [] is_a: OBI:0002919 ! live arthropod specimen collection process [Term] id: OBI:0002905 name: animal-biting arthropod specimen collection by aspiration def: "An arthropod specimen collection by aspiration that occurs while the arthropod is biting an animal." [] synonym: "animal biting catch" EXACT [] is_a: OBI:0002912 ! arthropod specimen collection by aspiration [Term] id: OBI:0002906 name: animal-biting outdoor arthropod specimen collection by aspiration def: "An animal-biting arthropod specimen collection by aspiration that occurs outside a building." [] synonym: "animal biting catch - outdoors" EXACT [] is_a: OBI:0002905 ! animal-biting arthropod specimen collection by aspiration [Term] id: OBI:0002907 name: aquatic arthropod specimen collection process def: "An arthropod specimen collection process that has the objective of collecting mosquitoes from an aquatic environment." [] synonym: "aquatic environment catch" EXACT [] is_a: OBI:0002913 ! arthropod specimen collection process [Term] id: OBI:0002908 name: arthropod resting in animal house specimen collection by aspiration def: "An arthropod specimen collection by aspiration that catches specimens resting inside an animal house." [] synonym: "animal shed resting catch" EXACT [] is_a: OBI:0002912 ! arthropod specimen collection by aspiration [Term] id: OBI:0002909 name: arthropod resting outdoors on artificial support specimen collection by aspiration def: "An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on a processed material such as a wall or furniture." [] synonym: "outdoors shelter catch - artificial" EXACT [] is_a: OBI:0002911 ! arthropod resting outdoors specimen collection by aspiration [Term] id: OBI:0002910 name: arthropod resting outdoors on natural support specimen collection by aspiration def: "An arthropod resting outdoors specimen collection by aspiration that occurs while the arthropod rests on an unprocessed material such as a plant." [] synonym: "outdoors shelter catch - natural" EXACT [] is_a: OBI:0002911 ! arthropod resting outdoors specimen collection by aspiration [Term] id: OBI:0002911 name: arthropod resting outdoors specimen collection by aspiration def: "An animal-biting arthropod specimen collection by aspiration that occurs while the arthropod is resting outside a building during a period of inactivity." [] synonym: "outdoors shelter catch" EXACT [] is_a: OBI:0002905 ! animal-biting arthropod specimen collection by aspiration [Term] id: OBI:0002912 name: arthropod specimen collection by aspiration def: "A live arthropod specimen collection process that involves the use of an aspirator, a device which draws an arthropod by suction into a container." [] synonym: "catch by aspiration" EXACT [] is_a: OBI:0002904 ! adult arthropod specimen collection process [Term] id: OBI:0002913 name: arthropod specimen collection process def: "A specimen collection process that has the objective of collecting arthropods as specimens." [] synonym: "collection of arthropods" EXACT [] synonym: "field population catch" EXACT [] is_a: OBI:0000659 ! specimen collection process [Term] id: OBI:0002914 name: human-biting arthropod specimen collection by aspiration def: "An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human." [] synonym: "man biting catch" EXACT [] is_a: OBI:0002912 ! arthropod specimen collection by aspiration [Term] id: OBI:0002915 name: human-biting indoor arthropod specimen collection by aspiration def: "An arthropod specimen collection by aspiration that occurs while the arthropod is biting a human inside a building." [] synonym: "man biting catch - indoors" EXACT [] is_a: OBI:0002914 ! human-biting arthropod specimen collection by aspiration [Term] id: OBI:0002916 name: human-biting outdoor arthropod specimen collection by aspiration def: "An arthropod specimen collection by aspiration designed to catch specimens that are in the process of biting a human outside a building." [] synonym: "man biting catch - outdoors" EXACT [] is_a: OBI:0002914 ! human-biting arthropod specimen collection by aspiration [Term] id: OBI:0002917 name: knockdown arthropod specimen collection by pyrethrum spray def: "A knockdown arthropod specimen collection process in which the pesticide is pyrethrum." [] synonym: "pyrethrum spray catch" EXACT [] is_a: OBI:0002918 ! knockdown arthropod specimen collection process [Term] id: OBI:0002918 name: knockdown arthropod specimen collection process def: "An arthropod specimen collection process that involves exposing arthropods to pesticide, then collecting them once they become dead or immobilized." [] synonym: "knockdown collection" EXACT [] is_a: OBI:0002919 ! live arthropod specimen collection process [Term] id: OBI:0002919 name: live arthropod specimen collection process def: "An arthropod specimen collection process meant to collect live specimens." [] synonym: "catch of live specimens" EXACT [] is_a: OBI:0002913 ! arthropod specimen collection process [Term] id: OBI:0002920 name: arthropod trap def: "A device designed to catch arthropods." [] is_a: OBI:0000968 ! device [Term] id: OBI:0002921 name: artificial pit shelter def: "An arthropod trap, consisting of a pit dug in the ground to provide a space for arthropods to rest and be collected." [] is_a: OBI:0002939 ! resting arthropod trap [Term] id: OBI:0002922 name: baited net trap def: "An arthropod trap designed to work with an animal (which could be human) inside a netted structure. This structure is designed so that an arthropod, attracted by the animal, can fly into the netted structure but can neither escape nor reach the animal." [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002923 name: barrier trap def: "An arthropod trap consisting of a static physical barrier designed to funnel arthropods in flight into a container." [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002924 name: BG-Counter def: "A device manufactured by BioGents that is designed to count mosquitoes passing through the device, differentiating the mosquitoes from other arthropods." [] is_a: OBI:0000968 ! device [Term] id: OBI:0002925 name: BG-Sentinel trap def: "An arthropod trap that is manufactured by Biogents and is designed to attract arthropods through the use of a motorized fan to mimic convection currents produced by a human. The current also pulls arthropods into the trap, where a layer of gauze prevents the arthropods from escaping along with the air current." [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002926 name: Centers for Disease Control and Prevention light trap def: "A light trap that is designed similarly to the New Jersey trap—in that it uses motorized suction and light attractant—and is powered by a six-volt battery." [] synonym: "CDC light trap" EXACT [] is_a: OBI:0002930 ! light trap [Term] id: OBI:0002927 name: dipper for arthropod immatures def: "A device that is designed for the collection of arthropod larvae or pupae from water and has the shape of a ladle or a pan." [] synonym: "dipper for immatures" EXACT [] is_a: OBI:0000968 ! device [Term] id: OBI:0002928 name: encephalitis virus surveillance trap def: "A light trap that uses carbon dioxide as attractant. The trap consists of a container of dry ice with holes in the bottom to allow the carbon dioxide to flow downward into a separate container, in which a motorized fan creates suction to collect arthropods." [] synonym: "EVS trap" EXACT [] is_a: OBI:0002930 ! light trap [Term] id: OBI:0002929 name: gravid trap def: "An arthropod trap that is designed to collect gravid female arthropods or their eggs." [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002930 name: light trap def: "An arthropod trap that uses light as an attractant." [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002931 name: light trap for indoor use def: "A light trap designed to be placed inside a building." [] synonym: "indoor light trap" EXACT [] is_a: OBI:0002930 ! light trap [Term] id: OBI:0002932 name: light trap for outdoor use def: "A light trap designed to be placed outside a building." [] synonym: "outdoor light trap" EXACT [] is_a: OBI:0002930 ! light trap [Term] id: OBI:0002933 name: Mosquito Magnet Pro trap def: "An arthropod trap that is powered by propane and is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods." [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002934 name: MosquiTRAP def: "A gravid trap consisting of an arthropod attractant and adhesive surface." [] is_a: OBI:0002929 ! gravid trap [Term] id: OBI:0002935 name: New Jersey light trap def: "A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the light attractant." [] synonym: "New Jersey trap" EXACT [] is_a: OBI:0002930 ! light trap [Term] id: OBI:0002936 name: Onderstepoort Veterinary Institute light-suction trap def: "A light trap that is designed to use motorized suction to trap arthropods in a collection bag once they approach the attractant. The light is supplied by an 8 watt tube, and the fan providing the suction has an 11-centimeter diameter." [] synonym: "OVI light-suction trap" EXACT [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002937 name: outlet window trap def: "An arthropod trap that is positioned adjacent to a window of a building and is designed to collect arthropods flying out of the building." [] synonym: "outlet window trap" EXACT [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002938 name: ovitrap def: "An arthropod trap that consists of a container holding a mesh layer above water and is designed to trap arthropods hatched from eggs dropped over the water by gravid females." [] synonym: "oviposition trap" EXACT [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002939 name: resting arthropod trap def: "An arthropod trap that is designed to be attractive to an arthropod as a place to rest during a period of inactivity." [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002940 name: resting box trap def: "An arthropod trap that consists of a box that is open on one end. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity." [] synonym: "resting box catch" EXACT [] is_a: OBI:0002939 ! resting arthropod trap [Term] id: OBI:0002941 name: resting bucket def: "An arthropod trap that consists of a bucket, which is lined with fabric and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity (not actively seeking a host)." [] synonym: "resting bucket catch" EXACT [] is_a: OBI:0002939 ! resting arthropod trap [Term] id: OBI:0002942 name: Shannon trap def: "An arthropod trap that is made of cloth and netting and is designed to be suspended from above (e.g. from a tree). It is also designed so that the arthropod enters the trap from beneath, being attracted to some bait, and is prevented from escaping upward by the suspended cloth, which allows them to be collected from the upper interior of the trap." [] synonym: "shannon trap catch" EXACT [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0002943 name: sticky resting bucket def: "An arthropod trap that consists of a bucket, which is lined with adhesive and placed on its side, and a wet cloth inside the bucket. The placement of the box and modifications to it are done in such a way that it becomes attractive to an arthropod as a place to rest during a period of inactivity. The trap is designed for arthropods to become caught in the adhesive so that they can be collected." [] synonym: "sticky resting bucket catch" EXACT [] is_a: OBI:0002939 ! resting arthropod trap [Term] id: OBI:0002944 name: sticky trap def: "An arthropod trap that is designed to capture arthropods resting on a surface by coating the surface with adhesive." [] synonym: "sticky trap catch" EXACT [] is_a: OBI:0002939 ! resting arthropod trap [Term] id: OBI:0002945 name: population based design def: "A study design where the selection of the individuals that are included into the study are intended to be representative of all individuals in the a priori defined specific population and is done at the population level or among the population groups, generally to find the cause, incidence or spread of the disease or to see the response to the treatment, nutrition or environment." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0002946 name: fluorescence imaging-based apoptosis assay def: "A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with molecular processes of apoptosis." [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0002947 name: fluorescence imaging-based cell proliferation assay def: "A type of cell proliferation assay in which fluorescent dyes are ued to label and detect proteins or structures that can be used to count cells." [] synonym: "fluroescence imaging-based cell count assay" EXACT [] is_a: OBI:0000891 ! cell proliferation assay [Term] id: OBI:0002948 name: fluroescence imaging-based cell cycle state assay def: "A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with particular cell cycle states." [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0002949 name: fluorescence imaging-based cell viability assay def: "A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures associated with cell viability." [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0002950 name: fluorescence imaging-based drug synergy assay def: "A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures to determine if drugs applied to cells in combination have a greater effect together than the sum of their separate effects." [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0002951 name: fluorescence imaging-based cell morphology assay def: "A type of cytometry assay in which fluorescent dyes are used to label and detect proteins or structures in order to determine cell morphology." [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0002952 name: fluorescence imaging multiplex cytological profiling def: "A type of cytometry assay in which fluorescent dyes are used to stain seven major cellular components followed by automatic image capture and analysis which extracts shape, texture, and intensity parameters." [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0002953 name: protein state assay def: "A type of assay that measures the quantity and/or identity of proteins in their modficied and unmodified states where modifications include phosphorylation, methylation, acetylation, etc." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002954 name: fluorescence imaging-based protein phosphorylation state assay def: "A type of protein state assay that employs high-throughput microscopy to measure levels of proteins in different phosphorylation states." [] is_a: OBI:0002953 ! protein state assay [Term] id: OBI:0002955 name: mass spectrometry-based protein state assay def: "A type of protein state assay that employs mass spectrometry to measure levels of proteins in different phosphorylation states." [] is_a: OBI:0002953 ! protein state assay [Term] id: OBI:0002956 name: targeted, drug-modulated, mass spectrometry-based protein phoshporylation-state assay def: "A type of mass spectrometry protein state assay that measures levels of a targeted set of proteins in different phosphorylation states in response to drug perturbations." [] synonym: "P100 phosphoprotein quantification assay" EXACT [] is_a: OBI:0002955 ! mass spectrometry-based protein state assay [Term] id: OBI:0002957 name: reverse phase protein array profiling assay def: "A type of protein state assay where tissue or cell samples are lysed and then spotted onto a slide which is probed with antibodies specific to proteins with and without post-translational modifications." [] synonym: "reverse phase lysate array profiling assay" EXACT [] synonym: "RPLA assay" EXACT [] synonym: "RPPA assay" EXACT [] is_a: OBI:0002953 ! protein state assay [Term] id: OBI:0002958 name: SWATH-MS protein profiling assay def: "A type of mass spectrometry assay using a data-independent acquisition method to identify target peptides." [] synonym: "sequential window acquisition of all theoretical mass spectra protein profiling assay" EXACT [] is_a: OBI:0000615 ! protein expression profiling assay [Term] id: OBI:0002959 name: tandem mass tag mass spectrometry assay def: "A type of tandem mass spectrometry where isotopomer labels are employed for accurate quantification and identification of specific proteins." [] is_a: OBI:0003540 ! tandem mass spectrometry assay [Term] id: OBI:0002960 name: fluorescence imaging-based reporter gene assay def: "A type of reporter gene assay that employs fluorescence imaging to detect a reporter gene's expression." [] is_a: OBI:0002082 ! reporter gene assay [Term] id: OBI:0002961 name: global chromatin profiling by mass spectrometry assay def: "A type of epigenetic modification assay that employs targeted quantitative mass spectrometry to profile modifications of the core histones of chromatin." [] synonym: "GCP" EXACT [] synonym: "global chromatin epigenetic profiling" EXACT [] synonym: "global chromatin profiling" EXACT [] is_a: OBI:0002020 ! epigenetic modification assay [Term] id: OBI:0002962 name: kinase inhibitor assay def: "A type of assay that identifies compounds that inhibit the activity of kinases." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0002963 name: KINOMEscan assay def: "A type of proprietary kinase inhibitor assay that and employs a panel of kinases against which one can test compounds for their selectivity and potency in interactions with kinases, without the need to add ATP to the reactions." [] is_a: OBI:0002962 ! kinase inhibitor assay [Term] id: OBI:0002964 name: KiNativ assay def: "A type of proprietary in situ kinase inhibitor assay that employs biotinylated acyl phosphates of ATP and ADP." [] is_a: OBI:0002962 ! kinase inhibitor assay [Term] id: OBI:0002965 name: landmark transcript profiling assay def: "A type of transcription profiling assay in which a set of landmark transcripts that have been determined to provide a comprehensive profile of cell activity, plus numerous steady-state controls, are assayed via ligation-mediated amplification followed by capture on fluorescently labeled microspheres followed by detection of fluorescence." [] synonym: "L1000 mRNA profiling assay" EXACT [] is_a: OBI:0000424 ! transcription profiling assay [Term] id: OBI:0002966 name: microenvironment microarray assay def: "A type of cytometry assay where cells are incubated for three days with a standardized set of extracellular matrix proteins in combination with various ligands creating varying microenvironment perterbations for the cells. Immunofluorescent imaging of cells is used to measure features such as morphology, metabolism, cell cycle, and nuclear activity." [] synonym: "MEMA assay" EXACT [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0002967 name: microwestern meso-scale quantitative western blot assay def: "A western blot assay that provides a high-throughput, sensitive, and quantitative measurement of proteins from numerous samples via an array of small western blots on a single sheet of nitrocellulose." [] is_a: OBI:0000854 ! western blot assay [Term] id: OBI:0002968 name: positive/negative ion switching metabolite profiling assay def: "A type of metabolic profiling assay which employs a hybrid dual quadrupole linear ion trap mass spectrometer for steady-state profiling of endogenous polar metabolites from organic extractions from biological samples." [] synonym: "positive/negative ion switching metabolomic assay" EXACT [] is_a: OBI:0000366 ! metabolite profiling assay [Term] id: OBI:0002969 name: cyclic immunoflouroescence assay def: "A type of microscopy assay resulting in highly multiplexed immunofluorescence imaging through sequential rounds of imaging followed by fluorophore inactivation." [] is_a: OBI:0002119 ! microscopy assay [Term] id: OBI:0002970 name: multiplex bead-based protein state immunoassay def: "A type of protein state assay in which antibodies attached to different colored beads and fluorescent reporter dye labels are used in a multiplexed mixture to assay for proteins in specific states." [] is_a: OBI:0002953 ! protein state assay [Term] id: OBI:0002971 name: endotracheal tube specimen def: "A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected upon removal of the tube from the trachea." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002972 name: endotracheal aspirate specimen def: "A specimen that derives from a biofilm that forms on the inner surface of an endotracheal tube while the tube is in the trachea. The specimen is collected by suction without removing the tube." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0002975 name: input protein sequence start site def: "The position of the first amino acid in a protein sequence being analyzed (input protein sequence)." [] synonym: "input protein start" EXACT [] synonym: "query protein start site" EXACT [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002976 name: input protein sequence stop site def: "The position of the last amino acid in a protein sequence being analyzed (input protein sequence)." [] synonym: "input protein stop" EXACT [] synonym: "query protein stop site" EXACT [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002977 name: input gene sequence start site def: "The position of the first nucleotide in a gene sequence being analyzed (input gene sequence)." [] synonym: "input gene start" EXACT [] synonym: "query gene start site" EXACT [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002978 name: input gene sequence stop site def: "The position of the last nucelotide in a gene sequence being analyzed (input gene sequence)." [] synonym: "input gene stop" EXACT [] synonym: "query gene stop site" EXACT [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002979 name: reference protein sequence start site def: "The position of the first amino acid in a reference protein sequence (sequence being used for comparison)." [] synonym: "reference protein start" EXACT [] synonym: "subject protein start site" EXACT [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002980 name: reference protein sequence stop site def: "The position of the last amino acid in a reference protein sequence (sequence being used for comparison)." [] synonym: "reference protein stop" EXACT [] synonym: "subject protein stop site" EXACT [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002981 name: reference gene sequence start site def: "The position of the first nucleotide in a reference gene sequence (sequence being used for comparison)." [] synonym: "reference gene start" EXACT [] synonym: "subject gene start site" EXACT [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002982 name: reference gene sequence stop site def: "The position of the last nucelotide in a reference sequence (sequence being used for comparison)." [] synonym: "reference gene stop" EXACT [] synonym: "subject gene stop site" EXACT [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0002983 name: altitude measurement datum def: "A length measurement datum between a point at sea or ground level and some point above it." [] is_a: IAO:0000408 ! length measurement datum [Term] id: OBI:0002984 name: capture Hi-C assay def: "A Hi-C assay in which a selection step is performed on ligated fragments in order to enrich for ligation products containing specific regions of interest." [] synonym: "cHi-C" EXACT [] is_a: OBI:0002440 ! Hi-C assay [Term] id: OBI:0002985 name: magnetic resonance imaging assay def: "An imaging assay in which nuclear magnetic resonance is used to produce information about the interior structure and composition of an input material entity." [] synonym: "MRI" EXACT [] is_a: OBI:0000185 ! imaging assay [Term] id: OBI:0002986 name: computed tomography imaging assay def: "An imaging assay that uses a series of X-ray images to produce information about the interior structure and composition of an input material entity." [] synonym: "CAT scan" EXACT [] synonym: "computed tomography scan" EXACT [] synonym: "CT scan" EXACT [] is_a: OBI:0000185 ! imaging assay [Term] id: OBI:0002987 name: positron emission tomography imaging assay def: "An imaging assay in which positron-emitting radionuclides are used to visualize functional processes of an input material entity." [] synonym: "PET scan" EXACT [] synonym: "positron emission tomography scan" EXACT [] is_a: OBI:0000185 ! imaging assay [Term] id: OBI:0002988 name: specimen collection duration def: "A time measurement datum that is the count of collection cycles over which a specimen collection process occurs." [] synonym: "specimen collection duration" EXACT [] is_a: IAO:0000416 ! time measurement datum [Term] id: OBI:0002989 name: material supplier def: "A person or organization that provides material supplies to other people or organizations." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0002990 name: T cell receptor repertoire sequencing assay def: "A sequencing assay that determines the sequences of DNA or RNA molecules that encode the repertoire of T cell receptors within an input sample." [] synonym: "bulk TCR assay" EXACT [] synonym: "TCR repertoire sequencing assay" EXACT [] is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0002991 name: B cell receptor repertoire sequencing assay def: "A sequencing assay that determines the sequence of a DNA or RNA molecules that encode the repertoire of B cell receptors within an input sample." [] synonym: "Antibody repertoire sequencing assay" EXACT [] synonym: "BCR repertoire sequencing assay" EXACT [] synonym: "bulk BCR assay" EXACT [] is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0002992 name: prevalence of pathogen in specimens def: "A data item that is the frequency of detection of a specified pathogenic organism in collected specimens." [] synonym: "prevalence of pathogen" EXACT [] is_a: IAO:0000027 ! data item [Term] id: OBI:0002993 name: prevalence of blood meal specimens from a host organism def: "A data item that is the frequency of blood whose source is from a specified host organism in collected blood meal specimens." [] synonym: "host blood index" EXACT [] is_a: IAO:0000027 ! data item [Term] id: OBI:0002994 name: presence of blood from host organism in blood meal specimen def: "A data item that indicates whether blood in a blood meal specimen came from a specified host organism." [] synonym: "presence of blood meal host organism" EXACT [] is_a: IAO:0000027 ! data item [Term] id: OBI:0002995 name: blood meal source organism def: "An organism that is the source of a blood meal." [] synonym: "blood meal host organism" EXACT [] is_a: OBI:0100026 ! organism [Term] id: OBI:0002996 name: blood meal source role def: "A role borne by an organism that is gained during a process in which another organism ingests blood as food from the organism." [] is_a: BFO:0000023 ! role [Term] id: OBI:0002997 name: arthropod attractor role def: "A role of a material entity realized in drawing an arthropod in the direction of the material." [] synonym: "attractant" EXACT [] is_a: BFO:0000023 ! role [Term] id: OBI:0002998 name: arthropod collection process with automated identification def: "An arthropod specimen collection process that involves a device that produces data specifying the types of arthropod collected." [] is_a: OBI:0002913 ! arthropod specimen collection process [Term] id: OBI:0002999 name: gravid female arthropod specimen collection process def: "An arthropod specimen collection process that has the objective of collecting gravid female arthropods." [] is_a: OBI:0002913 ! arthropod specimen collection process [Term] id: OBI:0003000 name: resting flight-capable arthropod specimen collection process def: "An arthropod specimen collection process that occurs while an arthropod that is capable of flight is resting outdoors during a period of inactivity." [] is_a: OBI:0002913 ! arthropod specimen collection process [Term] id: OBI:0003001 name: daytime arthropod specimen collection by aspiration def: "An arthropod specimen collection by aspiration that occurs in the daytime." [] is_a: OBI:0002912 ! arthropod specimen collection by aspiration [Term] id: OBI:0003002 name: arthropod resting in human house specimen collection by aspiration def: "An arthropod specimen collection by aspiration that catches specimens resting inside a human house." [] is_a: OBI:0002912 ! arthropod specimen collection by aspiration [Term] id: OBI:0003003 name: landing arthropod specimen collection process def: "An arthropod specimen collection process that occurs while the arthropods land on a surface." [] synonym: "collection of landing insects" EXACT [] is_a: OBI:0002904 ! adult arthropod specimen collection process [Term] id: OBI:0003004 name: flying adult arthropod collection process by passive interception def: "An adult arthropod specimen collection process that has the objective of collecting arthropods capable of flight, through the use of a barrier trap." [] is_a: OBI:0002904 ! adult arthropod specimen collection process [Term] id: OBI:0003005 name: device for collection of resting adult arthropods def: "A device that is designed to provide a solid surface that is attractive to an arthropod as a place to rest during a period of inactivity." [] is_a: OBI:0000968 ! device [Term] id: OBI:0003006 name: well net for arthropod immatures def: "A device that is designed for the collection of arthropod larvae or pupae from water and consists of a conical net." [] is_a: OBI:0000968 ! device [Term] id: OBI:0003007 name: arthropod trap containing small non-human animal bait def: "An arthropod trap that uses as attractant an animal that is not human and is the size of a chicken or smaller." [] synonym: "trap containing small non-human animal bait" EXACT [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0003008 name: trap for emerging adult arthropods def: "An arthropod trap that is designed to trap an arthropod as it emerges from water at the beginning of its adult stage." [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0003009 name: ferritin assay def: "An assay that measures ferritin" [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003010 name: fibrinogen assay def: "An assay that measures fibrinogen" [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003011 name: iron assay def: "An analyte assay that measures the abundance of iron" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003012 name: ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003013 name: transferrin assay def: "An analyte assay that measures the abundance of transferrin" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:0003014 name: uric acid assay def: "An analyte assay that measures the abundance of uric acid" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003015 name: globulin assay def: "An analyte assay that measures the abundance of globulin" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003016 name: myelocyte assay def: "A cytometry assay that measures the abundance and/or characteristics of myelocytes" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003017 name: metamyelocyte assay def: "A cytometry assay that measures the abundance and/or characteristics of metamyelocytes" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003018 name: hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003019 name: promyelocyte assay def: "A cytometry assay that measures the abundance and/or characteristics of promyelocytes" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003021 name: basophil assay def: "A cytometry assay that measures the abundance and/or characteristics of basophils" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003022 name: neutrophil assay def: "A cytometry assay that measures the abundance and/or characteristics of neutrophils" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003023 name: eosinophil assay def: "A cytometry assay that measures the abundance and/or characteristics of eosinophils" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003024 name: lymphocyte assay def: "A cytometry assay that measures the abundance and/or characteristics of lymphocytes" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003025 name: monocyte assay def: "A cytometry assay that measures the abundance and/or characteristics of monocytes" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003026 name: reticulocyte assay def: "A cytometry assay that measures the abundance and/or characteristics of reticulocytes" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003027 name: macrophage assay def: "A cytometry assay that measures the abundance and/or characteristics of macrophages" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003028 name: platelet assay def: "A cytometry assay that measures the abundance and/or characteristics of platelets" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003029 name: barcode target locus role def: "An evaluant role that is realized in a taxonomic diversity assessment by targeted gene survey involving sequencing a small defined region of genome amplified by PCR." [] is_a: OBI:0000067 ! evaluant role [Term] id: OBI:0003030 name: oligonucleotide primer set def: "A processed material that consists of oligonucleotides that bear a primer role." [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0003031 name: fluorogenic PCR assay def: "A polymerase chain reaction assay that uses target specific probes labeled with fluorogenic chromophores." [] synonym: "TaqMan" EXACT [] is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0003032 name: genotyping by PCR assay def: "A genotyping assay that uses polymerase chain reaction." [] is_a: OBI:0000435 ! genotyping assay is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0003033 name: cleavage under targets and release using nuclease assay def: "A type of DNA sequencing assay employing in situ chromatin profiling in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the the supernatant for sequencing." [] synonym: "CUT&RUN assay" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0003034 name: cleavage under targets and tagmentation def: "A type of DNA sequencing assay employing in situ chromatin profiling in which a chromatin protein is bound in situ by a specific antibody, which then tethers to a protein A-Tn5 hyperactive transposase fusion protein (pA-Tn5) loaded with sequence adapters. Activation of pA-Tn5 results in factor-targeted tagmentation, generating fragments ready for PCR enrichment and DNA sequencing." [] synonym: "CUT&Tag assay" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0003035 name: coma severity assay def: "A physical examination of an organism that has the objective to determine the severity of coma in a patient." [] is_a: OBI:0002441 ! physical examination of an organism [Term] id: OBI:0003036 name: Plasmodium gametocyte detection assay def: "An assay that detects Plasmodium gametocytes in a specimen." [] is_a: OBI:0003038 ! parasite detection assay [Term] id: OBI:0003037 name: malaria rapid diagnosis assay def: "An assay that is quick and easy in the diagnosis of malaria by detecting evidence of malaria parasites (antigens) in human blood." [] synonym: "malaria rapid diagnosis test" EXACT [] is_a: OBI:0003038 ! parasite detection assay is_a: OBI:0003040 ! blood assay [Term] id: OBI:0003038 name: parasite detection assay def: "An assay that detects parasite in a specimen." [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0003039 name: feces microbiology assay def: "An organism detection assay that detects microorganisms in a feces specimen." [] synonym: "stool test for microorganisms" EXACT [] is_a: OBI:0003237 ! feces assay is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0003040 name: blood assay def: "An assay that has a blood specimen as evaulant." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003041 name: falcivax rapid diagnostic test def: "A parasite detection assay that can quickly establish the diagnosis of P. falciparum or P. vivax malaria infection by detecting the antigens in a person's blood." [] is_a: OBI:0003038 ! parasite detection assay is_a: OBI:0003040 ! blood assay [Term] id: OBI:0003042 name: optimal-IT rapid diagnostic test def: "A parasite detection assay that is rapid, sensitive, and able to differentiate between P. falciparum and other malaria parasites." [] is_a: OBI:0003038 ! parasite detection assay is_a: OBI:0003040 ! blood assay [Term] id: OBI:0003043 name: urine assay def: "An assay that has a urine specimen as evaluant." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003044 name: parasite species identification by PCR assay def: "A parasite detection by PCR assay that identifies the species of parasite." [] is_a: OBI:0003045 ! parasite detection by PCR assay [Term] id: OBI:0003045 name: parasite detection by PCR assay def: "A parasite detection assay that uses PCR." [] is_a: OBI:0002692 ! polymerase chain reaction assay is_a: OBI:0003038 ! parasite detection assay [Term] id: OBI:0003046 name: free-standing window trap def: "An arthropod trap that consists of a transparent window placed in a box that holds a liquid solution deadly to arthropods. This trap is designed to stop an arthropod in flight, causing it to fall into the liquid and die." [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0003048 name: BG-lure scent dispenser def: "A device manufactured by BioGents that is designed for operation with the BG-Sentinel trap and releases an attractant that mimics the scent of human skin." [] synonym: "BG-lure" EXACT [] is_a: OBI:0000968 ! device [Term] id: OBI:0003049 name: hand-held sweep net def: "A device that consists of a network of mesh and is designed to capture adult arthropods." [] is_a: OBI:0000968 ! device [Term] id: OBI:0003050 name: Centers for Disease Control and Prevention gravid trap def: "A gravid trap that consists of a pan holding a hay infusion, motorized fan, and collection bag. This trap is designed to attract gravid female arthropods to the infused material, which would serve as an oviposition medium, and then draw them into the bag with the current generated by the fan." [] synonym: "CDC gravid trap" EXACT [] is_a: OBI:0002929 ! gravid trap [Term] id: OBI:0003051 name: egg specimen collection process def: "An arthropod specimen collection process in which the arthropods are in the embryo stage." [] synonym: "collection of eggs" EXACT [] is_a: OBI:0002907 ! aquatic arthropod specimen collection process [Term] id: OBI:0003052 name: larval specimen collection process def: "An arthropod specimen collection process in which the arthropods are in the larval stage." [] synonym: "collection of larvae" EXACT [] is_a: OBI:0002907 ! aquatic arthropod specimen collection process [Term] id: OBI:0003053 name: pupal specimen collection process def: "An arthropod specimen collection process in which the arthropods are in the pupal stage." [] synonym: "collection of pupae" EXACT [] is_a: OBI:0002907 ! aquatic arthropod specimen collection process [Term] id: OBI:0003054 name: blood specimen in vacutainer def: "A blood specimen that is located in a vacutainer." [] synonym: "Vacutainer sample" EXACT [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:0003055 name: blood specimen on filter paper def: "A blood specimen that is located on a filter paper." [] synonym: "Filter paper sample" EXACT [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:0003056 name: proportion mapped reads def: "A sequence datum that is the specified output of a read mapping and is the ratio of the count of mapped reads to the total count of reads." [] is_a: OBI:0000973 ! sequence data [Term] id: OBI:0003057 name: antibiotic administration process def: "Administering substance in vivo where an antibiotic substance is administered to a living organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003063 name: insecticide resistance datum def: "A data item that is about resistance to an insecticide." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003064 name: organism detection datum def: "A data item that is the specified output of an organism detection assay." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003066 name: easting coordinate measurement datum def: "A one dimensional Cartesian spatial coordinate datum that is the eastward component of a distance from a point on a map projection." [] is_a: IAO:0000401 ! one dimensional cartesian spatial coordinate datum [Term] id: OBI:0003067 name: northing coordinate measurement datum def: "A one dimensional Cartesian spatial coordinate datum that is the northward component of a distance from a point on a map projection." [] is_a: IAO:0000401 ! one dimensional cartesian spatial coordinate datum [Term] id: OBI:0003068 name: clinical study center def: "Organization that undertakes a clinical study at some point in time." [] is_a: OBI:0000245 ! organization [Term] id: OBI:0003069 name: sequencing protocol def: "A protocol that, when concretized, is realized in an assay that uses chemical or biological means to infer the sequence of a biomaterial." [] is_a: OBI:0000272 ! protocol [Term] id: OBI:0003070 name: specimen collection protocol def: "A protocol that specifies processes to fulfill a specimen collection objective." [] is_a: OBI:0000272 ! protocol [Term] id: OBI:0003071 name: participant identifier def: "A symbol that denotes a participant under investigation." [] is_a: IAO:0000028 ! symbol [Term] id: OBI:0003072 name: axillary temperature measurement datum def: "A temperature measurement datum that is about an axilla." [] is_a: OBI:0003079 ! temperature measurement datum [Term] id: OBI:0003073 name: organismal body temperature measurement datum def: "A temperature measurement datum that is about an organism." [] is_a: OBI:0003079 ! temperature measurement datum [Term] id: OBI:0003074 name: common name of organism def: "A textual entity refers to a taxon or organism that is based on the normal language of everyday life; this kind of name is often contrasted with the scientific name for the same organism, which is Latinized." [] is_a: IAO:0000300 ! textual entity [Term] id: OBI:0003075 name: age since birth at time of enrollment def: "An age since birth measurement datum at the time of subject enrollment." [] is_a: OBI:0001169 ! age since birth measurement datum [Term] id: OBI:0003076 name: age since birth at time of visit def: "An age since birth measurement datum at the time of a clinical visit." [] is_a: OBI:0001169 ! age since birth measurement datum [Term] id: OBI:0003077 name: entomological data item def: "A data item that is about a collection of insects." [] synonym: "entomological measurement datum" EXACT [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003079 name: temperature measurement datum def: "A scalar measurement datum that is the result of measuring temperature." [] is_a: IAO:0000032 ! scalar measurement datum [Term] id: OBI:0003080 name: organismal body temperature measurement assay def: "An assay that detects body temperature of an organism." [] is_a: OBI:0002140 ! temperature measurement assay [Term] id: OBI:0003081 name: extraction date def: "A time measurement datum that specifies when some material was extracted from an input material." [] is_a: IAO:0000416 ! time measurement datum [Term] id: OBI:0003082 name: extraction duration time def: "A time measurement datum that is the result of measuring the duration of an extraction process." [] is_a: IAO:0000416 ! time measurement datum [Term] id: OBI:0003083 name: specimen collection time post disease onset def: "A specimen collection time measurement datum that is the measure of a time when specimens are collected after the onset of disease in a host." [] is_a: OBI:0001619 ! specimen collection time measurement datum [Term] id: OBI:0003084 name: specimen collection time post infection def: "A specimen collection time measurement datum that is the measure of a time when specimens are collected after an infection starts." [] is_a: OBI:0001619 ! specimen collection time measurement datum [Term] id: OBI:0003085 name: laboratory postal address def: "A postal address used as a directive to deliver something to a laboratory." [] synonym: "laboratory address" EXACT [] is_a: IAO:0000422 ! postal address [Term] id: OBI:0003086 name: laboratory-based population def: "A population where the collection of individuals is located and maintained in a laboratory, research, or production facility." [] is_a: OBI:0000181 ! population [Term] id: OBI:0003087 name: autofluorescence assay def: "A fluorescence detection assay in which the light that is naturally emitted by a sample is visualized after excitation of the sample with light at a suitable wavelength." [] synonym: "intrinsic fluorescence assay" EXACT [] is_a: OBI:0001501 ! fluorescence detection assay [Term] id: OBI:0003088 name: autofluorescence microscopy assay def: "An autofluorescence assay in which the light that is naturally emitted by a sample is visualized via microscopy after excitation of the sample with light at a suitable wavelength." [] is_a: OBI:0003087 ! autofluorescence assay [Term] id: OBI:0003089 name: bulk assay for transposase-accessible chromatin using sequencing def: "An assay for transposase-accessible chromatin using sequencing in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells." [] synonym: "bulk ATAC-seq" EXACT [] is_a: OBI:0002039 ! assay for transposase-accessible chromatin using sequencing [Term] id: OBI:0003090 name: bulk RNA-seq assay def: "An RNA-seq assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells." [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0003091 name: multiplexed fluorescent antibody imaging assay def: "An imaging assay in which multiple cycles consisting of fluorescent labeling, imaging, and fluorophor deactivation are used to detect multiple proteins and their locations in a given sample of tissues or cells." [] is_a: OBI:0000185 ! imaging assay [Term] id: OBI:0003092 name: Cell DIVE multiplexed imaging assay def: "A multiplexed fluorescent antibody imaging assay that involves an iterative staining, imaging and dye inactivation workflow for over 60 biomarkers on a single fixed tissue section." [] is_a: OBI:0003091 ! multiplexed fluorescent antibody imaging assay [Term] id: OBI:0003093 name: co-detection by indexing assay def: "A multiplexed fluorescent antibody imaging assay that involves a highly multiplexed analysis of up to 40 proteins in a tissue using cyclic detection of DNA-indexed antibody panels." [] synonym: "CODEX" EXACT [] is_a: OBI:0003091 ! multiplexed fluorescent antibody imaging assay [Term] id: OBI:0003094 name: fluorescence in-situ hybridization assay def: "An in-situ hybridization assay in which fluorescently labeled molecules are used to localize specific DNA or RNA sequences." [] synonym: "FISH" EXACT [] is_a: OBI:0001686 ! in-situ hybridization assay [Term] id: OBI:0003095 name: decoding amplified targeted transcripts with fluorescence in situ hybridization assay def: "A fluorescence in-situ hybridization assay which involves multiplex in situ digital quantification of targeted RNA transcripts in fresh or frozen tissue providing an understanding of the spatial organization of different cell types." [] synonym: "DARTFISH" EXACT [] is_a: OBI:0000424 ! transcription profiling assay is_a: OBI:0003094 ! fluorescence in-situ hybridization assay [Term] id: OBI:0003096 name: imaging mass cytometry assay def: "A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. The sample is then ablated with a laser and the labeled material is detected by cytometry time of flight mass spectrometry." [] synonym: "imaging CyTOF" EXACT [] synonym: "IMC" EXACT [] is_a: OBI:0002115 ! cytometry time of flight assay [Term] id: OBI:0003097 name: liquid chromatography mass spectrometry assay def: "A mass spectrometry assay where a sample mixture is first separated by liquid chromatography before being converted into ions which are characterized by using mass spectrometry based on their mass-to-charge ratio and relative abundance." [] synonym: "LC-MS" EXACT [] is_a: OBI:0000470 ! mass spectrometry assay [Term] id: OBI:0003098 name: lightsheet fluorescence microscopy assay def: "A fluorescence microscopy that involves capturing of photons emitted by fluorophores excited with a thin sheet of laser light in a sample only in a relatively narrow plane by a detection objective oriented perpendicularly to the light sheet and imaged onto a detection device such as a CCD camera." [] is_a: CHMO:0000087 ! fluorescence microscopy assay [Term] id: OBI:0003099 name: matrix assisted laser desorption ionization imaging mass spectrometry assay def: "A mass spectrometry assay that involves collection of spatially resolved mass spectra of a sample during microscopy where a pulse laser is used to produce both ionisation and vaporization. The sample is held in a matrix (such as dihydrobenzoic acid) to protect it from direct laser illumination and to separate the sample molecules. The spectra are used to visualise the spatial distribution of biomolecules by their molecular masses." [] synonym: "MALDI-IMS" EXACT [] is_a: OBI:0000470 ! mass spectrometry assay [Term] id: OBI:0003100 name: multiplexed ion beam imaging assay def: "A cytometry time of flight assay in which molecules of interest on or in cells are imaged through a system in which samples are labeled with multiple different rare-earth tagged antibodies. A primary ion beam is ued to rasterize sections under vacuum, releasing showers of secondary ions detected by cytometry time of flight mass spectrometry." [] synonym: "MIBI" EXACT [] is_a: OBI:0002115 ! cytometry time of flight assay [Term] id: OBI:0003101 name: nanospray desorption electrospray ionization assay def: "A mass spectrometry assay that analyzes organic and biological molecules on a substrate by desorption of an analyte into a solvent bridge formed between two capillaries and the analysis surface. One capillary supplies solvent to create and maintain the bridge, while the second capillary transports the dissolved analyte from the bridge to the mass spectrometer. A high voltage applied between the inlet of mass spectrometer and the primary capillary creates a self-aspirating nanospray." [] synonym: "NanoDESI" EXACT [] is_a: OBI:0000470 ! mass spectrometry assay [Term] id: OBI:0003102 name: nanodroplet processing in one pot for trace samples assay def: "A protein expression profiling assay in which proteomics sample processing is performed in nanoliter volumes. Flow cytometry or laser microdissection is employed to isolate a small population or single cells into a nanoPOTS chip. Then, liquid chromatography mass spectrometry is used to measure the global protein expression." [] synonym: "NanoPOTS" EXACT [] is_a: OBI:0000615 ! protein expression profiling assay [Term] id: OBI:0003103 name: periodic acid-Schiff staining assay def: "A histological assay which is used on tissue samples to demonstrate the presence of carbohydrates and carbohydrate compounds such as polysaccharides, mucin, glycogen, or fungal cell wall components." [] synonym: "PAS staining" EXACT [] is_a: OBI:0600020 ! histological assay [Term] id: OBI:0003104 name: single cell combinatorial indexing assay for transposase-accessessable chromatin using sequencing def: "An assay for transposase-accessible chromatin that uses sequencing which involves single cell combinatorial indexing ('sci-') strategy where nucleic acids from each of many cells are uniquely tagged through several rounds of split-pool barcoding which enables identification of single cells without single cell isolation." [] synonym: "sciATACseq" EXACT [] is_a: OBI:0002039 ! assay for transposase-accessible chromatin using sequencing [Term] id: OBI:0003105 name: single-cell combinatorial indexing RNA sequencing assay def: "A single-cell RNA sequencing assay that involves single cell combinatorial indexing ('sci-') strategy to profile the transcriptomes of single cells or nuclei without single cell isolation." [] synonym: "sciRNAseq" EXACT [] is_a: OBI:0002631 ! single-cell RNA sequencing assay [Term] id: OBI:0003106 name: sequential fluorescence in-situ hybridization assay def: "A fluorescence in-situ hybridization assay that involves ultra-resolution imaging of cell activity by targetting thousands of single molecules with fluorescent probes which find and hybridize with complementary DNA or RNA sequences in the tissue sample, thus enabling identification of those molecules directly in single cells with their spatial context preserved." [] synonym: "seqFISH" EXACT [] is_a: OBI:0003094 ! fluorescence in-situ hybridization assay [Term] id: OBI:0003107 name: slide-seq assay def: "An RNA-seq assay that involves transfer of RNA from tissue sections onto a surface covered in DNA-barcoded beads with known positions, allowing the locations of the RNA to be inferred by sequencing." [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0003108 name: single-nucleus chromatin accessibility and mRNA expression sequencing assay def: "A single-nucleus RNA sequencing assay that involves joint profiling of accessible chromatin and RNA within the same cells which enables direct matching of transcriptional regulation to its outputs." [] synonym: "SNARE-seq" EXACT [] synonym: "SNAREseq" EXACT [] is_a: OBI:0003109 ! single-nucleus RNA sequencing assay [Term] id: OBI:0003109 name: single-nucleus RNA sequencing assay def: "A RNA-seq assay that is used for profiling gene expression in individual nuclei with optimized next generation sequencing (NGS) technologies. This allows the RNA-seq profiling of cell types that are more vulnerable to the tissue dissociation process, and that are therefore underrepresented in the final data set in single cell sequencing." [] synonym: "single nuclei RNA sequencing" EXACT [] synonym: "snRNA-seq" EXACT [] synonym: "sNuc-seq" EXACT [] is_a: OBI:0001271 ! RNA-seq assay [Term] id: OBI:0003110 name: gas chromatography mass spectrometry assay def: "A mass spectrometry assay combining mass spectrometry and gas chromatography for the qualitative as well as quantitative determination of compounds." [] synonym: "GC-MS" EXACT [] is_a: OBI:0000470 ! mass spectrometry assay [Term] id: OBI:0003111 name: SOMAscan assay def: "An analyte assay that uses aptamers to detect protein analytes in serum." [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003112 name: Olink assay def: "A proximity extension assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of proteins using a high-multiplex, high-throughput protein biomarker platform. The assay utilizes two distinct oligonucleotide-labeled antibodies (‘probes’) that bind at different sites for each detected protein. When the two probes are in close proximity, a new PCR target sequence is formed by a proximity-dependent DNA polymerization event. The resulting sequence is subsequently detected and quantified using standard real-time PCR." [] is_a: OBI:0003113 ! proximity extension assay [Term] id: OBI:0003113 name: proximity extension assay def: "An analyte assay that uses quantitative polymerase chain reaction (qPCR) technology to determine the concentration/presence of an analyte or analyte complex." [] is_a: OBI:0000443 ! analyte assay is_a: OBI:0002692 ! polymerase chain reaction assay [Term] id: OBI:0003114 name: Illumina MiniSeq def: "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." [] synonym: "MiniSeq" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0003115 name: antigen detection by cytometric bead array assay def: "A cytometric bead array assay in which a series of beads are coated with antibodies specific to antigens of interest. Antigens of interest attach to antibodies on the beads. Fluorescent labeled secondary antibodies are used to detect the antigens of interest." [] is_a: OBI:0000920 ! cytometric bead array assay [Term] id: OBI:0003116 name: antibody detection by cytometric bead array assay def: "A cytometric bead array assay that detects antigen-specific antibodies. In the assay a series of beads are coated with antigens which capture antibodies specific to the antigens. Fluorescent labeled secondary antibodies are used to detect the antibodies of interest." [] is_a: OBI:0000920 ! cytometric bead array assay [Term] id: OBI:0003117 name: 3D molecular structure determination assay def: "An assay that determines the 3-dimensional configuration of a molecular entity or molecular complex." [] is_a: OBI:0600045 ! 