format-version: 1.2 data-version: releases/2018-08-21 date: 08:21:2018 11:52 saved-by: rctauber subsetdef: go_groupings "Grouping classes used by GO" subsetdef: valid_with_biological_process "GO biological process terms should be used in the GO with/from field" subsetdef: valid_with_cellular_component "GO cellular component terms should be used in the GO with/from field" subsetdef: valid_with_chemical_entity "Chemical entity IDs should be used in the GO with/from field" subsetdef: valid_with_gene "Gene IDs should be used in the GO with/from field" subsetdef: valid_with_molecular_function "GO molecular function terms should be used in the GO with/from field" subsetdef: valid_with_protein "Protein IDs should be used in the GO with/from field" subsetdef: valid_with_protein_complex "Protein complex IDs should be used in the GO with/from field" subsetdef: valid_with_transcript "Transcript IDs should be used in the GO with/from field" default-namespace: eco remark: ECO (https://github.com/evidenceontology/evidenceontology) is released into the public domain under CC0 1.0 Universal (CC0 1.0). Anyone is free to copy, modify, or distribute the work, even for commercial purposes, without asking permission. Please see the Public Domain Dedication (https://creativecommons.org/publicdomain/zero/1.0/) for an easy-to-read description of CC0 1.0 or the full legal code (https://creativecommons.org/publicdomain/zero/1.0/legalcode) for more detailed information. To get a sense of why ECO is CC0 as opposed to licensed under CC-BY, please read this thoughtful discussion (https://github.com/OBOFoundry/OBOFoundry.github.io/issues/285) on the OBO Foundry GitHub site. ontology: eco property_value: http://purl.org/dc/elements/1.1/description "The Evidence & Conclusion Ontology (ECO) describes types of scientific evidence within the biological research domain that arise from laboratory experiments, computational methods, literature curation, or other means." xsd:string property_value: http://purl.org/dc/elements/1.1/title "Evidence & Conclusion Ontology (ECO)" xsd:string property_value: http://purl.org/dc/terms/license https://creativecommons.org/publicdomain/zero/1.0/ [Term] id: BFO:0000001 name: entity property_value: BFO:0000179 "entity" xsd:string property_value: BFO:0000180 "Entity" xsd:string property_value: IAO:0000112 "Julius Caesar" xsd:string property_value: IAO:0000112 "the Second World War" xsd:string property_value: IAO:0000112 "Verdi’s Requiem" xsd:string property_value: IAO:0000112 "your body mass index" xsd:string property_value: IAO:0000116 "BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81" xsd:string property_value: IAO:0000116 "Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000004", comment="per discussion with Barry Smith", http://www.w3.org/2000/01/rdf-schema#seeAlso="http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf"} property_value: IAO:0000600 "An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/001-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [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 property_value: BFO:0000179 "continuant" xsd:string property_value: BFO:0000180 "Continuant" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240" xsd:string property_value: IAO:0000116 "Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000007"} property_value: IAO:0000600 "A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} property_value: IAO:0000601 "if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} property_value: IAO:0000601 "if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} property_value: IAO:0000601 "if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/009-002"} property_value: IAO:0000602 "(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/126-001"} property_value: IAO:0000602 "(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/008-002"} property_value: IAO:0000602 "(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/011-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [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 property_value: BFO:0000179 "occurrent" xsd:string property_value: BFO:0000180 "Occurrent" xsd:string property_value: IAO:0000116 "BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region" xsd:string property_value: IAO:0000116 "BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players." xsd:string property_value: IAO:0000116 "Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000006", comment="per discussion with Barry Smith"} property_value: IAO:0000116 "Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000012"} property_value: IAO:0000600 "An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/077-002"} property_value: IAO:0000601 "b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: IAO:0000601 "Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} property_value: IAO:0000602 "(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/108-001"} property_value: IAO:0000602 "(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/079-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000004 name: independent continuant def: "A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything." [] def: "b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000020 {http://www.w3.org/1999/02/22-rdf-syntax-ns#type="owl:AllDisjointClasses"} ! specifically dependent continuant disjoint_from: BFO:0000020 ! specifically dependent continuant disjoint_from: BFO:0000031 ! generically dependent continuant property_value: BFO:0000179 "ic" xsd:string property_value: BFO:0000180 "IndependentContinuant" xsd:string property_value: IAO:0000112 "a chair" xsd:string property_value: IAO:0000112 "a heart" xsd:string property_value: IAO:0000112 "a leg" xsd:string property_value: IAO:0000112 "a molecule" xsd:string property_value: IAO:0000112 "a spatial region" xsd:string property_value: IAO:0000112 "an atom" xsd:string property_value: IAO:0000112 "an orchestra." xsd:string property_value: IAO:0000112 "an organism" xsd:string property_value: IAO:0000112 "the bottom right portion of a human torso" xsd:string property_value: IAO:0000112 "the interior of your mouth" xsd:string property_value: IAO:0000601 "For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} property_value: IAO:0000601 "For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} property_value: IAO:0000602 "(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/018-002"} property_value: IAO:0000602 "(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/134-001"} property_value: IAO:0000602 "(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/017-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000015 name: process def: "An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t." [] def: "p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} is_a: BFO:0000003 ! occurrent property_value: BFO:0000179 "process" xsd:string property_value: BFO:0000180 "Process" xsd:string property_value: IAO:0000112 "a process of cell-division, \\ a beating of the heart" xsd:string property_value: IAO:0000112 "a process of meiosis" xsd:string property_value: IAO:0000112 "a process of sleeping" xsd:string property_value: IAO:0000112 "the course of a disease" xsd:string property_value: IAO:0000112 "the flight of a bird" xsd:string property_value: IAO:0000112 "the life of an organism" xsd:string property_value: IAO:0000112 "your process of aging." xsd:string property_value: IAO:0000116 "BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)" xsd:string property_value: IAO:0000602 "(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/083-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000016 name: disposition is_a: BFO:0000017 ! realizable entity disjoint_from: BFO:0000023 ! role property_value: BFO:0000179 "disposition" xsd:string property_value: BFO:0000180 "Disposition" xsd:string property_value: IAO:0000112 "an atom of element X has the disposition to decay to an atom of element Y" xsd:string property_value: IAO:0000112 "certain people have a predisposition to colon cancer" xsd:string property_value: IAO:0000112 "children are innately disposed to categorize objects in certain ways." xsd:string property_value: IAO:0000112 "the cell wall is disposed to filter chemicals in endocytosis and exocytosis" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type." xsd:string property_value: IAO:0000600 "b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} property_value: IAO:0000601 "If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} property_value: IAO:0000602 "(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/063-002"} property_value: IAO:0000602 "(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/062-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [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 property_value: BFO:0000179 "realizable" xsd:string property_value: BFO:0000180 "RealizableEntity" xsd:string property_value: IAO:0000112 "the disposition of this piece of metal to conduct electricity." xsd:string property_value: IAO:0000112 "the disposition of your blood to coagulate" xsd:string property_value: IAO:0000112 "the function of your reproductive organs" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the role of this boundary to delineate where Utah and Colorado meet" xsd:string property_value: IAO:0000600 "To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: IAO:0000601 "All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/060-002"} property_value: IAO:0000602 "(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/058-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000019 name: quality is_a: BFO:0000020 ! specifically dependent continuant property_value: BFO:0000179 "quality" xsd:string property_value: BFO:0000180 "Quality" xsd:string property_value: IAO:0000112 "the ambient temperature of this portion of air" xsd:string property_value: IAO:0000112 "the color of a tomato" xsd:string property_value: IAO:0000112 "the length of the circumference of your waist" xsd:string property_value: IAO:0000112 "the mass of this piece of gold." xsd:string property_value: IAO:0000112 "the shape of your nose" xsd:string property_value: IAO:0000112 "the shape of your nostril" xsd:string property_value: IAO:0000600 "a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} property_value: IAO:0000601 "If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} property_value: IAO:0000602 "(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/105-001"} property_value: IAO:0000602 "(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/055-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000020 name: specifically dependent continuant def: "A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same." [] def: "b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} def: "b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} is_a: BFO:0000002 ! continuant disjoint_from: BFO:0000031 ! generically dependent continuant property_value: BFO:0000179 "sdc" xsd:string property_value: BFO:0000180 "SpecificallyDependentContinuant" xsd:string property_value: IAO:0000112 "of one-sided specifically dependent continuants: the mass of this tomato" xsd:string property_value: IAO:0000112 "of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates." xsd:string property_value: IAO:0000112 "Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key" xsd:string property_value: IAO:0000112 "the disposition of this fish to decay" xsd:string property_value: IAO:0000112 "the function of this heart: to pump blood" xsd:string property_value: IAO:0000112 "the mutual dependence of proton donors and acceptors in chemical reactions [79" xsd:string property_value: IAO:0000112 "the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction" xsd:string property_value: IAO:0000112 "the pink color of a medium rare piece of grilled filet mignon at its center" xsd:string property_value: IAO:0000112 "the role of being a doctor" xsd:string property_value: IAO:0000112 "the shape of this hole." xsd:string property_value: IAO:0000112 "the smell of this portion of mozzarella" xsd:string property_value: IAO:0000116 "Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc." xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/0000005", comment="per discussion with Barry Smith"} property_value: IAO:0000602 "(iff (RelationalSpecificallyDependentContinuant a) (and (SpecificallyDependentContinuant a) (forall (t) (exists (b c) (and (not (SpatialRegion b)) (not (SpatialRegion c)) (not (= b c)) (not (exists (d) (and (continuantPartOfAt d b t) (continuantPartOfAt d c t)))) (specificallyDependsOnAt a b t) (specificallyDependsOnAt a c t)))))) // axiom label in BFO2 CLIF: [131-004] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/131-004"} property_value: IAO:0000602 "(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/050-003"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [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 property_value: BFO:0000179 "role" xsd:string property_value: BFO:0000180 "Role" xsd:string property_value: IAO:0000112 "John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married." xsd:string property_value: IAO:0000112 "the priest role" xsd:string property_value: IAO:0000112 "the role of a boundary to demarcate two neighboring administrative territories" xsd:string property_value: IAO:0000112 "the role of a building in serving as a military target" xsd:string property_value: IAO:0000112 "the role of a stone in marking a property boundary" xsd:string property_value: IAO:0000112 "the role of subject in a clinical trial" xsd:string property_value: IAO:0000112 "the student role" xsd:string property_value: IAO:0000116 "BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives." xsd:string property_value: IAO:0000600 "b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: IAO:0000602 "(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/061-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000029 name: site is_a: BFO:0000141 ! immaterial entity property_value: BFO:0000179 "site" xsd:string property_value: BFO:0000180 "Site" xsd:string property_value: IAO:0000112 "a hole in the interior of a portion of cheese" xsd:string property_value: IAO:0000112 "a rabbit hole" xsd:string property_value: IAO:0000112 "an air traffic control region defined in the airspace above an airport" xsd:string property_value: IAO:0000112 "Manhattan Canyon)" xsd:string property_value: IAO:0000112 "the cockpit of an aircraft" xsd:string property_value: IAO:0000112 "the Grand Canyon" xsd:string property_value: IAO:0000112 "the hold of a ship" xsd:string property_value: IAO:0000112 "the interior of a kangaroo pouch" xsd:string property_value: IAO:0000112 "the interior of the trunk of your car" xsd:string property_value: IAO:0000112 "the interior of your bedroom" xsd:string property_value: IAO:0000112 "the interior of your office" xsd:string property_value: IAO:0000112 "the interior of your refrigerator" xsd:string property_value: IAO:0000112 "the lumen of your gut" xsd:string property_value: IAO:0000112 "the Piazza San Marco" xsd:string property_value: IAO:0000112 "your left nostril (a fiat part – the opening – of your left nasal cavity)" xsd:string property_value: IAO:0000600 "b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} property_value: IAO:0000602 "(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/034-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000031 name: generically dependent continuant def: "A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time." [] def: "b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001])" [] {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} is_a: BFO:0000002 ! continuant property_value: BFO:0000179 "gdc" xsd:string property_value: BFO:0000180 "GenericallyDependentContinuant" xsd:string property_value: IAO:0000112 "The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity." xsd:string property_value: IAO:0000112 "the pdf file on your laptop, the pdf file that is a copy thereof on my laptop" xsd:string property_value: IAO:0000112 "the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule." xsd:string property_value: IAO:0000602 "(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/074-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000034 name: function is_a: BFO:0000016 ! disposition property_value: BFO:0000179 "function" xsd:string property_value: BFO:0000180 "Function" xsd:string property_value: IAO:0000112 "the function of a hammer to drive in nails" xsd:string property_value: IAO:0000112 "the function of a heart pacemaker to regulate the beating of a heart through electricity" xsd:string property_value: IAO:0000112 "the function of amylase in saliva to break down starch into sugar" xsd:string property_value: IAO:0000116 "BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc." xsd:string property_value: IAO:0000600 "A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} property_value: IAO:0000602 "(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/064-001"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [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 property_value: BFO:0000179 "material" xsd:string property_value: BFO:0000180 "MaterialEntity" xsd:string property_value: IAO:0000112 "a flame" xsd:string property_value: IAO:0000112 "a forest fire" xsd:string property_value: IAO:0000112 "a human being" xsd:string property_value: IAO:0000112 "a hurricane" xsd:string property_value: IAO:0000112 "a photon" xsd:string property_value: IAO:0000112 "a puff of smoke" xsd:string property_value: IAO:0000112 "a sea wave" xsd:string property_value: IAO:0000112 "a tornado" xsd:string property_value: IAO:0000112 "an aggregate of human beings." xsd:string property_value: IAO:0000112 "an energy wave" xsd:string property_value: IAO:0000112 "an epidemic" xsd:string property_value: IAO:0000112 "the undetached arm of a human being" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity." xsd:string property_value: IAO:0000116 "BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here." xsd:string property_value: IAO:0000600 "A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: IAO:0000601 "every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} property_value: IAO:0000601 "Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])" xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/021-002"} property_value: IAO:0000602 "(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/020-002"} property_value: IAO:0000602 "(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] " xsd:string {http://purl.obolibrary.org/obo/IAO_0010000="http://purl.obolibrary.org/obo/bfo/axiom/019-002"} property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [Term] id: BFO:0000141 name: immaterial entity is_a: BFO:0000004 ! independent continuant property_value: BFO:0000179 "immaterial" xsd:string property_value: BFO:0000180 "ImmaterialEntity" xsd:string property_value: IAO:0000116 "BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl [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 property_value: IAO:0000111 "ATP" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [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 property_value: IAO:0000111 "peptide" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [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 property_value: IAO:0000111 "deoxyribonucleic acid" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [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 