3D structure determination assay [Term] id: OBI:0003118 name: electron-microscopy 3D molecular structure determination assay def: "A 3D molecular structure determination assay that uses electron microscopy imaging." [] is_a: OBI:0003117 ! 3D molecular structure determination assay [Term] id: OBI:0003119 name: antigen:antibody complex def: "A complex of molecular entitites which is the result of an antibody binding to an antigen." [] is_a: COB:0000080 ! complex of molecular entities [Term] id: OBI:0003120 name: epitope:MHC:TCR complex def: "A complex of molecular entities which is the result of a T cell receptor binding to a MHC-epitope complex." [] is_a: COB:0000080 ! complex of molecular entities [Term] id: OBI:0003121 name: MHC:ligand complex def: "A complex of molecular entities which is the result of a MHC molecule binding with a ligand." [] is_a: COB:0000080 ! complex of molecular entities [Term] id: OBI:0003122 name: 3D cell structure determination assay def: "A 3D structure determination assay that determines the 3-dimensional configuration of a cell." [] is_a: OBI:0001977 ! cytometry assay is_a: OBI:0600045 ! 3D structure determination assay [Term] id: OBI:0003123 name: 3D neural cell structure determination assay def: "A 3D cell structure determination assay that determines the 3-dimensional configuration of a neural cell." [] is_a: OBI:0003122 ! 3D cell structure determination assay [Term] id: OBI:0003124 name: neuron morphology assay def: "A 3D neural cell structure determination assay that determines the 3-dimensional configuration of a neuron." [] is_a: OBI:0003123 ! 3D neural cell structure determination assay [Term] id: OBI:0003125 name: mosaicism with repeat frameshift genetic sparse labeling def: "A 3D neural cell structure determination assay where sparse and stochastic methods are used to label genetically-defined neurons." [] synonym: "MORF genetic sparse labeling" EXACT [] is_a: OBI:0003123 ! 3D neural cell structure determination assay [Term] id: OBI:0003126 name: neuron morphology reconstruction assay def: "A neuron morphology assay where the morphology or structure of a neuron is represented. Often, this assay is a combination of different assays (sparse labelling, fluorescent labeling, fMOST)." [] is_a: OBI:0003124 ! neuron morphology assay [Term] id: OBI:0003127 name: B cell epitope assay def: "An immune epitope assay that characterizes the structrue of an antibody-epitope complex, or measures the binding of an antibody receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope." [] synonym: "B cell assay|any method" EXACT [] is_a: OBI:1110128 ! immune epitope assay [Term] id: OBI:0003128 name: T cell epitope assay def: "An immune epitope assay that characterizes the structrue of an epitope-T cell receptor complex, or measures the binding of a T cell receptor to epitope, or the immune response process resulting from such a binding event or the recognition of the epitope." [] synonym: "T cell assay|any method" EXACT [] is_a: OBI:1110128 ! immune epitope assay [Term] id: OBI:0003129 name: chemical mutagenesis def: "A form of random mutagenesis that produces a mutation by introducing the organism to a chemical mutagen." [] is_a: OBI:0002620 ! random mutagenesis [Term] id: OBI:0003130 name: irradiation mutagenesis def: "A form of random mutagenesis that produces a random mutation by exposing the organism to radiation." [] synonym: "radiation induced mutagenesis" EXACT [] is_a: OBI:0002620 ! random mutagenesis [Term] id: OBI:0003131 name: directed mutagenesis def: "An induced mutation in which a specific gene(s) or part of a gene(s) is altered." [] is_a: OBI:0001154 ! induced mutagenesis [Term] id: OBI:0003132 name: endonuclease mediated mutagenesis def: "A directed mutagenesis in which guide RNAs and an endonuclease (cas9, TALEN) are used to introduce a mutation at a specific location in a gene." [] is_a: OBI:0003131 ! directed mutagenesis [Term] id: OBI:0003133 name: cas mediated mutagenesis def: "An endonuclease mediated mutagenesis in which guide RNAs and cas are used to introduce a mutation at a specific location in the genome." [] synonym: "CRISPR mediated mutagenesis" EXACT [] synonym: "CRISPR/cas mediated mutagenesis" EXACT [] is_a: OBI:0003132 ! endonuclease mediated mutagenesis [Term] id: OBI:0003134 name: TALEN mediated mutagenesis def: "An endonuclease mediated mutagenesis in which guide RNAs and transcription activator-like effector nucleases (TALENs) are used to introduce a mutation at a specific location in the genome." [] is_a: OBI:0003132 ! endonuclease mediated mutagenesis [Term] id: OBI:0003135 name: zinc finger mediated mutagenesis def: "An endonuclease mediated mutagenesis in which synthetic zinc-finger proteins designed to target specific DNA sequences are used to introduce a mutation at a specific location in the genome." [] synonym: "ZFN mediated mutagenesis" EXACT [] is_a: OBI:0003132 ! endonuclease mediated mutagenesis [Term] id: OBI:0003136 name: transgenic mutagenesis def: "A form of random mutagenesis that produces a mutation by introducing a construct into the genome of an organism in a random or semi-random fashion." [] is_a: OBI:0002620 ! random mutagenesis [Term] id: OBI:0003137 name: gene-trap mutagenesis def: "A transgenic mutagenesis that produces a mutation by introducing a construct designed to capture the expression of an endogenous gene by creating a spliced fusion transcript when inserted into the genome of an organism." [] is_a: OBI:0003136 ! transgenic mutagenesis [Term] id: OBI:0003138 name: enhancer-trap mutagenesis def: "A transgenic mutagenesis that produces a mutation by introducing a construct designed to monitor transcriptionally active regions when inserted into the genome of an organism by inserting a reporter gene that requires cis-acting DNA sequences in the genome to activate reporter gene expression." [] is_a: OBI:0003136 ! transgenic mutagenesis [Term] id: OBI:0003139 name: targeted mutagenesis def: "A directed mutation in which a construct is used to introduce a mutation into a specific genome location through homologous recombination." [] synonym: "gene targeting by homologous recombination" EXACT [] is_a: OBI:0003131 ! directed mutagenesis [Term] id: OBI:0003140 name: transposon-induced mutagenesis def: "A random mutagenesis in which expression of a transposase causes the mobilization of an artificial or modified transposable element with the insertion of the element into the genome creating a mutation." [] is_a: OBI:0002620 ! random mutagenesis [Term] id: OBI:0003141 name: categorical binding datum def: "A binding datum that is expressed as a categorical value." [] synonym: "qualitative binding datum" EXACT [] is_a: OBI:0001181 ! binding datum [Term] id: OBI:0003142 name: quantitative binding datum def: "A binding datum that is expressed using numbers." [] is_a: OBI:0001181 ! binding datum [Term] id: OBI:0003143 name: EC50 binding datum def: "A quantitative binding datum that is expressed as a half-maximal effective concentration (EC50)." [] is_a: OBI:0001180 ! half maximal effective concentration (EC50) is_a: OBI:0003142 ! quantitative binding datum [Term] id: OBI:0003144 name: IC50 binding datum def: "A quantitative binding datum that is expressed as a half-maximal inhibitory concentration (IC50)." [] is_a: OBI:0001191 ! half maximal inhibitory concentration (IC50) is_a: OBI:0003142 ! quantitative binding datum [Term] id: OBI:0003145 name: assay measuring quantitative binding of a MHC:ligand complex def: "An assay that detects the binding of a MHC molecule with a ligand, and produces a quantitative measurement of the binding as an output." [] synonym: "quantitative binding|binding assay" EXACT [] is_a: OBI:1110126 ! assay measuring binding of a MHC:ligand complex [Term] id: OBI:0003146 name: assay measuring quantitative binding of an antigen:antibody complex def: "An assay that detects the binding of an antigen with an antibody, and produces a quantitative measurement of the binding as an output." [] synonym: "quantitative binding|binding assay" EXACT [] is_a: OBI:1110127 ! assay measuring binding of a B cell epitope:antibody complex [Term] id: OBI:0003147 name: assay measuring quantitative binding of an epitope:MHC:TCR complex def: "An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a quantitative measurement of the binding as an output." [] synonym: "quantitative binding|binding assay" EXACT [] is_a: OBI:1110037 ! assay measuring binding of a T cell epitope:MHC:TCR complex [Term] id: OBI:0003148 name: albumin concentration assay def: "An albumin assay that measures the concentration of albumin in a specimen." [] is_a: OBI:2100022 ! albumin assay [Term] id: OBI:0003149 name: basophil percentage assay def: "A basophil assay that measures the percentage of basophils in a specimen." [] is_a: OBI:0003021 ! basophil assay [Term] id: OBI:0003150 name: calcium cation concentration assay def: "A calcium cation assay that measures the concentration of calcium cations in a specimen." [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:0003151 name: chloride concentration assay def: "A chloride assay that measures the concentration of chloride in a specimen." [] is_a: OBI:2100010 ! chloride assay [Term] id: OBI:0003152 name: cholesterol concentration assay def: "A cholesterol assay that measures the concentration of cholesterol in a specimen." [] is_a: OBI:2100031 ! cholesterol assay [Term] id: OBI:0003153 name: creatinine concentration assay def: "A creatinine assay that measures the concentration of creatinine in a specimen." [] is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:0003154 name: eosinophil percentage assay def: "An eosinophil assay that measures the percentage of eosinophils in a specimen." [] is_a: OBI:0003023 ! eosinophil assay [Term] id: OBI:0003155 name: globulin concentration assay def: "A globulin assay that measures the concentration of globulin in a specimen." [] is_a: OBI:0003015 ! globulin assay [Term] id: OBI:0003156 name: hemoglobin concentration assay def: "A hemoglobin assay that measures the amount of hemoglobin in a specimen." [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:0003157 name: high-density lipoprotein cholesterol concentration assay def: "A high-density lipoprotein cholesterol assay that measures the concentration of high-density lipoprotein cholesterol in a specimen." [] is_a: OBI:2100030 ! high-density lipoprotein cholesterol assay [Term] id: OBI:0003158 name: iron concentration assay def: "An iron assay that measures the concentration of iron cation in a specimen." [] is_a: OBI:0003011 ! iron assay [Term] id: OBI:0003159 name: low-density lipoprotein cholesterol concentration assay def: "A low-density lipoprotein cholesterol assay that measures the concentration of low-density lipoprotein cholesterol in a specimen." [] is_a: OBI:2100032 ! low-density lipoprotein cholesterol assay [Term] id: OBI:0003160 name: lymphocyte percentage assay def: "A lymphocyte assay that measures the percentage of lymphocytes in a specimen." [] is_a: OBI:0003024 ! lymphocyte assay [Term] id: OBI:0003161 name: metamyelocyte count assay def: "A metamyelocyte assay that measures the number of metamyelocytes in a specimen." [] is_a: OBI:0003017 ! metamyelocyte assay [Term] id: OBI:0003162 name: metamyelocyte percentage assay def: "A metamyelocyte assay that measures the percentage of metamyelocytes in a specimen." [] is_a: OBI:0003017 ! metamyelocyte assay [Term] id: OBI:0003163 name: methemoglobin percentage assay def: "A methemoglobin assay that measures the percentage of methemoglobin in a specimen." [] is_a: OBI:2100040 ! methemoglobin assay [Term] id: OBI:0003164 name: monocyte percentage assay def: "A monocyte assay that measures the percentage of monocytes in a specimen." [] is_a: OBI:0003025 ! monocyte assay [Term] id: OBI:0003165 name: myelocyte count assay def: "A myelocyte assay that measures the number of myelocytes in a specimen." [] is_a: OBI:0003016 ! myelocyte assay [Term] id: OBI:0003166 name: neutrophil percentage assay def: "A neutrophil assay that measures the percentage of neutrophils in a specimen." [] is_a: OBI:0003022 ! neutrophil assay [Term] id: OBI:0003167 name: phosphate ion concentration assay def: "A phosphate ion assay that measures the concentration of phosphate ions in a specimen." [] is_a: OBI:2100015 ! phosphate ion assay [Term] id: OBI:0003168 name: potassium(1+) concentration assay def: "A potassium(1+) assay that measures the concentration of potassium(1+) in a specimen." [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:0003170 name: reticulocyte percentage assay def: "A reticulocyte assay that measures the percentage of reticulocytes in a specimen." [] is_a: OBI:0003026 ! reticulocyte assay [Term] id: OBI:0003171 name: sodium(1+) concentration assay def: "A sodium(1+) assay that measures the concentration of sodium(1+) in a specimen." [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:0003172 name: thyroid stimulating hormone concentration assay def: "A thyroid stimulating hormone assay that measures the concentration of thyroid stimulating hormone in a specimen." [] is_a: OBI:2100033 ! thyroid stimulating hormone assay [Term] id: OBI:0003173 name: triglyceride concentration assay def: "A triglyceride assay that measures the concentration of triglycerides in a specimen." [] is_a: OBI:2100029 ! triglyceride assay [Term] id: OBI:0003174 name: 3,3',5'-triiodothyronine concentration assay def: "A 3,3',5'-triiodothyronine assay that measures the concentration of 3,3',5'-triiodothyronine in a specimen." [] is_a: OBI:2100046 ! 3,3',5'-triiodothyronine assay [Term] id: OBI:0003175 name: fibrinogen concentration assay def: "A fibrinogen assay that measures the concentration of fibrinogen in a specimen." [] is_a: OBI:0003010 ! fibrinogen assay [Term] id: OBI:0003176 name: free thyroxine concentration assay def: "A thyroxine assay that measures the concentration of free thyroxine in a specimen." [] is_a: OBI:2100035 ! thyroxine assay [Term] id: OBI:0003177 name: total thyroxine concentration assay def: "A thyroxine assay that measures the concentration of total thyroxine in a specimen." [] is_a: OBI:2100035 ! thyroxine assay [Term] id: OBI:0003180 name: direct bilirubin concentration assay def: "A bilirubin IXalpha assay that measures the concentration of direct bilirubin in a specimen." [] is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:0003181 name: indirect bilirubin concentration assay def: "A bilirubin IXalpha assay that measures the concentration of indirect bilirubin in a specimen." [] is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:0003182 name: total bilirubin concentration assay def: "A bilirubin IXalpha assay that measures the concentration of total bilirubin in a specimen." [] is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:0003183 name: mean cell hemoglobin assay def: "A hemoglobin assay that measures the average concentration of hemoglobin in a population of erythrocytes." [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:0003184 name: mean cell hemoglobin concentration assay def: "A hemoglobin assay that measures the concentration of hemoglobin in a specimen." [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:0003185 name: mean platelet volume assay def: "A platelet assay that measures the average volume of platelets in a specimen." [] is_a: OBI:0003028 ! platelet assay [Term] id: OBI:0003186 name: immature neutrophil count assay def: "A neutrophil assay that measures the number of immature neutrophils in a specimen." [] is_a: OBI:0003022 ! neutrophil assay [Term] id: OBI:0003187 name: immature neutrophil percentage assay def: "An neutrophil assay that measures the percentage of immature neutrophils in a specimen." [] is_a: OBI:0003022 ! neutrophil assay [Term] id: OBI:0003188 name: nucleated erythrocyte percentage assay def: "An erythrocyte assay that measures the percentage of nucleated erythrocytes in a specimen." [] is_a: OBI:0003190 ! erythrocyte assay [Term] id: OBI:0003189 name: mean cell volume assay def: "An erythrocyte assay that measures the average volume of erythrocytes in a specimen." [] is_a: OBI:0003190 ! erythrocyte assay [Term] id: OBI:0003190 name: erythrocyte assay def: "A cytometry assay that measures the abundance and/or characteristics of erythrocytes." [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:0003191 name: manual hematocrit assay def: "A hematocrit assay that measures the percentage of erythrocytes in a specimen by manual processes." [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:0003192 name: adiponectin assay def: "An analyte assay that measures the abundance of adiponectin" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:0003193 name: adiponectin concentration assay def: "An adiponectin assay that measures the concentration of adiponectin in a specimen." [] is_a: OBI:0003192 ! adiponectin assay [Term] id: OBI:0003194 name: creatine assay def: "An analyte assay that measures the abundance of creatine" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003195 name: creatine concentration assay def: "A creatine assay that measures the concentration of creatine in a specimen." [] is_a: OBI:0003194 ! creatine assay [Term] id: OBI:0003196 name: estradiol assay def: "An analyte assay that measures the abundance of estradiol" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003197 name: estradiol concentration assay def: "An estradiol assay that measures the concentration of estradiol in a specimen." [] is_a: OBI:0003196 ! estradiol assay [Term] id: OBI:0003202 name: leptin assay def: "An analyte assay that measures the abundance of leptin" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:0003203 name: leptin concentration assay def: "An leptin assay that measures the concentration of leptin in a specimen." [] is_a: OBI:0003202 ! leptin assay [Term] id: OBI:0003204 name: lipoprotein concentration assay def: "An analyte assay that measures the abundance of lipoprotein" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003205 name: high-density lipoprotein concentration assay def: "A lipoprotein concentration assay that measures the concentration of high-density lipoprotein in a specimen." [] is_a: OBI:0003204 ! lipoprotein concentration assay [Term] id: OBI:0003206 name: low-density lipoprotein concentration assay def: "A lipoprotein concentration assay that measures the concentration of low-density lipoprotein in a specimen." [] is_a: OBI:0003204 ! lipoprotein concentration assay [Term] id: OBI:0003207 name: very-low-density lipoprotein concentration assay def: "A lipoprotein concentration assay that measures the concentration of very-low-density lipoprotein in a specimen." [] is_a: OBI:0003204 ! lipoprotein concentration assay [Term] id: OBI:0003208 name: luteinizing hormone assay def: "An analyte assay that measures the abundance of luteinizing hormone" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003209 name: luteinizing hormone concentration assay def: "A luteinizing hormone assay that measures the concentration of luteinizing hormone in a specimen." [] is_a: OBI:0003208 ! luteinizing hormone assay [Term] id: OBI:0003210 name: nitrite assay def: "An analyte assay that measures the abundance of nitrite" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003211 name: nitrite concentration assay def: "A nitrite assay that measures the concentration of nitrite in a specimen." [] is_a: OBI:0003210 ! nitrite assay [Term] id: OBI:0003212 name: phospholipid assay def: "An analyte assay that measures the abundance of phospholipid" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003213 name: phospholipid concentration assay def: "A phospholipid assay that measures the concentration of phospholipids in a specimen." [] is_a: OBI:0003212 ! phospholipid assay [Term] id: OBI:0003214 name: progesterone assay def: "An analyte assay that measures the abundance of progesterone" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003215 name: progesterone concentration assay def: "A progesterone assay that measures the concentration of progesterone in a specimen." [] is_a: OBI:0003214 ! progesterone assay [Term] id: OBI:0003216 name: testosterone assay def: "An analyte assay that measures the abundance of testosterone" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003217 name: testosterone concentration assay def: "A testosterone assay that measures the concentration of testosterone in a specimen." [] is_a: OBI:0003216 ! testosterone assay [Term] id: OBI:0003218 name: bile salt assay def: "An analyte assay that measures the abundance of bile salt" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003219 name: bile salt concentration assay def: "A bile salt assay that measures the concentration of bile salt in a specimen." [] is_a: OBI:0003218 ! bile salt assay [Term] id: OBI:0003220 name: fatty acid assay def: "An analyte assay that measures the abundance of fatty acid" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003221 name: free fatty acid concentration assay def: "A fatty acid assay that measures the concentration of free fatty acids in a specimen." [] is_a: OBI:0003220 ! fatty acid assay [Term] id: OBI:0003222 name: insulin assay def: "An analyte assay that measures the abundance of insulin" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003223 name: insulin concentration assay def: "A insulin assay that measures the concentration of insulin in a specimen." [] is_a: OBI:0003222 ! insulin assay [Term] id: OBI:0003224 name: follicle stimulating hormone assay def: "An analyte assay that measures the abundance of follicle stimulating hormone" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:0003225 name: follicle stimulating hormone concentration assay def: "A follicle stimulating hormone assay that measures the concentration of follicle stimulating hormone in a specimen." [] is_a: OBI:0003224 ! follicle stimulating hormone assay [Term] id: OBI:0003226 name: total lymphocyte count assay def: "A lymphocyte assay that measures the number of lymphocytes and large unstained cells in a specimen." [] is_a: OBI:0003024 ! lymphocyte assay [Term] id: OBI:0003227 name: total lymphocyte percentage assay def: "A lymphocyte assay that measures the percentage of lymphocytes and large unstained cells in a specimen." [] is_a: OBI:0003024 ! lymphocyte assay [Term] id: OBI:0003228 name: fluorescent immunospot assay def: "A cytometry assay that detects the presence of cells that secrete a material of interest (analyte). In the assay, a plate is coated with an antibody specific to the analyte of interest. These antibodies capture the analytes secreted by the cells. The analytes are then detected using fluorescent labeled secondary antibodies." [] synonym: "FLUOROSPOT" EXACT [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003229 name: plasma proteomics assay def: "A proteomics profiling assay that detects proteins in a blood plasma specimen." [] is_a: OBI:0001318 ! proteomic profiling by array assay [Term] id: OBI:0003230 name: T cell activation induced marker assay def: "A flow cytometry assay that detects the presence/amount of antigen-specific T cells without the need to identify their cytokine production. Instead, antigen-specific T cells are detected on the basis of upregulation of TCR stimulation-induced surface markers." [] is_a: OBI:0000916 ! flow cytometry assay [Term] id: OBI:0003231 name: leukapheresis def: "A blood harvesting process in which white blood cells are separated from a blood specimen." [] is_a: OBI:1110095 ! blood harvesting [Term] id: OBI:0003232 name: cerebrospinal fluid assay def: "An assay that has a cerebrospinal fluid specimen as evaluant." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003233 name: endotracheal aspirate assay def: "An assay that has an endotracheal aspirate specimen as evaluant." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003234 name: induced sputum assay def: "An assay that has an induced sputum specimen as evaluant." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003235 name: lung assay def: "An assay that has a lung specimen as evaluant." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003236 name: milk assay def: "An assay that has a milk specimen as evaluant." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003237 name: feces assay def: "An assay that has a feces specimen as evaluant." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003238 name: umbilical cord blood assay def: "An assay that has an umbilical cord blood specimen as evaluant." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003239 name: saliva assay def: "An assay that has a saliva specimen as evaluant." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003240 name: cerebrospinal fluid microbiology assay def: "An organism detection assay that detects microorganisms in a cerebrospinal fluid specimen." [] is_a: OBI:0003232 ! cerebrospinal fluid assay is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0003241 name: endotracheal tube aspirate microbiology assay def: "An organism detection assay that detects microorganisms in an endotracheal aspirate specimen." [] is_a: OBI:0003233 ! endotracheal aspirate assay is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0003242 name: induced sputum microbiology assay def: "An organism detection assay that detects microorganisms in an induced sputum specimen." [] is_a: OBI:0003234 ! induced sputum assay is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0003243 name: blood assay datum def: "A data item that is the specified output of a blood assay." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003244 name: blood microbiology datum def: "An organism detection datum that is the specified output of a blood microbiology assay." [] is_a: OBI:0003064 ! organism detection datum is_a: OBI:0003243 ! blood assay datum [Term] id: OBI:0003245 name: feces assay datum def: "A data item that is the specified output of a feces assay." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003246 name: feces microbiology datum def: "An organism detection datum that is the specified output of a feces microbiology assay." [] is_a: OBI:0003064 ! organism detection datum is_a: OBI:0003245 ! feces assay datum [Term] id: OBI:0003247 name: urine assay datum def: "A data item that is the specified output of a urine assay." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003248 name: urine microbiology datum def: "An organism detection datum that is the specified output of a urine microbiology assay." [] is_a: OBI:0003064 ! organism detection datum is_a: OBI:0003247 ! urine assay datum [Term] id: OBI:0003249 name: induced sputum assay datum def: "A data item that is the specified output of a induced sputum assay." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003250 name: biomedical laboratory organization def: "An organization that performs assays, processes specimens, analyses data and conducts planned processes relevant to the life sciences." [] synonym: "laboratory" EXACT [] is_a: OBI:0000245 ! organization [Term] id: OBI:0003251 name: induced sputum microbiology datum def: "An organism detection datum that is the specified output of an induced sputum microbiology assay." [] is_a: OBI:0003064 ! organism detection datum is_a: OBI:0003249 ! induced sputum assay datum [Term] id: OBI:0003252 name: cerebrospinal fluid assay datum def: "A data item that is the specified output of a cerebrospinal fluid assay." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003253 name: cerebrospinal fluid microbiology datum def: "An organism detection datum that is the specified output of a cerebrospinal fluid microbiology assay." [] is_a: OBI:0003064 ! organism detection datum is_a: OBI:0003252 ! cerebrospinal fluid assay datum [Term] id: OBI:0003254 name: endotracheal aspirate assay datum def: "An organism detection datum that is the specified output of an endotracheal aspirate assay." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003255 name: endotracheal tube aspirate microbiology datum def: "An organism detection datum that is the specified output of an endotracheal tube aspirate microbiology assay." [] is_a: OBI:0003064 ! organism detection datum is_a: OBI:0003254 ! endotracheal aspirate assay datum [Term] id: OBI:0003256 name: lung microbiology datum def: "An organism detection datum that is the specified output of a lung microbiology assay." [] is_a: OBI:0003064 ! organism detection datum [Term] id: OBI:0003257 name: nasopharyngeal or oropharyngeal swab microbiology datum def: "An organism detection datum that is the specified output of a nasopharyngeal or oropharyngeal swab microbiology assay." [] is_a: OBI:0003064 ! organism detection datum [Term] id: OBI:0003258 name: pleural fluid microbiology datum def: "An organism detection datum that is the specified output of a pleural fluid microbiology assay." [] is_a: OBI:0003064 ! organism detection datum [Term] id: OBI:0003259 name: umbilical cord blood assay datum def: "A data item that is the specified output of an umbilical cord blood assay." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003260 name: umbilical cord blood microbiology datum def: "An organism detection datum that is the specified output of an umbilical cord blood microbiology assay." [] is_a: OBI:0003244 ! blood microbiology datum is_a: OBI:0003259 ! umbilical cord blood assay datum [Term] id: OBI:0003261 name: bacteria in blood datum def: "A blood microbiology datum that is about bacteria." [] is_a: OBI:0003244 ! blood microbiology datum [Term] id: OBI:0003262 name: virus in blood datum def: "A blood microbiology datum that is about a virus." [] is_a: OBI:0003244 ! blood microbiology datum [Term] id: OBI:0003263 name: eukaryota in blood datum def: "A blood microbiology datum that is about eukaryota." [] is_a: OBI:0003244 ! blood microbiology datum [Term] id: OBI:0003264 name: bacteria in feces datum def: "A feces microbiology datum that is about bacteria." [] is_a: OBI:0003246 ! feces microbiology datum [Term] id: OBI:0003265 name: eukaryota in feces datum def: "A feces microbiology datum that is about eukaryota." [] is_a: OBI:0003246 ! feces microbiology datum [Term] id: OBI:0003266 name: virus in feces datum def: "A feces microbiology datum that is about a virus." [] is_a: OBI:0003246 ! feces microbiology datum [Term] id: OBI:0003267 name: eukaryota in urine datum def: "A urine microbiology datum that is about eukaryota." [] is_a: OBI:0003248 ! urine microbiology datum [Term] id: OBI:0003268 name: bacteria in induced sputum datum def: "An induced sputum microbiology datum that is about bacteria." [] is_a: OBI:0003251 ! induced sputum microbiology datum [Term] id: OBI:0003269 name: eukaryota in induced sputum datum def: "An induced sputum microbiology datum that is about eukaryota." [] is_a: OBI:0003251 ! induced sputum microbiology datum [Term] id: OBI:0003270 name: virus in induced sputum datum def: "An induced sputum microbiology datum that is about a virus." [] is_a: OBI:0003251 ! induced sputum microbiology datum [Term] id: OBI:0003271 name: bacteria in endotracheal tube aspirate datum def: "An endotracheal tube aspirate microbiology datum that is about bacteria." [] is_a: OBI:0003255 ! endotracheal tube aspirate microbiology datum [Term] id: OBI:0003272 name: bacteria in lung datum def: "A lung microbiology datum that is about bacteria." [] is_a: OBI:0003256 ! lung microbiology datum [Term] id: OBI:0003273 name: eukaryota in lung datum def: "A lung microbiology datum that is about eukaryota." [] is_a: OBI:0003256 ! lung microbiology datum [Term] id: OBI:0003274 name: virus in lung datum def: "A lung microbiology datum that is about a virus." [] is_a: OBI:0003256 ! lung microbiology datum [Term] id: OBI:0003275 name: bacteria in nasopharyngeal or oropharyngeal swab datum def: "A nasopharyngeal or oropharyngeal swab microbiology datum that is about bacteria." [] is_a: OBI:0003257 ! nasopharyngeal or oropharyngeal swab microbiology datum [Term] id: OBI:0003276 name: eukaryota in nasopharyngeal or oropharyngeal swab datum def: "A nasopharyngeal or oropharyngeal swab microbiology datum that is about eukaryota." [] is_a: OBI:0003257 ! nasopharyngeal or oropharyngeal swab microbiology datum [Term] id: OBI:0003277 name: virus in nasopharyngeal or oropharyngeal swab datum def: "A nasopharyngeal or oropharyngeal swab microbiology datum that is about a virus." [] is_a: OBI:0003257 ! nasopharyngeal or oropharyngeal swab microbiology datum [Term] id: OBI:0003278 name: bacteria in pleural fluid datum def: "A pleural fluid microbiology datum that is about bacteria." [] is_a: OBI:0003258 ! pleural fluid microbiology datum [Term] id: OBI:0003279 name: eukaryota in pleural fluid datum def: "A pleural fluid microbiology datum that is about eukaryota." [] is_a: OBI:0003258 ! pleural fluid microbiology datum [Term] id: OBI:0003280 name: virus in pleural fluid datum def: "A pleural fluid microbiology datum that is about a virus." [] is_a: OBI:0003258 ! pleural fluid microbiology datum [Term] id: OBI:0003281 name: eukaryota in umbilical cord blood datum def: "An umbilical cord blood microbiology datum that is about eukaryota." [] is_a: OBI:0003260 ! umbilical cord blood microbiology datum is_a: OBI:0003263 ! eukaryota in blood datum [Term] id: OBI:0003282 name: lung microbiology assay def: "An organism detection assay that detects microorganisms in a lung specimen." [] is_a: OBI:0003235 ! lung assay is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0003283 name: pleural fluid microbiology assay def: "An organism detection assay that detects microorganisms in a pleural fluid specimen." [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0003284 name: umbilical cord blood microbiology assay def: "An organism detection assay that detects microorganisms in an umbilical cord blood specimen." [] is_a: OBI:0002649 ! blood microbiology assay is_a: OBI:0003238 ! umbilical cord blood assay [Term] id: OBI:0003285 name: nasopharyngeal or oropharyngeal swab microbiology assay def: "An organism detection assay that detects microorganisms in a nasopharyngeal or oropharyngeal swab specimen." [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0003286 name: urine microbiology assay def: "An organism detection assay that detects microorganisms in a urine specimen." [] is_a: OBI:0003043 ! urine assay is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0003287 name: multiplex real time polymerase chain reaction assay def: "A real time polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle." [] synonym: "multiplexed real time polymerase chain reaction assay" EXACT [] is_a: OBI:0000893 ! real time polymerase chain reaction assay [Term] id: OBI:0003288 name: multiplex real time reverse-transcription polymerase chain reaction assay def: "A real time reverse-transcription polymerase chain reaction assay in which multiple DNA sequences are amplified in a single cycle." [] synonym: "multiplexed real time reverse-transcription polymerase chain reaction assay" EXACT [] is_a: OBI:0000911 ! real time reverse-transcription polymerase chain reaction assay [Term] id: OBI:0003289 name: mosquito membrane feeding device def: "A device that contains blood in a membrane penetrable to mosquitoes, designed to feed mosquitoes without the need for an animal host." [] is_a: OBI:0000968 ! device [Term] id: OBI:0003290 name: mosquito membrane feeding assay def: "An assay that evaluates host-to-mosquito transmission of a parasite organism by feeding a specimen of host blood infected with the parasite organism to a collection of mosquitoes through a mosquito membrane feeding device and, after a given time, dissecting the mosquitoes and counting the number of parasite organisms within them." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003291 name: in silico design def: "A study design that is executed primarily on a computer." [] is_a: OBI:0500000 ! study design [Term] id: OBI:0003292 name: cytometric bead array assay measuring epitope specific granulysin release by T cells def: "A cytometric bead array assay that detects epitope specific granulysin release by T cells." [] synonym: "granulysin release|cytometric bead array" EXACT [] is_a: OBI:0001810 ! assay measuring epitope specific granulysin release by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0003293 name: cytometric bead array assay measuring epitope specific perforin release by T cells def: "A cytometric bead array assay that detects epitope specific perforin release by T cells." [] synonym: "perforin release|cytometric bead array" EXACT [] is_a: OBI:0001497 ! assay measuring epitope specific perforin release by T cells is_a: OBI:0003115 ! antigen detection by cytometric bead array assay [Term] id: OBI:0003294 name: modified acid-fast stain microscopy assay def: "A microscopy assay that uses staining to identify acid-fast organisms in a specimen and does not require heating." [] is_a: OBI:0002119 ! microscopy assay [Term] id: OBI:0003295 name: positive binding datum def: "A categorical binding datum that states that there is a significant disposition of two or more entities to form a complex." [] is_a: OBI:0003141 ! categorical binding datum [Term] id: OBI:0003296 name: antibodies from lymphocyte secretions assay def: "An assay that evaluates a blood specimen for antibodies currently being produced by lymphocytes in the specimen, by separating peripheral blood mononuclear cells, culturing them, and then collecting the supernatant containing the antibodies secreted from those cells." [] synonym: "ALS assay" EXACT [] synonym: "antibodies from lymphocyte supernatant assay" EXACT [] is_a: OBI:0003040 ! blood assay [Term] id: OBI:0003297 name: tyramide signal amplification sequencing assay def: "A DNA sequencing assay that uses tyramide signal amplification (TSA) to assess distance of DNA regions to a targeted nuclear compartment or protein, typically on a scale of 100-1000 nm." [] synonym: "TSA-seq" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0003298 name: DNA adenine methyltransferase identification assay def: "An assay for identifying DNA binding sites for a protein by fusing it to Dam methylase, and expressing it so that bound DNA gets methylated. The methylated DNA can then be isolated and analyzed." [] synonym: "DamID assay" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003299 name: DamID-seq def: "A DNA adenine methyltransferase identification (DamID) assay in which DamID-generated DNA fragments undergo high-throughput sequencing to determine a protein's DNA-binding site." [] is_a: OBI:0003298 ! DNA adenine methyltransferase identification assay [Term] id: OBI:0003300 name: nucleolus-associated domain sequencing assay def: "A DNA sequencing assay in which nucleoli are isolated and the DNA associated with them is sequenced to identify nucleoli-associating domains." [] synonym: "NAD-seq" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0003301 name: DNase Hi-C assay def: "A Hi-C assay in which DNase I is used for digesting DNA fragments rather than a restriction enzyme, which can result in a higher resolution of mapped chromosome contacts." [] is_a: OBI:0002440 ! Hi-C assay [Term] id: OBI:0003302 name: micro-C assay def: "A Hi-C assay which uses micrococcal nuclease digestion in place of the restriction enzyme digestion step." [] is_a: OBI:0002440 ! Hi-C assay [Term] id: OBI:0003303 name: single cell combinatorial indexing Hi-C assay def: "A Hi-C assay performed on massively multiplexed single-cell samples." [] synonym: "sci-Hi-C" EXACT [] is_a: OBI:0002440 ! Hi-C assay [Term] id: OBI:0003304 name: single nucleus Hi-C assay def: "A Hi-C assay performed on isolated nuclei." [] synonym: "sn-Hi-C" EXACT [] is_a: OBI:0002440 ! Hi-C assay [Term] id: OBI:0003305 name: single cell Hi-C assay def: "A Hi-C assay performed on a single cell." [] is_a: OBI:0002440 ! Hi-C assay [Term] id: OBI:0003306 name: bulk Hi-C assay def: "A Hi-C assay in which the sample that is sequenced is derived from a collection of cells, such as a tissue sample or entire cell culture, and therefore provides results representative of the aggregate of sample cells." [] is_a: OBI:0002440 ! Hi-C assay [Term] id: OBI:0003307 name: multi-contact Hi-C assay def: "A Hi-C assay that assesses interactions between multiple DNA fragments rather than only pairwise interactions as in traditional Hi-C. The experimental procedure of cross-linking, digestion, and ligation is performed similarly to traditional Hi-C, but after DNA is purified a long-read library is produced in which many ligated fragments may be contained in a single molecule. The library is then sequenced on a long read sequencer." [] synonym: "MC-3C" EXACT [] synonym: "MC-HI-C" EXACT [] is_a: OBI:0002440 ! Hi-C assay [Term] id: OBI:0003309 name: transposase-mediated analysis of chromatin looping assay def: "A DNA sequencing assay designed to detect interacting genomic regions. Rather than the traditional Hi-C approach of digestion and proximity ligation, the procedure involves transposase-mediated insertion of an oligonucleotide linker between the pair of interacting regions." [] synonym: "TrAC-Loop" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0003310 name: split-pool recognition of interactions and tag extension assay def: "A sequencing assay designed to detect multi-way interactions between nucleic acids. The procedure involves crosslinking nuclei, and then splitting the lysate among wells in a 96-well or other multi-well plate. A different barcode is ligated to the fragments in each well, and the lysates are pooled together again. This sequence of splitting, tagging, and re-combining is repeated several times so that fragments with the same sequences of barcodes represent fragments that have co-associated throughout the experiment. Finally, a sequencing library is constructed and high-throughput sequencing is performed." [] synonym: "SPRITE" EXACT [] is_a: OBI:0600047 ! sequencing assay [Term] id: OBI:0003311 name: DNA split-pool recognition of interactions and tag extension assay def: "A split-pool recognition of interactions and tag extension (SPRITE) assay that only assays interactions between regions of genomic DNA." [] synonym: "DNA SPRITE" EXACT [] is_a: OBI:0003310 ! split-pool recognition of interactions and tag extension assay [Term] id: OBI:0003312 name: RNA-DNA split-pool recognition of interactions and tag extension assay def: "A split-pool recognition of interactions and tag extension (SPRITE) assay in which RNA in the cross-linked complexes is converted to cDNA before the initial splitting step, allowing analysis of RNA-DNA interactions." [] synonym: "RNA-DNA SPRITE" EXACT [] is_a: OBI:0003310 ! split-pool recognition of interactions and tag extension assay [Term] id: OBI:0003313 name: genome architecture mapping assay def: "A DNA sequencing assay designed to analyze 3D chromatin structure without relying on digestion and ligation. The procedure involves cryosectioning samples in random orientation, and then single nuclear profiles are isolated by laser microdissection. Each nuclear profile then undergoes high-throughput sequencing, and subsequent analysis can generate a matrix of inferred proximity between genomic regions." [] synonym: "GAM" EXACT [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:0003314 name: mapping RNA-genome interactions assay def: "A nuclear ligation assay for probing RNA-DNA interactions in the nucleus. Nuclei are crosslinked, and RNA fragments are ligated to proximal DNA fragments via a special linker molecule. After reverse transcription, high-throughput sequencing is performed." [] synonym: "MARGI" EXACT [] is_a: OBI:0002438 ! nuclear ligation assay [Term] id: OBI:0003315 name: assay measuring epitope specific amphiregulin production by T cells def: "A T cell epitope specific cytokine production assay that detects amphiregulin production by T cells." [] synonym: "amphiregulin release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0003316 name: ELISA measuring epitope specific amphiregulin production by T cells def: "An enzyme-linked immunosorbent assay that detects amphiregulin production by T cells." [] synonym: "amphiregulin release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0003315 ! assay measuring epitope specific amphiregulin production by T cells [Term] id: OBI:0003317 name: perforin release during T cell degranulation def: "The release of perforin during cytotoxic T cell degranulation." [] is_a: GO:0035944 ! perforin production [Term] id: OBI:0003318 name: granzyme A release during T cell degranulation def: "The release of granzyme A during cytotoxic T cell degranulation." [] is_a: GO:0035746 ! granzyme A production [Term] id: OBI:0003319 name: granzyme B release during T cell degranulation def: "The release of granzyme B during cytotoxic T cell degranulation." [] is_a: GO:0071613 ! granzyme B production [Term] id: OBI:0003320 name: granulysin release during T cell degranulation def: "The release of granulysin during cytotoxic T cell degranulation." [] is_a: GO:0036262 ! granulysin production [Term] id: OBI:0003321 name: venous blood microbiology assay def: "A blood microbiology assay that detects a microorganism in a venous blood specimen." [] is_a: OBI:0002649 ! blood microbiology assay [Term] id: OBI:0003323 name: high throughput multiplexed assay measuring binding of a B cell epitope:antibody complex def: "A B cell epitope assay that measures the binding of an antibody receptor to an epitope using a high throughput multiplexed assay." [] synonym: "antibody binding|High throughput multiplexed assay" EXACT [] is_a: OBI:1110127 ! assay measuring binding of a B cell epitope:antibody complex [Term] id: OBI:0003324 name: high throughput multiplexed assay measuring binding of a T cell epitope:MHC:TCR complex def: "A T cell epitope assay that measures the binding of T cell receptor to an epitope using a high throughput multiplexed assay." [] synonym: "T cell binding|High throughput multiplexed assay" EXACT [] is_a: OBI:1110037 ! assay measuring binding of a T cell epitope:MHC:TCR complex [Term] id: OBI:0003325 name: high throughput multiplexed assay measuring binding of a MHC:ligand complex def: "A MHC ligand assay that detects the binding of a ligand to an MHC molecule using a high throughput multiplexed assay." [] synonym: "MHC binding|High throughput multiplexed assay" EXACT [] is_a: OBI:1110126 ! assay measuring binding of a MHC:ligand complex [Term] id: OBI:0003326 name: high throughput multiplexed assay measuring MHC ligand processing and presentation def: "A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them using a high throughput multiplexed assay." [] synonym: "ligand presentation|High throughput multiplexed assay" EXACT [] is_a: OBI:1110125 ! assay measuring MHC ligand processing and presentation [Term] id: OBI:0003327 name: image data set def: "A data set that is comprised of multidimensional structured measurements and metadata required for a morphological representation of an entity. An image data set can be the source from which an image (such as a 2D image using pixels or a 3D image using voxels) is produced." [] is_a: IAO:0000100 ! data set [Term] id: OBI:0003328 name: magnetic resonance image data set def: "An image data set whose information content originates from some MR imaging assay and is about some MRI participant." [] is_a: OBI:0003327 ! image data set [Term] id: OBI:0003329 name: magnetic resonance imaging participant def: "The subject being scanned in an MRI study, and bearor of data derived from that study." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0003330 name: magnetic resonance imaging evaluant role def: "An evaluant role that inheres in a material entity that is realized in a MR imaging assay in which MR imaging data is generated about the bearer of the evaluant role." [] is_a: OBI:0000067 ! evaluant role [Term] id: OBI:0003331 name: raw image data set def: "An image data set that encodes measurement values produced by some instrument before undergoing a data transformation." [] is_a: OBI:0003327 ! image data set [Term] id: OBI:0003332 name: magnetic resonance pulse sequence protocol def: "The NMR/MRI machine protocol about the radiofrequency pulse sequence." [] is_a: OBI:0000272 ! protocol [Term] id: OBI:0003333 name: computed image data set def: "An image data set that is the output of an image data set analysis." [] is_a: OBI:0003327 ! image data set [Term] id: OBI:0003334 name: reconstructed magnetic resonance image data set def: "An image data set that is the direct output of a raw magnetic resonance image data set reconstruction or a transformation of another MR image data set." [] is_a: OBI:0003328 ! magnetic resonance image data set is_a: OBI:0003333 ! computed image data set [Term] id: OBI:0003335 name: diffusion weighted magnetic resonance image data set def: "A type of magnetic resonance image data set collected using at least three diffusion gradients of some factor \"b,\" which is a function of the amplitude, duration, and interval of the gradiants." [] is_a: OBI:0003334 ! reconstructed magnetic resonance image data set [Term] id: OBI:0003336 name: functional magnetic resonance image data set def: "An magnetic resonance image data set collected as a 4D time series representing changes in brain metabolism (i.e. BOLD), typically used as a proxy for brain activity." [] is_a: OBI:0003334 ! reconstructed magnetic resonance image data set [Term] id: OBI:0003337 name: resting state functional magnetic resonance image data set def: "A type of functional MRI in which the participant is not given a task, but just rests during acquisision" [] is_a: OBI:0003336 ! functional magnetic resonance image data set [Term] id: OBI:0003338 name: task-based functional magnetic resonance image data set def: "A type of functional MRI in which the participant is given a task or tasks, which are timed with the acquisition" [] is_a: OBI:0003336 ! functional magnetic resonance image data set [Term] id: OBI:0003339 name: perfusion weighted magnetic resonance image data set def: "An magnetic resonance image data set that captures volume and flow of blood in the brain." [] is_a: OBI:0003334 ! reconstructed magnetic resonance image data set [Term] id: OBI:0003340 name: proton density magnetic resonance image data set def: "An magnetic resonance image data set in which the contrast emphasizes density of protons, supressing T1 and T2 effects" [] is_a: OBI:0003334 ! reconstructed magnetic resonance image data set [Term] id: OBI:0003341 name: T1 weighted magnetic resonance image data set def: "An magnetic resonance image acquired using a T1 weighted magnetic resonance image acquisition sequence." [] is_a: OBI:0003334 ! reconstructed magnetic resonance image data set [Term] id: OBI:0003342 name: post-Gd T1 weighted magnetic resonance image data set def: "A T1 weighted image data set where gadolidium contrast agent has been administered to the participant before image acquistion." [] is_a: OBI:0003341 ! T1 weighted magnetic resonance image data set [Term] id: OBI:0003343 name: T1 weighted GRE magnetic resonance image data set def: "T1 weighted image data set collected using a gradient recall echo sequence." [] is_a: OBI:0003341 ! T1 weighted magnetic resonance image data set [Term] id: OBI:0003344 name: high resolution T1 weighted magnetic resonance image data set def: "A T1-weighted image data set acquired from an NMR/MRI machine with at least a 3 Tesla magnet and in which the voxel size is isotropic." [] is_a: OBI:0003343 ! T1 weighted GRE magnetic resonance image data set [Term] id: OBI:0003345 name: baseline high resolution T1 weighted magnetic resonance image data set def: "A T1w image data set collected at an evaluant's first visit in a study." [] is_a: OBI:0003343 ! T1 weighted GRE magnetic resonance image data set [Term] id: OBI:0003346 name: follow-up high resolution T1 weighted magnetic resonance image data set def: "A T1w image data set collected at a later time than the evaluant's first scan." [] is_a: OBI:0003343 ! T1 weighted GRE magnetic resonance image data set [Term] id: OBI:0003347 name: T1 weighted SE magnetic resonance image data set def: "A T1 weighted image data set acquired using a spin echo sequence." [] is_a: OBI:0003341 ! T1 weighted magnetic resonance image data set [Term] id: OBI:0003348 name: T2 weighted magnetic resonance image data set def: "A magnetic resonance image produced by a T2 weighted magnetic resonance image acquisition sequence." [] is_a: OBI:0003334 ! reconstructed magnetic resonance image data set [Term] id: OBI:0003349 name: T2 weighted FLAIR magnetic resonance image data set def: "A T2 weighted image data set collected using a FLAIR sequence." [] is_a: OBI:0003348 ! T2 weighted magnetic resonance image data set [Term] id: OBI:0003350 name: T2 weighted FSE magnetic resonance image data set def: "T2 weighted image collected using a fast/turbo spin echo sequence." [] synonym: "T2 weighted TSE magnetic resonance image data set" EXACT [] is_a: OBI:0003348 ! T2 weighted magnetic resonance image data set [Term] id: OBI:0003351 name: T2 weighted SE magnetic resonance image data set def: "A type of T2-weighted image in which the acquisition is performed using a 2D spin-echo technique" [] is_a: OBI:0003348 ! T2 weighted magnetic resonance image data set [Term] id: OBI:0003352 name: T2 weighted STIR magnetic resonance image data set def: "A T2 weighted magnetic resonance image data set collected using a STIR sequence to suppress the signal coming from fat." [] is_a: OBI:0003348 ! T2 weighted magnetic resonance image data set [Term] id: OBI:0003353 name: T2* weighted GRE magnetic resonance image data set def: "T2* weighted image data set collected using a gradient echo sequence." [] is_a: OBI:0003348 ! T2 weighted magnetic resonance image data set [Term] id: OBI:0003354 name: raw magnetic resonance image data set def: "An image data set that is the direct output of an magnetic resonance imaging assay and whose values encode spatial frequencies produced by the NMR or MRI instrument." [] is_a: OBI:0003328 ! magnetic resonance image data set is_a: OBI:0003331 ! raw image data set [Term] id: OBI:0003355 name: image data set analysis def: "The process of deriving a data item from an image data set using computer algorithms. The produced data item can be an image data set, data measurement, or any other data item." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0003356 name: raw magnetic resonance image data set reconstruction def: "A process that transforms raw magnetic resonance image data from an NMR/MRI machine into a reconstructed magnetic resonance image data set." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0003355 ! image data set analysis [Term] id: OBI:0003357 name: brain region atlas image data set def: "An image data set consisting of values computed from multiple image data sets encoded to represent the spatial location of individual functional or structural regions of a canonical brain." [] is_a: OBI:0003333 ! computed image data set [Term] id: OBI:0003358 name: probabilistic brain region atlas image dataset def: "A brain atlas consisting of weighted values that respresent the probability that a voxel X is part of some brain component Y, typically derived from multiple image data sets." [] is_a: OBI:0003357 ! brain region atlas image data set [Term] id: OBI:0003359 name: deterministic brain region atlas image data set def: "A brain atlas consisting of discrete integer values where a value X denotes a voxel is part of some brain component Y." [] is_a: OBI:0003357 ! brain region atlas image data set [Term] id: OBI:0003360 name: image segmentation map def: "An image data set of integer values in which each value corresponds to some shared characteristic or computed property. The values often belong to a group of pixels or voxels that share the same characteristic, such as a tissue type or anatomical region." [] is_a: OBI:0003333 ! computed image data set [Term] id: OBI:0003361 name: lesion mask def: "An image data set where voxel intensity values greater than zero encode the location of some brain lesion and voxels outside the lesion have an intensity value of zero." [] is_a: OBI:0003360 ! image segmentation map [Term] id: OBI:0003362 name: T1 lesion mask def: "A lesion mask where the lesions are derived from a T1 weighted image data set." [] is_a: OBI:0003361 ! lesion mask [Term] id: OBI:0003363 name: T2 FLAIR lesion mask def: "A lesion mask where the lesions are derived from a T2 FLAIR image data set." [] is_a: OBI:0003361 ! lesion mask [Term] id: OBI:0003365 name: milk assay datum def: "A data item that is the specified output of a milk assay." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003366 name: organism diagnostic process def: "A drawing a conclusion based on data that involves the interpretation of data about a given organism (human, animal, or plant) and the assertion to the effect that the organism has or had a disease, disorder, or syndrome of a certain type, or none of these as output." [] is_a: OBI:0000338 ! drawing a conclusion based on data [Term] id: OBI:0003367 name: diagnosis of an organism def: "A conclusion based on data about that an organism has a disease, disorder, or syndrome of a certain type, or none of these." [] is_a: OBI:0001909 ! conclusion based on data [Term] id: OBI:0003368 name: detection technique def: "An assay (A) that is part of another assay (B), where the target entities of A and B are disjoint, and the target entity of A is a proxy for the target of assay B." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003369 name: assay kit def: "A device that consists of reagents and devices that enable the performance of a specific type of assay, which could, in addition, require specific instruments not included in the kit." [] is_a: OBI:0000968 ! device [Term] id: OBI:0003371 name: epitope specific XCL1 release by T cells def: "A biological process where T cells produce XCL1 resulting from the recognition of a T cell epitope." [] is_a: GO:0140779 ! XCL1 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:0003372 name: assay measuring epitope specific lymphotactin production by T cells def: "A T cell epitope specific cytokine production assay that detects lymphotactin production by T cells." [] synonym: "lymphotactin release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0003373 name: ELISA measuring epitope specific lymphotactin production by T cells def: "An enzyme-linked immunosorbent assay that detects lymphotactin production by T cells." [] synonym: "lymphotactin release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0003372 ! assay measuring epitope specific lymphotactin production by T cells [Term] id: OBI:0003374 name: remote patient assessment def: "An organism diagnostic process which involves a remote assessment of a patient by a clinician." [] synonym: "telehealth patient assessment" EXACT [] is_a: OBI:0003366 ! organism diagnostic process [Term] id: OBI:0003380 name: placental blood specimen def: "A specimen that is derived from placental blood." [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:0003381 name: placental blood microbiology assay def: "A blood microbiology assay that detects microorganisms in a placental blood specimen." [] is_a: OBI:0002649 ! blood microbiology assay [Term] id: OBI:0003382 name: placental blood microbiology datum def: "An organism detection datum that is the specified output of a placental blood microbiology assay." [] is_a: OBI:0003244 ! blood microbiology datum [Term] id: OBI:0003383 name: eukaryota in placental blood datum def: "A placental blood microbiology datum that is about eukaryota." [] is_a: OBI:0003263 ! eukaryota in blood datum is_a: OBI:0003382 ! placental blood microbiology datum [Term] id: OBI:0003384 name: synaptosome preparation process def: "A material component separation process where a synaptic terminal is isolated from a neuron by mild homogenization of nervous tissue under isotonic conditions and subsequent fractionation using differential and density gradient centrifugation." [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0003386 name: Illumina HiSeq 1500 def: "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." [] synonym: "HiSeq 1500" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0003387 name: NextSeq 550 def: "A DNA sequencer manufactured by the Illumina corporation, which provides the increased flexibility of microarray scanning in addition to sequencing." [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0003388 name: Agilent-026655 Whole Mouse Genome Microarray 4x44K v2 def: "A DNA microarray manufactured with Agilent 60-mer SurePrint Technology .The SurePrint G3 Mouse Gene Expression 4x44K v2 Microarray provide full coverage of the mouse transcriptome using the latest annotation databases, including long non-coding RNA(lncRNA). Each glass slide is formatted with four high-definition 44K arrays." [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003389 name: Agilent-030493 SurePrint G3 Mouse Exon 4x180K Microarray def: "A DNA microarray manufactured with Agilent 60-mer SurePrint Technology for studying exon-level gene expression changes. The SurePrint G3 Mouse Exon 4x180K Microarray include probes targeting individual exons. Each glass slide formatted with four 180K arrays." [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003390 name: Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray def: "A DNA microarray manufactured with Agilent 60-mer SurePrint technology which provides comprehensive coverage of genes and transcripts using the latest annotation databases. The SurePrint G3 Mouse Gene Expression 8x60K v2 Microarray features complete coverage of established RefSeq coding transcripts (NM) from the latest build and updated long non-coding RNA (lncRNA) content to ensure relevant research.Each glass slide formatted with eight high-definition 60K arrays." [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003391 name: Affymetrix Mouse Genome 430 2.0 Array def: "A DNA microarray manufactured by Affymetrix, which includes complete coverage of the GeneChip Mouse Expression Set 430, for analysis of over 39,000 transcripts and variants from more than 34,000 well-characterized mouse genes and UniGene clusters, on a single array. The sequences for this array were selected from GenBank™, dbEST, and RefSeq., and sequence clusters cretaed from the UniGene database." [] synonym: "GeneChip Mouse Genome 430 2.0 Array" EXACT [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003392 name: Affymetrix Mouse Genome 430A 2.0 Array def: "A DNA microarray manufactured by Affymetrix for gene expression analysis focusing on approximately 14,000 well-characterized genes in the transcribed mouse genome using single-array cartridge. Sequences used in the design of the array were selected from GenBank™, dbEST, and RefSeq. The sequence clusters were created from the UniGene database." [] synonym: "GeneChip Mouse Genome 430A 2.0 Array" EXACT [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003393 name: Affymetrix Mouse Gene 1.0 ST Array def: "A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA). This whole-transcript array design provides a complete expression profile of mRNA as well as the intermediary lincRNA transcripts that impact the mRNA expression profile." [] synonym: "GeneChip Mouse Gene 1.0 ST Array" EXACT [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003394 name: Affymetrix Mouse Gene 2.1 ST Array def: "A DNA microarray manufactured by Affymetrix, which is a whole-transcript array that includes probes to measure both messenger (mRNA) and long intergenic non-coding RNA transcripts (lincRNA).To supplement the lincRNA data contained in RefSeq, we used sequence and transcript data from lncRNA db." [] synonym: "GeneChip Mouse Gene 2.1 ST Array" EXACT [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003395 name: Affymetrix Rhesus Macaque Genome Array def: "A DNA microarray manufactured by Affymetrix,which is a single-labeled high-density oligonucleotide array, designed to study gene expression in the rhesus animal model and to interrogate rhesus transcripts orthologous to the 3' end of human transcripts. The array consists of over 52,000 probe sets representing more than 20,000 genes, and several relevant viral organisms for studying host-disease immune response." [] synonym: "GeneChip Rhesus Macaque Genome Array" EXACT [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003396 name: Affymetrix Human Transcriptome Array 2.0 def: "A DNA microarray manufactured by Affymetrix, to go beyond gene-level expression profiling to accurately detect all known transcript isoforms produced by a gene. The array design covers >245,000 coding transcripts, >40,000 non-coding transcripts and >339,000 probe sets covering exon-exon junctions, thus ensuring uniform coverage of the transcriptome." [] synonym: "GeneChip Human Transcriptome Array 2.0" EXACT [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003397 name: Affymetrix Human Genome U219 Array def: "A DNA microarray manufactured by Affymetrix, which comprises more than 530,000 probes covering more than 36,000 transcripts and variants, which represent more than 20,000 genes mapped through RefSeq or via UniGene annotation. Sequences used in the design of the array were selected from the RefSeq version 36, UniGene database 219, and full-length human mRNAs from GenBank™." [] synonym: "Applied Biosystems GeneChip PrimeView Human Gene Expression Array" EXACT [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003398 name: Affymetrix Human Gene 2.0 ST Array def: "A DNA microarray manufactured by Affymetrix, which provides the most accurate, sensitive, and comprehensive measurement of protein coding (mRNA) and long intergenic non-coding RNA (lincRNA) transcripts. The array design covers >33,500 coding transcripts and >11,000 lincRNA transcripts thus enabling researchers to understand whole-transcriptome gene expression at the gene and exon levels, which allows the study of transcript variants and alternative splicing events." [] synonym: "GeneChip Human Gene 2.0 ST Array" EXACT [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003399 name: Affymetrix Clariom S Assay, Human def: "A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the human transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers , and to quickly assess changes in key genes and pathways." [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003400 name: Affymetrix Clariom S Assay, Mouse def: "A DNA microarray manufactured by Affymetrix, to obtain a gene-level view of the mouse transcriptome. The assay design covers >20,000 well-annotated genes, providing researchers with the ability to perform gene-level expression profiling studies, to identify expression biomarkers, and to quickly assess changes in key genes and pathways." [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003401 name: Illumina HumanHT-12 V4.0 expression beadchip def: "An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling and expression-based quantitative trait loci (eQTL) studies. This BeadChip contains 12 arrays, each featuring more than 48,000 probes, targeting more than 31,000 annotated genes, providing genome-wide coverage of well-characterized genes, gene candidates, and splice variants." [] is_a: OBI:0001869 ! Illumina BeadChip [Term] id: OBI:0003402 name: Illumina MouseRef-8 v2.0 beadchip def: "An Illumina BeadChip which employs direct-hybridization assay, for whole-genome expression profiling in the mouse.This Beadchip contains 8 microarrays, featuring more than 25,000 probes per array, derived from the NCBI RefSeq database and supplemented with MEEBO and RIKEN FANTOM2 content." [] is_a: OBI:0001869 ! Illumina BeadChip [Term] id: OBI:0003403 name: Affymetrix Mouse Exon Junction Array def: "A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the mouse transcriptome." [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003404 name: Affymetrix Human Exon Junction Array def: "A DNA microarray manufactured by Affymetrix, used to identify exon-exon junctions associated with alternate splice variants in the human transcriptome." [] is_a: OBI:0400148 ! DNA microarray [Term] id: OBI:0003413 name: administering substance in vivo to cause disease def: "An administration of substance in vivo with the intention to induce disease in the organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003414 name: administering substance in vivo to reduce or prevent disease def: "An administration of substance in vivo with the intention to reduce the symptoms of or prevent development of a disease in the organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003415 name: peripheral blood mononuclear cell specimen def: "A processed specimen that is extracted from whole blood using gradient centrifugation that separates the blood into a layer of peripheral blood mononuclear cells under the top layer of plasma. It contains lymphocytes, monocytes or macrophages that are critical components in the immune system." [] synonym: "PBMC specimen" EXACT [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0003416 name: mid-upper arm circumference datum def: "A length measurement datum that is the specified output of an assay measuring the length around an upper arm, taken midway along the upper arm." [] is_a: IAO:0000408 ! length measurement datum [Term] id: OBI:0003417 name: antigen specific antibodies assay datum def: "A data item that is the specified output of an antigen specific antibodies assay." [] is_a: IAO:0000027 ! data item [Term] id: OBI:0003418 name: antigen specific antibodies in blood assay def: "An antigen specific antibodies assay that has a blood specimen as evaluant." [] is_a: OBI:0002145 ! antigen specific antibodies assay is_a: OBI:0003040 ! blood assay [Term] id: OBI:0003419 name: antigen specific antibodies in milk assay def: "An antigen specific antibodies assay that has a milk specimen as evaluant." [] is_a: OBI:0002145 ! antigen specific antibodies assay is_a: OBI:0003236 ! milk assay [Term] id: OBI:0003420 name: antigen specific antibodies in blood assay datum def: "An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in blood assay." [] is_a: OBI:0003243 ! blood assay datum is_a: OBI:0003417 ! antigen specific antibodies assay datum [Term] id: OBI:0003421 name: antigen specific antibodies in milk assay datum def: "An antigen specific antibodies assay datum that is the specified output of an antigen specific antibodies in milk assay." [] is_a: OBI:0003365 ! milk assay datum is_a: OBI:0003417 ! antigen specific antibodies assay datum [Term] id: OBI:0003422 name: enzymatic activity level assay def: "An assay in which the level of catalytic activity of an enzyme is determined." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003423 name: 5'-nucleotidase activity level assay def: "An enzymatic activity level assay that measures the activity of 5'-nucleotidase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003424 name: alanine aminotransferase activity level assay def: "An enzymatic activity level assay that measures the activity of alanine aminotransferase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003425 name: alkaline phosphatase activity level assay def: "An enzymatic activity level assay that measures the activity of alkaline phosphatase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003426 name: amylase activity level assay def: "An enzymatic activity level assay that measures the activity of amylase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003427 name: aspartate aminotransferase activity level assay def: "An enzymatic activity level assay that measures the activity of aspartate aminotransferase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003428 name: cholinesterase activity level assay def: "An enzymatic activity level assay that measures the activity of cholinesterase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003429 name: creatine kinase activity level assay def: "An enzymatic activity level assay that measures the activity of creatine kinase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003430 name: gamma-glutamyltransferase activity level assay def: "An enzymatic activity level assay that measures the activity of gamma-glutamyltransferase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003431 name: glutamate dehydrogenase activity level assay def: "An enzymatic activity level assay that measures the activity of glutamate dehydrogenase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003432 name: isocitrate dehydrogenase activity level assay def: "An enzymatic activity level assay that measures the activity of isocitrate dehydrogenase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003433 name: lactate dehydrogenase activity level assay def: "An enzymatic activity level assay that measures the activity of lactate dehydrogenase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003434 name: sorbitol dehydrogenase activity level assay def: "An enzymatic activity level assay that measures the activity of sorbitol dehydrogenase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003435 name: acyl-CoA oxidase activity level assay def: "An enzymatic activity level assay that measures the activity of Acyl-CoA oxidase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003436 name: N-acetyl-beta-glucosaminidase activity level assay def: "An enzymatic activity level assay that measures the activity of N-acetyl-beta-glucosaminidase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003437 name: ribonuclease activity level assay def: "An enzymatic activity level assay that measures the activity of ribonuclease in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003438 name: galactosidase activity level assay def: "An enzymatic activity level assay that measures the activity of galactosidase in a sample." [] is_a: OBI:0003422 ! enzymatic activity level assay [Term] id: OBI:0003454 name: Mosquito Magnet Liberty Plus trap def: "An arthropod trap that is designed to emit a combination of carbon dioxide, heat, water, and oct-1-en-3-ol attractants while simultaneously using suction to trap arthropods. This trap has the same design as the Mosquito Magnet Pro trap but is smaller, is more lightweight, and uses a main line electricity supply instead of propane to power itself. Both use propane to produce the arthropod attractor." [] is_a: OBI:0002920 ! arthropod trap [Term] id: OBI:0003455 name: tumor challenge def: "The administration of a malignant cell to a host." [] is_a: OBI:0003456 ! in vivo challenge [Term] id: OBI:0003456 name: in vivo challenge def: "The administration of a challenge to a live host." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003457 name: epitope protection from infectious challenge experiment based on survival def: "An epitope protection from infectious challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls." [] synonym: "survival after infectious challenge" EXACT [] is_a: OBI:0001179 ! epitope protection from infectious challenge experiment [Term] id: OBI:0003458 name: epitope protection from tumor challenge experiment based on burden def: "An epitope protection from tumor challenge experiment in which the readout is a reduction in the presence of malignant cells in the host compared to controls." [] synonym: "burden after tumor challenge" EXACT [] is_a: OBI:0001183 ! epitope protection from tumor challenge experiment [Term] id: OBI:0003459 name: epitope protection from tumor challenge experiment based on survival def: "An epitope protection from tumor challenge experiment that determines the success of the epitope intervention based on increased survival of the host compared to controls." [] synonym: "survival after tumor challenge" EXACT [] is_a: OBI:0001183 ! epitope protection from tumor challenge experiment [Term] id: OBI:0003460 name: in vivo assay measuring T cell epitope specific protection from pathogen challenge def: "An in vivo assay measuring T cell epitope specific protection from pathogen challenge." [] synonym: "protection from pathogen challenge|in vivo assay" EXACT [] is_a: OBI:0001179 ! epitope protection from infectious challenge experiment is_a: OBI:0002073 ! in vivo assay measuring T cell epitope specific protection from challenge [Term] id: OBI:0003461 name: in vivo assay measuring T cell epitope specific protection from tumor challenge def: "An in vivo assay measuring T cell epitope specific protection from tumor challenge." [] synonym: "protection from tumor challenge|in vivo assay" EXACT [] is_a: OBI:0001183 ! epitope protection from tumor challenge experiment is_a: OBI:0002073 ! in vivo assay measuring T cell epitope specific protection from challenge [Term] id: OBI:0003462 name: in vivo assay measuring T cell epitope specific protection from other challenge def: "An in vivo assay measuring T cell epitope specific protection from a challenge other than pathogen, infection, or tumor." [] synonym: "protection from other challenge|in vivo assay" EXACT [] is_a: OBI:0002073 ! in vivo assay measuring T cell epitope specific protection from challenge [Term] id: OBI:0003463 name: in vivo assay measuring T cell epitope specific survival after tumor challenge def: "An in vivo assay measuring T cell epitope specific protection from tumor challenge using survival." [] synonym: "survival from tumor challenge|in vivo assay" EXACT [] is_a: OBI:0003459 ! epitope protection from tumor challenge experiment based on survival is_a: OBI:0003461 ! in vivo assay measuring T cell epitope specific protection from tumor challenge [Term] id: OBI:0003464 name: in vivo assay measuring T cell epitope specific survival after pathogen challenge def: "An in vivo assay measuring T cell epitope specific protection from pathogen challenge using survival." [] synonym: "survival from pathogen challenge|in vivo assay" EXACT [] is_a: OBI:0003457 ! epitope protection from infectious challenge experiment based on survival is_a: OBI:0003460 ! in vivo assay measuring T cell epitope specific protection from pathogen challenge [Term] id: OBI:0003465 name: in vivo assay measuring B cell epitope specific protection from pathogen challenge def: "An in vivo assay measuring B cell epitope specific protection from pathogen challenge." [] synonym: "protection from pathogen challenge|in vivo assay" EXACT [] is_a: OBI:0001179 ! epitope protection from infectious challenge experiment is_a: OBI:0001710 ! in vivo assay measuring B cell epitope specific protection from challenge [Term] id: OBI:0003466 name: in vivo assay measuring B cell epitope specific protection from tumor challenge def: "An in vivo assay measuring B cell epitope specific protection from tumor challenge." [] synonym: "protection from tumor challenge|in vivo assay" EXACT [] is_a: OBI:0001183 ! epitope protection from tumor challenge experiment is_a: OBI:0001710 ! in vivo assay measuring B cell epitope specific protection from challenge [Term] id: OBI:0003467 name: in vivo assay measuring B cell epitope specific protection from other challenge def: "An in vivo assay measuring B cell epitope specific protection from a challenge other than pathogen, infection, or tumor." [] synonym: "protection from other challenge|in vivo assay" EXACT [] is_a: OBI:0001710 ! in vivo assay measuring B cell epitope specific protection from challenge [Term] id: OBI:0003468 name: in vivo assay measuring B cell epitope specific survival after pathogen challenge def: "An in vivo assay measuring B cell epitope specific protection from pathogen challenge using survival." [] synonym: "survival from pathogen challenge|in vivo assay" EXACT [] is_a: OBI:0003457 ! epitope protection from infectious challenge experiment based on survival is_a: OBI:0003465 ! in vivo assay measuring B cell epitope specific protection from pathogen challenge [Term] id: OBI:0003469 name: in vivo assay measuring B cell epitope specific survival after tumor challenge def: "An in vivo assay measuring B cell epitope specific protection from tumor challenge using survival." [] synonym: "survival from tumor challenge|in vivo assay" EXACT [] is_a: OBI:0003459 ! epitope protection from tumor challenge experiment based on survival is_a: OBI:0003466 ! in vivo assay measuring B cell epitope specific protection from tumor challenge [Term] id: OBI:0003470 name: in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells def: "An in vivo assay measuring a T cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells." [] synonym: "protection from pathogen challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001179 ! epitope protection from infectious challenge experiment is_a: OBI:0002637 ! in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells [Term] id: OBI:0003471 name: in vivo assay measuring T cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific T cells based on survival def: "An in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells using survival." [] synonym: "survival after pathogen challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0003464 ! in vivo assay measuring T cell epitope specific survival after pathogen challenge is_a: OBI:0003470 ! in vivo assay measuring T cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific T cells [Term] id: OBI:0003472 name: in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells def: "An in vivo assay measuring a T cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific T cells." [] synonym: "protection from tumor challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001183 ! epitope protection from tumor challenge experiment is_a: OBI:0002637 ! in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells [Term] id: OBI:0003473 name: in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells based on survival def: "An in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells using survival." [] synonym: "survival after tumor challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0003463 ! in vivo assay measuring T cell epitope specific survival after tumor challenge is_a: OBI:0003472 ! in vivo assay measuring T cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific T cells [Term] id: OBI:0003474 name: in vivo assay measuring T cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific T cells def: "An in vivo assay measuring a T cell epitope specific protection from other challenge after adoptive transfer of epitope specific T cells." [] synonym: "protection from other challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0002637 ! in vivo assay measuring T cell epitope specific protection from challenge resulting from the adoptive transfer of epitope specific T cells [Term] id: OBI:0003475 name: in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells def: "An in vivo assay measuring a B cell epitope specific protection from a pathogen challenge after adoptive transfer of epitope specific antibodies or B cells." [] synonym: "protection from pathogen challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001179 ! epitope protection from infectious challenge experiment is_a: OBI:0002638 ! in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0003476 name: in vivo assay measuring B cell epitope specific pathogen protection from challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival def: "An in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival." [] synonym: "survival after pathogen challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0003468 ! in vivo assay measuring B cell epitope specific survival after pathogen challenge is_a: OBI:0003475 ! in vivo assay measuring B cell epitope specific protection from pathogen challenge resulting from the adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0003477 name: in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells def: "An in vivo assay measuring a B cell epitope specific protection from a tumor challenge after adoptive transfer of epitope specific antibodies or B cells." [] synonym: "protection from tumor challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0001183 ! epitope protection from tumor challenge experiment is_a: OBI:0002638 ! in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0003478 name: in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells based on survival def: "An in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells using survival." [] synonym: "survival after tumor challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0003469 ! in vivo assay measuring B cell epitope specific survival after tumor challenge is_a: OBI:0003477 ! in vivo assay measuring B cell epitope specific protection from tumor challenge resulting from the adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0003479 name: in vivo assay measuring B cell epitope specific protection from other challenge resulting from the adoptive transfer of epitope specific antibodies or B cells def: "An in vivo assay measuring a B cell epitope specific protection from other challenge after adoptive transfer of epitope specific antibodies or B cells." [] synonym: "protection from other challenge after adoptive transfer|in vivo assay" EXACT [] is_a: OBI:0002638 ! in vivo assay measuring B cell epitope specific protection from challenge resulting from adoptive transfer of epitope specific antibodies or B cells [Term] id: OBI:0003480 name: Gram stain assay def: "An organism detection assay that identifies bacteria based on the differential retention of a crystal violet-iodine complex within the cell wall." [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0003481 name: cow-baited arthropod trap def: "A resting arthropod trap that consists of a tent inside which an adult cow is tethered to the ground, in order to attract arthropods and collect those that rest on the interior walls of the tent." [] is_a: OBI:0000968 ! device [Term] id: OBI:0003482 name: lymph specimen def: "A specimen that is derived from a portion of lymph collected from an organism." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0003483 name: digestive tract specimen def: "A specimen that is derived from part of a digestive tract." [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:0003484 name: assay measuring epitope specific interleukin-25 production by T cells def: "A T cell epitope specific cytokine production assay that detects interleukin-25 production by T cells." [] synonym: "IL-25 release|biological activity" EXACT [] is_a: OBI:1110129 ! assay measuring epitope specific cytokine production by T cells [Term] id: OBI:0003485 name: detection of specific nucleic acids with complementary probes assay measuring epitope specific interleukin-25 production by T cells def: "A detection of specific nucleic acid polymers with complementary probes that detects interleukin-25 production by T cells." [] synonym: "IL-25 release|RNA/DNA detection" EXACT [] is_a: OBI:0000874 ! detection of specific nucleic acid polymers with complementary probes is_a: OBI:0003484 ! assay measuring epitope specific interleukin-25 production by T cells [Term] id: OBI:0003486 name: intracellular cytokine staining assay measuring epitope specific interleukin-25 production by T cells def: "A flow cytometry assay that detects interleukin-25 production by T cells." [] synonym: "IL-25 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0003484 ! assay measuring epitope specific interleukin-25 production by T cells [Term] id: OBI:0003487 name: ELISA measuring epitope specific interleukin-25 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-25 production by T cells." [] synonym: "IL-25 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0003484 ! assay measuring epitope specific interleukin-25 production by T cells [Term] id: OBI:0003488 name: cell culture analyte detection bioassay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells def: "A reporter cell line analyte detection bioassay that detects tumor necrosis factor superfamily cytokine production by T cells." [] synonym: "TNF release|bioassay" EXACT [] is_a: OBI:0000904 ! reporter cell line analyte detection bioassay is_a: OBI:0001400 ! assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:0003489 name: Scrub Typhus Detect IgM ELISA kit def: "An assay kit that is manufactured by InBios International to use ELISA to test for IgM antibodies for Orientia tsutsugamushi strains Karp, Kato, Gilliam, and TA 716, with a protein microarray that has a 96-well plate and the 56-kDa type-specific antigen." [] is_a: OBI:0003369 ! assay kit [Term] id: OBI:0003490 name: Panbio Dengue IgM capture ELISA kit def: "An assay kit that is manufactured by Abbott to test for IgM antibodies for Dengue with a two-plate protein microarray. One plate contains stabilized Dengue viruses 1 through 4, and the other plate contains anti-human IgM antibody." [] is_a: OBI:0003369 ! assay kit [Term] id: OBI:0003491 name: Panbio Dengue Early ELISA kit def: "An assay kit that is manufactured by Abbott to detect the NS1 Dengue viral protein with a protein microarray and an anti-NS1 monoclonal antibody." [] is_a: OBI:0003369 ! assay kit [Term] id: OBI:0003492 name: SD Bioline Chikungunya IgM RDT kit def: "A device manufactured by Abbott for rapid detection of human IgM antibodies for Chikungunya virus in blood, using analytical chromatography." [] is_a: OBI:0003369 ! assay kit [Term] id: OBI:0003493 name: SD Bioline Chikungunya IgM capture ELISA kit def: "An assay kit that is manufactured by Abbott to detect human IgM antibodies for Chikungunya with a protein microarray and ELISA." [] is_a: OBI:0003369 ! assay kit [Term] id: OBI:0003494 name: Advantage Chikungunya IgM Card kit def: "An assay kit that is manufactured by J. Mitra to detect human IgM antibodies for Chikungunya virus with a protein microarray and double-antigen sandwich ELISA." [] is_a: OBI:0003369 ! assay kit [Term] id: OBI:0003498 name: organism detection assay def: "An assay that detects a type of organism and/or the quantity of individuals of a type of organism." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003501 name: functional assessment of individual def: "A physical examination of an organism's ability to perform functional activities." [] is_a: OBI:0002441 ! physical examination of an organism [Term] id: OBI:0003502 name: facial atrophy assessment def: "An observational assessment of the loss of facial muscle tissue due to inactivity or disease." [] is_a: OBI:0003536 ! observational assessment of individual [Term] id: OBI:0003503 name: tongue atrophy assessment def: "An observational assessment of the loss of muscle tissue related to tongue movement due to inactivity or disease." [] is_a: OBI:0003536 ! observational assessment of individual [Term] id: OBI:0003504 name: forced cough assessment def: "A functional assessment of an individual's ability to cough forcefully." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003505 name: speech test assessment def: "A functional assessment of an individual's ability to understandably repeat spoken sentences." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003506 name: finger to finger assessment def: "A functional assessment of an individual's ability to touch index fingers together in front of the sternum without oscillation for a specified duration of time" [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003507 name: nose to finger assessment def: "A functional assessment of an individual's ability to touch their own nose and then touch an examiners finger in front of them and then touch their own nose once more." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003508 name: dysmetria assessment def: "A functional assessment of an individual's ability to accurately touch a moving target with their finger and then touch their own chin a number of times in a row." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003509 name: rapid alternating hands assessment def: "A functional assessment of an individual's ability to alternate the forearm between pronation and suppination as quickly as possible during a specified duration of time" [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003510 name: finger taps assessment def: "A functional assessment of an individual's ability to touch their finger-tip to thumb as many times as possible during a specified duration of time." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003511 name: heel along shin assessment def: "A functional assessment of an individual's ability to slide their heel back and forth along their contralateral tibia from the patella to the ankle with the contralateral leg extended." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003512 name: heel to shin assessment def: "A functional assessment of an individual's ability to tap their heel to the midpoint of the contralateral shin a number of times." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003513 name: muscle atrophy assessment def: "An observational assesment of an individual's muscle tissue loss due to inactivity or disease." [] is_a: OBI:0003536 ! observational assessment of individual [Term] id: OBI:0003514 name: muscle weakness assessment def: "A functional assessment of an individual's ability to perform muscle movement to overcome gravity or physical resistence." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003515 name: vibratory sense assessment def: "A functional assessment of an individual's ability to sense vibration." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003516 name: position sense assessment def: "A functional assessment of an individual's ability to sense the position of a finger or toe that has been manipulated by minimal random movements." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003517 name: deep tendon reflex assessment def: "A functional assessment of an individual's muscle contraction when a muscle is triggered by a signal from a muscle spindle in response to a stimulus applied to a specific trigger point on the body." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003518 name: limits of stability assessment def: "The functional assessment of an individual's ability to maintain balance, posture or upright stability." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003519 name: sitting posture assessment def: "A limits of stability assessment designed to assess an individual's ability to maintain unsupported posture while sitting over a given time period." [] is_a: OBI:0003518 ! limits of stability assessment [Term] id: OBI:0003520 name: stance feet apart assessment def: "A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet 20 cm apart." [] is_a: OBI:0003518 ! limits of stability assessment [Term] id: OBI:0003521 name: stance feet apart assessment, with eyes closed def: "A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with their eyes closed." [] is_a: OBI:0003518 ! limits of stability assessment [Term] id: OBI:0003522 name: stance feet together assessment def: "A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet together." [] is_a: OBI:0003518 ! limits of stability assessment [Term] id: OBI:0003523 name: stance feet together assessment, with eyes closed def: "A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet together and eyes closed." [] is_a: OBI:0003518 ! limits of stability assessment [Term] id: OBI:0003524 name: tandem stance assessment def: "A limits of stability assessment designed to assess an individual's ability to maintain a stable stance with feet in tandem placement." [] is_a: OBI:0003518 ! limits of stability assessment [Term] id: OBI:0003525 name: stance on one foot assessment def: "A limits of stability assessment designed to assess an individual's ability to maintain a stable stance on one foot." [] is_a: OBI:0003518 ! limits of stability assessment [Term] id: OBI:0003526 name: tandem walk assessment def: "A limits of stability assessment designed to assess an individual's ability to maintain balance while walking in a straight line placing steps in tandem." [] is_a: OBI:0003518 ! limits of stability assessment [Term] id: OBI:0003527 name: gait assessment def: "A limits of stability assessment designed to assess an individual's manner or pattern of walking." [] is_a: OBI:0003518 ! limits of stability assessment [Term] id: OBI:0003528 name: bulbar assessment def: "A functional assessment of an individual's lower cranial nerve function via proxy of facial muscle performance." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003529 name: spontaneous speech assessment def: "A functional assessment of an individual's ability to articulate spoken words." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003530 name: limb coordination assessment def: "A functional assessment of an individual's ability to coordinate limb movement." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003531 name: upper limb coordination assessment def: "A limb coordination assessment designed to assess an individual's ability to coordinate upper limb movement." [] is_a: OBI:0003530 ! limb coordination assessment [Term] id: OBI:0003532 name: lower limb coordination assessment def: "A limb coordination assessment designed to assess an individual's ability to coordinate lower limb movement." [] is_a: OBI:0003530 ! limb coordination assessment [Term] id: OBI:0003533 name: nervous system functionality assessment def: "A functional assesment of an individual's nerve performance. Specifically the nerves connecting the sensory and motor structures with the central nervous system." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003534 name: upright stability assessment def: "A functional assessment of an individual's ability to maintain upright body posture." [] is_a: OBI:0003501 ! functional assessment of individual [Term] id: OBI:0003535 name: deep tendon reflex assessment of the knee joint def: "A deep tendon reflex assessment of an individual's reaction to stimulus applied to a knee joint." [] is_a: OBI:0003517 ! deep tendon reflex assessment [Term] id: OBI:0003536 name: observational assessment of individual def: "A physical examination of an organism through visual assesment." [] is_a: OBI:0002441 ! physical examination of an organism [Term] id: OBI:0003537 name: deep tendon reflex assessment of the ankle joint def: "A deep tendon reflex assessment of an individual's reaction to stimulus applied to an ankle joint." [] is_a: OBI:0003517 ! deep tendon reflex assessment [Term] id: OBI:0003538 name: deep tendon reflex assessment of the tendon of biceps brachii def: "A deep tendon reflex assessment of an individual's reaction to stimulus applied to a tendon of biceps brachii." [] is_a: OBI:0003517 ! deep tendon reflex assessment [Term] id: OBI:0003539 name: deep tendon reflex assessment of the brachioradialis def: "A deep tendon reflex assessment of an individual's reaction to stimulus applied to a brachioradialis." [] is_a: OBI:0003517 ! deep tendon reflex assessment [Term] id: OBI:0003540 name: tandem mass spectrometry assay def: "A mass spectrometry assay that uses two or more analyzers separated by a region in which ions can be induced to fragment by transfer of energy (frequently by collision with other molecules)." [] is_a: OBI:0000470 ! mass spectrometry assay [Term] id: OBI:0003541 name: ELISA measuring Orientia tsutsugamushi IgM antibody def: "An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Orientia tsutsugamushi." [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay [Term] id: OBI:0003542 name: microarray assay measuring Dengue IgM antibody def: "A microarray assay that detects the IgM antibody that binds Dengue." [] is_a: OBI:0001985 ! microarray assay [Term] id: OBI:0003543 name: microarray assay measuring NS1 def: "A microarray assay that detects NS1." [] is_a: OBI:0001985 ! microarray assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:0003544 name: analytical chromatography measuring Chikungunya IgM antibody def: "Analytical chromatography that detects the IgM antibody that binds Chikungunya." [] is_a: OBI:0001630 ! analytical chromatography [Term] id: OBI:0003545 name: ELISA measuring Chikungunya IgM antibody def: "An enzyme-linked immunosorbent assay that detects the IgM antibody that binds Chikungunya." [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay [Term] id: OBI:0003546 name: microarray ELISA measuring Chikungunya IgM antibody def: "An enzyme-linked immunosorbent assay that uses a microarray as the solid support and detects the IgM antibody that binds Chikungunya." [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay [Term] id: OBI:0003547 name: liquid chromatography def: "A preparative chromatography in which material components are separated in a liquid solution." [] is_a: OBI:0600046 ! preparative chromatography [Term] id: OBI:0003548 name: upper limit of detection def: "A value specification that specifies the largest concentration/amount of a substance that can be quantified in an analyte assay." [] is_a: OBI:0001933 ! value specification [Term] id: OBI:0003549 name: lower limit of detection def: "A value specification that specifies the smallest concentration/amount of a substance that can be detected in an analyte assay." [] is_a: OBI:0001933 ! value specification [Term] id: OBI:0003550 name: odor baited CDC light trap def: "A CDC light trap that uses odorous gas from a human being as an attractant, by pumping it from the room where the human being sleeps into the trap." [] synonym: "human odour baited light trap" EXACT [] is_a: OBI:0002926 ! Centers for Disease Control and Prevention light trap [Term] id: OBI:0003551 name: resting clay pot trap def: "A resting arthropod trap that consists of a container composed primarily of clay." [] synonym: "resting clay pot catch" EXACT [] is_a: OBI:0002939 ! resting arthropod trap [Term] id: OBI:0003552 name: proximity ligation-assisted ChIP-seq def: "A chromosome conformation capture assay in which proximity ligation is conducted in nuclei prior to chromatin shearing and immunoprecipitation. Immunopreciptation with an antibody that targets a transcription factor or histone modification allows for selection and enrichment of specific genomic regions for investigation of long-range chromosomal interactions." [] synonym: "PLAC-seq" EXACT [] is_a: OBI:0002439 ! chromosome conformation capture assay [Term] id: OBI:0003553 name: intragastric administration def: "An administration of a substance into the stomach of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003554 name: intracolonic administration def: "An administration of a substance into the colon of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003555 name: vaginal administration def: "An administration of a substance into the vagina of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003556 name: topical administration def: "An administration of a substance onto the surface of the skin of an organism." [] synonym: "percutaneous administration" EXACT [] synonym: "transcutaneous administration" EXACT [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003557 name: cervical administration def: "An administration of a substance to the cervix of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003558 name: conjunctival administration def: "An administration of a substance to the conjunctiva of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003559 name: intratracheal administration def: "An administration of a substance into the trachea of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003560 name: intra-amniotic administration def: "An administration of a substance into the amnion of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003561 name: intra-arterial administration def: "An administration of a substance into the artery of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003562 name: intracerebral administration def: "An administration of a substance into the cerebrum of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003563 name: intracranial administration def: "An administration of a substance into the cranium of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003564 name: intraepidermal administration def: "An administration of a substance into the epidermis of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003565 name: intralymphatic administration def: "An administration of a substance into the lymphatic system of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003566 name: lymph node administration def: "An intralymphatic administration in which the substance is administered into a lymph node." [] is_a: OBI:0003565 ! intralymphatic administration [Term] id: OBI:0003567 name: urethral administration def: "An administration of a substance into the urethra of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003568 name: skin scarification administration def: "An intraepidermal administration in which the skin is scratched before the substance is administered to the skin." [] is_a: OBI:0003564 ! intraepidermal administration [Term] id: OBI:0003569 name: intrauteral administration def: "An adminstration of a substance into the uterus of an organism. " [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003570 name: intracarotid administration def: "An intra-arterial administration in which the substance is administered into the carotid artery." [] synonym: "i.c." EXACT [] synonym: "i.c. administration" EXACT [] is_a: OBI:0003561 ! intra-arterial administration [Term] id: OBI:0003571 name: intraocular administration def: "An administration of a substance to the eye of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003572 name: intraplacental administration def: "An administration of a substance into the placenta of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003573 name: intrarectal administration def: "An administration of a substance into the rectum of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003574 name: intrasplenic administration def: "An administration of a substance into the spleen of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003575 name: scratching def: "A process in which the target material entity is scraped by another material entity." [] synonym: "abrading" EXACT [] is_a: BFO:0000015 ! process [Term] id: OBI:0003576 name: skin of body microbiology assay def: "An organism detection assay that detects microorganisms in a skin of body specimen." [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0003577 name: skin of body microbiology datum def: "An organism detection datum that is the specified output of a skin of body microbiology assay." [] is_a: OBI:0003064 ! organism detection datum [Term] id: OBI:0003578 name: bone marrow microbiology assay def: "An organism detection assay that detects microorganisms in a bone marrow specimen." [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0003579 name: bone marrow microbiology datum def: "An organism detection datum that is the specified output of a bone marrow microbiology assay." [] is_a: OBI:0003064 ! organism detection datum [Term] id: OBI:0003580 name: nasal aspirate microbiology assay def: "An organism detection assay that detects microorganisms in a nasal aspirate specimen." [] is_a: OBI:0003498 ! organism detection assay [Term] id: OBI:0003581 name: nasal aspirate microbiology datum def: "An organism detection datum that is the specified output of a nasal aspirate microbiology assay." [] is_a: OBI:0003064 ! organism detection datum [Term] id: OBI:0003582 name: cell proliferation assay using carboxyfluorescein succinimidyl ester staining def: "A cell proliferation assay that uses carboxyfluorescein succinimidyl ester staining to detect cell division." [] is_a: OBI:0000891 ! cell proliferation assay is_a: OBI:0002106 ! carboxyfluorescein succinimidyl ester staining assay [Term] id: OBI:0003583 name: cell viability assay def: "A cytometry assay which measures the number of living cells in a population." [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:0003584 name: cell viability assay using Annexin V staining def: "A cell viability assay that uses Annexin V staining to detect apoptotic cells." [] is_a: OBI:0003583 ! cell viability assay [Term] id: OBI:0003585 name: carboxyfluorescein succinimidyl ester staining def: "Staining using carboxyfluorescein succinimidyl ester." [] is_a: OBI:0302887 ! staining [Term] id: OBI:0003586 name: Annexin V staining def: "Staining using Annexin V to detect apoptotic cells." [] is_a: OBI:0302887 ! staining [Term] id: OBI:0003587 name: cell culture assay def: "An assay that has cell culture as an input." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003589 name: serum anti-Epstein-Barr virus antibody level assay def: "An antigen specific antibodies assay that is meant to detect antibodies that bind to Epstein-Barr virus (EBV) antigens in a serum sample." [] synonym: "EBV" EXACT [] is_a: OBI:0002145 ! antigen specific antibodies assay [Term] id: OBI:0003590 name: serum anti-cytomegalovirus antibody level assay def: "A CMV antibody assay that has serum as an input." [] synonym: "CMV" EXACT [] is_a: OBI:0002154 ! CMV antibody assay [Term] id: OBI:0003591 name: chronic allograft damage index score def: "A clinical data item that quantifies the degree of tissue damage in biopsies taken from transplanted kidneys." [] synonym: "CADI" EXACT [] is_a: OGMS:0000123 ! clinical data item [Term] id: OBI:0003592 name: sequential organ failure assessment score def: "A clinical data item that quantifies the degree of function of a critically ill patient's organs." [] synonym: "SOFA score" EXACT [] is_a: OGMS:0000123 ! clinical data item [Term] id: OBI:0003593 name: physician's global assessment of disease activity def: "A clinical data item that quantifies a physician's judgement of the overall activity of some specific disease in a patient." [] synonym: "MD global, PGA" EXACT [] is_a: OGMS:0000123 ! clinical data item [Term] id: OBI:0003594 name: human leukocyte antigen mismatch count def: "A genetic characteristics information that is about the number of dissimilarities in the human leukocyte antigen gene complexes of two humans." [] synonym: "HLA mismatch count, HLA mismatch" EXACT [] is_a: OBI:0001404 ! genetic characteristics information [Term] id: OBI:0003595 name: nasal lavage fluid def: "A specimen collected through nasal cavity lavage that contains the reagents used to for the lavage process, organisms, cells, cellular secretions, and other biomaterials present in the nasal cavity space." [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0003598 name: single cell B cell receptor repertoire sequencing assay def: "A B cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of B cell receptors that can be traced to a single cell of origin." [] synonym: "single-cell BCR assay" EXACT [] is_a: OBI:0002991 ! B cell receptor repertoire sequencing assay [Term] id: OBI:0003599 name: single cell T cell receptor repertoire sequencing assay def: "A T cell receptor repertoire sequencing assay that determines the sequence of DNA or RNA molecules that encode the repertoire of T cell receptors that can be traced to a single cell of origin." [] synonym: "single-cell TCR assay" EXACT [] is_a: OBI:0002990 ! T cell receptor repertoire sequencing assay [Term] id: OBI:0003600 name: hypertension grade def: "A categorical value specification that indicates the severity of hypertension." [] is_a: OBI:0001930 ! categorical value specification [Term] id: OBI:0003601 name: quartz crystal microbalance assay def: "An assay that measures the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator." [] synonym: "QCM" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:0003602 name: quartz crystal microbalance assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex def: "A quartz crystal microbalance assay that measures the dissociation constant [KD] of an antigen binding with an antibody." [] synonym: "dissociation constant KD|quartz crystal microbalance|nM" EXACT [] synonym: "QCM measuring KD" EXACT [] is_a: OBI:0001708 ! assay measuring the dissociation constant [KD] of a B cell epitope:antibody complex is_a: OBI:0003601 ! quartz crystal microbalance assay [Term] id: OBI:0003603 name: intratumoral administration def: "An administration of a substance into a tumor of an organism." [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:0003604 name: multiplexed error-robust fluorescence in situ hybridization assay def: "A fluorescence in-situ hybridization assay that uses combinatorial FISH labeling with error resistant encoding schemes for highly multiplexed single-molecule imaging." [] synonym: "MERFISH" EXACT [] is_a: OBI:0003094 ! fluorescence in-situ hybridization assay [Term] id: OBI:0003605 name: single molecule fluorescence in situ hybridization def: "A fluorescence in-situ hybridization assay that detects single RNA molecules in fixed cells, allowing for both the quantification and localization at the single-cell level and single-molecule resolution." [] synonym: "smFISH" EXACT [] is_a: OBI:0003094 ! fluorescence in-situ hybridization assay [Term] id: OBI:0003606 name: Illumina NextSeq 1000 def: "A DNA sequencer which is manufactured by the Illumina corporation using sequence-by-synthesis chemistry that fits on a benchtop and uses P1 and P2 flow cells." [] synonym: "NextSeq 1000" EXACT [] is_a: OBI:0400103 ! DNA sequencer [Term] id: OBI:0003607 name: disease causation objective def: "An objective specification that is fulfilled by causing a disease in a particular organism." [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0003608 name: disease severity reduction objective def: "An objective specification that is fulfilled by reducing the severity of a disease in a particular organism." [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0003609 name: disease prevention objective def: "An objective specification that is fulfilled by preventing the development of a disease in a particular organism." [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0003610 name: reactant role def: "A role borne by a biological or chemical entity that participates or has molecular components that participate in a chemical reaction." [] is_a: BFO:0000023 ! role [Term] id: OBI:0003611 name: precursor role def: "A role borne by a biological or chemical entity which serves as the core component of a chemical reaction process, upon which other reactants, like reagents or solvents, act." [] is_a: OBI:0003610 ! reactant role [Term] id: OBI:0003612 name: electron microscopy assay determining the 3D structure of a T cell epitope:MHC:TCR complex def: "An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a T cell epitope:MHC:TCR complex." [] synonym: "3D structure|electron microscopy" EXACT [] is_a: OBI:0001999 ! 3D molecular structure determination assay of a T cell epitope:MHC:TCR complex is_a: OBI:0003118 ! electron-microscopy 3D molecular structure determination assay [Term] id: OBI:0003613 name: electron microscopy assay determining the 3D structure of a MHC:ligand complex def: "An electron-microscopy 3D molecular structure determination assay that characterizes the 3-dimensional molecular structrue of a MHC:ligand complex." [] synonym: "3D structure|electron microscopy" EXACT [] is_a: OBI:0002050 ! 3D molecular structure determination assay of a MHC:ligand complex is_a: OBI:0003118 ! electron-microscopy 3D molecular structure determination assay [Term] id: OBI:0003614 name: disease prevalence reduction objective def: "An objective specification that is fulfilled by reducing the prevalence of a disease in a population of organisms." [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0003615 name: antibody purification of MHC protein complex def: "A purification to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0001505 ! purification [Term] id: OBI:0003616 name: antibody purification of MHC class I protein complex def: "An antibody purification of MHC protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC class I protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003615 ! antibody purification of MHC protein complex [Term] id: OBI:0003617 name: antibody purification of human MHC class I protein complex def: "An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of human MHC class I protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003635 ! antibody purification of pig MHC class I protein complex, cattle MHC class I protein complex, and/or human MHC class I protein complex [Term] id: OBI:0003618 name: antibody purification of HLA protein complex with A2 serotype def: "An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A2 serotype, while others contain impurities and are not of interest." [] is_a: OBI:0003620 ! antibody purification of HLA protein complex with A2 serotype and/or HLA protein complex with A28 serotype [Term] id: OBI:0003619 name: antibody purification of HLA protein complex with A24 serotype def: "An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A24 serotype, while others contain impurities and are not of interest." [] is_a: OBI:0003617 ! antibody purification of human MHC class I protein complex [Term] id: OBI:0003620 name: antibody purification of HLA protein complex with A2 serotype and/or HLA protein complex with A28 serotype def: "An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A2 serotype and/or HLA protein complex with A28 serotype, while others contain impurities and are not of interest." [] is_a: OBI:0003617 ! antibody purification of human MHC class I protein complex [Term] id: OBI:0003621 name: antibody purification of HLA protein complex with A29 serotype def: "An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with A29 serotype, while others contain impurities and are not of interest." [] is_a: OBI:0003617 ! antibody purification of human MHC class I protein complex [Term] id: OBI:0003622 name: antibody purification of HLA protein complex with B27 serotype def: "An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with B27 serotype, while others contain impurities and are not of interest." [] is_a: OBI:0003617 ! antibody purification of human MHC class I protein complex [Term] id: OBI:0003623 name: antibody purification of HLA-C protein complex def: "An antibody purification of human MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA-C protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003617 ! antibody purification of human MHC class I protein complex [Term] id: OBI:0003624 name: antibody purification of pig MHC class I protein complex def: "An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of pig MHC class I protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003635 ! antibody purification of pig MHC class I protein complex, cattle MHC class I protein complex, and/or human MHC class I protein complex [Term] id: OBI:0003625 name: antibody purification of cattle MHC class I protein complex def: "An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of cattle MHC class I protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003635 ! antibody purification of pig MHC class I protein complex, cattle MHC class I protein complex, and/or human MHC class I protein complex [Term] id: OBI:0003626 name: antibody purification of rat MHC class I protein complex def: "An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of rat MHC class I protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003616 ! antibody purification of MHC class I protein complex [Term] id: OBI:0003627 name: antibody purification of mouse MHC class I protein complex def: "An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class I protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003616 ! antibody purification of MHC class I protein complex [Term] id: OBI:0003628 name: antibody purification of H2-Dd protein complex def: "An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Dd protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003632 ! antibody purification of H2-Dd protein complex and/or H2-Kd protein complex [Term] id: OBI:0003629 name: antibody purification of H2-Db protein complex def: "An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Db protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003631 ! antibody purification of H2-Ld protein complex, H2-Db protein complex, and/or H2-Dq protein complex is_a: OBI:0003633 ! antibody purification of mouse MHC class I protein complex with H2-b haplotype and/or mouse MHC protein complex with H2-p haplotype [Term] id: OBI:0003630 name: antibody purification of H2-Kd protein complex def: "An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Kd protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003632 ! antibody purification of H2-Dd protein complex and/or H2-Kd protein complex [Term] id: OBI:0003631 name: antibody purification of H2-Ld protein complex, H2-Db protein complex, and/or H2-Dq protein complex def: "An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Ld protein complex, H2-Db protein complex, and/or H2-Dq protein complex while others contain impurities and are not of interest." [] is_a: OBI:0003627 ! antibody purification of mouse MHC class I protein complex [Term] id: OBI:0003632 name: antibody purification of H2-Dd protein complex and/or H2-Kd protein complex def: "An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-Dd protein complex and/or H2-Kd protein complex while others contain impurities and are not of interest." [] is_a: OBI:0003627 ! antibody purification of mouse MHC class I protein complex [Term] id: OBI:0003633 name: antibody purification of mouse MHC class I protein complex with H2-b haplotype and/or mouse MHC protein complex with H2-p haplotype def: "An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class I protein complex with H2-b haplotype and/or mouse MHC protein complex with H2-p haplotype while others contain impurities and are not of interest." [] is_a: OBI:0003627 ! antibody purification of mouse MHC class I protein complex [Term] id: OBI:0003634 name: antibody purification of H2-Kb protein complex, H2-Ks protein complex, and/or H2-Kq protein complex def: "An antibody purification of mouse MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse H2-Kb protein complex, H2-Ks protein complex, and/or H2-Kq protein complex while others contain impurities and are not of interest." [] is_a: OBI:0003627 ! antibody purification of mouse MHC class I protein complex [Term] id: OBI:0003635 name: antibody purification of pig MHC class I protein complex, cattle MHC class I protein complex, and/or human MHC class I protein complex def: "An antibody purification of MHC class I protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of pig MHC class I protein complex, cattle MHC class I protein complex, and/or human MHC class I protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003616 ! antibody purification of MHC class I protein complex [Term] id: OBI:0003636 name: antibody purification of MHC class II protein complex def: "An antibody purification of MHC protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of MHC class II protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003615 ! antibody purification of MHC protein complex [Term] id: OBI:0003637 name: antibody purification of cattle MHC class II protein complex def: "An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of cattle MHC class II protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003636 ! antibody purification of MHC class II protein complex [Term] id: OBI:0003638 name: antibody purification of human MHC class II protein complex def: "An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of human MHC class II protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003636 ! antibody purification of MHC class II protein complex [Term] id: OBI:0003639 name: antibody purification of HLA-DP protein complex def: "An antibody purification of human MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA-DP protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003638 ! antibody purification of human MHC class II protein complex [Term] id: OBI:0003640 name: antibody purification of HLA-DR protein complex def: "An antibody purification of human MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA-DR protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003638 ! antibody purification of human MHC class II protein complex [Term] id: OBI:0003641 name: antibody purification of HLA protein complex with DQ3 serotype def: "An antibody purification of human MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of HLA protein complex with DQ3 serotype, while others contain impurities and are not of interest." [] is_a: OBI:0003638 ! antibody purification of human MHC class II protein complex [Term] id: OBI:0003642 name: antibody purification of mouse MHC class II protein complex def: "An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class II protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003646 ! antibody purification of mouse MHC class II protein complex and/or rat MHC class II protein complex with RT1-A haplotype [Term] id: OBI:0003643 name: antibody purification of H2-IA protein complex def: "An antibody purification of mouse MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-IA protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003642 ! antibody purification of mouse MHC class II protein complex [Term] id: OBI:0003644 name: antibody purification of H2-IAg7 protein complex def: "An antibody purification of mouse MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-IAg7 protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003643 ! antibody purification of H2-IA protein complex [Term] id: OBI:0003645 name: antibody purification of H2-IAd protein complex def: "An antibody purification of mouse MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of H2-IAd protein complex, while others contain impurities and are not of interest." [] is_a: OBI:0003643 ! antibody purification of H2-IA protein complex [Term] id: OBI:0003646 name: antibody purification of mouse MHC class II protein complex and/or rat MHC class II protein complex with RT1-A haplotype def: "An antibody purification of MHC class II protein complex to separate a material entity into different compositions of which one fraction contains a higher concentration of mouse MHC class II protein complex and/or rat MHC class II protein complex with RT1-A haplotype, while others contain impurities and are not of interest." [] is_a: OBI:0003636 ! antibody purification of MHC class II protein complex [Term] id: OBI:0003647 name: tandem mass spectrometry analysis is_a: OBI:0200085 ! mass spectrometry analysis [Term] id: OBI:0003648 name: liquid chromatrography mass spectrometry analysis is_a: OBI:0200085 ! mass spectrometry analysis [Term] id: OBI:0003649 name: liquid chromatography-tandem mass spectrometry analysis is_a: OBI:0003647 ! tandem mass spectrometry analysis is_a: OBI:0003648 ! liquid chromatrography mass spectrometry analysis [Term] id: OBI:0003650 name: Illumina Infinium MethylationEPIC v2.0 BeadChip def: "An Illumina methylation BeadChip that targets 935,000 methylation sites per sample at single-nucleotide resolution." [] is_a: OBI:0001870 ! Illumina methylation BeadChip [Term] id: OBI:0003651 name: multidimensional fatigue inventory score def: "A clinical data item that quantifies the severity of a person's fatigue as measured by a 20-item self-report instrument." [] is_a: OGMS:0000123 ! clinical data item [Term] id: OBI:0005246 name: injection function def: "The function of a device realized when administering a substance in vivo, applied particularly to the forcible insertion of a liquid or gas by means of a syringe, pump, etc." [] is_a: BFO:0000034 ! function [Term] id: OBI:0100010 name: Epstein Barr virus transformed B cell def: "A material entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity" [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0100014 name: chimera def: "An organism which contains cells or tissues with a different genotype" [] is_a: OBI:0100026 ! organism [Term] id: OBI:0100015 name: obsolete_anatomical entity def: "An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue'" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0100016 name: blood plasma specimen def: "a material entity which corresponds to the liquid component of blood, in which the blood cells are suspended." [] synonym: "plasma" EXACT [] is_a: OBI:0000953 ! processed specimen [Term] id: OBI:0100017 name: blood serum specimen def: "A material entity which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors." [] is_a: OBI:0000953 ! processed specimen [Term] id: OBI:0100026 name: organism def: "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." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0100035 name: obsolete_immortal cell def: "a cell derived from a multicellular organism that has the potential to replicate indefinitely" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0100039 name: obsolete_fragment derived from protein def: "A material entity which is derived from a protein" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0100046 name: phosphate buffered saline solution def: "Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and in some preparations potassium chloride and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic)." [] synonym: "PBS buffer" EXACT [] is_a: OBI:0302729 ! chemical solution [Term] id: OBI:0100051 name: specimen def: "A material entity that has the specimen role." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0100055 name: obsolete_cell line cell def: "A material entity that represents generations of a primary culture." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0100056 name: obsolete_immortal cell line culture def: "A cell line that is expected to be capable of indefinite propagation in an vitro culture." [] synonym: "immortal cell line sample" EXACT [] synonym: "permanent cell line" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: CLO:0009828 [Term] id: OBI:0100058 name: xenograft def: "A material entity which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species." [] synonym: "xenotransplant" EXACT [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0100060 name: cultured cell population def: "A processed material comprised of a collection of cultured cells that has been continuously maintained together in culture and shares a common propagation history." [] comment: The extent of a 'cultured cell population' is restricted only in that all cell members must share a propagation history (ie be derived through a common lineage of passages from an initial culture). In being defined in this way, this class can be used to refer to the populations that researchers actually use in the practice of science - ie are the inputs to culturing, experimentation, and sharing. The cells in such populations will be a relatively uniform population as they have experienced similar selective pressures due to their continuous co-propagation. And this population will also have a single passage number, again owing to their common passaging history. Cultured cell populations represent only a collection of cells (ie do not include media, culture dishes, etc), and include populations of cultured unicellular organisms or cultured multicellular organism cells. They can exist under active culture, stored in a quiescent state for future use, or applied experimentally. synonym: "cell culture sample" EXACT [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0100061 name: primary cultured cell population def: "A cultured cell population comprised of cells expanded directly from living tissue prior to being passaged." [] synonym: "primary cell culture" EXACT [] synonym: "primary cell culture sample" EXACT [] is_a: OBI:0100060 ! cultured cell population [Term] id: OBI:0100062 name: obsolete_cell line def: "A secondary cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (ie has been successively passaged together in culture)." [] synonym: "cell line sample" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: CLO:0000031 [Term] id: OBI:0100063 name: cultured clonal cell population def: "A cultured cell population comprised of cells which can all be traced back to a single ancestor cell, and which therefore can be treated as identical." [] synonym: "clonal cell culture sample" EXACT [] is_a: OBI:0100060 ! cultured cell population [Term] id: OBI:0100064 name: screening library def: "a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process?" [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0100065 name: synthetic peptide def: "a synthetic peptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment" [] is_a: CHEBI:16670 ! peptide is_a: OBI:0000047 ! processed material [Term] id: OBI:0100066 name: organ section def: "A processed material which derives from an organ and results from a process of dissection or histological sample preparation a portion(formerly an organ section is portion of an organ removed from the context of the organ)" [] is_a: OBI:0000047 ! processed material [Term] id: OBI:0100067 name: bronchial alveolar lavage def: "Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space." [] synonym: "BAL" EXACT [] is_a: OBI:0100051 ! specimen [Term] id: OBI:0100069 name: obsolete_polymer def: "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." [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0100086 name: glucose in solution def: "A scattered aggregate of glucose molecules in a liquid" [] synonym: "glucose molecules" EXACT [] is_a: BFO:0000040 ! material entity [Term] id: OBI:0200000 name: data transformation def: "A planned process that produces output data from input data." [] synonym: "data analysis" EXACT [] synonym: "data processing" EXACT [] is_a: OBI:0000011 ! planned process disjoint_from: OBI:0600013 ! information acquisition [Term] id: OBI:0200001 name: geometric mean calculation def: "A data transformation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations)." [] comment: A geometric mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the nth root of the product of all of the observations in a data (n being the number of all observations). is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200181 ! center calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation [Term] id: OBI:0200002 name: logistic-log curve fitting def: "A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n)." [] is_a: OBI:0200072 ! curve fitting data transformation [Term] id: OBI:0200003 name: logit-log curve fitting def: "A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points." [] is_a: OBI:0200072 ! curve fitting data transformation [Term] id: OBI:0200004 name: log-log curve fitting def: "A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points." [] is_a: OBI:0200072 ! curve fitting data transformation [Term] id: OBI:0200005 name: feature extraction objective def: "A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200006 name: biexponential transformation def: "A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200072 ! curve fitting data transformation is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200007 name: box-cox transformation def: "A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200008 name: hyperlog transformation def: "A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200010 name: loess scale group transformation one-channel def: "A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar." [] is_a: OBI:0200025 ! loess scale group transformation [Term] id: OBI:0200011 name: logical transformation def: "A logical transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200012 name: loess scale group transformation two-channel def: "A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar." [] is_a: OBI:0200025 ! loess scale group transformation [Term] id: OBI:0200013 name: loess global transformation one-channel def: "A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays." [] is_a: OBI:0200023 ! loess global transformation [Term] id: OBI:0200014 name: split-scale transformation def: "A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuous with a continuous derivative at the transition point t." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200015 name: loess global transformation two-channel def: "A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay." [] is_a: OBI:0200023 ! loess global transformation [Term] id: OBI:0200016 name: sine transformation def: "A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200017 name: cosine transformation def: "A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200018 name: loess group transformation one-channel def: "A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays." [] is_a: OBI:0200024 ! loess group transformation [Term] id: OBI:0200019 name: loess group transformation two-channel def: "A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay." [] is_a: OBI:0200024 ! loess group transformation [Term] id: OBI:0200020 name: homogeneous polynomial transformation def: "A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree." [] is_a: OBI:0200093 ! polynomial transformation [Term] id: OBI:0200021 name: linlog transformation def: "A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200022 name: variance stabilizing transformation def: "A variance stabilizing transformation is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper." [] synonym: "variance stabilising transformation" EXACT [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200023 name: loess global transformation def: "A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possibly all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation." [] is_a: OBI:0200071 ! loess transformation [Term] id: OBI:0200024 name: loess group transformation def: "A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs." [] is_a: OBI:0200071 ! loess transformation [Term] id: OBI:0200025 name: loess scale group transformation def: "A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling." [] is_a: OBI:0200185 ! scaling data transformation [Term] id: OBI:0200026 name: total intensity transformation single def: "A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200027 name: total intensity transformation paired def: "A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors)." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200028 name: quantile transformation def: "A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200169 ! normalization data transformation is_a: OBI:0200181 ! center calculation data transformation [Term] id: OBI:0200029 name: mean centering def: "A mean centering is a data transformation that takes as input an n-dimensional (real) vector, performs a mean calculation on its components, and subtracts the resulting mean from each component of the input." [] synonym: "mean centring" EXACT [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200030 name: median centering def: "A median centering is a data transformation that takes as input an n-dimensional (real) vector, performs a median calculation on its components, and subtracts the resulting median from each component of the input." [] synonym: "median centring" EXACT [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200031 name: differential expression analysis objective def: "A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200032 name: K-fold cross validation method def: "K-fold cross-validation randomly partitions the original sample into K subsamples. Of the K subsamples, a single subsample is retained as the validation data for testing the model, and the remaining K - 1 subsamples are used as training data. The cross-validation process is then repeated K times (the folds), with each of the K subsamples used exactly once as the validation data. The K results from the folds then can be averaged (or otherwise combined) to produce a single estimation. The advantage of this method over repeated random sub-sampling is that all observations are used for both training and validation, and each observation is used for validation exactly once. 10-fold cross-validation is commonly used" [] is_a: OBI:0000792 ! statistical model validation [Term] id: OBI:0200033 name: leave one out cross validation method def: "is a data transformation : leave-one-out cross-validation (LOOCV) involves using a single observation from the original sample as the validation data, and the remaining observations as the training data. This is repeated such that each observation in the sample is used once as the validation data" [] is_a: OBI:0000792 ! statistical model validation [Term] id: OBI:0200034 name: jackknifing method def: "Jacknifing is a re-sampling data transformation process used to estimate the precision of sampling statistics and is a resampling method" [] synonym: "jackknifing" EXACT [] is_a: OBI:0000792 ! statistical model validation [Term] id: OBI:0200035 name: boostrapping def: "Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient" [] is_a: OBI:0000792 ! statistical model validation [Term] id: OBI:0200036 name: Benjamini and Hochberg false discovery rate correction method def: "A data transformation process in which the Benjamini and Hochberg method sequential p-value procedure is applied with the aim of correcting false discovery rate" [] is_a: OBI:0200163 ! false discovery rate correction method [Term] id: OBI:0200037 name: pareto scaling def: "A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200040 name: modular decomposition def: "Molecular decomposition is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins." [] is_a: OBI:0200080 ! network analysis [Term] id: OBI:0200041 name: k-means clustering def: "A k-means clustering is a data transformation which achieves a class discovery or partitioning objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed)." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200171 ! partitioning data transformation is_a: OBI:0200175 ! class discovery data transformation [Term] id: OBI:0200042 name: hierarchical clustering def: "A hierarchical clustering is a data transformation which achieves a class discovery objective, which takes as input data item and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root)." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200175 ! class discovery data transformation [Term] id: OBI:0200043 name: average linkage hierarchical clustering def: "An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster." [] is_a: OBI:0200154 ! agglomerative hierarchical clustering [Term] id: OBI:0200044 name: complete linkage hierarchical clustering def: "an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster." [] is_a: OBI:0200154 ! agglomerative hierarchical clustering [Term] id: OBI:0200045 name: single linkage hierarchical clustering def: "A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster." [] is_a: OBI:0200154 ! agglomerative hierarchical clustering [Term] id: OBI:0200049 name: Benjamini and Yekutieli false discovery rate correction method def: "A data transformation in which the Benjamini and Yekutieli method is applied with the aim of correcting false discovery rate" [] is_a: OBI:0200163 ! false discovery rate correction method [Term] id: OBI:0200050 name: dimensionality reduction def: "A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, ..., x_m) into an output n-dimensional vector (y_1, y_2, ..., y_n), where n is smaller than m." [] synonym: "data projection" EXACT [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200175 ! class discovery data transformation [Term] id: OBI:0200051 name: principal components analysis dimensionality reduction def: "A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones." [] synonym: "pca data reduction" EXACT [] is_a: OBI:0200050 ! dimensionality reduction [Term] id: OBI:0200052 name: probabilistic algorithm def: "A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200053 name: expectation maximization def: "EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximated probability function." [] is_a: OBI:0200052 ! probabilistic algorithm [Term] id: OBI:0200054 name: global modularity calculation def: "A network graph quality calculation in which an input data set of subgraph modules and their in-degree and out-degree qualities is used to calculate the average modularity of subgraphs within the network." [] is_a: OBI:0200147 ! network graph quality calculation [Term] id: OBI:0200055 name: dye swap merge def: "A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and vice versa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met." [] is_a: OBI:0200057 ! replicate analysis [Term] id: OBI:0200056 name: moving average def: "A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set." [] is_a: OBI:0200170 ! averaging data transformation [Term] id: OBI:0200057 name: replicate analysis def: "A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200058 name: b cell epitope prediction def: "A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope." [] is_a: OBI:0200187 ! sequence analysis data transformation [Term] id: OBI:0200059 name: mhc binding prediction def: "An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule." [] is_a: OBI:0200187 ! sequence analysis data transformation [Term] id: OBI:0200060 name: t cell epitope prediction def: "A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope." [] is_a: OBI:0200187 ! sequence analysis data transformation [Term] id: OBI:0200061 name: data imputation def: "Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200062 name: continuum mass spectrum analysis def: "A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion." [] is_a: OBI:0200085 ! mass spectrometry analysis [Term] id: OBI:0200063 name: characteristic path length calculation def: "Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices" [] is_a: OBI:0200085 ! mass spectrometry analysis [Term] id: OBI:0200064 name: centroid mass spectrum analysis def: "A centroid mass spectrum is a data transformation in which many points are used to delineate a mass spectral peak, is converted into mass-centroided data by a data compression algorithm. The centroided mass peak is located at the weighted center of mass of the profile peak. The normalized area of the peak provides the mass intensity data." [] synonym: "centroid mass spectrum calculation" EXACT [] synonym: "centroiding" EXACT [] is_a: OBI:0200085 ! mass spectrometry analysis [Term] id: OBI:0200066 name: Holm-Bonferroni family-wise error rate correction method def: "a data transformation that performs more than one hypothesis test simultaneously, a closed-test procedure, that controls the familywise error rate for all the k hypotheses at level α in the strong sense. Objective: multiple testing correction" [] is_a: OBI:0200073 ! family wise error rate correction method [Term] id: OBI:0200070 name: edge weighting def: "Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network." [] is_a: OBI:0200080 ! network analysis [Term] id: OBI:0200071 name: loess transformation def: "A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200072 name: curve fitting data transformation def: "A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200073 name: family wise error rate correction method def: "A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive." [] synonym: "FWER correction" EXACT [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200089 ! multiple testing correction method [Term] id: OBI:0200074 name: submatrix extraction def: "A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.)" [] is_a: OBI:0200050 ! dimensionality reduction [Term] id: OBI:0200075 name: row submatrix extraction def: "A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows." [] is_a: OBI:0200074 ! submatrix extraction [Term] id: OBI:0200076 name: column submatrix extraction def: "A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns." [] is_a: OBI:0200074 ! submatrix extraction [Term] id: OBI:0200077 name: gating def: "Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry." [] is_a: OBI:0200171 ! partitioning data transformation is_a: OBI:0200182 ! data vector reduction data transformation [Term] id: OBI:0200078 name: descriptive statistical calculation objective def: "A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200079 name: arithmetic mean calculation def: "An arithmetic mean calculation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the 'center of gravity' for the data set. It is also known as the first moment." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200170 ! averaging data transformation is_a: OBI:0200181 ! center calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation [Term] id: OBI:0200080 name: network analysis def: "A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network." [] synonym: "network topology analysis" EXACT [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200081 name: sequence analysis objective def: "A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200082 name: longitudinal data analysis def: "Longitudinal analysis is a data transformation used to perform repeated observations of the same items over long periods of time." [] synonym: "correlation analysis" EXACT [] synonym: "longitudinal data analysis" EXACT [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200083 name: survival analysis objective def: "A data transformation objective which has the data transformation aims to model time to event data (where events are e.g. death and or disease recurrence); the purpose of survival analysis is to model the underlying distribution of event times and to assess the dependence of the event time on other explanatory variables" [] synonym: "survival analysis" EXACT [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200085 name: mass spectrometry analysis def: "A data transformation which has the objective of spectrum analysis." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200086 name: spread calculation data transformation def: "A spread calculation is a data transformation that has objective spread calculation." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200088 name: Kaplan Meier def: "a nonparametric (actuarial) data transformation technique for estimating time-related events. It is a univariate analysis that estimates the probability of the proportion of subjects in remission at a particular time, starting from the initiation of active date (time zero), and takes into account those lost to follow-up or not yet in remission at end of study (censored)" [] is_a: OBI:0200194 ! survival analysis data transformation [Term] id: OBI:0200089 name: multiple testing correction method def: "A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate" [] synonym: "multiple testing procedure" EXACT [] is_a: OBI:0000668 ! error correction data transformation [Term] id: OBI:0200091 name: inter-rater reliability objective def: "a data transformation objective of determining the concordance or agreement between human judges." [] synonym: "inter-rater agreement" EXACT [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200092 name: Westfall and Young family wise error rate correction def: "Is a data transformation process in which the Westfall and Young method is applied with the aim of controlling for multiple testing" [] synonym: "Westfall and Young FWER correction" EXACT [] is_a: OBI:0200073 ! family wise error rate correction method [Term] id: OBI:0200093 name: polynomial transformation def: "A polynomial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200094 name: logarithmic transformation def: "A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200095 name: exponential transformation def: "An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200097 name: non-negative matrix factorization def: "Non negative matrix factorization is a data transformation in which factorises a matrix and which forces that all elements must be equal to or greater than zero." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200098 name: soft independent modeling of class analogy analysis def: "Soft independent modeling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes." [] synonym: "SIMCA" EXACT [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200099 name: discriminant function analysis def: "Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0000663 ! class prediction data transformation is_a: OBI:0200106 ! discriminant analysis is_a: OBI:0200175 ! class discovery data transformation [Term] id: OBI:0200100 name: canonical variate analysis def: "canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form." [] synonym: "CVA" EXACT [] is_a: OBI:0200106 ! discriminant analysis is_a: OBI:0200171 ! partitioning data transformation [Term] id: OBI:0200101 name: linear discriminant functional analysis def: "Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0000663 ! class prediction data transformation is_a: OBI:0200106 ! discriminant analysis is_a: OBI:0200175 ! class discovery data transformation [Term] id: OBI:0200102 name: regression analysis method def: "Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200103 name: multiple linear regression analysis def: "multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term epsilon. The model can be written as\n Y = \\beta_0 + \\beta_1 X_1 + \\beta_2 X_2 + \\cdots +\\beta_p X_p + \\varepsilon\nwhere \\beta_0 = 0 is the intercept (\"constant\" term), the \\beta_i s are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression." [] is_a: OBI:0200102 ! regression analysis method [Term] id: OBI:0200104 name: principal component regression def: "The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200102 ! regression analysis method is_a: OBI:0200175 ! class discovery data transformation [Term] id: OBI:0200105 name: partial least square regression analysis def: "Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that\nY = b0 + b1X1 + b2X2 + ... + bpXp\nIn this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data." [] synonym: "PLS-RA" EXACT [] is_a: OBI:0200102 ! regression analysis method [Term] id: OBI:0200106 name: discriminant analysis def: "Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200107 name: partial least square discriminant analysis def: "PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information." [] synonym: "PLS-DA" EXACT [] is_a: OBI:0200106 ! discriminant analysis [Term] id: OBI:0200108 name: eh transformation def: "An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200109 name: b transformation def: "A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200110 name: s transformation def: "An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization." [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200111 name: data visualization def: "A planned process with the objective to graphically represent some data by inputing the data and outputting images, diagrams or animations." [] synonym: "data encoding as image" EXACT [] synonym: "visualization" EXACT [] is_a: OBI:0000011 ! planned process [Term] id: OBI:0200113 name: similarity calculation def: "A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0000663 ! class prediction data transformation is_a: OBI:0200175 ! class discovery data transformation [Term] id: OBI:0200114 name: euclidean distance calculation def: "An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered." [] is_a: OBI:0200113 ! similarity calculation [Term] id: OBI:0200115 name: pearson correlation coefficient calculation def: "A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the \"sample correlation coefficient\" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered." [] is_a: OBI:0200113 ! similarity calculation [Term] id: OBI:0200116 name: loess fitting def: "A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between 1/4 and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda)." [] is_a: OBI:0200072 ! curve fitting data transformation [Term] id: OBI:0200117 name: mode calculation def: "A mode calculation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200181 ! center calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation [Term] id: OBI:0200118 name: quantile calculation def: "A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details." [] is_a: OBI:0200184 ! descriptive statistical calculation data transformation [Term] id: OBI:0200119 name: median calculation def: "A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values." [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200181 ! center calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation [Term] id: OBI:0200120 name: variance calculation def: "A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment." [] is_a: OBI:0200086 ! spread calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation [Term] id: OBI:0200121 name: standard deviation calculation def: "A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean." [] is_a: OBI:0200086 ! spread calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation [Term] id: OBI:0200122 name: interquartile-range calculation def: "The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data." [] is_a: OBI:0200086 ! spread calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation [Term] id: OBI:0200123 name: skewness calculation def: "A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment" [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200181 ! center calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation [Term] id: OBI:0200124 name: kurtosis calculation def: "A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html" [] is_a: OBI:0200086 ! spread calculation data transformation is_a: OBI:0200184 ! descriptive statistical calculation data transformation [Term] id: OBI:0200125 name: data combination def: "A data transformation in which individual input data elements and values are merged together into a output set of data elements and values." [] synonym: "data pooling" EXACT [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200126 name: network graph construction def: "A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph." [] is_a: OBI:0200080 ! network analysis [Term] id: OBI:0200127 name: weighted network graph construction def: "A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph." [] is_a: OBI:0200126 ! network graph construction [Term] id: OBI:0200128 name: directed network graph construction def: "A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph." [] is_a: OBI:0200126 ! network graph construction [Term] id: OBI:0200129 name: node quality calculation def: "A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network." [] is_a: OBI:0200080 ! network analysis [Term] id: OBI:0200130 name: node degree calculation def: "A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node." [] is_a: OBI:0200129 ! node quality calculation [Term] id: OBI:0200131 name: quantitative node degree calculation def: "A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node." [] is_a: OBI:0200129 ! node quality calculation [Term] id: OBI:0200132 name: node in-degree calculation def: "A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node." [] is_a: OBI:0200129 ! node quality calculation [Term] id: OBI:0200133 name: node out-degree calculation def: "A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node." [] is_a: OBI:0200129 ! node quality calculation [Term] id: OBI:0200134 name: node shortest path identification def: "A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arrive at a specific target node in the network." [] is_a: OBI:0200129 ! node quality calculation [Term] id: OBI:0200135 name: edge quality calculation def: "A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network." [] is_a: OBI:0200080 ! network analysis [Term] id: OBI:0200136 name: edge betweenness calculation def: "An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge." [] is_a: OBI:0200135 ! edge quality calculation [Term] id: OBI:0200137 name: network subgraph quality calculation def: "A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network." [] is_a: OBI:0200080 ! network analysis [Term] id: OBI:0200138 name: subgraph degree calculation def: "A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph." [] is_a: OBI:0200137 ! network subgraph quality calculation [Term] id: OBI:0200139 name: quantitative subgraph degree calculation def: "A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph." [] is_a: OBI:0200137 ! network subgraph quality calculation [Term] id: OBI:0200140 name: mathematical feature def: "feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation" [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200141 name: log base def: "The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1." [] synonym: "logarithm base" EXACT [] synonym: "logarithmic base" EXACT [] is_a: OBI:0200140 ! mathematical feature [Term] id: OBI:0200143 name: subgraph in-degree calculation def: "A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph." [] is_a: OBI:0200137 ! network subgraph quality calculation [Term] id: OBI:0200144 name: subgraph out-degree calculation def: "A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph." [] is_a: OBI:0200137 ! network subgraph quality calculation [Term] id: OBI:0200145 name: intra subgraph connectivity calculation def: "A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph." [] is_a: OBI:0200137 ! network subgraph quality calculation [Term] id: OBI:0200146 name: subgraph modularity calculation def: "A network subgraph quality calculation in which an input data set of subgraph in-degree and out-degree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity." [] is_a: OBI:0200137 ! network subgraph quality calculation [Term] id: OBI:0200147 name: network graph quality calculation def: "A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole." [] is_a: OBI:0200080 ! network analysis [Term] id: OBI:0200149 name: unit-variance scaling def: "A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable." [] synonym: "autoscaling" EXACT [] is_a: OBI:0200169 ! normalization data transformation [Term] id: OBI:0200150 name: MA transformation def: "An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200151 name: exponential base def: "The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1)." [] is_a: OBI:0200140 ! mathematical feature [Term] id: OBI:0200152 name: polynomial degree def: "The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted." [] is_a: OBI:0200140 ! mathematical feature [Term] id: OBI:0200153 name: number of variables def: "The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space." [] is_a: OBI:0200140 ! mathematical feature [Term] id: OBI:0200154 name: agglomerative hierarchical clustering def: "An agglomerative hierarchical clustering is a hierarchical clustering which starts with separate clusters and then successively combines these clusters until there is only one cluster remaining." [] synonym: "bottom-up hierarchical clustering" EXACT [] is_a: OBI:0200042 ! hierarchical clustering [Term] id: OBI:0200155 name: divisive hierarchical clustering def: "A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster and then successively splits resulting clusters until only clusters of individual objects remain." [] synonym: "top-down hierarchical clustering" EXACT [] is_a: OBI:0200042 ! hierarchical clustering [Term] id: OBI:0200156 name: data partitioning def: "Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200157 name: data vector reduction objective def: "Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200160 name: generalized family wise error rate correction method def: "A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer." [] synonym: "gFWER correction" EXACT [] is_a: OBI:0200089 ! multiple testing correction method [Term] id: OBI:0200161 name: quantile number of false positives correction method def: "A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed'" [] synonym: "QNFP" EXACT [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200089 ! multiple testing correction method [Term] id: OBI:0200162 name: tail probability for the proportion of false positives correction method def: "A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1." [] synonym: "TPPFP correction method" EXACT [] is_a: OBI:0200089 ! multiple testing correction method [Term] id: OBI:0200163 name: false discovery rate correction method def: "The false discovery rate is a data transformation used in multiple hypothesis testing to correct for multiple comparisons. It controls the expected proportion of incorrectly rejected null hypotheses (type I errors) in a list of rejected hypotheses. It is a less conservative comparison procedure with greater power than familywise error rate (FWER) control, at a cost of increasing the likelihood of obtaining type I errors. ." [] synonym: "FDR correction method" EXACT [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200089 ! multiple testing correction method [Term] id: OBI:0200164 name: proportion of expected false positives correction method def: "A proportion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses." [] synonym: "PEFP correction method" EXACT [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200089 ! multiple testing correction method [Term] id: OBI:0200165 name: quantile proportion of false positives correction method def: "A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distribution of the proportion of false positives among the rejected hypothesis (false discovery rate)." [] synonym: "QPFP correction method" EXACT [] is_a: APOLLO_SV:00000796 ! dataset creating is_a: OBI:0200089 ! multiple testing correction method [Term] id: OBI:0200166 name: data transformation objective def: "An objective specification to transformation input data into output data" [] is_a: IAO:0000005 ! objective specification [Term] id: OBI:0200167 name: data normalization objective def: "A normalization objective is a data transformation objective where the aim is to remove\nsystematic sources of variation to put the data on equal footing in order\nto create a common base for comparisons." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200168 name: correction objective def: "A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself" [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200169 name: normalization data transformation def: "A normalization data transformation is a data transformation that has objective normalization." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200170 name: averaging data transformation def: "An averaging data transformation is a data transformation that has objective averaging." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200171 name: partitioning data transformation def: "A partitioning data transformation is a data transformation that has objective partitioning." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200172 name: partitioning objective def: "A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200173 name: background correction objective def: "A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation." [] is_a: OBI:0200168 ! correction objective [Term] id: OBI:0200174 name: curve fitting objective def: "A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200175 name: class discovery data transformation def: "A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery." [] synonym: "clustering data transformation" EXACT [] synonym: "unsupervised classification data transformation" EXACT [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200176 name: Fisher's exact test def: "Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two Fisher's exact test is a statistical significance test used in the analysis of contingency tables where sample sizes are small where the significance of the deviation from a null hypothesis can be calculated exactly, rather than relying on an approximation that becomes exact in the limit as the sample size grows to infinity, as with many statistical tests." [] is_a: OBI:0000673 ! statistical hypothesis test [Term] id: OBI:0200177 name: center calculation objective def: "A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200178 name: class discovery objective def: "A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic." [] synonym: "clustering objective" EXACT [] synonym: "discriminant analysis objective" EXACT [] synonym: "unsupervised classification objective" EXACT [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200179 name: class prediction objective def: "A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and\nclass labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data." [] synonym: "classification objective" EXACT [] synonym: "supervised classification objective" EXACT [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200180 name: spread calculation objective def: "is a data transformation objective whereby the aim is to the calculate the spread of a dataset, spread is a descriptive statistic which describes the variability of values in a data set." [] is_a: OBI:0200166 ! data transformation objective [Term] id: OBI:0200181 name: center calculation data transformation def: "A center calculation data transformation is a data transformation that has objective of center calculation." [] is_a: OBI:0200000 ! data transformation [Term] id: OBI:0200182 name: data vector reduction data transformation def: "A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of output vectors j, where jcells; output=>cell_lysate" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0600028 name: artificially induced reverse transcription def: "a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA)" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0600029 name: isolation of cell culture supernatant def: "a protocol which results in the separation of supernatant material from a cell culture" [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0600030 name: experimental disease induction def: "a protocol application to induce a specific disease in an organism" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0600031 name: enzyme-linked immunospot assay def: "A cytometry assay in which cells are cultured on a surface coated with a capture antibody binding a secretory material of interest which subsequently gets stained resulting in a spot for each cell producing the secretory material of interest." [] synonym: "ELISPOT assay" EXACT [] is_a: OBI:0001977 ! cytometry assay is_a: OBI:0003587 ! cell culture assay [Term] id: OBI:0600032 name: artificially induced DNA repair def: "a protocol application to repair damaged DNA molecules" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0600033 name: cell permeabilization def: "A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0600034 name: precipitation def: "a protocol application to cause a material to precipitate (becoming a solid) out of solution. Input is a solution, output is a solution plus a solid component (the precipitate)" [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0600036 name: establishing cell culture def: "a process through which a new type of cell culture or cell line is created, either through the isolation and culture of one or more cells from a fresh source, or the deliberate experimental modification of an existing cell culture (e.g passaging a primary culture to become a secondary culture or line, or the immortalization or stable genetic modification of an existing culture or line)." [] comment: A 'cell culture' as used here referes to a new lineage of cells in culture deriving from a single biological source.. New cultures are established through the initial isolation and culturing of cells from an organismal source, or through changes in an existing cell culture or line that result in a new culture with unique characteristics. This can occur through the passaging/selection of a primary culture into a secondary culture or line, or experimental modifications of an existing cell culture or line such as an immortalization process or other stable genetic modification. This class covers establishment of cultures of either multicellular organism cells or unicellular organisms. is_a: OBI:0000094 ! material processing [Term] id: OBI:0600037 name: cell culture splitting def: "The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing" [] comment: An active cell culture is typically split when it has grown to confluence in its culture dish. Cell culture splitting of a cell culture sample results in an increase in its passage number, which measures how long a sample has been propagated in vitro, and therefore how many selective or genetic changes it is likely to have undergone. synonym: "cell culture passaging" EXACT [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0600038 name: addition of molecular label def: "a material processing technique intended to add a molecular label to some input material entity, to allow detection of the molecular target of this label in a detection of molecular label assay" [] synonym: "labeling" EXACT [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0600039 name: artificially induced methylation def: "A planned process of adding methyl groups to polymers" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0600040 name: synthesis def: "the construction of a biomaterial from simpler biomaterials" [] synonym: "synthesize" EXACT [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0600041 name: concentrate def: "a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material" [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0600042 name: recombinant plasmid cloning def: "the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial" [] is_a: OBI:0600064 ! recombinant vector cloning [Term] id: OBI:0600043 name: genetic transformation def: "the introduction. alteration or integration of genetic material into a cell or organism" [] synonym: "genetic modification" EXACT [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0600044 name: lavage def: "A protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid" [] is_a: OBI:0600005 ! collecting specimen from organism is_a: OBI:0600014 ! material component separation [Term] id: OBI:0600045 name: 3D structure determination assay def: "An assay that determines the 3-dimensional configuration of an input material." [] is_a: OBI:0000070 ! assay [Term] id: OBI:0600046 name: preparative chromatography def: "the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity" [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0600047 name: sequencing assay def: "An assay the uses chemical or biochemical means to infer the sequence of a biomaterial" [] is_a: OBI:0000070 ! assay [Term] id: OBI:0600048 name: vector mediated amplification def: "The process of creating a copy of some biological entity in cell culture" [] is_a: OBI:0600064 ! recombinant vector cloning [Term] id: OBI:0600049 name: DNA polymerase amplification def: "DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA contained in biomaterial used as input" [] is_a: OBI:0600058 ! enzymatic amplification [Term] id: OBI:0600050 name: specific enzymatic cleavage def: "an enzymatic cleavage that uses an enzyme with a strong affinity for specific cleavage sites in the input material" [] is_a: OBI:0000231 ! enzymatic cleavage [Term] id: OBI:0600051 name: gradient separation def: "a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities" [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0600052 name: dialysis def: "a protocol application that uses diffusion through a semi-permeable membrane to separate an input material into two fractions of different composition" [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0600053 name: electrophoresis def: "a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge" [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:0600054 name: selection by survival def: "the use of environmental conditions to select for the organism or cells that have a certain trait" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0600055 name: DNA restriction enzyme digestion def: "A specific enzymatic cleavage of DNA molecules using endonucleases that cleave DNA molecules at specific sites based on the surrounding nucleotide sequence" [] synonym: "restriction enzyme assay" EXACT [] is_a: OBI:0600050 ! specific enzymatic cleavage [Term] id: OBI:0600056 name: protease cleavage def: "protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments)." [] is_a: OBI:0000231 ! enzymatic cleavage [Term] id: OBI:0600057 name: enzymatic DNA replication def: "the use of enzymes to duplicate DNA molecule any process used to make additional copies of a biomaterial" [] is_a: OBI:0600058 ! enzymatic amplification [Term] id: OBI:0600058 name: enzymatic amplification def: "the use of enzymes to increase the number of molecules of a biomaterial" [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0600059 name: DNA transduction def: "a genetic transformation which relies on the use of lysogenic infection to transfer DNA sequences into an organism" [] is_a: OBI:0600043 ! genetic transformation [Term] id: OBI:0600060 name: DNA transfection def: "a transfection which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell" [] is_a: OBI:0001152 ! transfection [Term] id: OBI:0600063 name: vector mediated expression def: "vector mediated expression sis the generation of copies of biomaterial by in a cell_culture modified for this purpose by insertion of an expression vector" [] is_a: OBI:0600064 ! recombinant vector cloning [Term] id: OBI:0600064 name: recombinant vector cloning def: "a planned process with the objective to insert genetic material into a cloning vector for future replication of the inserted material" [] synonym: "molecular cloning" EXACT [] is_a: OBI:0000094 ! material processing [Term] id: OBI:0600065 name: obsolete_defined processes def: "Place holder class, see editor note" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:0600067 name: specific labeling def: "a labeling in which the labeling reagent used has a specificity to bind only certain components of the input material" [] is_a: OBI:0600038 ! addition of molecular label [Term] id: OBI:0666666 name: RNA extraction def: "A RNA extraction is a nucleic acid extraction where the desired output material is RNA" [] is_a: OBI:0666667 ! nucleic acid extraction [Term] id: OBI:0666667 name: nucleic acid extraction def: "a material separation to recover the nucleic acid fraction of an input material" [] is_a: OBI:0302884 ! extraction [Term] id: OBI:1000023 name: cell culture supernatant def: "Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell." [] is_a: OBI:0000047 ! processed material [Term] id: OBI:1000024 name: cell pellet def: "A material entity which results from the aggregation of cells produced by the application of centrifugal force to a liquid containing cells in suspension" [] is_a: OBI:0000047 ! processed material [Term] id: OBI:1000029 name: phage display library def: "a phage display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified." [] synonym: "display library" EXACT [] is_a: OBI:0000731 ! recombinant vector [Term] id: OBI:1000036 name: cell lysate def: "a cell lysate is a material entity which is output of a cell lysis process" [] synonym: "lysate" EXACT [] synonym: "lysed material" EXACT [] is_a: OBI:0000047 ! processed material [Term] id: OBI:1000042 name: peptide construct def: "a material entity synthesized to contain a number of peptides conjugated together in a non-linear fashion" [] is_a: OBI:0000047 ! processed material [Term] id: OBI:1000048 name: transgenic organism def: "a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it" [] is_a: OBI:0302859 ! genetically modified organism [Term] id: OBI:1000049 name: whole mount tissue def: "A whole organism preparation resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide" [] synonym: "whole mount sample" EXACT [] is_a: OBI:0000680 ! whole organism preparation is_a: OBI:0000953 ! processed specimen is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:1000207 name: assay bead def: "A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules." [] synonym: "bead" EXACT [] is_a: OBI:0000047 ! processed material [Term] id: OBI:1110001 name: epitope def: "A material entity with the disposition to be bound by an adaptive immune receptor." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:1110002 name: obsolete_occurrence of disease def: "An occurrence of disease is a process involving pathologic changes within an organism" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: OBI:1110003 name: host exposure to infectious agent def: "a process in which an infectious agent comes into physical contact with a host organism." [] is_a: GO:0008150 ! biological_process [Term] id: OBI:1110007 name: administration in vivo with infectious agent def: "is an administration of an infectious agent to a host organism" [] is_a: OBI:0600007 ! administering substance in vivo [Term] id: OBI:1110008 name: occurrence of infectious disease def: "Is an occurrence of a disease caused by an infection" [] is_a: OGMS:0000063 ! disease course [Term] id: OBI:1110010 name: disposition to cause an allergic reaction def: "The role borne by a material entity that is realized when it is recognized by the immune system and results in the occurrence of an allergic disease." [] synonym: "allergenic disposition" EXACT [] is_a: BFO:0000016 ! disposition [Term] id: OBI:1110011 name: allergic reaction def: "an allergic reaction is an pathologic immune response by an organism to a non-self entity that is normally harmless(the allergen)" [] is_a: OBI:1110122 ! pathologic process [Term] id: OBI:1110012 name: occurrence of allergy def: "The process of an allergic disease occurring in an organism." [] is_a: OGMS:0000063 ! disease course [Term] id: OBI:1110013 name: ELISPOT assay measuring epitope specific interleukin-2 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|ELISPOT" EXACT [] is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:1110014 name: epitope binding by adaptive immune receptor def: "is the process in which an adaptive immune receptor binds to a material entity (realizing its disposition). The binding affinity is significant enough to trigger an immune response. Specifically, transient non-specific binding of adaptive immune receptors occurring during immune surveillance is not considered significant binding." [] is_a: GO:0008150 ! biological_process [Term] id: OBI:1110015 name: Immunization in vivo def: "Process of administering an object playing the role of immunogen to a living organism" [] is_a: OBI:1110094 ! immunization [Term] id: OBI:1110016 name: adaptive immune effector function def: "A function realized as an immune response, which inheres in a T cell, B cell or antibody which derives from or is produced by a cell with prior antigen experience." [] is_a: BFO:0000034 ! function [Term] id: OBI:1110017 name: living with infected household contact def: "a process in which a a human being lives in the same household as another human being that is known to be infected with an infectious agent" [] is_a: OBI:1110111 ! environmental proximity to infectious agent [Term] id: OBI:1110018 name: living in endemic area def: "a process in which a potential host organism lives in a geographic area in which an infectious agent is present to such a degree of frequency that contact is likely" [] is_a: OBI:1110111 ! environmental proximity to infectious agent [Term] id: OBI:1110019 name: pathogen release in laboratory accident def: "a process in which a an infectious agent maintained in a laboratory setting is not contained as planned, leading to potential exposure of human beings to the agent" [] is_a: OBI:1110111 ! environmental proximity to infectious agent [Term] id: OBI:1110020 name: Immunization in vitro def: "A planned process with the objective to administer an object playing the role of immunogen to a cell culture." [] is_a: OBI:0000094 ! material processing [Term] id: OBI:1110021 name: infection process def: "the detrimental process in which an infectious agent colonizes or replicates in a host environment" [] is_a: OBI:1110122 ! pathologic process [Term] id: OBI:1110022 name: adaptive immune receptor def: "is a receptor produced by cells of the adaptive immune system with the purpose of binding epitopes." [] is_a: GO:0032991 ! protein-containing complex [Term] id: OBI:1110023 name: immunogen def: "a material entity bearing the immunogen role" [] is_a: BFO:0000040 ! material entity [Term] id: OBI:1110024 name: environmental exposure to infectious agent def: "Is a process in which an infectious agent is in direct contact with a potential host organism in its habitat. This is preceded by proximity to the infectious agent" [] is_a: GO:0008150 ! biological_process [Term] id: OBI:1110026 name: host of immune response def: "An organism in which an immune response process occurs." [] is_a: OBI:0100026 ! organism [Term] id: OBI:1110028 name: 293-T cell line def: "A cell line derived from human embryonic kidney cells. This cell line contains the SV40 Large T-antigen, allowing episomal replication of transfected plasmids containing the SV40 origin of replication." [] is_a: CLO:0009828 ! immortal cell line [Term] id: OBI:1110029 name: C1R cell line def: "A cell line derived from human B cells. This cell line was created by EBV transformation (B-lymphoblastoid cell-line (BLCL))." [] is_a: CLO:0009828 ! immortal cell line [Term] id: OBI:1110030 name: experimental infection of cell culture def: "is the administration of an infectious agent to a cell culture with the objective to have the agent colonize and replicate in culture" [] is_a: OBI:0600000 ! adding substance to cell culture [Term] id: OBI:1110031 name: EL-4 cell line def: "A cell line derived from mouse (C57BL/6N) lymphoma cells." [] is_a: CLO:0009828 ! immortal cell line [Term] id: OBI:1110032 name: HeLa cell line def: "A cell line derived from human cervical cancer cells." [] is_a: CLO:0009828 ! immortal cell line [Term] id: OBI:1110033 name: JAWS II cell line def: "A cell line derived from mouse dendritic cells." [] is_a: CLO:0009828 ! immortal cell line [Term] id: OBI:1110034 name: antigen def: "A material entity that has the antigen role." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:1110035 name: Jurkat cell line def: "A cell line derived from human T cells." [] is_a: CLO:0009828 ! immortal cell line [Term] id: OBI:1110036 name: JY cell line def: "The JY cell line is an Epstein-Barr virus (EBV)-immortalised b cell lymphoblastoid line.(wikipedia)" [] is_a: CLO:0009828 ! immortal cell line [Term] id: OBI:1110037 name: assay measuring binding of a T cell epitope:MHC:TCR complex def: "A T cell epitope assay that measures the binding of T cell receptor to an epitope." [] synonym: "T cell binding|any method" EXACT [] is_a: OBI:0003128 ! T cell epitope assay [Term] id: OBI:1110038 name: RMA cell line def: "A cell line derived from a mouse lymphoma, specifically a Rauscher virus-induced tumor.This cell ine is antigen processing-defective and expresses a very low level of MHC molecules on its surface." [] is_a: CLO:0009828 ! immortal cell line [Term] id: OBI:1110039 name: T2 cell line def: "A human T-B lymphoblastoid hybrid cell line" [] is_a: CLO:0009828 ! immortal cell line [Term] id: OBI:1110040 name: infectious disease def: "is a disease caused by an infectious agent" [] is_a: OGMS:0000031 ! disease [Term] id: OBI:1110041 name: lymph node cell specimen def: "A cell specimen comprised of a mixed population of cells obtained by processing whole lymph node into individual cells, typically performed using a sieve. This population includes T cells, B cells, macrophages, and other cell types." [] is_a: OBI:0000953 ! processed specimen is_a: OBI:0001468 ! cell specimen [Term] id: OBI:1110043 name: cultured adherent cell population def: "A mixed cell population that is characterized by its ability to bind to tissue culture flasks or plates. This population typically contains macrophages and other cells capable of playing the antigen presenting cell role." [] synonym: "adherent cell culture sample" EXACT [] is_a: OBI:0100060 ! cultured cell population [Term] id: OBI:1110044 name: cultured PBMC cell population def: "A mixed cell population obtained by processing whole blood. The cells are characterized by having a similar density and are largely mononuclear cells (includes T cells, B cells, and other cell types)." [] synonym: "PBMC cell culture sample" EXACT [] is_a: OBI:0001875 ! cultured immune cell population [Term] id: OBI:1110045 name: disposition to be bound by an adaptive immune receptor def: "Is the disposition borne by a material entity that is realized in a process of being bound by a adaptive immune receptor." [] synonym: "epitope disposition" EXACT [] is_a: BFO:0000016 ! disposition [Term] id: OBI:1110046 name: organ harvesting def: "The process of removing an organ from its source organism" [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:1110047 name: cultured CD3+ T cell population def: "A T cell population characterized by expressing the CD3 molecule on its surface." [] synonym: "CD3+ T cell culture sample" EXACT [] is_a: OBI:0001875 ! cultured immune cell population [Term] id: OBI:1110048 name: cultured CD3- T cell population def: "A T cell population characterized by not expressing the CD3 molecule on its surface." [] synonym: "CD3- T cell culture sample" EXACT [] is_a: OBI:0001875 ! cultured immune cell population [Term] id: OBI:1110049 name: allergy def: "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" [] is_a: OGMS:0000031 ! disease [Term] id: OBI:1110050 name: cultured CD4- T cell population def: "A T cell population characterized by not expressing the CD4 molecule on its surface." [] synonym: "CD4- T cell culture sample" EXACT [] is_a: OBI:0001875 ! cultured immune cell population [Term] id: OBI:1110051 name: cultured CD8- T cell population def: "A T cell population characterized by not expressing the CD8 molecule on its surface." [] synonym: "CD8- T cell culture sample" EXACT [] is_a: OBI:0001875 ! cultured immune cell population [Term] id: OBI:1110052 name: cultured CD4-/CD8- T cell population def: "A T cell population characterized by not expressing the CD4 nor the CD8 molecule on its surface." [] synonym: "CD4-/CD8- T cell culture sample" EXACT [] is_a: OBI:1110050 ! cultured CD4- T cell population is_a: OBI:1110051 ! cultured CD8- T cell population [Term] id: OBI:1110053 name: cancer def: "A disease characterized by abnormal and uncontrolled cell division" [] is_a: OGMS:0000031 ! disease [Term] id: OBI:1110054 name: autoimmune disease def: "Is a disease characterized by an immune response of an organism against parts of itself" [] is_a: OGMS:0000031 ! disease [Term] id: OBI:1110055 name: obsolete_disease def: "placeholder to be imported from disease ontology" [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: OGMS:0000031 [Term] id: OBI:1110056 name: epitope specific IL-2 release by T cells def: "A biological process where T cells produce IL-2 resulting from the recognition of a T cell epitope." [] is_a: GO:0032623 ! interleukin-2 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:1110057 name: MHC:epitope complex binding to TCR def: "a process of an MHC molecule binding to an entity playing the role of epitope to create an MHC:epitope complex which is then bound by a TCR molecule." [] is_a: OBI:0001588 ! binding is_a: OBI:1110014 ! epitope binding by adaptive immune receptor [Term] id: OBI:1110059 name: ELISPOT assay measuring epitope specific interferon-gamma production by T cells def: "An enzyme-linked immunospot assay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|ELISPOT" EXACT [] is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:1110061 name: exposure resulting in immune reactivity def: "a process in which an organism (host) is exposed to some material entity, which results in an immune reactivity" [] is_a: GO:0008150 ! biological_process [Term] id: OBI:1110082 name: immunogen role def: "A role of a material entity that is realized when the material elicits an immune response targeting itself in whole or in part." [] is_a: BFO:0000023 ! role [Term] id: OBI:1110083 name: host of immune response role def: "is a role borne by an organism. It is realized by the organism during an immunization or an immune response taking place inside or on the surface of the organism, and in which the responding or stimulated immune system is part of the host." [] is_a: BFO:0000023 ! role [Term] id: OBI:1110084 name: effector T cell function def: "The function inhering in a T cell that is realized in an immune response that results from the T cell receptor binding to the MHC:epitope complex." [] is_a: OBI:1110016 ! adaptive immune effector function [Term] id: OBI:1110085 name: antigen presentation function def: "a function inhering in a cell that expresses MHC molecules which is realized in the process of antigen processing and presentation of antigen derived parts by MHC molecules on the cell surface." [] synonym: "APC" EXACT [] is_a: BFO:0000034 ! function [Term] id: OBI:1110086 name: restricting MHC role def: "The role played by an MHC molecule by binding a material entity playing the role of epitope when that epitope/MHC molecule pair are recognized (bound) by a TCR molecule on the surface of a cell playing the role of effector cell." [] is_a: BFO:0000023 ! role [Term] id: OBI:1110087 name: donor role def: "A role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro." [] synonym: "donor role" EXACT [] is_a: BFO:0000023 ! role [Term] id: OBI:1110091 name: immune epitope carrier role def: "A role inhering in a material entity that is covalently bound to an epitope in order to increase the epitopes immunogenicity." [] is_a: BFO:0000023 ! role [Term] id: OBI:1110092 name: adjuvant role def: "Adjuvant role is a role that inheres in a material entity and which is realized through a process of modifying a biological response." [] synonym: "adjuvent role" EXACT [] is_a: BFO:0000023 ! role [Term] id: OBI:1110093 name: disposition to infect an organism def: "Is a role borne by an agent, and realized when in contact with or inside another organism in which it is capable of replicating and causing disease" [] is_a: BFO:0000016 ! disposition [Term] id: OBI:1110094 name: immunization def: "The process of an epitope that is part of or derived from an immunogen coming into contact with adaptive immune cells resulting in these cells acquiring immune effector functions specific for the epitope." [] is_a: GO:0008150 ! biological_process [Term] id: OBI:1110095 name: blood harvesting def: "A material separation where blood is taken from an organism." [] is_a: OBI:0600014 ! material component separation [Term] id: OBI:1110099 name: L cell line def: "A cell line derived from mouse fibroblasts." [] is_a: CLO:0009828 ! immortal cell line [Term] id: OBI:1110106 name: cultured antigen presenting cell population def: "a cell culture including cells that have an antigen presentation function" [] synonym: "antigen presenting cell culture sample" EXACT [] is_a: OBI:0001875 ! cultured immune cell population [Term] id: OBI:1110107 name: cultured effector T cell population def: "A cell culture including cells that have an effector T cell function" [] synonym: "culture of effector T cells" EXACT [] synonym: "effector T cell culture sample" EXACT [] is_a: OBI:0001875 ! cultured immune cell population [Term] id: OBI:1110108 name: material to be added def: "A material entity that is added to another material entity in an “adding a material entity into a target” process." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:1110109 name: target of material addition def: "A material entity that receives the addition of another material entity in an “adding a material entity into a target” process." [] is_a: BFO:0000040 ! material entity [Term] id: OBI:1110111 name: environmental proximity to infectious agent def: "Is a process in which an infectious agent comes close enough to a potential host organism in its habitat that a contact can result" [] is_a: GO:0008150 ! biological_process [Term] id: OBI:1110114 name: contact to pathogen carrying biological vector def: "a process in which a vector carrying an infectious agent comes close enough to a potential host organism that a contact can result" [] is_a: OBI:1110111 ! environmental proximity to infectious agent [Term] id: OBI:1110116 name: splenocyte specimen def: "A cell specimen comprised of a mixed cell population obtained by processing whole spleen into individual cells, typically performed using a sieve or blender. This population includes T cells, B cells, macrophages, and other cell types." [] is_a: OBI:0000953 ! processed specimen is_a: OBI:0001468 ! cell specimen [Term] id: OBI:1110118 name: P815 cell line def: "A cell line derived from mouse mastocytoma." [] is_a: CLO:0009828 ! immortal cell line [Term] id: OBI:1110120 name: assay antigen role def: "An antigen role that is realized as part of an assay, where immune recognition of the material with the assay antigen role is being detected as part of the assay." [] is_a: OBI:0000237 ! antigen role [Term] id: OBI:1110122 name: pathologic process def: "abnormal, harmful processes caused by or associated with a disease" [] is_a: GO:0008150 ! biological_process [Term] id: OBI:1110124 name: assay measuring qualitative binding of a T cell epitope:MHC:TCR complex def: "An assay that detects the binding of a MHC:epitope complex with a T cell receptor, and produces a qualitative measurement of the binding as an output." [] synonym: "qualitative binding|binding assay" EXACT [] is_a: OBI:1110037 ! assay measuring binding of a T cell epitope:MHC:TCR complex [Term] id: OBI:1110125 name: assay measuring MHC ligand processing and presentation def: "A MHC ligand assay that determines what ligands are processed and loaded onto MHC molecules by eluting ligands and identifying them." [] synonym: "ligand presentation|any method" EXACT [] is_a: OBI:0002075 ! MHC ligand assay [Term] id: OBI:1110126 name: assay measuring binding of a MHC:ligand complex def: "A MHC ligand assay that detects the binding of a ligand to an MHC molecule." [] synonym: "MHC binding|any method" EXACT [] is_a: OBI:0002075 ! MHC ligand assay [Term] id: OBI:1110127 name: assay measuring binding of a B cell epitope:antibody complex def: "A B cell epitope assay that measures the binding of an antibody receptor to an epitope." [] synonym: "antibody binding|any method" EXACT [] is_a: OBI:0003127 ! B cell epitope assay [Term] id: OBI:1110128 name: immune epitope assay def: "An assay that detects the binding of an epitope to an adaptive immune receptor, or an immune process resulting from such a binding event, or characterizes the structrue of the complex resulting from such a binding event." [] synonym: "immune epitope assay" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:1110129 name: assay measuring epitope specific cytokine production by T cells def: "A T cell epitope assay that detects cytokine production by T cells." [] synonym: "cytokine release|biological activity" EXACT [] is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:1110130 name: assay measuring epitope specific T cell killing def: "A T cell epitope dependent biological activity assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC." [] synonym: "cytotoxicity|biological activity" EXACT [] is_a: OBI:0000882 ! cell-cell killing assay is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:1110131 name: assay measuring epitope specific proliferation of T cells def: "A T cell epitope dependent biological activity assay that detects T cell proliferation." [] synonym: "proliferation|biological activity" EXACT [] is_a: OBI:0002055 ! assay measuring biological activity resulting from T cell epitope:MHC:TCR binding [Term] id: OBI:1110132 name: obsolete CD8 receptor def: "A transmembrane glycoprotein that serves as a co-receptor for the T cell receptor." [] synonym: "CD8" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true replaced_by: PR:000025402 [Term] id: OBI:1110150 name: 51 chromium assay measuring epitope specific T cell killing def: "A chromium release assay that detects the killing of an antigen presenting cell (APC) by a T cell whose TCR recognizes an epitope presented by the APC." [] synonym: "cytotoxicity|51 chromium" EXACT [] is_a: OBI:0002062 ! in vitro assay measuring epitope specific T cell killing is_a: OBI:9999994 ! chromium release assay [Term] id: OBI:1110151 name: ELISA measuring epitope specific interferon-gamma production by T cells def: "An enzyme-linked immunosorbent assay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells [Term] id: OBI:1110152 name: ELISA measuring epitope specific interleukin-2 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells [Term] id: OBI:1110153 name: ELISA measuring epitope specific interleukin-4 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-4 production by T cells." [] synonym: "IL-4 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001450 ! assay measuring epitope specific interleukin-4 production by T cells [Term] id: OBI:1110154 name: ELISA measuring epitope specific interleukin-5 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-5 production by T cells." [] synonym: "IL-5 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001230 ! assay measuring epitope specific interleukin-5 production by T cells [Term] id: OBI:1110155 name: ELISA measuring epitope specific tumor necrosis factor alpha production by T cells def: "An enzyme-linked immunosorbent assay that detects tumor necrosis factor alpha production by T cells." [] synonym: "TNFa release|ELISA" EXACT [] is_a: OBI:0001246 ! ELISA measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor alpha production by T cells [Term] id: OBI:1110156 name: ELISA measuring epitope specific interleukin-10 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001209 ! assay measuring epitope specific interleukin-10 production by T cells [Term] id: OBI:1110157 name: ELISA measuring epitope specific granulocyte macrophage colony-stimulating factor production by T cells def: "An enzyme-linked immunosorbent assay that detects granulocyte macrophage colony stimulating factor production by T cells." [] synonym: "GM-CSF release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001233 ! assay measuring epitope specific granulocyte macrophage colony stimulating factor production by T cells [Term] id: OBI:1110158 name: ELISA measuring epitope specific interleukin-6 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-6 production by T cells." [] synonym: "IL-6 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001451 ! assay measuring epitope specific interleukin-6 production by T cells [Term] id: OBI:1110159 name: ELISA measuring epitope specific interleukin-13 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-13 production by T cells." [] synonym: "IL-13 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001251 ! assay measuring epitope specific interleukin-13 production by T cells [Term] id: OBI:1110160 name: ELISA measuring epitope specific interleukin-12 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-12 production by T cells." [] synonym: "IL-12 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001391 ! assay measuring epitope specific interleukin-12 production by T cells [Term] id: OBI:1110161 name: ELISA measuring epitope specific interleukin-1 beta production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-1 beta production by T cells." [] synonym: "IL-1b release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001449 ! assay measuring epitope specific interleukin-1 beta production by T cells [Term] id: OBI:1110162 name: ELISA measuring epitope specific interleukin-17 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-17 production by T cells." [] synonym: "IL-17 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:1110163 name: ELISA measuring epitope specific interleukin-18 production by T cells def: "An enzyme-linked immunosorbent assay that detects interleukin-18 production by T cells." [] synonym: "IL-18 release|ELISA" EXACT [] is_a: OBI:0000661 ! enzyme-linked immunosorbent assay is_a: OBI:0001380 ! assay measuring epitope specific interleukin-18 production by T cells [Term] id: OBI:1110167 name: ELISPOT assay measuring epitope specific interleukin-4 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-4 production by T cells." [] synonym: "IL-4 release|ELISPOT" EXACT [] is_a: OBI:0001450 ! assay measuring epitope specific interleukin-4 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:1110168 name: ELISPOT assay measuring epitope specific tumor necrosis factor alpha production by T cells def: "An enzyme-linked immunospot assay that detects tumor necrosis factor alpha production by T cells" [] synonym: "TNFa release|ELISPOT" EXACT [] is_a: OBI:0001272 ! ELISPOT assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor alpha production by T cells [Term] id: OBI:1110170 name: ELISPOT assay measuring epitope specific interleukin-10 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|ELISPOT" EXACT [] is_a: OBI:0001209 ! assay measuring epitope specific interleukin-10 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:1110171 name: ELISPOT assay measuring epitope specific interleukin-13 production by T cells def: "An enzyme-linked immunospot assay that detects interleukin-13 production by T cells." [] synonym: "IL-13 release|ELISPOT" EXACT [] is_a: OBI:0001251 ! assay measuring epitope specific interleukin-13 production by T cells is_a: OBI:0600031 ! enzyme-linked immunospot assay [Term] id: OBI:1110172 name: intracellular cytokine staining assay measuring epitope specific interferon-gamma production by T cells def: "A flow cytometry assay that detects interferon-gamma production by T cells." [] synonym: "IFNg release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001414 ! assay measuring epitope specific interferon-gamma production by T cells [Term] id: OBI:1110173 name: intracellular cytokine staining assay measuring epitope specific interleukin-2 production by T cells def: "A flow cytometry assay that detects interleukin-2 production by T cells." [] synonym: "IL-2 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001445 ! assay measuring epitope specific interleukin-2 production by T cells [Term] id: OBI:1110174 name: intracellular cytokine staining assay measuring epitope specific tumor necrosis factor alpha production by T cells def: "A flow cytometry assay that detects tumor necrosis factor alpha production by T cells." [] synonym: "TNFa release|ICS" EXACT [] is_a: OBI:0001385 ! intracellular cytokine staining assay measuring epitope specific tumor necrosis factor superfamily cytokine production by T cells is_a: OBI:0001416 ! assay measuring epitope specific tumor necrosis factor alpha production by T cells [Term] id: OBI:1110175 name: intracellular cytokine staining assay measuring epitope specific interleukin-4 production by T cells def: "A flow cytometry assay that detects interleukin-4 production by T cells." [] synonym: "IL-4 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001450 ! assay measuring epitope specific interleukin-4 production by T cells [Term] id: OBI:1110177 name: intracellular cytokine staining assay measuring epitope specific interleukin-10 production by T cells def: "A flow cytometry assay that detects interleukin-10 production by T cells." [] synonym: "IL-10 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001209 ! assay measuring epitope specific interleukin-10 production by T cells [Term] id: OBI:1110178 name: intracellular cytokine staining assay measuring epitope specific interleukin-17 production by T cells def: "A flow cytometry assay that detects interleukin-17 production by T cells." [] synonym: "IL-17 release|ICS" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001295 ! assay measuring epitope specific interleukin-17 production by T cells [Term] id: OBI:1110179 name: MHC tetramer/multimer assay measuring binding of a T cell epitope:MHC:TCR complex def: "A MHC tetramer/multimer assay that measures the binding of an epitope:MHC complex binding with a T cell receptor." [] synonym: "qualitative binding|multimer/tetramer" EXACT [] is_a: OBI:0000916 ! flow cytometry assay is_a: OBI:0001501 ! fluorescence detection assay is_a: OBI:1110124 ! assay measuring qualitative binding of a T cell epitope:MHC:TCR complex [Term] id: OBI:1110180 name: 3H-thymidine assay measuring epitope specific proliferation of T cells def: "A tritiated thymidine incorporation assay that detects T cell epitope specific proliferation in vitro." [] synonym: "proliferation|3H-thymidine" EXACT [] is_a: OBI:0000669 ! tritiated thymidine incorporation assay is_a: OBI:0002071 ! in vitro assay measuring epitope specific proliferation of T cells [Term] id: OBI:1110181 name: BrdU assay measuring epitope specific proliferation of T cells def: "A BrdU incorporation assay that detects T cell epitope specific proliferation in vitro." [] synonym: "proliferation|BrdU" EXACT [] is_a: OBI:0000664 ! BrdU incorporation assay is_a: OBI:0002071 ! in vitro assay measuring epitope specific proliferation of T cells [Term] id: OBI:1110182 name: epitope specific T cell proliferation def: "A biological process where T cells proliferate resulting from the recognition of a T cell epitope." [] is_a: GO:0042098 ! T cell proliferation [Term] id: OBI:1110184 name: epitope specific GM-CSF release by T cells def: "A biological process where T cells produce GM-CSF resulting from the recognition of a T cell epitope." [] is_a: GO:0032604 ! granulocyte macrophage colony-stimulating factor production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:1110185 name: epitope specific IFN-g release by T cells def: "A biological process where T cells produce IFNg resulting from the recognition of a T cell epitope." [] is_a: GO:0032609 ! interferon-gamma production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:1110187 name: epitope specific IL-10 release by T cells def: "A biological process where T cells produce IL-10 resulting from the recognition of a T cell epitope." [] is_a: GO:0032613 ! interleukin-10 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:1110190 name: epitope specific IL-12 release by T cells def: "A biological process where T cells produce IL-12 resulting from the recognition of a T cell epitope." [] is_a: GO:0032615 ! interleukin-12 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:1110191 name: epitope specific IL-13 release by T cells def: "A biological process where T cells produce IL-13 resulting from the recognition