property_value: IAO:0000111 "molecular entity" xsd:string property_value: IAO:0000116 "We are assuming that every molecular entity has to be completely connected by chemical bonds. This excludes protein complexes, which are comprised of minimally two separate molecular entities. We will follow up with Chebi to ensure this is their understanding as well" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:23528 name: cytochalasin is_a: CHEBI:23367 ! molecular entity property_value: IAO:0000111 "cytochalasin" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [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 property_value: IAO:0000111 "acrylamide" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [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 property_value: IAO:0000111 "atom" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [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 property_value: IAO:0000111 "nucleic acid" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [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 property_value: IAO:0000111 "ribonucleic acid" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [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." [] is_a: CHEBI:23367 ! molecular entity property_value: IAO:0000111 "macromolecule" xsd:string property_value: IAO:0000118 "polymer" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHEBI:4705 name: double-stranded DNA is_a: CHEBI:16991 ! deoxyribonucleic acid property_value: IAO:0000111 "double-stranded DNA" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [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 property_value: IAO:0000111 "5-bromo-2'-deoxyuridine" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [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 property_value: IAO:0000111 "chromium-51" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [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 property_value: IAO:0000111 "tritiated thymidine" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/chebi.owl [Term] id: CHMO:0000087 name: fluorescence microscopy def: "Any type of microscopy 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." [] is_a: OBI:0002119 ! microscopy assay property_value: IAO:0000118 "fluorescence imaging" xsd:string property_value: IAO:0000118 "fluorescence microscopic imaging" xsd:string property_value: IAO:0000118 "FM" xsd:string property_value: IAO:0000119 "CHMO" xsd:string [Term] id: CHMO:0000102 name: light microscopy def: "Microscopy where the specimen is illuminated with visible light and a system of lenses is used to produce an image." [] is_a: OBI:0002119 ! microscopy assay property_value: IAO:0000118 "light microscopy" xsd:string property_value: IAO:0000118 "OM" xsd:string property_value: IAO:0000118 "optical microscopy" xsd:string property_value: IAO:0000119 "CHMO" xsd:string [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 property_value: IAO:0000111 "cell" xsd:string property_value: IAO:0000111 "cell" xsd:string property_value: IAO:0000112 "PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. \"...Epithelial cells were harvested from histologically confirmed adenocarcinomas ..\"" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl [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 property_value: IAO:0000111 "cultured cell" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl [Term] id: CL:0000236 name: B cell def: "A lymphocyte of B lineage with the phenotype CD19-positive, CD20-positive, and capable of B cell mediated immunity." [] is_a: CL:0000542 ! lymphocyte property_value: IAO:0000111 "B cell" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl [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 property_value: IAO:0000111 "lymphocyte" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl [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 relationship: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing property_value: IAO:0000111 "experimentally modified cell in vitro" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl [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 property_value: IAO:0000111 "mononuclear cell" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/cl.owl [Term] id: ECO:0000000 name: evidence def: "A type of information that is used to support an assertion." [ECO:MCC] synonym: "evidence code" RELATED [] synonym: "evidence_code" RELATED [] disjoint_from: ECO:0000217 ! assertion method [Term] id: ECO:0000001 name: inference from background scientific knowledge def: "A type of curator inference where conclusions are drawn based on the background scientific knowledge of the curator." [ECO:SN] is_a: ECO:0000205 ! curator inference [Term] id: ECO:0000002 name: direct assay evidence alt_id: ECO:0005006 def: "A type of experimental evidence resulting from the direct measurement of some aspect of a biological feature." [ECO:SN] is_a: ECO:0000006 ! experimental evidence is_a: IAO:0000030 {is_inferred="true"} ! information content entity relationship: IAO:0000136 GO:0008150 ! is about biological_process relationship: OBI:0000312 OBI:0000070 ! is_specified_output_of assay [Term] id: ECO:0000003 name: reconstitution assay evidence def: "A type of direct assay evidence based on reconstructing a biological sample from its disassociated state to its original state." [ECO:KAV, PMID:26029343] is_a: ECO:0000002 ! direct assay evidence [Term] id: ECO:0000004 name: cell fractionation evidence def: "A type of fractionation evidence where sub-cellular components are separated based on their physical properties such as density in a sucrose density gradient." [ECO:KIM, TAIR:TED] comment: If using this term for Gene Ontology annotation, it would be used most typically for annotations to the cellular component ontology. synonym: "IDA: cell fractionation" RELATED [] is_a: ECO:0000100 ! fractionation evidence [Term] id: ECO:0000005 name: enzyme assay evidence alt_id: ECO:0005001 def: "A type of protein assay evidence where the catalytic activity of an enzyme is determined." [url:http\://www.sciencedirect.com/science/article/pii/S2213020914000068] synonym: "IDA: enzyme assays" RELATED [] xref: MI:0415 "enzymatic study" is_a: ECO:0000039 ! protein assay evidence relationship: IAO:0000136 GO:0003824 ! is about catalytic activity [Term] id: ECO:0000006 name: experimental evidence alt_id: ECO:0005023 def: "A type of evidence resulting from manipulation of variables in order to discover cause and effect." [url:http\://holah.co.uk/page/experimental/] subset: go_groupings is_a: BFO:0000002 {is_inferred="true"} ! continuant is_a: ECO:0000000 ! evidence relationship: OBI:0000312 OBI:0000070 ! is_specified_output_of assay [Term] id: ECO:0000007 name: immunofluorescence evidence def: "A type of protein detection assay evidence where a fluorescently labeled antibody is used to detect the presence or localization of a biomolecule within a cell." [ECO:MCC, TAIR:TED] synonym: "IDA: immunofluorescence" RELATED [] is_a: ECO:0005517 ! protein detection assay evidence [Term] id: ECO:0000008 name: expression pattern evidence def: "A type of experimental evidence that is based on characterization of gene expression." [ECO:MCC, GO:IEP] comment: Use this evidence type when the annotation is inferred from the timing or location of expression of a gene. It may be difficult to determine whether the expression pattern truly indicates that a gene plays a role in a given process. is_a: ECO:0000006 ! experimental evidence [Term] id: ECO:0000009 name: transcript expression evidence alt_id: ECO:0000048 def: "A type of expression pattern evidence where abundance of a transcript is analyzed." [ECO:RCT] synonym: "transcript expression level evidence" EXACT [] is_a: ECO:0000008 ! expression pattern evidence is_a: IAO:0000030 {is_inferred="true"} ! information content entity relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0000424 ! is_specified_output_of transcription profiling assay [Term] id: ECO:0000010 name: protein expression evidence def: "A type of expression pattern evidence resulting from protein abundance quantification techniques." [PMC:4029002, url:https\://www.thermofisher.com/us/en/home/life-science/protein-biology/protein-biology-learning-center/protein-biology-resource-library/pierce-protein-methods/overview-protein-expression-systems.html] is_a: ECO:0000008 ! expression pattern evidence is_a: ECO:0000039 ! protein assay evidence [Term] id: ECO:0000011 name: genetic interaction evidence def: "A type of experimental phenotypic evidence resulting from the effect that a given gene has on another gene or genes, and the products." [ECO:RCT, PMID:11822023] xref: TAIR:TED is_a: ECO:0000059 ! experimental phenotypic evidence [Term] id: ECO:0000012 name: functional complementation evidence def: "A type of genetic interaction evidence where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background." [PMID:27403640] synonym: "IGI: functional complementation" RELATED [] is_a: ECO:0000011 ! genetic interaction evidence [Term] id: ECO:0000013 name: transgenic rescue experiment evidence def: "A type of functional complementation evidence resulting from the introduction of a transgene to prevent, or \"rescue\" an organism from a condition." [url:http\://www.mdpi.com/1420-3049/19/9/13932/pdf, url:http\://www.nature.com/gt/journal/v11/n15/full/3302282a.html] is_a: ECO:0000012 ! functional complementation evidence [Term] id: ECO:0000015 name: mutant phenotype evidence def: "A type of experimental phenotypic evidence derived from the difference in two alleles of a corresponding gene that result from one or more changes in the genome." [GO:IMP] is_a: ECO:0000059 ! experimental phenotypic