of a T cell epitope." [] is_a: GO:0032616 ! interleukin-13 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:1110193 name: epitope specific IL-17 release by T cells def: "A biological process where T cells produce IL-17 resulting from the recognition of a T cell epitope." [] is_a: GO:0032620 ! interleukin-17 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:1110195 name: epitope specific IL-18 release by T cells def: "A biological process where T cells produce IL-18 resulting from the recognition of a T cell epitope." [] is_a: GO:0032621 ! interleukin-18 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:1110196 name: epitope specific IL-1b release by T cells def: "A biological process where T cells produce IL-1b resulting from the recognition of a T cell epitope." [] is_a: GO:0032611 ! interleukin-1 beta production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:1110199 name: epitope specific IL-4 release by T cells def: "A biological process where T cells produce IL-4 resulting from the recognition of a T cell epitope." [] is_a: GO:0032633 ! interleukin-4 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:1110201 name: allergen def: "A material entity bearing the disposition to cause an allergic reaction" [] is_a: BFO:0000040 ! material entity [Term] id: OBI:1110202 name: epitope specific IL-5 release by T cells def: "A biological process where T cells produce IL-5 resulting from the recognition of a T cell epitope." [] is_a: GO:0032634 ! interleukin-5 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:1110203 name: epitope specific IL-6 release by T cells def: "A biological process where T cells produce IL-6 resulting from the recognition of a T cell epitope." [] is_a: GO:0032635 ! interleukin-6 production is_a: OBI:0001193 ! epitope specific cytokine production by T cells [Term] id: OBI:1110204 name: epitope specific killing by T cells def: "A biological process where T cells lyse antigen presenting cells resulting from the recognition of a T cell epitope on MHC molecules of the antigen presenting cell." [] is_a: GO:0001913 ! T cell mediated cytotoxicity [Term] id: OBI:1110206 name: epitope specific TNF release by T cells def: "A biological process where T cells produce TNF resulting from the recognition of a T cell epitope." [] is_a: GO:0032640 ! tumor necrosis factor production is_a: OBI:0001351 ! epitope specific tumor necrosis factor superfamily cytokine production by T cells [Term] id: OBI:1110207 name: assay detecting IFN-gamma production def: "An assay that determines information about the production of the cytokine interferon gamma" [] synonym: "IFNg release" EXACT [] is_a: OBI:0000070 ! assay [Term] id: OBI:1110300 name: direct submission to IEDB def: "A report about experiments in an investigation that characterize immune epitopes, and was submitted directly by the authors to the Immune Epitope Database (IEDB)" [] is_a: IAO:0000088 ! report [Term] id: OBI:1200000 name: FFPE specimen def: "A specimen that has been fixed in formalin and embedded in paraffin." [] synonym: "formalin-fixed paraffin-embeded specimen" EXACT [] is_a: OBI:0000950 ! paraffin specimen [Term] id: OBI:2000000 name: uterine cervix specimen def: "A specimen that is derived from some uterine cervix" [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:2000001 name: urethra specimen def: "A specimen that is derived from some urethra" [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:2000002 name: cervical mucus specimen def: "A specimen that is derived from some cervical mucus" [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:2000003 name: throat specimen def: "A specimen that is derived from some throat" [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:2000004 name: eye specimen def: "A specimen that is derived from some eye" [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:2000005 name: respiratory system specimen def: "A specimen that is derived from some respiratory system" [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:2000006 name: upper respiratory tract specimen def: "A specimen that is derived from some upper respiratory tract" [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:2000007 name: nasopharynx specimen def: "A specimen that is derived from some nasopharynx" [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:2000008 name: semen specimen def: "A specimen that is derived from some semen" [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:2000009 name: bodily fluid specimen def: "A specimen that is derived from some bodily fluid" [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:2000010 name: chorionic villus specimen def: "A specimen that is derived from some chorionic villus" [] is_a: OBI:0001479 ! specimen from organism [Term] id: OBI:2000011 name: meconium specimen def: "A specimen that is derived from some meconium" [] is_a: OBI:0002503 ! feces specimen [Term] id: OBI:2000012 name: umbilical cord blood specimen def: "A specimen that is derived from some umbilical cord blood" [] is_a: OBI:2000013 ! arterial blood specimen [Term] id: OBI:2000013 name: arterial blood specimen def: "A specimen that is derived from some arterial blood" [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:2000014 name: venous blood specimen def: "A specimen that is derived from some venous blood" [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:2000015 name: capillary blood specimen def: "A specimen that is derived from some capillary blood" [] is_a: OBI:2000009 ! bodily fluid specimen [Term] id: OBI:2000016 name: erythrocyte specimen def: "A specimen that is derived from some erythrocytes" [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:2000017 name: reticulocyte specimen def: "A specimen that is derived from some reticulocytes" [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:2000018 name: leukocyte specimen def: "A specimen that is derived from some leukocytes" [] is_a: OBI:0002599 ! swab specimen [Term] id: OBI:2100001 name: carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100002 name: sodium(1+) assay def: "An analyte assay that measures the abundance of sodium(1+)" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100003 name: creatinine assay def: "An analyte assay that measures the abundance of creatinine" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100004 name: potassium(1+) assay def: "An analyte assay that measures the abundance of potassium(1+)" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100005 name: basophil count assay def: "A cytometry assay that measures the count of basophils" [] is_a: OBI:0003021 ! basophil assay [Term] id: OBI:2100006 name: neutrophil count assay def: "A cytometry assay that measures the count of neutrophils" [] is_a: OBI:0003022 ! neutrophil assay [Term] id: OBI:2100007 name: eosinophil count assay def: "A cytometry assay that measures the count of eosinophils" [] is_a: OBI:0003023 ! eosinophil assay [Term] id: OBI:2100008 name: lymphocyte count assay def: "A cytometry assay that measures the count of lymphocytes" [] is_a: OBI:0003024 ! lymphocyte assay [Term] id: OBI:2100009 name: monocyte count assay def: "A cytometry assay that measures the count of monocytes" [] is_a: OBI:0003025 ! monocyte assay [Term] id: OBI:2100010 name: chloride assay def: "An analyte assay that measures the abundance of chloride" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100011 name: erythrocyte count assay def: "A cytometry assay that measures the count of erythrocytes" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100012 name: platelet count assay def: "A cytometry assay that measures the count of platelets" [] is_a: OBI:0003028 ! platelet assay [Term] id: OBI:2100013 name: leukocyte count assay def: "A cytometry assay that measures the count of leukocytes" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100014 name: hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100015 name: phosphate ion assay def: "An analyte assay that measures the abundance of phosphate ion" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100016 name: alanine aminotransferase assay def: "An analyte assay that measures the abundance of alanine aminotransferase" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100017 name: alkaline phosphatase (human) assay def: "An analyte assay that measures the abundance of alkaline phosphatase (human)" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100018 name: bilirubin IXalpha assay def: "An analyte assay that measures the abundance of bilirubin IXalpha" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100019 name: aspartate aminotransferase (human) assay def: "An analyte assay that measures the abundance of aspartate aminotransferase (human)" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100020 name: glucose assay def: "An analyte assay that measures the abundance of glucose" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100021 name: magnesium cation assay def: "An analyte assay that measures the abundance of magnesium cation" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100022 name: albumin assay def: "An analyte assay that measures the abundance of albumin" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100023 name: protein assay def: "An analyte assay that measures the abundance of protein" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100024 name: calcium cation assay def: "An analyte assay that measures the abundance of calcium cation" [] is_a: OBI:0003012 ! ionized calcium assay [Term] id: OBI:2100025 name: creatine kinase assay def: "An analyte assay that measures the abundance of creatine kinase" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100026 name: nucleate erythrocyte count assay def: "A cytometry assay that measures the count of nucleate erythrocytes" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100027 name: segmented neutrophil of bone marrow count assay def: "A cytometry assay that measures the count of segmented neutrophil of bone marrows" [] is_a: OBI:0003022 ! neutrophil assay [Term] id: OBI:2100028 name: lactate dehydrogenase complex assay def: "An assay that measures lactate dehydrogenase complex" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100029 name: triglyceride assay def: "An analyte assay that measures the abundance of triglyceride" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100030 name: high-density lipoprotein cholesterol assay def: "An analyte assay that measures the abundance of high-density lipoprotein cholesterol" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100031 name: cholesterol assay def: "An analyte assay that measures the abundance of cholesterol" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100032 name: low-density lipoprotein cholesterol assay def: "An analyte assay that measures the abundance of low-density lipoprotein cholesterol" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100033 name: thyroid stimulating hormone assay def: "An analyte assay that measures the abundance of thyroid stimulating hormone" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100034 name: prostate-specific antigen assay def: "An analyte assay that measures the abundance of prostate-specific antigen" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100035 name: thyroxine assay def: "An analyte assay that measures the abundance of thyroxine" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100036 name: elemental oxygen assay def: "An analyte assay that measures the abundance of elemental oxygen" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100037 name: folic acids assay def: "An analyte assay that measures the abundance of folic acids" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100038 name: reticulocyte count assay def: "A cytometry assay that measures the count of reticulocytes" [] is_a: OBI:0003026 ! reticulocyte assay [Term] id: OBI:2100039 name: osmolality assay def: "An assay that measures osmolality" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100040 name: methemoglobin assay def: "An analyte assay that measures the abundance of methemoglobin" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100041 name: cytosolic creatine kinase complex, MB-type assay def: "An assay that measures cytosolic creatine kinase complex, MB-type" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100042 name: rac-lactic acid assay def: "An assay that measures rac-lactic acid" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100043 name: hydrogencarbonate assay def: "An analyte assay that measures the abundance of hydrogencarbonate" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100044 name: vancomycin assay def: "An analyte assay that measures the abundance of vancomycin" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100045 name: tobramycin assay def: "An analyte assay that measures the abundance of tobramycin" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100046 name: 3,3',5'-triiodothyronine assay def: "An analyte assay that measures the abundance of 3,3',5'-triiodothyronine" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100047 name: C-reactive protein assay def: "An analyte assay that measures the abundance of C-reactive protein" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100048 name: megakaryocyte count assay def: "A cytometry assay that measures the count of megakaryocytes" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100049 name: mesothelial cell count assay def: "A cytometry assay that measures the count of mesothelial cells" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100050 name: macrophage count assay def: "A cytometry assay that measures the count of macrophages" [] is_a: OBI:0003027 ! macrophage assay [Term] id: OBI:2100051 name: 3-hydroxybutyric acid assay def: "An analyte assay that measures the abundance of 3-hydroxybutyric acid" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100052 name: panel5 venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a panel5 order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100053 name: panel5 venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a panel5 order" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100054 name: panel5 venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a panel5 order" [] is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100055 name: panel5 venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a panel5 order" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100056 name: automated differential venous blood basophil count assay def: "A cytometry assay that measures the count of basophils in venous blood as part of a automated differential order" [] is_a: OBI:0003021 ! basophil assay [Term] id: OBI:2100057 name: automated differential venous blood neutrophil count assay def: "A cytometry assay that measures the count of neutrophils in venous blood as part of a automated differential order" [] is_a: OBI:0003022 ! neutrophil assay [Term] id: OBI:2100058 name: automated differential venous blood eosinophil count assay def: "A cytometry assay that measures the count of eosinophils in venous blood as part of a automated differential order" [] is_a: OBI:0003023 ! eosinophil assay [Term] id: OBI:2100059 name: automated differential venous blood lymphocyte count assay def: "A cytometry assay that measures the count of lymphocytes in venous blood as part of a automated differential order" [] is_a: OBI:0003024 ! lymphocyte assay [Term] id: OBI:2100060 name: automated differential venous blood monocyte count assay def: "A cytometry assay that measures the count of monocytes in venous blood as part of a automated differential order" [] is_a: OBI:0003025 ! monocyte assay [Term] id: OBI:2100061 name: venous blood chloride assay def: "An analyte assay that measures the abundance of chloride in venous blood" [] is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100062 name: CBC with automated differential venous blood RBC count assay def: "A cytometry assay that measures the count of RBCs in venous blood as part of a CBC with automated differential order" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100063 name: CBC with automated differential venous blood platelet count assay def: "A cytometry assay that measures the count of platelets in venous blood as part of a CBC with automated differential order" [] is_a: OBI:0003028 ! platelet assay [Term] id: OBI:2100064 name: CBC with automated differential venous blood WBC count assay def: "A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with automated differential order" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100065 name: CBC with automated differential venous blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC with automated differential order" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100066 name: CBC with automated differential venous blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC with automated differential order" [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100067 name: venous blood phosphate assay def: "An analyte assay that measures the abundance of phosphate in venous blood" [] is_a: OBI:2100015 ! phosphate ion assay [Term] id: OBI:2100068 name: liver injury venous blood alanine aminotransferase assay def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver injury order" [] is_a: OBI:2100016 ! alanine aminotransferase assay [Term] id: OBI:2100069 name: liver injury venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver injury order" [] is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100070 name: liver injury venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver injury order" [] is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:2100071 name: liver injury venous blood human aspartate aminotransferase assay def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver injury order" [] is_a: OBI:2100019 ! aspartate aminotransferase (human) assay [Term] id: OBI:2100072 name: venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100073 name: venous blood magnesium assay def: "An analyte assay that measures the abundance of magnesium in venous blood" [] is_a: OBI:2100021 ! magnesium cation assay [Term] id: OBI:2100074 name: CBC venous blood RBC count assay def: "A cytometry assay that measures the count of RBCs in venous blood as part of a CBC order" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100075 name: CBC venous blood WBC count assay def: "A cytometry assay that measures the count of WBCs in venous blood as part of a CBC order" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100076 name: CBC venous blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a CBC order" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100077 name: CBC venous blood platelet count assay def: "A cytometry assay that measures the count of platelets in venous blood as part of a CBC order" [] is_a: OBI:0003028 ! platelet assay [Term] id: OBI:2100078 name: CBC venous blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a CBC order" [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100079 name: corrected venous blood leukocyte count assay def: "A cytometry assay that measures the count of leukocytes in venous blood as part of a corrected order" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100080 name: liver evaluation venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver evaluation order" [] is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:2100081 name: liver evaluation venous blood globulin assay def: "An analyte assay that measures the abundance of globulin in venous blood as part of a liver evaluation order" [] is_a: OBI:0003015 ! globulin assay [Term] id: OBI:2100082 name: liver evaluation venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a liver evaluation order" [] is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100083 name: liver evaluation venous blood human aspartate aminotransferase assay def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver evaluation order" [] is_a: OBI:2100019 ! aspartate aminotransferase (human) assay [Term] id: OBI:2100084 name: liver evaluation venous blood alanine aminotransferase assay def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver evaluation order" [] is_a: OBI:2100016 ! alanine aminotransferase assay [Term] id: OBI:2100085 name: liver evaluation venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver evaluation order" [] is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100086 name: liver evaluation venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a liver evaluation order" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100087 name: basic metabolic panel venous blood chloride assay def: "An analyte assay that measures the abundance of chloride in venous blood as part of a basic metabolic panel order" [] is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100088 name: basic metabolic panel venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a basic metabolic panel order" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100089 name: basic metabolic panel venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a basic metabolic panel order" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100090 name: basic metabolic panel venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a basic metabolic panel order" [] is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100091 name: basic metabolic panel venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a basic metabolic panel order" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100092 name: basic metabolic panel venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a basic metabolic panel order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100093 name: basic metabolic panel venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a basic metabolic panel order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100094 name: venous blood creatine kinase assay def: "An analyte assay that measures the abundance of creatine kinase in venous blood" [] is_a: OBI:2100025 ! creatine kinase assay [Term] id: OBI:2100095 name: venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100096 name: venous blood ferritin assay def: "An assay that measures ferritin in venous blood" [] is_a: OBI:0003009 ! ferritin assay [Term] id: OBI:2100097 name: total venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a total order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100098 name: venous blood iron assay def: "An analyte assay that measures the abundance of iron in venous blood" [] is_a: OBI:0003011 ! iron assay [Term] id: OBI:2100099 name: CBC with manual differential venous blood band neutrophil count assay def: "A cytometry assay that measures the count of band neutrophils in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003022 ! neutrophil assay [Term] id: OBI:2100100 name: CBC with manual differential venous blood WBC count assay def: "A cytometry assay that measures the count of WBCs in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100101 name: CBC with manual differential venous blood eosinophil count assay def: "A cytometry assay that measures the count of eosinophils in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003023 ! eosinophil assay [Term] id: OBI:2100102 name: CBC with manual differential venous blood lymphocyte count assay def: "A cytometry assay that measures the count of lymphocytes in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003024 ! lymphocyte assay [Term] id: OBI:2100103 name: CBC with manual differential venous blood nucleated RBC count assay def: "A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100104 name: CBC with manual differential venous blood monocyte count assay def: "A cytometry assay that measures the count of monocytes in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003025 ! monocyte assay [Term] id: OBI:2100105 name: CBC with manual differential venous blood segmented neutrophil count assay def: "A cytometry assay that measures the count of segmented neutrophils in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003022 ! neutrophil assay [Term] id: OBI:2100106 name: CBC with manual differential venous blood basophil count assay def: "A cytometry assay that measures the count of basophils in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003021 ! basophil assay [Term] id: OBI:2100107 name: venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood" [] is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100108 name: cardiac enzymes venous blood creatine kinase assay def: "An analyte assay that measures the abundance of creatine kinase in venous blood as part of a cardiac enzymes order" [] is_a: OBI:2100025 ! creatine kinase assay [Term] id: OBI:2100109 name: venous blood haptoglobin assay def: "An analyte assay that measures the abundance of haptoglobin in venous blood" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100110 name: venous blood lactate dehydrogenase assay def: "An assay that measures lactate dehydrogenase in venous blood" [] is_a: OBI:2100028 ! lactate dehydrogenase complex assay [Term] id: OBI:2100111 name: venous blood prealbunin assay def: "An analyte assay that measures the abundance of prealbunin in venous blood" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100112 name: lipid panel venous blood triglyceride assay def: "An analyte assay that measures the abundance of triglyceride in venous blood as part of a lipid panel order" [] is_a: OBI:2100029 ! triglyceride assay [Term] id: OBI:2100113 name: lipid panel venous blood high density lipoprotein assay def: "An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a lipid panel order" [] is_a: OBI:2100030 ! high-density lipoprotein cholesterol assay [Term] id: OBI:2100114 name: lipid panel venous blood cholesterol assay def: "An analyte assay that measures the abundance of cholesterol in venous blood as part of a lipid panel order" [] is_a: OBI:2100031 ! cholesterol assay [Term] id: OBI:2100115 name: lipid panel venous blood low density lipoprotein assay def: "An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a lipid panel order" [] is_a: OBI:2100032 ! low-density lipoprotein cholesterol assay [Term] id: OBI:2100116 name: venous blood hemoglobin A1c assay def: "An assay that measures hemoglobin A1c in venous blood" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100117 name: venous blood uric acid assay def: "An analyte assay that measures the abundance of uric acid in venous blood" [] is_a: OBI:0003014 ! uric acid assay [Term] id: OBI:2100118 name: total venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a total order" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100119 name: venous blood thyroid stimulating hormone assay def: "An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood" [] is_a: OBI:2100033 ! thyroid stimulating hormone assay [Term] id: OBI:2100120 name: venous blood prostate specific antigen assay def: "An analyte assay that measures the abundance of prostate specific antigen in venous blood" [] is_a: OBI:2100034 ! prostate-specific antigen assay [Term] id: OBI:2100121 name: 24 hour total urine volume assay def: "An assay that measures volume in urine as part of a 24 hour total order" [] is_a: OBI:0003043 ! urine assay [Term] id: OBI:2100122 name: T4 uptake venous blood T4 assay def: "An analyte assay that measures the abundance of T4 in venous blood as part of a T4 uptake order" [] is_a: OBI:2100035 ! thyroxine assay [Term] id: OBI:2100123 name: arterial blood glucose assay def: "An analyte assay that measures the abundance of glucose in arterial blood" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100124 name: CBC with manual differential venous blood cell count assay def: "A cytometry assay that measures the count of cells in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100125 name: hemoglobin oxygen saturation arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a hemoglobin oxygen saturation order" [] is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100126 name: hemoglobin oxygen saturation arterial blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a hemoglobin oxygen saturation order" [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100127 name: inpatient profile venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a inpatient profile order" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100128 name: inpatient profile venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a inpatient profile order" [] is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100129 name: inpatient profile venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a inpatient profile order" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100130 name: inpatient profile venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a inpatient profile order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100131 name: venous blood folic acid assay def: "An analyte assay that measures the abundance of folic acid in venous blood" [] is_a: OBI:2100037 ! folic acids assay [Term] id: OBI:2100132 name: count venous blood reticulocyte count assay def: "A cytometry assay that measures the count of reticulocytes in venous blood as part of a count order" [] is_a: OBI:0003026 ! reticulocyte assay [Term] id: OBI:2100133 name: venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100134 name: venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100135 name: venous blood transferrin assay def: "An analyte assay that measures the abundance of transferrin in venous blood" [] is_a: OBI:0003013 ! transferrin assay [Term] id: OBI:2100136 name: venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100137 name: random electrolytes urine sodium assay def: "An analyte assay that measures the abundance of sodium in urine as part of a random electrolytes order" [] is_a: OBI:0003043 ! urine assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100138 name: random electrolytes urine potassium assay def: "An analyte assay that measures the abundance of potassium in urine as part of a random electrolytes order" [] is_a: OBI:0003043 ! urine assay is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100139 name: urine creatinine assay def: "An analyte assay that measures the abundance of creatinine in urine" [] is_a: OBI:0003043 ! urine assay is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100140 name: urine osmolality assay def: "An assay that measures osmolality in urine" [] is_a: OBI:0003043 ! urine assay is_a: OBI:2100039 ! osmolality assay [Term] id: OBI:2100141 name: cooximitery arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a cooximitery order" [] is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100142 name: cooximitery arterial blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a cooximitery order" [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100143 name: cooximitery arterial blood methemoglobin assay def: "An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a cooximitery order" [] is_a: OBI:2100040 ! methemoglobin assay [Term] id: OBI:2100144 name: electrolytes urine sodium assay def: "An analyte assay that measures the abundance of sodium in urine as part of a electrolytes order" [] is_a: OBI:0003043 ! urine assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100145 name: electrolytes urine potassium assay def: "An analyte assay that measures the abundance of potassium in urine as part of a electrolytes order" [] is_a: OBI:0003043 ! urine assay is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100146 name: Biosite cardiac panel arterial blood creatine kinase MB assay def: "An assay that measures creatine kinase MB in arterial blood as part of a Biosite cardiac panel order" [] is_a: OBI:2100041 ! cytosolic creatine kinase complex, MB-type assay [Term] id: OBI:2100147 name: venous blood fibrinogen assay def: "An assay that measures fibrinogen in venous blood" [] is_a: OBI:0003010 ! fibrinogen assay [Term] id: OBI:2100148 name: comprehensive metabolic panel venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a comprehensive metabolic panel order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100149 name: comprehensive metabolic panel venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a comprehensive metabolic panel order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100150 name: comprehensive metabolic panel venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a comprehensive metabolic panel order" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100151 name: comprehensive metabolic panel venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a comprehensive metabolic panel order" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100152 name: comprehensive metabolic panel venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a comprehensive metabolic panel order" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100153 name: comprehensive metabolic panel venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a comprehensive metabolic panel order" [] is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100154 name: comprehensive metabolic panel venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a comprehensive metabolic panel order" [] is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100155 name: comprehensive metabolic panel venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a comprehensive metabolic panel order" [] is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:2100156 name: comprehensive metabolic panel venous blood chloride assay def: "An analyte assay that measures the abundance of chloride in venous blood as part of a comprehensive metabolic panel order" [] is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100157 name: comprehensive metabolic panel venous blood human aspartate aminotransferase assay def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a comprehensive metabolic panel order" [] is_a: OBI:2100019 ! aspartate aminotransferase (human) assay [Term] id: OBI:2100158 name: comprehensive metabolic panel venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a comprehensive metabolic panel order" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100159 name: comprehensive metabolic panel venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a comprehensive metabolic panel order" [] is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100160 name: comprehensive metabolic panel venous blood alanine aminotransferase assay def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a comprehensive metabolic panel order" [] is_a: OBI:2100016 ! alanine aminotransferase assay [Term] id: OBI:2100161 name: venous blood LDH assay def: "An assay that measures LDH in venous blood" [] is_a: OBI:2100028 ! lactate dehydrogenase complex assay [Term] id: OBI:2100162 name: venous blood creatine kinase MB assay def: "An assay that measures creatine kinase MB in venous blood" [] is_a: OBI:2100041 ! cytosolic creatine kinase complex, MB-type assay [Term] id: OBI:2100163 name: venous blood lactic acid assay def: "An assay that measures lactic acid in venous blood" [] is_a: OBI:2100042 ! rac-lactic acid assay [Term] id: OBI:2100164 name: venous blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in venous blood" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100165 name: venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood" [] is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100166 name: blood gas venous blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in venous blood as part of a blood gas order" [] is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100167 name: ionized venous blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ionized order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100168 name: blood gas venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a blood gas order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100169 name: blood gas venous blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in venous blood as part of a blood gas order" [] is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100170 name: arterial blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in arterial blood" [] is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100171 name: venous blood tacrolimus assay def: "An analyte assay that measures the abundance of tacrolimus in venous blood" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100172 name: random venous blood vancomycin assay def: "An analyte assay that measures the abundance of vancomycin in venous blood as part of a random order" [] is_a: OBI:2100044 ! vancomycin assay [Term] id: OBI:2100173 name: venous blood mycophenolic acid assay def: "An analyte assay that measures the abundance of mycophenolic acid in venous blood" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100174 name: non-vented blood gas arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a non-vented blood gas order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100175 name: non-vented blood gas arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a non-vented blood gas order" [] is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100176 name: non-vented blood gas arterial blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a non-vented blood gas order" [] is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100177 name: quantitative venous blood IgG assay def: "An assay that measures IgG in venous blood as part of a quantitative order" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100178 name: quantitative venous blood IgM assay def: "An assay that measures IgM in venous blood as part of a quantitative order" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100179 name: quantitative venous blood IgA assay def: "An assay that measures IgA in venous blood as part of a quantitative order" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100180 name: arterial blood sodium assay def: "An analyte assay that measures the abundance of sodium in arterial blood" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100181 name: arterial blood potassium assay def: "An analyte assay that measures the abundance of potassium in arterial blood" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100182 name: ionized arterial blood calcium assay def: "An analyte assay that measures the abundance of calcium in arterial blood as part of a ionized order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100183 name: vented blood gas arterial blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a vented blood gas order" [] is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100184 name: vented blood gas arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a vented blood gas order" [] is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100185 name: vented blood gas arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a vented blood gas order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100186 name: arterial blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in arterial blood" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100187 name: arterial blood chloride assay def: "An analyte assay that measures the abundance of chloride in arterial blood" [] is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100188 name: arterial blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in arterial blood" [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100189 name: GEM premier blood gas venous blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a GEM premier blood gas order" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100190 name: GEM premier blood gas venous blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in venous blood as part of a GEM premier blood gas order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100191 name: GEM premier blood gas venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a GEM premier blood gas order" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100192 name: GEM premier blood gas venous blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in venous blood as part of a GEM premier blood gas order" [] is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100193 name: GEM premier blood gas venous blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a GEM premier blood gas order" [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100194 name: GEM premier blood gas venous blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in venous blood as part of a GEM premier blood gas order" [] is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100195 name: GEM premier blood gas venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a GEM premier blood gas order" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100196 name: GEM premier blood gas venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a GEM premier blood gas order" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100197 name: GEM premier blood gas venous blood lactic acid assay def: "An assay that measures lactic acid in venous blood as part of a GEM premier blood gas order" [] is_a: OBI:2100042 ! rac-lactic acid assay [Term] id: OBI:2100198 name: GEM premier blood gas venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a GEM premier blood gas order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100199 name: trough venous blood tobramycin assay def: "An analyte assay that measures the abundance of tobramycin in venous blood as part of a trough order" [] is_a: OBI:2100045 ! tobramycin assay [Term] id: OBI:2100200 name: random venous blood tobramycin assay def: "An analyte assay that measures the abundance of tobramycin in venous blood as part of a random order" [] is_a: OBI:2100045 ! tobramycin assay [Term] id: OBI:2100201 name: CBC with manual differential venous blood metamyelocyte count assay def: "A cytometry assay that measures the count of metamyelocytes in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003017 ! metamyelocyte assay [Term] id: OBI:2100202 name: arterial blood lactic acid assay def: "An assay that measures lactic acid in arterial blood" [] is_a: OBI:2100042 ! rac-lactic acid assay [Term] id: OBI:2100203 name: venous blood 25-hydroxyvitamin D2 assay def: "An analyte assay that measures the abundance of 25-hydroxyvitamin D2 in venous blood" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100204 name: venous blood digoxin assay def: "An analyte assay that measures the abundance of digoxin in venous blood" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100205 name: urine protein assay def: "An analyte assay that measures the abundance of protein in urine" [] is_a: OBI:0003043 ! urine assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100206 name: venous blood tobramycin assay def: "An analyte assay that measures the abundance of tobramycin in venous blood" [] is_a: OBI:2100045 ! tobramycin assay [Term] id: OBI:2100207 name: CBC with manual differential venous blood myelocyte count assay def: "A cytometry assay that measures the count of myelocytes in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003165 ! myelocyte count assay [Term] id: OBI:2100208 name: SPEP protein electrophoresis venous blood beta-globin assay def: "An analyte assay that measures the abundance of beta-globin in venous blood as part of a SPEP protein electrophoresis order" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100209 name: SPEP protein electrophoresis venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a SPEP protein electrophoresis order" [] is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100210 name: SPEP protein electrophoresis venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a SPEP protein electrophoresis order" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100211 name: trough venous blood vancomycin assay def: "An analyte assay that measures the abundance of vancomycin in venous blood as part of a trough order" [] is_a: OBI:2100044 ! vancomycin assay [Term] id: OBI:2100212 name: hepatic panel venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a hepatic panel order" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100213 name: hepatic panel venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a hepatic panel order" [] is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:2100214 name: hepatic panel venous blood alanine aminotransferase assay def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a hepatic panel order" [] is_a: OBI:2100016 ! alanine aminotransferase assay [Term] id: OBI:2100215 name: hepatic panel venous blood human aspartate aminotransferase assay def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a hepatic panel order" [] is_a: OBI:2100019 ! aspartate aminotransferase (human) assay [Term] id: OBI:2100216 name: hepatic panel venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a hepatic panel order" [] is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100217 name: hepatic panel venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a hepatic panel order" [] is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100218 name: estimated venous blood glomerular filtration assay def: "An assay that measures glomerular filtration in venous blood as part of a estimated order" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100219 name: DT60 venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a DT60 order" [] is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100220 name: fasting venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a fasting order" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100221 name: random venous blood amikacin assay def: "An analyte assay that measures the abundance of amikacin in venous blood as part of a random order" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100222 name: venous blood ammonia assay def: "An analyte assay that measures the abundance of ammonia in venous blood" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100223 name: venous blood GGT assay def: "An analyte assay that measures the abundance of GGT in venous blood" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100224 name: chem11 venous blood phosphate assay def: "An analyte assay that measures the abundance of phosphate in venous blood as part of a chem11 order" [] is_a: OBI:2100015 ! phosphate ion assay [Term] id: OBI:2100225 name: chem11 venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a chem11 order" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100226 name: chem11 venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a chem11 order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100227 name: chem11 venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a chem11 order" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100228 name: chem11 venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem11 order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100229 name: chem11 venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a chem11 order" [] is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100230 name: chem11 venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a chem11 order" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100231 name: chem11 venous blood magnesium assay def: "An analyte assay that measures the abundance of magnesium in venous blood as part of a chem11 order" [] is_a: OBI:2100021 ! magnesium cation assay [Term] id: OBI:2100232 name: chem11 venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a chem11 order" [] is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100233 name: chem11 venous blood chloride assay def: "An analyte assay that measures the abundance of chloride in venous blood as part of a chem11 order" [] is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100234 name: total venous blood IgE assay def: "An assay that measures IgE in venous blood as part of a total order" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100235 name: chem16 venous blood human aspartate aminotransferase assay def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a chem16 order" [] is_a: OBI:2100019 ! aspartate aminotransferase (human) assay [Term] id: OBI:2100236 name: chem16 venous blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in venous blood as part of a chem16 order" [] is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100237 name: chem16 venous blood magnesium assay def: "An analyte assay that measures the abundance of magnesium in venous blood as part of a chem16 order" [] is_a: OBI:2100021 ! magnesium cation assay [Term] id: OBI:2100238 name: chem16 venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a chem16 order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100239 name: chem16 venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a chem16 order" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100240 name: chem16 venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a chem16 order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100241 name: chem16 venous blood triglyceride assay def: "An analyte assay that measures the abundance of triglyceride in venous blood as part of a chem16 order" [] is_a: OBI:2100029 ! triglyceride assay [Term] id: OBI:2100242 name: chem16 venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a chem16 order" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100243 name: chem16 venous blood phosphate assay def: "An analyte assay that measures the abundance of phosphate in venous blood as part of a chem16 order" [] is_a: OBI:2100015 ! phosphate ion assay [Term] id: OBI:2100244 name: chem16 venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a chem16 order" [] is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100245 name: chem16 venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a chem16 order" [] is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100246 name: chem16 venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a chem16 order" [] is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:2100247 name: chem16 venous blood chloride assay def: "An analyte assay that measures the abundance of chloride in venous blood as part of a chem16 order" [] is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100248 name: chem16 venous blood alanine aminotransferase assay def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a chem16 order" [] is_a: OBI:2100016 ! alanine aminotransferase assay [Term] id: OBI:2100249 name: chem16 venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a chem16 order" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100250 name: POC chem8 arterial blood glucose assay def: "An analyte assay that measures the abundance of glucose in arterial blood as part of a POC chem8 order" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100251 name: POC chem8 arterial blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a POC chem8 order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100252 name: POC chem8 arterial blood potassium assay def: "An analyte assay that measures the abundance of potassium in arterial blood as part of a POC chem8 order" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100253 name: POC chem8 arterial blood sodium assay def: "An analyte assay that measures the abundance of sodium in arterial blood as part of a POC chem8 order" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100254 name: POC chem8 arterial blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC chem8 order" [] is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100255 name: POC chem8 arterial blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a POC chem8 order" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100256 name: POC chem8 arterial blood chloride assay def: "An analyte assay that measures the abundance of chloride in arterial blood as part of a POC chem8 order" [] is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100257 name: peak venous blood tobramycin assay def: "An analyte assay that measures the abundance of tobramycin in venous blood as part of a peak order" [] is_a: OBI:2100045 ! tobramycin assay [Term] id: OBI:2100258 name: 24 hour urine creatinine assay def: "An analyte assay that measures the abundance of creatinine in urine as part of a 24 hour order" [] is_a: OBI:0003043 ! urine assay is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100259 name: intact venous blood PTH assay def: "An analyte assay that measures the abundance of PTH in venous blood as part of a intact order" [] is_a: OBI:2100034 ! prostate-specific antigen assay [Term] id: OBI:2100260 name: total venous blood PSA assay def: "An analyte assay that measures the abundance of PSA in venous blood as part of a total order" [] is_a: OBI:2100034 ! prostate-specific antigen assay [Term] id: OBI:2100261 name: total venous blood T3 assay def: "An analyte assay that measures the abundance of T3 in venous blood as part of a total order" [] is_a: OBI:2100046 ! 