evidence [Term] id: ECO:0000016 name: loss-of-function mutant phenotype evidence def: "A type of mutant phenotype evidence where a phenotype is associated with altered gene product which lacks the molecular function of the wild-type gene." [SO:0002054] is_a: ECO:0000015 ! mutant phenotype evidence [Term] id: ECO:0000017 name: ectopic expression evidence def: "A type of experimental phenotypic evidence where a transgenic strain carrying the construct of a promoter cDNA fusion in which a gene of interest is driven by a defined promoter or enhancer is ectopically expressed in the defined pattern to characterize potential cellular properties and functions of a protein of interest." [PMID:10948520, PMID:19301619] synonym: "IMP: analysis of overexpression/ectopic expression phenotype" RELATED [] is_a: ECO:0000059 ! experimental phenotypic evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay [Term] id: ECO:0000018 name: anti-sense experiment evidence def: "A type of mutant phenotype evidence where a phenotype is observed while expressing an anti-sense version of a gene product in a wild-type (for that gene product) background." [ECO:SN] synonym: "IMP: anti-sense experiments" RELATED [] is_a: ECO:0000015 ! mutant phenotype evidence relationship: IAO:0000136 GO:0009300 ! is about antisense RNA transcription relationship: OBI:0000312 OBI:0001672 ! is_specified_output_of gene knock-down assay [Term] id: ECO:0000019 name: RNAi evidence def: "A type of mutant phenotype evidence where an RNA construct is introduced into a cell and the expression of the gene bearing its complementary sequence is suppressed." [ECO:MCC] synonym: "IMP: RNAi experiment" RELATED [] is_a: ECO:0000015 ! mutant phenotype evidence relationship: IAO:0000136 GO:0070549 ! is about negative regulation of translation involved in RNA interference relationship: OBI:0000312 OBI:0001672 ! is_specified_output_of gene knock-down assay [Term] id: ECO:0000020 name: specific protein inhibition evidence def: "A type of protein assay evidence based on the inhibition of the molecular function of a protein." [ECO:MCC] is_a: ECO:0000039 ! protein assay evidence [Term] id: ECO:0000021 name: physical interaction evidence alt_id: ECO:0005025 def: "A type of experimental evidence that is based on characterization of an interaction between a gene product and another molecule." [ECO:SN] comment: Molecules interacted with might include protein, nucleic acid, ion, or complex. xref: MI:0045 "experimental interaction detection" is_a: ECO:0000006 ! experimental evidence [Term] id: ECO:0000022 name: co-purification evidence def: "A type of physical interaction evidence where a cellular component subunit is isolated as part of purification of its larger complex." [TAIR:TED] synonym: "IPI: co-purification" RELATED [] xref: MI:0025 "copurification" is_a: ECO:0000021 ! physical interaction evidence relationship: OBI:0000312 OBI:0001505 ! is_specified_output_of purification [Term] id: ECO:0000023 name: affinity evidence def: "A type of physical interaction evidence that depends on the strength of the interaction between two entities." [ECO:MCC, PSI-MI:MI\:0400] synonym: "ligand binding evidence" NARROW [] xref: MI:0400 "affinity technology" is_a: ECO:0000021 ! physical interaction evidence [Term] id: ECO:0000024 name: protein binding evidence def: "A type of affinity evidence resulting from the binding of a molecule to a protein or protein complex." [GO:0005515, url:https\://en.wikipedia.org/wiki/Mutation] is_a: ECO:0000023 ! affinity evidence is_a: ECO:0000039 ! protein assay evidence [Term] id: ECO:0000025 name: hybrid interaction evidence def: "A type of affinity evidence where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein." [ECO:MCC, PSI-MI:MI\:0090] comment: Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode. xref: MI:0090 "protein complementation assay" is_a: ECO:0000023 ! affinity evidence [Term] id: ECO:0000026 name: nucleic acid hybridization evidence def: "A type of experimental genomic evidence resulting from a process in which single stranded nucleic acids are allowed to interact so that complexes, or hybrids, are formed by molecules with sufficiently similar, complementary sequences." [OBI:0302903] comment: This term has been made obsolete with the clean up of experimental genomic evidence branch. is_obsolete: true [Term] id: ECO:0000027 name: structural similarity evidence def: "A type of similarity evidence based on structural similarity of an annotated gene or gene product to another gene or group of genes." [ECO:MCC, TAIR:TED] comment: For GO annotation, in the case of a single gene, an accession for the related gene's sequence is entered in the evidence_with field. is_a: ECO:0000057 ! phenotypic similarity evidence [Term] id: ECO:0000028 name: motif similarity evidence def: "A type of match to sequence model evidence that is