3,3',5'-triiodothyronine assay [Term] id: OBI:2100262 name: 24 hour urine protein assay def: "An analyte assay that measures the abundance of protein in urine as part of a 24 hour order" [] is_a: OBI:0003043 ! urine assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100263 name: total venous blood cholesterol assay def: "An analyte assay that measures the abundance of cholesterol in venous blood as part of a total order" [] is_a: OBI:2100031 ! cholesterol assay [Term] id: OBI:2100264 name: venous blood triglyceride assay def: "An analyte assay that measures the abundance of triglyceride in venous blood" [] is_a: OBI:2100029 ! triglyceride assay [Term] id: OBI:2100265 name: tube 4 count cerebrospinal fluid cell count assay def: "A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 4 count order" [] is_a: OBI:0001977 ! cytometry assay is_a: OBI:0003232 ! cerebrospinal fluid assay [Term] id: OBI:2100266 name: cerebrospinal fluid protein assay def: "An analyte assay that measures the abundance of protein in cerebrospinal fluid" [] is_a: OBI:0003232 ! cerebrospinal fluid assay is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100267 name: cerebrospinal fluid glucose assay def: "An analyte assay that measures the abundance of glucose in cerebrospinal fluid" [] is_a: OBI:0003232 ! cerebrospinal fluid assay is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100268 name: tube 1 count cerebrospinal fluid cell count assay def: "A cytometry assay that measures the count of cells in cerebrospinal fluid as part of a tube 1 count order" [] is_a: OBI:0001977 ! cytometry assay is_a: OBI:0003232 ! cerebrospinal fluid assay [Term] id: OBI:2100269 name: venous blood dehydroepiandrosterone assay def: "An analyte assay that measures the abundance of dehydroepiandrosterone in venous blood" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100270 name: venous blood cortisol assay def: "An analyte assay that measures the abundance of cortisol in venous blood" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100271 name: ABL90 panel arterial blood sodium assay def: "An analyte assay that measures the abundance of sodium in arterial blood as part of a ABL90 panel order" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100272 name: ABL90 panel arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABL90 panel order" [] is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100273 name: ABL90 panel arterial blood glucose assay def: "An analyte assay that measures the abundance of glucose in arterial blood as part of a ABL90 panel order" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100274 name: ABL90 panel arterial blood lactic acid assay def: "An assay that measures lactic acid in arterial blood as part of a ABL90 panel order" [] is_a: OBI:2100042 ! rac-lactic acid assay [Term] id: OBI:2100275 name: ABL90 panel arterial blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a ABL90 panel order" [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100276 name: ABL90 panel arterial blood chloride assay def: "An analyte assay that measures the abundance of chloride in arterial blood as part of a ABL90 panel order" [] is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100277 name: ABL90 panel arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABL90 panel order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100278 name: ABL90 panel arterial blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a ABL90 panel order" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100279 name: ABL90 panel arterial blood calcium assay def: "An analyte assay that measures the abundance of calcium in arterial blood as part of a ABL90 panel order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100280 name: ABL90 panel arterial blood temperature assay def: "An assay that measures temperature in arterial blood as part of a ABL90 panel order" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100281 name: ABL90 panel arterial blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a ABL90 panel order" [] is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100282 name: ABL90 panel arterial blood potassium assay def: "An analyte assay that measures the abundance of potassium in arterial blood as part of a ABL90 panel order" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100283 name: CBC with manual differential venous blood promyelocyte count assay def: "A cytometry assay that measures the count of promyelocytes in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003019 ! promyelocyte assay [Term] id: OBI:2100284 name: ABL90 panel venous blood glucose assay def: "An analyte assay that measures the abundance of glucose in venous blood as part of a ABL90 panel order" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100285 name: ABL90 panel venous blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a ABL90 panel order" [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100286 name: ABL90 panel venous blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in venous blood as part of a ABL90 panel order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100287 name: ABL90 panel venous blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in venous blood as part of a ABL90 panel order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100288 name: ABL90 panel venous blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a ABL90 panel order" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100289 name: ABL90 panel venous blood sodium assay def: "An analyte assay that measures the abundance of sodium in venous blood as part of a ABL90 panel order" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100290 name: ABL90 panel venous blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in venous blood as part of a ABL90 panel order" [] is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100291 name: ABL90 panel venous blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in venous blood as part of a ABL90 panel order" [] is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100292 name: ABL90 panel venous blood lactic acid assay def: "An assay that measures lactic acid in venous blood as part of a ABL90 panel order" [] is_a: OBI:2100042 ! rac-lactic acid assay [Term] id: OBI:2100293 name: ABL90 panel venous blood chloride assay def: "An analyte assay that measures the abundance of chloride in venous blood as part of a ABL90 panel order" [] is_a: OBI:2100010 ! chloride assay [Term] id: OBI:2100294 name: venous blood T4 assay def: "An analyte assay that measures the abundance of T4 in venous blood" [] is_a: OBI:2100035 ! thyroxine assay [Term] id: OBI:2100295 name: free venous blood T4 assay def: "An analyte assay that measures the abundance of T4 in venous blood as part of a free order" [] is_a: OBI:2100035 ! thyroxine assay [Term] id: OBI:2100296 name: ABL90 panel venous blood potassium assay def: "An analyte assay that measures the abundance of potassium in venous blood as part of a ABL90 panel order" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100297 name: urine sodium assay def: "An analyte assay that measures the abundance of sodium in urine" [] is_a: OBI:0003043 ! urine assay is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100298 name: bone profile venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a bone profile order" [] is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100299 name: bone profile venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a bone profile order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100300 name: bone profile venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a bone profile order" [] is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100301 name: bone profile venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a bone profile order" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100302 name: bone profile venous blood phosphate assay def: "An analyte assay that measures the abundance of phosphate in venous blood as part of a bone profile order" [] is_a: OBI:2100015 ! phosphate ion assay [Term] id: OBI:2100303 name: ABG/electrolytes arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a ABG/electrolytes order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100304 name: ABG/electrolytes arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a ABG/electrolytes order" [] is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100305 name: ABG/electrolytes arterial blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a ABG/electrolytes order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100306 name: CBC with automated differential venous blood nucleated RBC count assay def: "A cytometry assay that measures the count of nucleated RBCs in venous blood as part of a CBC with automated differential order" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100307 name: ABL90 panel venous blood methemoglobin assay def: "An analyte assay that measures the abundance of methemoglobin in venous blood as part of a ABL90 panel order" [] is_a: OBI:2100040 ! methemoglobin assay [Term] id: OBI:2100308 name: ABL90 panel arterial blood methemoglobin assay def: "An analyte assay that measures the abundance of methemoglobin in arterial blood as part of a ABL90 panel order" [] is_a: OBI:2100040 ! methemoglobin assay [Term] id: OBI:2100309 name: venous blood valproic acid assay def: "An analyte assay that measures the abundance of valproic acid in venous blood" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100310 name: high sensitivity cardiac/neonatal venous blood c-reactive protein assay def: "An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a high sensitivity cardiac/neonatal order" [] is_a: OBI:2100047 ! C-reactive protein assay [Term] id: OBI:2100311 name: POC arterial blood creatinine assay def: "An analyte assay that measures the abundance of creatinine in arterial blood as part of a POC order" [] is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100312 name: GEM4000 ANLCOOX arterial blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4000 ANLCOOX order" [] is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100313 name: GEM4000 ANLCOOX arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4000 ANLCOOX order" [] is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100314 name: GEM4000 ANLCOOX arterial blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4000 ANLCOOX order" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100315 name: GEM4000 ANLCOOX arterial blood temperature assay def: "An assay that measures temperature in arterial blood as part of a GEM4000 ANLCOOX order" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100316 name: GEM4000 ANLCOOX arterial blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4000 ANLCOOX order" [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100317 name: GEM4000 ANLCOOX arterial blood potassium assay def: "An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4000 ANLCOOX order" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100318 name: GEM4000 ANLCOOX arterial blood glucose assay def: "An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4000 ANLCOOX order" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100319 name: GEM4000 ANLCOOX arterial blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4000 ANLCOOX order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100320 name: GEM4000 ANLCOOX arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4000 ANLCOOX order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100321 name: GEM4000 ANLCOOX arterial blood sodium assay def: "An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4000 ANLCOOX order" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100322 name: ionized venous blood calcium assay def: "An analyte assay that measures the abundance of calcium in venous blood as part of a ionized order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100323 name: venous blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in venous blood" [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100324 name: CBC with manual differential venous blood megakaryocyte count assay def: "A cytometry assay that measures the count of megakaryocytes in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100325 name: non-cardiac venous blood c-reactive protein assay def: "An analyte assay that measures the abundance of c-reactive protein in venous blood as part of a non-cardiac order" [] is_a: OBI:2100047 ! C-reactive protein assay [Term] id: OBI:2100326 name: intraoperative venous blood PTH assay def: "An analyte assay that measures the abundance of PTH in venous blood as part of a intraoperative order" [] is_a: OBI:2100034 ! prostate-specific antigen assay [Term] id: OBI:2100327 name: venous blood parathyroid hormone assay def: "An analyte assay that measures the abundance of parathyroid hormone in venous blood" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100328 name: total bodily fluid protein assay def: "An analyte assay that measures the abundance of protein in bodily fluid as part of a total order" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100329 name: bodily fluid glucose assay def: "An analyte assay that measures the abundance of glucose in bodily fluid" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100330 name: count bodily fluid cell count assay def: "A cytometry assay that measures the count of cells in bodily fluid as part of a count order" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100331 name: manual differential bodily fluid segmented neutrophil count assay def: "A cytometry assay that measures the count of segmented neutrophils in bodily fluid as part of a manual differential order" [] is_a: OBI:0003022 ! neutrophil assay [Term] id: OBI:2100332 name: manual differential bodily fluid mesothelial cell count assay def: "A cytometry assay that measures the count of mesothelial cells in bodily fluid as part of a manual differential order" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100333 name: manual differential bodily fluid monocyte count assay def: "A cytometry assay that measures the count of monocytes in bodily fluid as part of a manual differential order" [] is_a: OBI:0003025 ! monocyte assay [Term] id: OBI:2100334 name: manual differential bodily fluid lymphocyte count assay def: "A cytometry assay that measures the count of lymphocytes in bodily fluid as part of a manual differential order" [] is_a: OBI:0003024 ! lymphocyte assay [Term] id: OBI:2100335 name: manual differential bodily fluid macrophage count assay def: "A cytometry assay that measures the count of macrophages in bodily fluid as part of a manual differential order" [] is_a: OBI:0003027 ! macrophage assay [Term] id: OBI:2100336 name: manual differential bodily fluid basophil count assay def: "A cytometry assay that measures the count of basophils in bodily fluid as part of a manual differential order" [] is_a: OBI:0003021 ! basophil assay [Term] id: OBI:2100337 name: manual differential bodily fluid eosinophil count assay def: "A cytometry assay that measures the count of eosinophils in bodily fluid as part of a manual differential order" [] is_a: OBI:0003023 ! eosinophil assay [Term] id: OBI:2100338 name: liver function venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a liver function order" [] is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:2100339 name: liver function venous blood alanine aminotransferase assay def: "An analyte assay that measures the abundance of alanine aminotransferase in venous blood as part of a liver function order" [] is_a: OBI:2100016 ! alanine aminotransferase assay [Term] id: OBI:2100340 name: liver function venous blood human aspartate aminotransferase assay def: "An analyte assay that measures the abundance of human aspartate aminotransferase in venous blood as part of a liver function order" [] is_a: OBI:2100019 ! aspartate aminotransferase (human) assay [Term] id: OBI:2100341 name: liver function venous blood albumin assay def: "An analyte assay that measures the abundance of albumin in venous blood as part of a liver function order" [] is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100342 name: liver function venous blood protein assay def: "An analyte assay that measures the abundance of protein in venous blood as part of a liver function order" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100343 name: liver function venous blood human alkaline phosphatase assay def: "An analyte assay that measures the abundance of human alkaline phosphatase in venous blood as part of a liver function order" [] is_a: OBI:2100017 ! alkaline phosphatase (human) assay [Term] id: OBI:2100344 name: vitamin B12 and Folate venous blood folic acid assay def: "An analyte assay that measures the abundance of folic acid in venous blood as part of a vitamin B12 and Folate order" [] is_a: OBI:2100037 ! folic acids assay [Term] id: OBI:2100345 name: bodily fluid cell count assay def: "A cytometry assay that measures the count of cells in bodily fluid" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100346 name: venous blood reticulocyte count assay def: "A cytometry assay that measures the count of reticulocytes in venous blood" [] is_a: OBI:0003026 ! reticulocyte assay [Term] id: OBI:2100347 name: bodily fluid cholesterol assay def: "An analyte assay that measures the abundance of cholesterol in bodily fluid" [] is_a: OBI:2100031 ! cholesterol assay [Term] id: OBI:2100348 name: TSH reflex Free T4 venous blood thyroid stimulating hormone assay def: "An analyte assay that measures the abundance of thyroid stimulating hormone in venous blood as part of a TSH reflex Free T4 order" [] is_a: OBI:2100033 ! thyroid stimulating hormone assay [Term] id: OBI:2100349 name: direct venous blood bilirubin assay def: "An analyte assay that measures the abundance of bilirubin in venous blood as part of a direct order" [] is_a: OBI:2100018 ! bilirubin IXalpha assay [Term] id: OBI:2100350 name: free venous blood T3 assay def: "An analyte assay that measures the abundance of T3 in venous blood as part of a free order" [] is_a: OBI:2100046 ! 3,3',5'-triiodothyronine assay [Term] id: OBI:2100351 name: bodily fluid albumin assay def: "An analyte assay that measures the abundance of albumin in bodily fluid" [] is_a: OBI:2100022 ! albumin assay [Term] id: OBI:2100352 name: bodily fluid triglyceride assay def: "An analyte assay that measures the abundance of triglyceride in bodily fluid" [] is_a: OBI:2100029 ! triglyceride assay [Term] id: OBI:2100353 name: hemoglobin and hematocrit venous blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in venous blood as part of a hemoglobin and hematocrit order" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100354 name: hemoglobin and hematocrit venous blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in venous blood as part of a hemoglobin and hematocrit order" [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100355 name: venous blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in venous blood" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100356 name: venous blood temperature assay def: "An assay that measures temperature in venous blood" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100357 name: venous blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in venous blood" [] is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100358 name: venous blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in venous blood" [] is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100359 name: venous blood osmolality assay def: "An assay that measures osmolality in venous blood" [] is_a: OBI:2100039 ! osmolality assay [Term] id: OBI:2100360 name: liver fibrosis (chronic viral hepatitis) venous blood platelet count assay def: "A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (chronic viral hepatitis) order" [] is_a: OBI:0003028 ! platelet assay [Term] id: OBI:2100361 name: venous blood T3 assay def: "An analyte assay that measures the abundance of T3 in venous blood" [] is_a: OBI:2100046 ! 3,3',5'-triiodothyronine assay [Term] id: OBI:2100362 name: CBC with manual differential venous blood neutrophil count assay def: "A cytometry assay that measures the count of neutrophils in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003022 ! neutrophil assay [Term] id: OBI:2100363 name: creatinine clearance urine creatinine assay def: "An analyte assay that measures the abundance of creatinine in urine as part of a creatinine clearance order" [] is_a: OBI:0003043 ! urine assay is_a: OBI:2100003 ! creatinine assay [Term] id: OBI:2100364 name: venous blood beta hydroxybutryic acid assay def: "An analyte assay that measures the abundance of beta hydroxybutryic acid in venous blood" [] is_a: OBI:2100051 ! 3-hydroxybutyric acid assay [Term] id: OBI:2100365 name: venous blood megakaryocyte count assay def: "A cytometry assay that measures the count of megakaryocytes in venous blood" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100366 name: venous blood nucleated RBC count assay def: "A cytometry assay that measures the count of nucleated RBCs in venous blood" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100367 name: venous blood WBC count assay def: "A cytometry assay that measures the count of WBCs in venous blood" [] is_a: OBI:0001977 ! cytometry assay [Term] id: OBI:2100368 name: automated count venous blood reticulocyte count assay def: "A cytometry assay that measures the count of reticulocytes in venous blood as part of a automated count order" [] is_a: OBI:0003026 ! reticulocyte assay [Term] id: OBI:2100369 name: total venous blood homocysteine assay def: "An analyte assay that measures the abundance of homocysteine in venous blood as part of a total order" [] is_a: OBI:0000443 ! analyte assay [Term] id: OBI:2100370 name: venous blood Ceruloplasmin assay def: "An analyte assay that measures the abundance of Ceruloplasmin in venous blood" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100371 name: GEM4 arterial blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a GEM4 order" [] is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100372 name: GEM4 arterial blood lactic acid assay def: "An assay that measures lactic acid in arterial blood as part of a GEM4 order" [] is_a: OBI:2100042 ! rac-lactic acid assay [Term] id: OBI:2100373 name: GEM4 arterial blood hemoglobin assay def: "An analyte assay that measures the abundance of hemoglobin in arterial blood as part of a GEM4 order" [] is_a: OBI:2100014 ! hemoglobin assay [Term] id: OBI:2100374 name: GEM4 arterial blood sodium assay def: "An analyte assay that measures the abundance of sodium in arterial blood as part of a GEM4 order" [] is_a: OBI:2100002 ! sodium(1+) assay [Term] id: OBI:2100375 name: GEM4 arterial blood potassium assay def: "An analyte assay that measures the abundance of potassium in arterial blood as part of a GEM4 order" [] is_a: OBI:2100004 ! potassium(1+) assay [Term] id: OBI:2100376 name: GEM4 arterial blood temperature assay def: "An assay that measures temperature in arterial blood as part of a GEM4 order" [] is_a: OBI:0000070 ! assay [Term] id: OBI:2100377 name: GEM4 arterial blood glucose assay def: "An analyte assay that measures the abundance of glucose in arterial blood as part of a GEM4 order" [] is_a: OBI:2100020 ! glucose assay [Term] id: OBI:2100378 name: GEM4 arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a GEM4 order" [] is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100379 name: GEM4 arterial blood hematocrit assay def: "A cytometry assay that measures the proportion of red blood cells in arterial blood as part of a GEM4 order" [] is_a: OBI:0003018 ! hematocrit assay [Term] id: OBI:2100380 name: GEM4 arterial blood ionized calcium assay def: "An analyte assay that measures the abundance of ionized calcium in arterial blood as part of a GEM4 order" [] is_a: OBI:2100024 ! calcium cation assay [Term] id: OBI:2100381 name: GEM4 arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a GEM4 order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100382 name: liver fibrosis (NAFLD) venous blood platelet count assay def: "A cytometry assay that measures the count of platelets in venous blood as part of a liver fibrosis (NAFLD) order" [] is_a: OBI:0003028 ! platelet assay [Term] id: OBI:2100383 name: venous blood beta hydroxybutric acid assay def: "An analyte assay that measures the abundance of beta hydroxybutric acid in venous blood" [] is_a: OBI:2100051 ! 3-hydroxybutyric acid assay [Term] id: OBI:2100384 name: CBC with manual differential venous blood plasma cell count assay def: "A cytometry assay that measures the count of plasma cells in venous blood as part of a CBC with manual differential order" [] is_a: OBI:0003024 ! lymphocyte assay [Term] id: OBI:2100385 name: venous blood erythropoietin assay def: "An analyte assay that measures the abundance of erythropoietin in venous blood" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100386 name: blood gas arterial blood oxygen assay def: "An analyte assay that measures the abundance of oxygen in arterial blood as part of a blood gas order" [] is_a: OBI:2100036 ! elemental oxygen assay [Term] id: OBI:2100387 name: blood gas arterial blood bicarbonate assay def: "An analyte assay that measures the abundance of bicarbonate in arterial blood as part of a blood gas order" [] is_a: OBI:2100043 ! hydrogencarbonate assay [Term] id: OBI:2100388 name: blood gas arterial blood carbon dioxide assay def: "An analyte assay that measures the abundance of carbon dioxide in arterial blood as part of a blood gas order" [] is_a: OBI:2100001 ! carbon dioxide assay [Term] id: OBI:2100389 name: free/total venous blood PSA assay def: "An analyte assay that measures the abundance of PSA in venous blood as part of a free/total order" [] is_a: OBI:2100034 ! prostate-specific antigen assay [Term] id: OBI:2100390 name: cerebrospinal fluid lymphocyte count assay def: "A cytometry assay that measures the count of lymphocytes in cerebrospinal fluid" [] is_a: OBI:0003024 ! lymphocyte assay is_a: OBI:0003232 ! cerebrospinal fluid assay [Term] id: OBI:2100391 name: cerebrospinal fluid segmented neutrophil count assay def: "A cytometry assay that measures the count of segmented neutrophils in cerebrospinal fluid" [] is_a: OBI:0003022 ! neutrophil assay is_a: OBI:0003232 ! cerebrospinal fluid assay [Term] id: OBI:2100392 name: cerebrospinal fluid mesothelial cell count assay def: "A cytometry assay that measures the count of mesothelial cells in cerebrospinal fluid" [] is_a: OBI:0001977 ! cytometry assay is_a: OBI:0003232 ! cerebrospinal fluid assay [Term] id: OBI:2100393 name: cerebrospinal fluid macrophage count assay def: "A cytometry assay that measures the count of macrophages in cerebrospinal fluid" [] is_a: OBI:0003027 ! macrophage assay is_a: OBI:0003232 ! cerebrospinal fluid assay [Term] id: OBI:2100394 name: cerebrospinal fluid basophil count assay def: "A cytometry assay that measures the count of basophils in cerebrospinal fluid" [] is_a: OBI:0003021 ! basophil assay is_a: OBI:0003232 ! cerebrospinal fluid assay [Term] id: OBI:2100395 name: cerebrospinal fluid monocyte count assay def: "A cytometry assay that measures the count of monocytes in cerebrospinal fluid" [] is_a: OBI:0003025 ! monocyte assay is_a: OBI:0003232 ! cerebrospinal fluid assay [Term] id: OBI:2100396 name: cerebrospinal fluid eosinophil count assay def: "A cytometry assay that measures the count of eosinophils in cerebrospinal fluid" [] is_a: OBI:0003023 ! eosinophil assay is_a: OBI:0003232 ! cerebrospinal fluid assay [Term] id: OBI:2100397 name: venous blood beta-2-microglobulin assay def: "An analyte assay that measures the abundance of beta-2-microglobulin in venous blood" [] is_a: OBI:2100023 ! protein assay [Term] id: OBI:2100398 name: lipid panel reflex direct venous blood low density lipoprotein assay def: "An analyte assay that measures the abundance of low density lipoprotein in venous blood as part of a Lipid panel reflex direct order" [] is_a: OBI:2100032 ! low-density lipoprotein cholesterol assay [Term] id: OBI:2100399 name: lipid panel reflex direct venous blood triglyceride assay def: "An analyte assay that measures the abundance of triglyceride in venous blood as part of a Lipid panel reflex direct order" [] is_a: OBI:2100029 ! triglyceride assay [Term] id: OBI:2100400 name: lipid panel reflex direct venous blood cholesterol assay def: "An analyte assay that measures the abundance of cholesterol in venous blood as part of a Lipid panel reflex direct order" [] is_a: OBI:2100031 ! cholesterol assay [Term] id: OBI:2100401 name: lipid panel reflex direct venous blood high density lipoprotein assay def: "An analyte assay that measures the abundance of high density lipoprotein in venous blood as part of a Lipid panel reflex direct order" [] is_a: OBI:2100030 ! high-density lipoprotein cholesterol assay [Term] id: OBI:2100402 name: pooled clone sequencing assay def: "A DNA sequencing assay in which the DNA input is derived from pooled clones (for example BACs and Fosmids) is sequenced." [] is_a: OBI:0000626 ! DNA sequencing assay [Term] id: OBI:9999994 name: chromium release assay def: "An in vitro cell killing assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died." [] is_a: OBI:0000903 ! in vitro cell killing assay [Term] id: OGMS:0000015 name: clinical history def: "A series of statements representing health-relevant qualities of a patient and of a patient's family." [] is_a: IAO:0000030 ! information content entity [Term] id: OGMS:0000023 name: phenotype def: "A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species." [] is_a: BFO:0000019 ! quality [Term] id: OGMS:0000031 name: disease def: "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." [] is_a: BFO:0000016 ! disposition [Term] id: OGMS:0000063 name: disease course def: "The totality of all processes through which a given disease instance is realized." [] is_a: GO:0008150 ! biological_process [Term] id: OGMS:0000073 name: diagnosis def: "The representation of a conclusion of a diagnostic process." [] is_a: IAO:0000027 ! data item [Term] id: OGMS:0000090 name: treatment def: "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" [] is_a: OBI:0000011 ! planned process [Term] id: OGMS:0000123 name: clinical data item def: "A data item that is about a patient and is the specified output of a health care process assay or diagnostic process" [] is_a: IAO:0000027 ! data item [Term] id: OMIABIS:0000050 name: fixed tissue specimen def: "A processed specimen that is the output of a fixation process." [] is_a: OBI:0000953 ! processed specimen [Term] id: OMIABIS:0000052 name: fixed tissue slide specimen def: "A fixed tissue specimen that is placed in a slide." [] is_a: OMIABIS:0000050 ! fixed tissue specimen [Term] id: OMRSE:00000012 name: health care provider role def: "A human health care role inhering in an organization or human being that is realized by a process of providing health care services to an organism." [] is_a: BFO:0000023 ! role [Term] id: OPL:0000232 name: parasite organism def: "An organism living in, with, or on another organism in parasitism. Individual members of parasite species, such as Leishmania, Plasmodium, Trypanosoma, etc. are members of this class." [] is_a: OBI:0100026 ! organism [Term] id: OPL:0000267 name: Plasmodium gametocyte def: "A Plasmodium that is located either in the bloodstream of the vertebrate host or midgut of mosquito vector during gametocyte stage. Gametocytes are the precursor cells of the macro- or microgametes" [] is_a: NCBITaxon:5820 ! Plasmodium [Term] id: ObsoleteClass name: Obsolete Class [Term] id: PATO:0000011 name: age def: "A time quality inhering in a bearer by virtue of how long the bearer has existed." [] is_a: PATO:0000165 ! time [Term] id: PATO:0000018 name: fluorescence def: "A luminous flux quality inhering in a bearer by virtue of the bearer's emitting longer wavelength light following the absorption of shorter wavelength radiation; fluorescence is common with aromatic compounds with several rings joined together." [] is_a: PATO:0001296 ! luminous flux [Term] id: PATO:0000025 name: composition def: "A single physical entity inhering in an bearer by virtue of the bearer's quantities or relative ratios of subparts." [] is_a: PATO:0000141 ! structure [Term] id: PATO:0000033 name: concentration of def: "A quality inhering in a substance by virtue of the amount of the bearer's there is mixed with another substance." [] is_a: PATO:0002182 ! molecular quality [Term] id: PATO:0000047 name: biological sex def: "An organismal quality inhering in a bearer by virtue of the bearer's ability to undergo sexual reproduction in order to differentiate the individuals or types involved." [] is_a: PATO:0001995 ! organismal quality [Term] id: PATO:0000051 name: morphology def: "A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure." [] is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0000117 name: size def: "A morphology quality inhering in a bearer by virtue of the bearer's physical magnitude." [] is_a: PATO:0000051 ! morphology [Term] id: PATO:0000122 name: length def: "A 1-D extent quality which is equal to the distance between two points." [] is_a: PATO:0000051 ! morphology [Term] id: PATO:0000125 name: mass def: "A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter." [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0000140 name: position def: "A spatial quality inhering in a bearer by virtue of the bearer's spatial location relative to other objects in the vicinity." [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0000141 name: structure def: "A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form." [] is_a: PATO:0000051 ! morphology [Term] id: PATO:0000146 name: temperature def: "A physical quality of the thermal energy of a system." [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0000165 name: time def: "A quality in which events occur in sequence." [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0000169 name: viability def: "An organismal quality inhering in a bearer or a population by virtue of the bearer's disposition to survive and develop normally or the number of surviving individuals in a given population." [] is_a: PATO:0001995 ! organismal quality [Term] id: PATO:0000186 name: behavioral quality def: "An organismal quality inhering in a bearer by virtue of the bearer's behavior aggregate of the responses or reactions or movements in a given situation." [] is_a: PATO:0001995 ! organismal quality [Term] id: PATO:0000383 name: female def: "A biological sex quality inhering in an individual or a population that only produces gametes that can be fertilised by male gametes." [] is_a: PATO:0001894 ! phenotypic sex [Term] id: PATO:0000384 name: male def: "A biological sex quality inhering in an individual or a population whose sex organs contain only male gametes." [] is_a: PATO:0001894 ! phenotypic sex [Term] id: PATO:0000918 name: volume def: "A 3-D extent quality inhering in a bearer by virtue of the bearer's amount of 3-dimensional space it occupies." [] is_a: PATO:0001710 ! 3-D extent [Term] id: PATO:0001018 name: physical quality def: "A quality of a physical entity that exists through action of continuants at the physical level of organisation in relation to other entities." [] is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0001020 name: damage def: "A structural quality inhering in a bearer by virtue of whether the bearer has been harmed or injured or spoiled." [] is_a: PATO:0000141 ! structure [Term] id: PATO:0001025 name: pressure def: "A physical quality that inheres in a bearer by virtue of the bearer's amount of force per unit area it exerts." [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0001161 name: diluted def: "A concentration which relatively low." [] is_a: PATO:0000033 ! concentration of [Term] id: PATO:0001167 name: damaged def: "A structural quality inhering in a bearer by virtue of the bearer being harmed or injured or spoiled, such that its functionality is impaired." [] is_a: PATO:0001020 ! damage [Term] id: PATO:0001193 name: lateral to def: "A spatial quality inhering in a bearer by virtue of the bearer's being located toward the side relative to another entity." [] is_a: PATO:0000140 ! position [Term] id: PATO:0001196 name: ventral to def: "A spatial quality inhering in a bearer by virtue of the bearer's being located toward the abdomen of an organism relative to another entity." [] is_a: PATO:0000140 ! position [Term] id: PATO:0001233 name: dorsal to def: "A spatial quality inhering in a bearer by virtue of the bearer's being located toward the back or upper surface of an organism relative to another entity." [] is_a: PATO:0000140 ! position [Term] id: PATO:0001241 name: physical object quality def: "A quality which inheres in a continuant." [] is_a: BFO:0000019 ! quality [Term] id: PATO:0001291 name: electromagnetic (EM) radiation quality def: "A physical quality that inheres in an bearer by virtue of how that bearer interacts with electromagnetic radiation." [] is_a: PATO:0001739 ! radiation quality [Term] id: PATO:0001296 name: luminous flux def: "A scalar optical quality which obtains by the magnitude of the light emitted by the bearer." [] is_a: PATO:0001300 ! optical quality [Term] id: PATO:0001300 name: optical quality def: "An EM radiation quality in which the EM radiation is within the fiat range of the spectrum visible deemed to be light." [] is_a: PATO:0001291 ! electromagnetic (EM) radiation quality [Term] id: PATO:0001335 name: bacterial mating type def: "A mating type that indicates whether the F plasmid has integrated into the chromosome." [] is_a: PATO:0001895 ! mating type [Term] id: PATO:0001337 name: yeast mating type def: "A yeast mating type." [] is_a: PATO:0001895 ! mating type [Term] id: PATO:0001338 name: mixed sex def: "A biological sex quality inhering in a population of multiple sexes." [] is_a: PATO:0002003 ! population quality [Term] id: PATO:0001339 name: biomaterial purity def: "A composition quality inhering in an bearer by virtue of the bearer's homogeneity of a biomaterial." [] is_a: PATO:0000025 ! composition [Term] id: PATO:0001340 name: hermaphrodite def: "A biological sex quality inhering in an organism or a population with both male and female sexual organs in one individual." [] is_a: PATO:0001894 ! phenotypic sex [Term] id: PATO:0001341 name: a mating type (yeast) def: "A S. cerevisiae mating type cells that secrete a pheromone that in alpha haploids stimulates processes that lead to mating." [] is_a: PATO:0001342 ! Saccharomyces cerevisiae mating type [Term] id: PATO:0001342 name: Saccharomyces cerevisiae mating type def: "A S. cerevisiae mating type." [] is_a: PATO:0001337 ! yeast mating type [Term] id: PATO:0001343 name: Schizosaccharomyces pombe mating type def: "A S. pombe mating type determined by the gene configuration on the mat1 locus." [] is_a: PATO:0001337 ! yeast mating type [Term] id: PATO:0001344 name: alpha mating type (yeast) def: "A S. cerevisiae mating type cells that secrete a pheromone that stimulates a haploids." [] is_a: PATO:0001342 ! Saccharomyces cerevisiae mating type [Term] id: PATO:0001345 name: h minus def: "A S. pombe mating type determined by the mat1-Mc and mat1-Mi on the mat1 locus." [] is_a: PATO:0001343 ! Schizosaccharomyces pombe mating type [Term] id: PATO:0001346 name: h plus def: "A S. pombe mating type determined by the mat1-Pc and mat1-Pi on the mat1 locus." [] is_a: PATO:0001343 ! Schizosaccharomyces pombe mating type [Term] id: PATO:0001347 name: F mating type def: "A bacterial mating type indicating the presence of F plasmid in a bacterial cell." [] is_a: PATO:0001335 ! bacterial mating type [Term] id: PATO:0001348 name: F minus mating type def: "A bacterial mating type indicating the absence of F plasmid in a bacterial cell." [] is_a: PATO:0001335 ! bacterial mating type [Term] id: PATO:0001374 name: ploidy def: "A cellular quality inhering in a bearer by virtue of the bearer's number of homologous sets of chromosomes in the nucleus or primary chromosome-containing compartment of the cell, each set essentially coding for all the biological traits of the organism." [] is_a: PATO:0001396 ! cellular quality [Term] id: PATO:0001375 name: haploid def: "A ploidy quality inhering in a bearer by virtue of the bearer's containing a single set of homologous chromosomes." [] is_a: PATO:0001393 ! euploid [Term] id: PATO:0001377 name: polyploid def: "A ploidy quality inhering in a bearer by virtue of the bearer's containing more than two homologous sets of chromosomes." [] is_a: PATO:0001393 ! euploid [Term] id: PATO:0001385 name: aneuploid def: "A ploidy quality inhering in a bearer by virtue of the bearer's containing a non-integral multiple of the monoploid number, due to extra or missing chromosomes." [] is_a: PATO:0001374 ! ploidy [Term] id: PATO:0001393 name: euploid def: "A ploidy quality inhering in a bearer by virtue of the bearer's containing an integral multiple of the monoploid number, possibly excluding the sex-determining chromosomes." [] is_a: PATO:0001374 ! ploidy [Term] id: PATO:0001394 name: diploid def: "A ploidy quality inhering in a bearer by virtue of the bearer's having two copies (homologs) of each chromosome, usually one from the mother and one from the father." [] is_a: PATO:0001393 ! euploid [Term] id: PATO:0001396 name: cellular quality def: "A monadic quality of continuant that exists at the cellular level of organisation." [] is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0001421 name: alive def: "A viability quality inhering in a bearer by virtue of the bearer's condition before death." [] is_a: PATO:0000169 ! viability [Term] id: PATO:0001422 name: dead def: "A viability quality inhering in a bearer by virtue of the cessation of the bearer's life." [] is_a: PATO:0000169 ! viability [Term] id: PATO:0001546 name: quality of a solid def: "A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity characterized by particles arranged such that their shape and volume are relatively stable." [] is_a: PATO:0002198 ! quality of a substance [Term] id: PATO:0001547 name: quality of a gas def: "A physical quality inhering in a bearer by virtue of the bearer's exhibiting the physical characteristics of an entity consisting of particles that have neither a defined volume nor defined shape." [] is_a: PATO:0002198 ! quality of a substance [Term] id: PATO:0001548 name: quality of a liquid def: "A physical quality inhering in an entity exhibiting the physical characteristics of an amorphous (non-crystalline) form of matter between a gas and a solid that has a definite volume, but no definite shape." [] is_a: PATO:0002198 ! quality of a substance [Term] id: PATO:0001574 name: flow rate def: "A physical quality inhering in a bearer by virtue of the bearer's motion characteristic." [] is_a: PATO:0001906 ! movement quality [Term] id: PATO:0001632 name: anterior to def: "A spatial quality inhering in a bearer by virtue of the bearer's being located toward the front of an organism relative to another entity." [] synonym: "frontal" EXACT [] is_a: PATO:0000140 ! position [Term] id: PATO:0001710 name: 3-D extent def: "A size quality inhering in an bearer by virtue of the bearer's extension in three dimensions." [] is_a: PATO:0000117 ! size [Term] id: PATO:0001739 name: radiation quality def: "A quality that inheres in an bearer by virtue of how that bearer interacts with radiation." [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0001740 name: activity (of a radionuclide) def: "A radiation quality inhering in a radioactive substance by virtue of its transformation (disintegration) rate." [] is_a: PATO:0001739 ! radiation quality [Term] id: PATO:0001741 name: radioactive def: "A radiation quality inhering in bearer by virtue of the bearer's exhibiting or being caused by radioactivity." [] is_a: PATO:0001740 ! activity (of a radionuclide) [Term] id: PATO:0001792 name: left side of def: "A spatial quality inhering in a bearer by virtue of the bearer's being located on left side of from the a another entity." [] is_a: PATO:0000140 ! position [Term] id: PATO:0001793 name: right side of def: "A spatial quality inhering in a bearer by virtue of the bearer's being located on right side of a another entity." [] is_a: PATO:0000140 ! position [Term] id: PATO:0001894 name: phenotypic sex def: "An organismal quality inhering in a bearer by virtue of the bearer's physical expression of sexual characteristics." [] is_a: PATO:0000047 ! biological sex [Term] id: PATO:0001895 name: mating type def: "A biological sex quality inhering in an individual or a population that undergo sexual reproduction." [] is_a: PATO:0000047 ! biological sex [Term] id: PATO:0001906 name: movement quality def: "A physical quality inhering in a bearer by virtue of the bearer's participation in movement." [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0001985 name: frozen def: "A quality inhering in a bearer by virtue of the bearer's being kept below its freezing point." [] is_a: PATO:0000146 ! temperature [Term] id: PATO:0001995 name: organismal quality def: "A quality that inheres in an entire organism or part of an organism." [] is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0002003 name: population quality def: "A quality that inheres in an entire population or part of a population." [] is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0002027 name: osmolality def: "A concentration quality inhering in a bearer by virtue of the bearer's amount of osmoles of solute per kilogram of solvent." [] is_a: PATO:0000033 ! concentration of [Term] id: PATO:0002182 name: molecular quality def: "A quality which inheres in a molecular entity, a single molecule, atom, ion, radical etc." [] is_a: PATO:0001241 ! physical object quality [Term] id: PATO:0002198 name: quality of a substance def: "A quality inhering in a bearer by virtue of its constitution." [] is_a: PATO:0001018 ! physical quality [Term] id: PATO:0002201 name: handedness def: "A behavioral quality inhering ina bearer by virtue of the bearer's unequal distribution of fine motor skill between its left and right hands or feet." [] is_a: PATO:0000186 ! behavioral quality [Term] id: PATO:0002202 name: left handedness def: "Handedness where the organism preferentially uses the left hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot." [] is_a: PATO:0002201 ! handedness [Term] id: PATO:0002203 name: right handedness def: "Handedness where the organism preferentially uses the right hand or foot for tasks requiring the use of a single hand or foot or a dominant hand or foot." [] is_a: PATO:0002201 ! handedness [Term] id: PATO:0002204 name: ambidextrous handedness def: "Handedness where the organism exhibits no overall dominance in the use of right or left hand or foot in the performance of tasks that require one hand or foot or a dominant hand or foot." [] is_a: PATO:0002201 ! handedness [Term] id: PATO:0002243 name: fluid flow rate def: "A physical quality inhering in a fluid (liquid or gas) by virtue of the amount of fluid which passes through a given surface per unit time." [] is_a: PATO:0001574 ! flow rate [Term] id: PR:000000001 name: protein def: "An amino acid chain that is produced de novo by ribosome-mediated translation of a genetically-encoded mRNA, and any derivatives thereof." [] is_a: CHEBI:16670 ! peptide [Term] id: PR:000001004 name: CD4 molecule def: "A protein that is a translation product of the human CD4 gene or a 1:1 ortholog thereof. CD4 is an accessory protein for MHC class-II antigen/T-cell receptor interaction. It is the primary receptor for HIV-1. CD4 has four immunoglobulin-like domains in its extracellular region that share the same structure, but can differ in sequence." [] is_a: PR:000000001 ! protein [Term] id: PR:000001018 name: CD3 subunit with immunoglobulin domain def: "A protein with a core domain composition consisting of an extracellular N-terminal domain that adopts an immunoglobulin fold, a transmembrane domain, and an intracellular C-terminal domain with a single copy of the Immunoreceptor tyrosine-based activation motif (Pfam:PF02189) (ITAM). It constitutes the invariant subunit of the T cell antigen receptor (TCR). TCR is a surface receptor on T cells responsible for recognizing MHC-restricted antigens and initiating the cellular immune response." [] is_a: PR:000000001 ! protein [Term] id: PR:000003015 name: prostate-specific antigen def: "A trypsin that is a translation product of the human KLK3 gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000003252 name: antithrombin-III def: "A serpin that is a translation product of the human SERPINC1 gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000003745 name: double-stranded RNA-specific adenosine deaminase def: "A protein that is a translation product of the human ADAR gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000003777 name: adiponectin def: "A protein that is a translation product of the human ADIPOQ gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000003918 name: albumin def: "A protein that is a translation product of the human ALB gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000004580 name: beta-2-microglobulin def: "A protein that is a translation product of the human B2M gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000005794 name: ceruloplasmin def: "A protein that is a translation product of the human CP gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000005897 name: C-reactive protein def: "A protein that is a translation product of the human CRP gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000006592 name: deoxyribonuclease-1 def: "A protein that is a translation product of the human DNASE1 gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000007141 name: erythropoietin def: "A protein that is a translation product of the human EPO gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000007928 name: glial cell line-derived neurotrophic factor def: "A protein that is a translation product of the human GDNF gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000008457 name: beta-globin def: "A hemoglobin subunit that is a translation product of the human HBB gene, a 1:1 ortholog thereof, or pro-orthologs thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000008725 name: haptoglobin def: "A protein that is a translation product of the human HP gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000009758 name: leptin def: "A protein that is a translation product of the human LEP gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000013429 name: parathyroid hormone def: "A protein that is a translation product of the human PTH gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000014060 name: ribonuclease T2 def: "A protein that is a translation product of the human RNASET2 gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000016261 name: serotransferrin def: "A protein that is a translation product of the human TF gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000016801 name: transthyretin def: "A protein that is a translation product of the human TTR gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000023089 name: DNA ligase def: "A protein that is a translation product of the Escherichia coli K-12 ligA gene or a 1:1 ortholog thereof." [] synonym: "ligase" EXACT [] is_a: OBI:0000427 ! enzyme is_a: PR:000000001 ! protein [Term] id: PR:000025402 name: T cell receptor co-receptor CD8 def: "A protein-containing complex that is a membrane-bound heterodimeric co-receptor for MHC class-I antigen/T-cell receptor interaction." [] is_a: PR:000000001 ! protein [Term] id: PR:000025467 name: guanyl-specific ribonuclease T1 def: "A protein that is a translation product of the Aspergillus oryzae RIB40 rntA gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000025471 name: nuclease S1 def: "A protein that is a translation product of the Aspergillus oryzae RIB40 nucS gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000025475 name: ribonuclease U2 def: "A protein that is a translation product of the Ustilago sphaerogena RNU2 gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000025477 name: ribonuclease V1 (cobra) def: "A protein with ribonuclease activity that is a constituent of cobra venom." [] is_a: PR:000000001 ! protein [Term] id: PR:000025478 name: ribonuclease CL3 (chicken) def: "A protein with ribonuclease activity that is purified from chicken liver." [] is_a: PR:000000001 ! protein [Term] id: PR:000027247 name: cytosolic creatine kinase complex, MB-type def: "A cytosolic creatine kinase complex that is a heterodimer of a B-type subunit and an M-type subunit." [] is_a: GO:0032991 ! protein-containing complex [Term] id: PR:000029971 name: creatine kinase def: "A protein that contains a single ATP:guanido phosphotransferase N-terminal domain (Pfam:PF02807) followed by a single ATP:guanido phosphotransferase C-terminal catalytic domain (Pfam:PF00217)." [] is_a: PR:000000001 ! protein [Term] id: PR:000029983 name: protein-glutamine gamma-glutamyltransferase is_a: PR:000000001 ! protein [Term] id: PR:000036824 name: NS1 def: "A dengue virus genome polyprotein proteolytic cleavage product that is the N-terminal most non-structural protein within the dengue virus genome polyprotein. Example: UniProtKB:P29990, 776-1127, Asn-905/Asn-982, MOD:00160." [] is_a: PR:000000001 ! protein [Term] id: PR:000050219 name: alanine aminotransferase def: "A protein that is a translation product of the human GPT or GPT2 genes, 1:1 orthologs thereof, or a semi-ortholog thereof." [] is_a: PR:000000001 ! protein [Term] id: PR:000050331 name: lactate dehydrogenase complex def: "A protein-containing complex that is composed of four subunits of L-lactate dehydrogenase, cytoplasmic." [] is_a: GO:0032991 ! protein-containing complex [Term] id: PR:000050343 name: alkaline phosphatase (human) def: "A protein that is a translation product of any of the following alkaline phosphatase genes in human: ALPG (encoding the germinal form; GCAP), ALPP (encoding the placental form; PLAP), ALPI (encoding the intestinal form; IAP), and ALPL (encoding the tissue non-specific form; TNAP)." [] is_a: PR:000000001 ! protein [Term] id: PR:000050353 name: aspartate aminotransferase (human) def: "A protein that is a translation product of any of the following genes in human: GOT1/GOT2." [] is_a: PR:000000001 ! protein [Term] id: PR:000050469 name: hemoglobin A1c def: "A hemoglobin complex that is composed of at least one beta-N-1-deoxy fructosyl hemoglobin subunit, in which the glycan is attached to the N-terminal valine (after initiator methionine removal) of one or both beta subunits." [] is_a: GO:0032991 ! protein-containing complex [Term] id: REO:0000171 name: obsolete molecular label role def: "A reagent role inhering in a molecular entity intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay." [] synonym: "molecular tracer role" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: REO:0000280 name: obsolete molecular label def: "A molecular reagent intended to associate with some molecular target to serve as a proxy for the presence, abundance, or location of this target in a detection of molecular label assay" [] synonym: "molecular tracer" EXACT [] is_a: ObsoleteClass ! Obsolete Class is_obsolete: true [Term] id: SO:0000001 name: region def: "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [] synonym: "primary structure of sequence macromolecule" EXACT [] synonym: "sequence" EXACT [] is_a: BFO:0000031 ! generically dependent continuant [Term] id: SO:0000104 name: polypeptide def: "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [] synonym: "polypeptide sequence" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0000148 name: supercontig def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000149 name: contig def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [] is_a: SO:0000353 ! sequence_assembly [Term] id: SO:0000235 name: TF_binding_site def: "A DNA site where a transcription factor binds." [] is_a: SO:0005836 ! regulatory_region [Term] id: SO:0000276 name: miRNA def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [] is_a: SO:0000001 ! region [Term] id: SO:0000353 name: sequence_assembly def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [] is_a: SO:0001248 ! assembly [Term] id: SO:0000988 name: circular def: "A quality of a nucleotide polymer that has no terminal nucleotide residues." [] is_a: PATO:0001241 ! physical object quality [Term] id: SO:0001248 name: assembly def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [] is_a: SO:0001410 ! experimental_feature [Term] id: SO:0001410 name: experimental_feature def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [] is_a: SO:0000001 ! region [Term] id: SO:0005836 name: regulatory_region def: "A region of sequence that is involved in the control of a biological process." [] is_a: SO:0000001 ! region [Term] id: UBERON:0000002 name: uterine cervix def: "Lower, narrow portion of the uterus where it joins with the top end of the vagina." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000007 name: pituitary gland def: "The pituitary gland is an endocrine gland that secretes hormones that regulate many other glands [GO]. An endocrine gland located ventral to the diencephalon and derived from mixed neuroectodermal and non neuroectodermal origin [ZFIN]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000010 name: peripheral nervous system def: "A major division of the nervous system that contains nerves which connect the central nervous system (CNS) with sensory organs, other organs, muscles, blood vessels and glands." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000029 name: lymph node def: "Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000057 name: urethra def: "The fibromuscular tubular canal through which urine is discharged from the bladder to the exterior via the external urinary meatus; in males, the urethra is joined by the ejaculatory ducts and serves as a passageway for semen during ejaculation, as well as a canal for urine during voiding; in females, the urethra is shorter and emerges above the vaginal opening." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000105 name: life cycle stage def: "A spatiotemporal region encompassing some part of the life cycle of an organism." [] is_a: GO:0008150 ! biological_process [Term] id: UBERON:0000165 name: mouth def: "The proximal portion of the digestive tract, containing the oral cavity and bounded by the oral opening. In vertebrates, this extends to the pharynx and includes gums, lips, tongue and parts of the palate. Typically also includes the teeth, except where these occur elsewhere (e.g. pharyngeal jaws) or protrude from the mouth (tusks)." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000173 name: amniotic fluid def: "Amniotic fluid is a bodily fluid consisting of watery liquid surrounding and cushioning a growing fetus within the amnion. It allows the fetus to move freely without the walls of the uterus being too tight against its body. Buoyancy is also provided. The composition of the fluid changes over the course of gestation. Initially, amniotic fluid is similar to maternal plasma, mainly water with electrolytes. As the fetus develops, proteins, carbohydrates, lipids, phospholipids originating from the lungs, fetal cells, and urea are deposited in the fluid." [] is_a: UBERON:0000463 ! organism substance [Term] id: UBERON:0000178 name: blood def: "A fluid that is composed of blood plasma and erythrocytes." [] is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0000305 name: amnion def: "The thin innermost layer of the extraembryonic membranes that contains the amniotic fluid; the membrane forms a closed sac in which the embryo and later, the fetus, is suspended and protected." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000310 name: breast def: "The upper ventral region of the torso of an organism." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000316 name: cervical mucus def: "A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation[WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus." [] is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0000341 name: throat def: "In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000362 name: renal medulla def: "The inner portion of the kidney consisting of the renal pyramids." [] is_a: UBERON:0000481 ! multi-tissue structure [Term] id: UBERON:0000463 name: organism substance def: "Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000465 name: material anatomical entity def: "Anatomical entity that has mass." [] is_a: BFO:0000040 ! material entity [Term] id: UBERON:0000473 name: testis def: "A gonad of a male animal. A gonad produces and releases sperm." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000477 name: anatomical cluster def: "Anatomical group whose component anatomical structures lie in close proximity to each other." [] is_a: BFO:0000040 ! material entity [Term] id: UBERON:0000479 name: tissue def: "Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000481 name: multi-tissue structure def: "Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000483 name: epithelium def: "Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina. Examples: simple squamous epithelium, glandular cuboidal epithelium, transitional epithelium, myoepithelium[CARO]." [] is_a: UBERON:0000479 ! tissue [Term] id: UBERON:0000945 name: stomach def: "An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000947 name: aorta def: "The main trunk of the systemic arterial system that carries blood from the heart to all the organs and other structures of the body, bringing oxygenated blood to all parts of the body in the systemic circulation." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000948 name: heart def: "A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000955 name: brain def: "The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000956 name: cerebral cortex def: "The thin layer of gray matter on the surface of the cerebral hemisphere that develops from the telencephalon. It consists of the neocortex (6 layered cortex or isocortex), the hippocampal formation and the olfactory cortex." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000970 name: eye def: "An organ that detects light." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000978 name: leg def: "The portion of the hindlimb that contains both the stylopod and zeugopod." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000992 name: ovary def: "The gonad of a female organism which contains germ cells." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000995 name: uterus def: "The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0000996 name: vagina def: "A fibromuscular tubular tract leading from the uterus to the exterior of the body in female placental mammals and marsupials, or to the cloaca in female birds, monotremes, and some reptiles[WP]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001003 name: skin epidermis def: "The outer epithelial layer of the skin that is superficial to the dermis." [] is_a: UBERON:0000483 ! epithelium [Term] id: UBERON:0001004 name: respiratory system def: "Functional system which consists of structures involved in respiration." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001013 name: adipose tissue def: "Portion of connective tissue composed of adipocytes enmeshed in areolar tissue." [] is_a: UBERON:0000479 ! tissue [Term] id: UBERON:0001037 name: strand of hair def: "A filament, mostly protein, that grows from follicles found in the dermis[WP]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001052 name: rectum def: "The terminal portion of the intestinal tube, terminating with the anus." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001087 name: pleural fluid def: "Transudate contained in the pleural cavity." [] is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0001088 name: urine def: "Excretion that is the output of a kidney." [] is_a: UBERON:0000463 ! organism substance [Term] id: UBERON:0001089 name: sweat def: "Secretion produced by a sweat gland." [] is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0001090 name: synovial fluid def: "Joint fluid is a transudate of plasma that is actively secreted by synovial cells." [] is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0001103 name: diaphragm def: "A thin musculomebranous barrier that separates the abdominal and thoracic cavities. Often used for breathing control." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001134 name: skeletal muscle tissue def: "Muscle tissue that consists primarily of skeletal muscle fibers." [] is_a: UBERON:0000479 ! tissue [Term] id: UBERON:0001155 name: colon def: "A portion of the large intestine before it becomes the rectum. In mammals, the colon is the most part of the large intestine, excluding the vermiform appendix, the rectum and the anal canal." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001159 name: sigmoid colon def: "The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001225 name: cortex of kidney def: "Outer cortical portion of the kidney, between the renal capsule and the renal medulla." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001255 name: urinary bladder def: "Distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001264 name: pancreas def: "An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating hormones[GO]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001268 name: peritoneal fluid def: "Transudate contained in the peritoneal cavity." [] is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0001323 name: tibial nerve def: "The tibial nerve is a branch of the sciatic nerve. The tibial nerve passes through the popliteal fossa to pass below the arch of soleus. In the popliteal fossa the nerve gives off branches to gastrocnemius, popliteus, soleus and plantaris muscles, an articular branch to the knee joint, and a cutaneous branch that will become the sural nerve. The sural nerve is joined by fibres from the common peroneal nerve and runs down the calf to supply the lateral side of the foot. Below the soleus muscle the nerve lies close to the tibia and supplies the tibialis posterior, the flexor digitorum longus and the flexor hallucis longus. The nerve passes into the foot running posterior to the medial malleolus. Here it is bound down by the flexor retinaculum in company with the posterior tibial artery. [WP,unvetted]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001359 name: cerebrospinal fluid def: "A clear, colorless, bodily fluid, that occupies the subarachnoid space and the ventricular system around and inside the brain and spinal cord." [] is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0001460 name: arm def: "The part of the forelimb extending from the shoulder to the autopod[cjm]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001485 name: knee joint def: "The knee joint joins the thigh with the leg and consists of two articulations: one between the femur and tibia, and one between the femur and patella. It is the largest and most complicated joint in the human body. The knee is a mobile trocho-ginglymus (i.e. a pivotal hinge joint), which permits flexion and extension as well as a slight medial and lateral rotation[WP,unvetted]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001488 name: ankle joint def: "A joint that connects the hindlimb autopod and zeugopod skeletons." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001530 name: common carotid artery plus branches def: "A bilaterally paired branched artery that originates from the aortic arches and divides into and includes as parts the internal and external carotid arteries[cjm]." [] is_a: UBERON:0001637 ! artery [Term] id: UBERON:0001555 name: digestive tract def: "A tube extending from the mouth to the anus." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001557 name: upper respiratory tract def: "The segment of the respiratory tract that starts proximally with the nose and ends distally with the cricoid cartilage, before continuing to the trachea." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001558 name: lower respiratory tract def: "The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001567 name: cheek def: "A fleshy subdivision of one side of the face bounded by an eye, ear and the nose." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001577 name: facial muscle def: "A muscle innervated by a facial nerve." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001621 name: coronary artery def: "An artery that supplies the myocardium." [] is_a: UBERON:0001637 ! artery [Term] id: UBERON:0001637 name: artery def: "An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001638 name: vein def: "Any of the tubular branching vessels that carry blood from the capillaries toward the heart." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001723 name: tongue def: "A muscular organ in the floor of the mouth." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001728 name: nasopharynx def: "The section of the pharynx that lies above the soft palate." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001729 name: oropharynx def: "The portion of the pharynx that lies between the soft palate and the upper edge of the epiglottis." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001797 name: vitreous humor def: "A transparent, semigelatinous substance that fills the cavity behind the crystalline lens of the eye and in front of the retina." [] is_a: UBERON:0000463 ! organism substance [Term] id: UBERON:0001811 name: conjunctiva def: "The mucous membrane that lines the inner surface of the eyelids and the front of the eyeball." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001826 name: nasal cavity mucosa def: "The mucous membrane that lines the nasal cavity[MP]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001830 name: minor salivary gland def: "One of the smaller, largely mucus-secreting, exocrine glands of the oral cavity, consisting of the labial, buccal, molar, lingual, and palatine glands[MP]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001836 name: saliva def: "A fluid produced in the oral cavity by salivary glands, typically used in predigestion, but also in other functions." [] is_a: UBERON:0000463 ! organism substance [Term] id: UBERON:0001873 name: caudate nucleus def: "Subcortical nucleus of telecephalic origin consisting of an elongated gray mass lying lateral to and bordering the lateral ventricle. It is divided into a head, body and tail in some species." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001874 name: putamen def: "Subcortical nucleus of telencephalic , which together with the caudate nucleus, forms the striatum. The putamen lies lateral to the internal capsule and medial to the external medullary lamina, and is separated from the caudate nucleus by the fibers of the internal capsule for most of its length, except at its anterior portion." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001893 name: telencephalon def: "Part of the forebrain consisting of paired olfactory bulbs and cerebral hemispheres." [] is_a: UBERON:0000481 ! multi-tissue structure [Term] id: UBERON:0001913 name: milk def: "An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation." [] is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0001968 name: semen def: "Organism substance that is composed of sperm cells suspended in seminal fluid." [] is_a: UBERON:0000463 ! organism substance [Term] id: UBERON:0001970 name: bile def: "Vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium." [] is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0001987 name: placenta def: "Organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0001988 name: feces def: "Portion of semisolid bodily waste discharged through the anus[MW,modified]." [] is_a: UBERON:0000463 ! organism substance [Term] id: UBERON:0002032 name: areola def: "Subdivision of breast which consists of skin, connective tissue and smooth muscle bundle and modified sebaceous glands and which surrounds the nipple." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002037 name: cerebellum def: "Part of the metencephalon that lies in the posterior cranial fossa behind the brain stem. It is concerned with the coordination of movement[MESH]. A large dorsally projecting part of the brain concerned especially with the coordination of muscles and the maintenance of bodily equilibrium, situated between the brain stem and the back of the cerebrum , and formed in humans of two lateral lobes and a median lobe[BTO]. Brain structure derived from the anterior hindbrain, and perhaps including posterior midbrain. The cerebellum plays a role in somatic motor function, the control of muscle tone, and balance[ZFA]." [] is_a: UBERON:0000481 ! multi-tissue structure [Term] id: UBERON:0002046 name: thyroid gland def: "A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002048 name: lung def: "Respiration organ that develops as an outpocketing of the esophagus." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002067 name: dermis def: "The dermis is a layer of skin between the epidermis (with which it makes up the skin) and subcutaneous tissues, and is composed of two layers, the papillary and reticular dermis[WP]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002072 name: hypodermis def: "Lowermost layer of the integumentary system in vertebrates. Types of cells that are found in the hypodermis are fibroblasts, adipose cells, and macrophages. It is derived from the mesoderm, but unlike the dermis, it is not derived from the dermatome region of the mesoderm. The hypodermis is used mainly for fat storage[WP]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002097 name: skin of body def: "The organ covering the body that consists of the dermis and epidermis." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002106 name: spleen def: "The organ that functions to filter blood and to store red corpuscles and platelets." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002107 name: liver def: "An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002116 name: ileum def: "The portion of the small intestine that extends from the jejunum to the colon." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002199 name: integument def: "The dermis, epidermis and hypodermis." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002358 name: peritoneum def: "A serous membrane that lines the peritoneal cavity[VHOG,modified]." [] is_a: UBERON:0000481 ! multi-tissue structure [Term] id: UBERON:0002367 name: prostate gland def: "The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002369 name: adrenal gland def: "Either of a pair of complex endocrine organs near the anterior medial border of the kidney consisting of a mesodermal cortex that produces glucocorticoid, mineralocorticoid, and androgenic hormones and an ectodermal medulla that produces epinephrine and norepinephrine[BTO]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002371 name: bone marrow def: "The soft tissue that fills the cavities of bones." [] is_a: UBERON:0000479 ! tissue [Term] id: UBERON:0002386 name: forelimb zeugopod def: "The middle limb segment of the pectoral free limb, between the autopod and stylopod segments. Includes as parts the forelimb zeugopodial skeleton, which includes as parts the radius and ulna, or their cartilage precursors, or evolutionary variants." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002389 name: manual digit def: "A digit that is part of a manus (hand)." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002391 name: lymph def: "Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]." [] is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0002409 name: pericardial fluid def: "Transudate contained in the pericardial cavity.[FMA]." [] is_a: UBERON:0006314 ! bodily fluid [Term] id: UBERON:0002415 name: tail def: "An external caudal extension of the body. In chordates, the tail is post-anal, in other animals the anus ends in the tail." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002465 name: lymphoid system def: "The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002469 name: esophagus mucosa def: "A mucosa that is part of a esophagus [Automatically generated definition]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002812 name: left cerebral hemisphere def: "A cerebral hemisphere that is in the left side of a brain." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0002813 name: right cerebral hemisphere def: "A cerebral hemisphere that is in the right side of a brain." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0003126 name: trachea def: "The trachea is the portion of the airway that attaches to the bronchi as it branches [GO:dph]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0003128 name: cranium def: "Upper portion of the skull that excludes the mandible (when present in the organism)." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0003688 name: omentum def: "A fold of peritoneum originating at the stomach and supporting the viscera." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0004648 name: esophagus muscularis mucosa def: "A muscularis mucosa that is part of a esophagus." [] is_a: UBERON:0000479 ! tissue [Term] id: UBERON:0005022 name: mucosa of nasopharynx def: "A mucosa that is part of a nasopharynx [Automatically generated definition]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0005023 name: mucosa of oropharynx def: "A mucosa that is part of a oropharynx [Automatically generated definition]." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0005921 name: middle nasal concha def: "The medial surface of the labyrinth of ethmoid consists of a thin lamella, which descends from the under surface of the cribriform plate, and ends below in a free, convoluted margin, the middle nasal concha. It is rough, and marked above by numerous grooves, directed nearly vertically downward from the cribriform plate; they lodge branches of the olfactory nerves, which are distributed to the mucous membrane covering the superior nasal concha." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0006314 name: bodily fluid def: "Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not." [] is_a: UBERON:0000463 ! organism substance [Term] id: UBERON:0006538 name: respiratory system fluid/secretion def: "A portion of organism substance that secreted_by a respiratory system." [] is_a: UBERON:0000463 ! organism substance [Term] id: UBERON:0006618 name: atrium auricular region def: "A small conical pouch projections located on the upper anterior portion of each atrium of the heart." [] is_a: UBERON:0000481 ! multi-tissue structure [Term] id: UBERON:0006911 name: digestive system secreted substance is_a: UBERON:0000463 ! organism substance [Term] id: UBERON:0007106 name: chorionic villus def: "One of the minute vascular projections of the fetal chorion that combines with maternal uterine tissue to form the placenta." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0007109 name: meconium def: "A dark greenish mass that accumulates in the bowel during fetal life and is discharged shortly after birth." [] is_a: UBERON:0001988 ! feces [Term] id: UBERON:0007311 name: sputum def: "Matter ejected from the lungs, bronchi, and trachea, through the mouth." [] is_a: UBERON:0006538 ! respiratory system fluid/secretion [Term] id: UBERON:0007610 name: tibial artery def: "The anterior and posterior arteries created at the bifurcation of the popliteal artery. The anterior tibial artery begins at the lower border of the popliteus muscle and lies along the tibia at the distal part of the leg to surface superficially anterior to the ankle joint. Its branches are distributed throughout the leg, ankle, and pes. The posterior tibial artery begins at the lower border of the popliteus muscle, lies behind the tibia in the lower part of its course, and is found situated between the medial malleolus and the medial process of the calcaneal tuberosity. Its branches are distributed throughout the leg and foot." [] is_a: UBERON:0001637 ! artery [Term] id: UBERON:0007650 name: esophagogastric junction def: "The junction between the esophagus and the stomach epithelium." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0008188 name: tendon of biceps brachii def: "A tendon that attaches_to a biceps brachii." [] is_a: UBERON:0000479 ! tissue [Term] id: UBERON:0010414 name: omental fat pad def: "Encapsulated adipose tissue associated with the fold of peritoneal tissue that extends from the stomach to the posterior abdominal wall after associating with the transverse colon." [] is_a: UBERON:0001013 ! adipose tissue [Term] id: UBERON:0011011 name: brachioradialis def: "Brachioradialis is a muscle of the forearm that acts to flex the forearm at the elbow. It is also capable of both pronation and supination, depending on the position of the forearm. It is attached to the distal styloid process of the radius by way of the brachioradialis tendon, and to the lateral supracondylar ridge of the humerus." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:0012168 name: umbilical cord blood def: "Blood that remains in the placenta and in the attached umbilical cord after childbirth[WP]." [] is_a: UBERON:0013755 ! arterial blood [Term] id: UBERON:0013755 name: arterial blood def: "A blood that is part of a artery." [] is_a: UBERON:0000178 ! blood [Term] id: UBERON:0013756 name: venous blood def: "A blood that is part of a vein." [] is_a: UBERON:0000178 ! blood [Term] id: UBERON:0013757 name: capillary blood def: "A blood that is part of a capillary." [] is_a: UBERON:0000178 ! blood [Term] id: UBERON:0036149 name: suprapubic skin def: "Area of skin in the hypoastric region of the abdomen." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:3000016 name: anterior nasal wall def: "Paired, vertical, and relatively straight plates that form the anterior limit of the nasal capsule." [] is_a: UBERON:0000465 ! material anatomical entity [Term] id: UBERON:8470000 name: placental blood def: "Blood located in the placenta." [] is_a: UBERON:0000178 ! blood [Term] id: UO:0000001 name: length unit def: "A unit which is a standard measure of the distance between two points." [] is_a: IAO:0000003 ! measurement unit label [Term] id: UO:0000002 name: mass unit def: "A unit which is a standard measure of the amount of matter/energy of a physical object." [] is_a: IAO:0000003 ! measurement unit label [Term] id: UO:0000003 name: time unit def: "A unit which is a standard measure of the dimension in which events occur in sequence." [] is_a: IAO:0000003 ! measurement unit label [Term] id: UO:0000005 name: temperature unit is_a: IAO:0000003 ! measurement unit label [Term] id: UO:0000006 name: substance unit is_a: IAO:0000003 ! measurement unit label [Term] id: UO:0000051 name: concentration unit is_a: IAO:0000003 ! measurement unit label [Term] id: UO:0000095 name: volume unit is_a: IAO:0000003 ! measurement unit label [Term] id: UO:0000105 name: frequency unit is_a: IAO:0000003 ! measurement unit label [Term] id: UO:0000109 name: pressure unit is_a: IAO:0000003 ! measurement unit label [Term] id: UO:0000270 name: volumetric flow rate unit is_a: IAO:0000003 ! measurement unit label [Term] id: UO:0000280 name: rate unit is_a: IAO:0000003 ! measurement unit label [Term] id: VO:0000001 name: vaccine def: "A vaccine is a processed material with the function that when administered, it prevents or ameliorates a disorder in a target organism by inducing or modifying adaptive immune responses specific to the antigens in the vaccine." [] is_a: BFO:0000040 ! material entity [Term] id: VO:0000002 name: vaccination def: "a process of administering substance in vivo that involves in adding a vaccine into a host (e.g., human) in vivo with the intent to invoke a protective or therapeutic adaptive immune response." [] is_a: OBI:0600007 ! administering substance in vivo [Typedef] id: BFO:0000050 name: part of def: "a core relation that holds between a part and its whole" [] synonym: "part_of" EXACT [] is_transitive: true inverse_of: BFO:0000051 ! has part [Typedef] id: BFO:0000051 name: has part def: "a core relation that holds between a whole and its part" [] synonym: "has_part" EXACT [] is_transitive: true [Typedef] id: BFO:0000054 name: realized in comment: Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process synonym: "is realized by" EXACT [] synonym: "realized_in" EXACT [] domain: BFO:0000017 ! realizable entity range: BFO:0000015 ! process inverse_of: BFO:0000055 ! realizes [Typedef] id: BFO:0000055 name: realizes comment: Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process domain: BFO:0000015 ! process range: BFO:0000017 ! realizable entity [Typedef] id: BFO:0000062 name: preceded by synonym: "is preceded by" EXACT [] synonym: "preceded_by" EXACT [] domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_transitive: true inverse_of: BFO:0000063 ! precedes [Typedef] id: BFO:0000063 name: precedes domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_transitive: true is_a: RO:0002222 ! temporal relation [Typedef] id: BFO:0000066 name: occurs in def: "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" [] comment: Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant synonym: "occurs_in" EXACT [] synonym: "unfolds in" EXACT [] synonym: "unfolds_in" EXACT [] domain: BFO:0000003 ! occurrent range: BFO:0000004 ! independent continuant holds_over_chain: BFO:0000050 BFO:0000066 inverse_of: BFO:0000067 ! contains process transitive_over: BFO:0000050 ! part of [Typedef] id: BFO:0000067 name: contains process def: "[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" [] comment: Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant [Typedef] id: IAO:0000039 name: has measurement unit label range: IAO:0000003 ! measurement unit label is_functional: true is_a: BFO:0000051 ! has part [Typedef] id: IAO:0000135 name: obsolete_specifically denotes def: "c specifically denotes r =def \nr is a portion of reality\n& c is a particular quality\n& c depends specifically on some independent continuant b \n& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly. \n\nMarked means there is a changed or additional quality of the bearer - the quality is the information carrier.\n\nCase 1\nMemory trace as mark created when reading some description of some friend. The trace can denote.\n\nCase 2\nPattern of ink arrayed on paper as mark when writing down a friend's name\n\nCase 3\nPattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file." [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: IAO:0000136 name: is about def: "A (currently) primitive relation that relates an information artifact to an entity." [] domain: IAO:0000030 ! information content entity [Typedef] id: IAO:0000142 name: mentions def: "An information artifact IA mentions an entity E exactly when it has a component/part that denotes E" [] is_a: IAO:0000136 ! is about [Typedef] id: IAO:0000219 name: denotes def: "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" [] domain: IAO:0000030 ! information content entity range: BFO:0000001 ! entity is_a: IAO:0000136 ! is about inverse_of: IAO:0000235 ! denoted by [Typedef] id: IAO:0000220 name: obsolete_materially denotes is_a: ObsoleteProperty is_obsolete: true [Typedef] id: IAO:0000221 name: is quality measurement of def: "m is a quality measurement of q at t. When q is a quality, there is a measurement process p that has specified output m, a measurement datum, that is about q" [] domain: IAO:0000109 ! measurement datum range: BFO:0000019 ! quality is_a: IAO:0000136 ! is about inverse_of: IAO:0000417 ! is quality measured as [Typedef] id: IAO:0000222 name: obsolete_describes is_a: ObsoleteProperty is_obsolete: true [Typedef] id: IAO:0000223 name: obsolete_represents is_a: ObsoleteProperty is_obsolete: true [Typedef] id: IAO:0000235 name: denoted by def: "inverse of the relation 'denotes'" [] domain: BFO:0000001 ! entity range: IAO:0000030 ! information content entity [Typedef] id: IAO:0000407 name: has coordinate unit label comment: relating a cartesian spatial coordinate datum to a unit label that together with the values represent a point domain: IAO:0000400 ! cartesian spatial coordinate datum range: UO:0000001 ! length unit is_functional: true is_a: BFO:0000051 ! has part [Typedef] id: IAO:0000413 name: is duration of def: "relates a process to a time-measurement-datum that represents the duration of the process" [] domain: IAO:0000416 ! time measurement datum range: BFO:0000015 ! process is_a: IAO:0000136 ! is about [Typedef] id: IAO:0000417 name: is quality measured as def: "inverse of the relation of is quality measurement of" [] [Typedef] id: IAO:0000418 name: is quality specification of def: "A relation between a data item and a quality of a material entity where the material entity is the specified output of a material transformation which achieves an objective specification that indicates the intended value of the specified quality." [] is_a: IAO:0000136 ! is about inverse_of: IAO:0000419 ! quality is specified as [Typedef] id: IAO:0000419 name: quality is specified as def: "inverse of the relation of is quality specification of" [] [Typedef] id: IAO:0000581 name: has time stamp def: "relates a time stamped measurement datum to the time measurement datum that denotes the time when the measurement was taken" [] domain: IAO:0000582 ! time stamped measurement datum range: IAO:0000416 ! time measurement datum is_functional: true is_a: BFO:0000051 ! has part [Typedef] id: IAO:0000583 name: has measurement datum def: "relates a time stamped measurement datum to the measurement datum that was measured" [] domain: IAO:0000582 ! time stamped measurement datum is_a: BFO:0000051 ! has part [Typedef] id: OBI:0000107 name: provides_service_consumer_with def: "A relation between a service and the primary processual part of the service that is performed by the provider for the consumer." [] domain: OBI:0001173 ! service is_a: BFO:0000051 ! has part [Typedef] id: OBI:0000124 name: is_supported_by_data def: "The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process" [] domain: OBI:0001909 ! conclusion based on data range: IAO:0000027 ! data item [Typedef] id: OBI:0000293 name: has_specified_input def: "The inverse property of is_specified_input_of" [] domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant inverse_of: OBI:0000295 ! is_specified_input_of [Typedef] id: OBI:0000294 name: obsolete_is_concretization_of def: "Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter." [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000295 name: is_specified_input_of def: "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." [] range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000297 name: obsolete_is_concretized_as def: "Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter." [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000298 name: obsolete_has_quality def: "A relation between an entity and a quality. For types: E has_quality Q iff: \nfor any eEt, exists qQt such that q inheres_in e at t. \nFor instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality [GOC:cjm]" [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000299 name: has_specified_output def: "The inverse property of is_specified_output_of" [] domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant inverse_of: OBI:0000312 ! is_specified_output_of [Typedef] id: OBI:0000300 name: obsolete_is_realized_by def: "Relation between a realizable and a process. Reciprocal relation of realizes [GOC:cjm]" [] synonym: "executed_during" EXACT [] synonym: "has_realization" EXACT [] synonym: "is_realized_as" EXACT [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000301 name: obsoleted_has_specified_output_information def: "A relation between a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data." [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000304 name: is_manufactured_by def: "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." [] synonym: "has_make" EXACT [] synonym: "has_manufacturer" EXACT [] domain: BFO:0000040 ! material entity range: OBI:0000835 ! manufacturer [Typedef] id: OBI:0000306 name: obsolete_has_function def: "Relation between an independent continuant and a function." [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000307 name: obsoleted_is_reagent_in def: "Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole" [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000308 name: obsolete_realizes def: "Relation between a process and a function, where the unfolding of the \nprocess requires the execution of the function. Class level: P realizes F iff: \ngiven any p that instantiates P, there exists some f, t such that f instantiates\n F at t and p *realizes* f. Here, *realizes* is the primitive \ninstance level relation [GOC:cjm]" [] synonym: "executes" EXACT [] synonym: "has_function_part" EXACT [] synonym: "involves_execution_of" EXACT [] synonym: "is_realization_of" EXACT [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000309 name: obsoleted_utilizes_reagent def: "Relationship between a protocol application and a substance that has role reagent that participates in the protocol application" [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000311 name: obsoleted_is_device_for def: "Relationship between a device and a protocol application in which it participates" [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000312 name: is_specified_output_of def: "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." [] range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000313 name: obsoleted_utilizes_device def: "Relationship between protocol application and an intrument in which it participates" [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000314 name: is_proxy_for def: "A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be." [] domain: BFO:0000002 ! continuant range: BFO:0000002 ! continuant [Typedef] id: OBI:0000315 name: obsoleted_has_specified_input_information def: "A relation between a process and a participant in that process, that consumes a data set . The process is the realization of a concretization of a directive information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data." [] synonym: "consumes data" EXACT [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000316 name: obsolete_has_role def: "A relation between a continuant C and a role R. The reciprocal relation of role_of." [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000365 name: obsolete_results_from is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000417 name: achieves_planned_objective def: "This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process." [] domain: OBI:0000011 ! planned process range: IAO:0000005 ! objective specification inverse_of: OBI:0000833 ! objective_achieved_by [Typedef] id: OBI:0000459 name: obsoleted_is_specified_information_output_of def: "A relation between a data set and the process in which it participates and was produced. Inverse of outputs_specified_data relation." [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000643 name: has grain def: "the relation of the cells in the finger of the skin to the finger, in which an indeterminate number of grains are parts of the whole by virtue of being grains in a collective that is part of the whole, and in which removing one granular part does not nec- essarily damage or diminish the whole. Ontological Whether there is a fixed, or nearly fixed number of parts - e.g. fingers of the hand, chambers of the heart, or wheels of a car - such that there can be a notion of a single one being missing, or whether, by contrast, the number of parts is indeterminate - e.g., cells in the skin of the hand, red cells in blood, or rubber molecules in the tread of the tire of the wheel of the car." [] is_a: BFO:0000051 ! has part [Typedef] id: OBI:0000644 name: obsoleted_is_specified_information_intput_of def: "Is the inverse relation of has_specfied_input_information" [] is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:0000645 name: is grain of def: "A relation between granular parts and the whole of which they are a part. Granular parts have indeterminate number such that removing one granular part does not necessarily damage or diminish the whole." [] is_a: BFO:0000050 ! part of [Typedef] id: OBI:0000646 name: provisions def: "A relation between an organisation or person and a material entity, where the organization or person provides or supplies the material entity for others to use" [] synonym: "supplies" EXACT [] inverse_of: OBI:0000647 ! has_supplier [Typedef] id: OBI:0000647 name: has_supplier def: "A relation between a material entity and an organisation or person who owned or has license to the material entity and there was a legal transfer of ownership or licensing of the material entity to the current owner." [] domain: BFO:0000040 ! material entity [Typedef] id: OBI:0000833 name: objective_achieved_by def: "This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." [] domain: IAO:0000005 ! objective specification range: OBI:0000011 ! planned process [Typedef] id: OBI:0000846 name: is member of organization def: "Relating a legal person or organization to an organization in the case where the legal person or organization has a role as member of the organization." [] range: OBI:0000245 ! organization inverse_of: OBI:0001688 ! has organization member [Typedef] id: OBI:0000999 name: has category label def: "A relation between a categorical measurement data item and the categorical label that indicates the value of that data item on the categorical scale." [] domain: OBI:0000938 ! categorical measurement datum range: OBI:0000963 ! categorical label is_a: BFO:0000051 ! has part [Typedef] id: OBI:0001637 name: has disposition to bind def: "A relationship between two material entitites that each have disposition to form a complex with the other." [] domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity is_symmetric: true [Typedef] id: OBI:0001688 name: has organization member def: "Relating an organization to a legal person or organization." [] domain: OBI:0000245 ! organization [Typedef] id: OBI:0001927 name: specifies value of def: "A relation between a value specification and an entity which the specification is about." [] domain: OBI:0001933 ! value specification is_a: IAO:0000136 ! is about [Typedef] id: OBI:0001938 name: has value specification def: "A relation between an information content entity and a value specification that specifies its value." [] domain: IAO:0000030 ! information content entity range: OBI:0001933 ! value specification is_a: BFO:0000051 ! has part [Typedef] id: OBI:0001950 name: has performer def: "A relation between a planned process and a continuant where the continuant can be a person, organization or device (such as a robot controlled by software workflow management system) that performs the planned process." [] comment: The 'has performer' relation covers the need to report on who performed a planned processed. It has to cover processes done by People or Devices (such as a robot controlled by software WF management system). domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant [Typedef] id: OBI:0003385 name: has assay target context def: "A relation between the target entity of an assay and a material entity, where the material entity is the environment in which the target entity of an assay is measured, such as a live mouse, cell culture, test tube, etc." [] range: BFO:0000040 ! material entity [Typedef] id: OBI:1110060 name: process is result of def: "is a relationship between a process and a preceding occurrent that directly caused the later one to occur" [] domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_a: RO:0002087 ! immediately preceded by [Typedef] id: OBI:1110112 name: obsolete_is_described_by is_a: ObsoleteProperty is_obsolete: true [Typedef] id: OBI:1110119 name: bound_to def: "A relationship between two material entities that form a complex based on a selective, non-covalent interaction." [] domain: BFO:0000040 ! material entity range: BFO:0000040 ! material entity [Typedef] id: RO:0000052 name: inheres in def: "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" [] synonym: "inheres_in" EXACT [] inverse_of: RO:0000053 ! bearer of [Typedef] id: RO:0000053 name: bearer of def: "a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence" [] synonym: "bearer_of" EXACT [] synonym: "is bearer of" EXACT [] range: BFO:0000020 ! specifically dependent continuant [Typedef] id: RO:0000056 name: participates in def: "a relation between a continuant and a process, in which the continuant is somehow involved in the process" [] synonym: "participates_in" EXACT [] domain: BFO:0000002 ! continuant range: BFO:0000003 ! occurrent inverse_of: RO:0000057 ! has participant [Typedef] id: RO:0000057 name: has participant def: "a relation between a process and a continuant, in which the continuant is somehow involved in the process" [] synonym: "has_participant" EXACT [] domain: BFO:0000003 ! occurrent range: BFO:0000002 ! continuant [Typedef] id: RO:0000058 name: is concretized as def: "A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants." [] domain: BFO:0000031 ! generically dependent continuant range: BFO:0000020 ! specifically dependent continuant inverse_of: RO:0000059 ! concretizes [Typedef] id: RO:0000059 name: concretizes def: "A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant." [] domain: BFO:0000020 ! specifically dependent continuant range: BFO:0000031 ! generically dependent continuant [Typedef] id: RO:0000079 name: function of def: "a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence" [] synonym: "function_of" EXACT [] synonym: "is function of" EXACT [] domain: BFO:0000034 ! function is_a: RO:0000052 ! inheres in inverse_of: RO:0000085 ! has function [Typedef] id: RO:0000080 name: quality of def: "a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence" [] synonym: "is quality of" EXACT [] synonym: "quality_of" EXACT [] is_a: RO:0000052 ! inheres in inverse_of: RO:0000086 ! has quality [Typedef] id: RO:0000081 name: role of def: "a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence" [] synonym: "is role of" EXACT [] synonym: "role_of" EXACT [] is_a: RO:0000052 ! inheres in inverse_of: RO:0000087 ! has role [Typedef] id: RO:0000085 name: has function def: "a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence" [] synonym: "has_function" EXACT [] domain: BFO:0000004 ! independent continuant range: BFO:0000034 ! function is_a: RO:0000053 ! bearer of [Typedef] id: RO:0000086 name: has quality def: "a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence" [] synonym: "has_quality" EXACT [] range: BFO:0000019 ! quality is_a: RO:0000053 ! bearer of [Typedef] id: RO:0000087 name: has role def: "a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence" [] synonym: "has_role" EXACT [] domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: RO:0000053 ! bearer of [Typedef] id: RO:0000091 name: has disposition def: "a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence" [] domain: BFO:0000004 ! independent continuant range: BFO:0000016 ! disposition is_a: RO:0000053 ! bearer of inverse_of: RO:0000092 ! disposition of [Typedef] id: RO:0000092 name: disposition of is_a: RO:0000052 ! inheres in [Typedef] id: RO:0001000 name: derives from def: "a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] synonym: "derives_from" EXACT [] domain: BFO:0000004 ! independent continuant range: BFO:0000004 ! independent continuant inverse_of: RO:0001001 ! derives into [Typedef] id: RO:0001001 name: derives into def: "a relation between two distinct material entities, the old entity and the new entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity" [] synonym: "derives_into" EXACT [] [Typedef] id: RO:0001015 name: location of def: "a relation between two independent continuants, the location and the target, in which the target is entirely within the location" [] synonym: "location_of" EXACT [] is_transitive: true inverse_of: RO:0001025 ! located in [Typedef] id: RO:0001025 name: located in def: "a relation between two independent continuants, the target and the location, in which the target is entirely within the location" [] synonym: "located_in" EXACT [] is_transitive: true [Typedef] id: RO:0002000 name: 2D boundary of def: "a relation between a 2D immaterial entity (the boundary) and a material entity, in which the boundary delimits the material entity" [] synonym: "2D_boundary_of" EXACT [] synonym: "boundary of" EXACT [] synonym: "is 2D boundary of" EXACT [] synonym: "is boundary of" EXACT [] inverse_of: RO:0002002 ! has 2D boundary [Typedef] id: RO:0002002 name: has 2D boundary def: "a relation between a material entity and a 2D immaterial entity (the boundary), in which the boundary delimits the material entity" [] synonym: "has boundary" EXACT [] synonym: "has_2D_boundary" EXACT [] domain: BFO:0000040 ! material entity range: BFO:0000141 ! immaterial entity [Typedef] id: RO:0002087 name: immediately preceded by comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) synonym: "starts_at_end_of" EXACT [] is_a: BFO:0000062 ! preceded by inverse_of: RO:0002090 ! immediately precedes [Typedef] id: RO:0002090 name: immediately precedes comment: X immediately_precedes_Y iff: end(X) simultaneous_with start(Y) synonym: "ends_at_start_of" EXACT [] synonym: "meets" EXACT [] is_a: BFO:0000063 ! precedes [Typedef] id: RO:0002180 name: has component def: "w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type." [] is_a: BFO:0000051 ! has part [Typedef] id: RO:0002215 name: capable of def: "A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process." [] synonym: "has function realized in" EXACT [] domain: BFO:0000004 ! independent continuant range: BFO:0000015 ! process [Typedef] id: RO:0002219 name: surrounded by def: "x surrounded_by y if and only if x is adjacent to y and for every region r that is adjacent to x, r overlaps y" [] is_a: RO:0002220 ! adjacent to [Typedef] id: RO:0002220 name: adjacent to [Typedef] id: RO:0002222 name: temporal relation comment: A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations. range: BFO:0000003 ! occurrent [Typedef] id: RO:0002223 name: starts def: "inverse of starts with" [] is_a: BFO:0000050 ! part of is_a: RO:0002222 ! temporal relation [Typedef] id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] synonym: "is member of" EXACT [] synonym: "member part of" EXACT [] is_a: BFO:0000050 ! part of inverse_of: RO:0002351 ! has member [Typedef] id: RO:0002351 name: has member def: "has member is a mereological relation between a collection and an item." [] is_a: BFO:0000051 ! has part