based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence." [ECO:SN] synonym: "ISS: recognized domains" RELATED [] is_a: ECO:0000202 ! match to sequence model evidence [Term] id: ECO:0000029 name: match to InterPro member signature evidence def: "A type of match to sequence model evidence resulting from a positive match of a protein, or set of proteins to a predictive model (signature) in the InterPro database." [PMC:2686546, url:http\://www.ncbi.nlm.nih.gov/mesh?term=Nucleic+Acid+Hybridization] is_a: ECO:0000202 ! match to sequence model evidence [Term] id: ECO:0000030 name: BLAST evidence used in manual assertion def: "A type of BLAST evidence that is used in a manual assertion." [ECO:MCC] synonym: "curated BLAST analysis" RELATED [] is_a: ECO:0000206 ! BLAST evidence is_a: ECO:0005560 {is_inferred="true"} ! pairwise sequence alignment evidence used in manual assertion intersection_of: ECO:0000206 ! BLAST evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion [Term] id: ECO:0000031 name: protein BLAST evidence used in manual assertion def: "A type of protein BLAST evidence that is used in a manual assertion." [ECO:SN] synonym: "curated protein BLAST analysis" RELATED [] xref: GO_REF:0000012 "Pairwise alignment (TIGR)" xref: GO_REF:0000027 "BLAST search criteria for ISS assignment in PAMGO_GAT" is_a: ECO:0000030 {is_inferred="true"} ! BLAST evidence used in manual assertion is_a: ECO:0000208 ! protein BLAST evidence intersection_of: ECO:0000208 ! protein BLAST evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion [Term] id: ECO:0000032 name: nucleotide BLAST evidence used in manual assertion def: "A type of nucleotide BLAST evidence that is used in a manual assertion." [ECO:SN] synonym: "curated nucleic acid BLAST analysis" RELATED [] is_a: ECO:0000030 {is_inferred="true"} ! BLAST evidence used in manual assertion is_a: ECO:0000207 ! nucleotide BLAST evidence intersection_of: ECO:0000207 ! nucleotide BLAST evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion [Term] id: ECO:0000033 name: author statement supported by traceable reference def: "A type of author statement in which the author makes a statement that is not supported by information in that particular publication, but rather can be traced to a reference cited by that publication." [ECO:RCT, GO:TAS] synonym: "traceable author statement" RELATED [] is_a: ECO:0000204 ! author statement disjoint_from: ECO:0000034 ! author statement without traceable support [Term] id: ECO:0000034 name: author statement without traceable support def: "A type of author statement that is not associated with results presented or a cited reference." [ECO:SN] synonym: "non-traceable author statement" RELATED [] is_a: ECO:0000204 ! author statement [Term] id: ECO:0000035 name: no biological data found def: "A curator inference that results from research where no information about a biological feature was found in the scientific literature, at biological databases, or within other resources." [ECO:SN] comment: An assertion of "no biological data found" carries the assumption that a more-or-less exhaustive search has been conducted. is_a: ECO:0000205 ! curator inference [Term] id: ECO:0000037 name: not_recorded comment: The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations. is_obsolete: true [Term] id: ECO:0000038 name: transient rescue experiment evidence is_a: ECO:0000012 ! functional complementation evidence [Term] id: ECO:0000039 name: protein assay evidence alt_id: ECO:0005022 def: "A type of direct assay evidence resulting from determining the presence, abundance, structure, function, or activity of proteins." [PMID:18429326] is_a: ECO:0000002 ! direct assay evidence [Term] id: ECO:0000040 name: immunological assay evidence alt_id: ECO:0005018 def: "A type of affinity evidence resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody." [ERO:0001362, url:http\://www.ncbi.nlm.nih.gov/books/NBK21589/\,http\://cores.ucsf.edu/protein-assay.html] is_a: ECO:0000023 ! affinity evidence [Term] id: ECO:0000041 name: similarity evidence def: "A type of evidence resulting from comparing likeness of distinct biological entities." [ECO:SN] synonym: "inferred from similarity" RELATED [] synonym: "IS" EXACT [] is_a: ECO:0000000 ! evidence [Term] id: ECO:0000042 name: gain-of-function mutant phenotype evidence def: "A type of mutant phenotype evidence resulting from a phenotype that is associated with the altered gene product which possesses a new molecular function or a new pattern of gene expression." [SO:0002053, url:http\://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614608/] is_a: ECO:0000015 ! mutant phenotype evidence [Term] id: ECO:0000044 name: sequence similarity evidence def: "A type of similarity based on biomolecular sequence." [ECO:MCC, TAIR:TED] comment: A sequence similarity analysis may involve a gene or a gene product, and it could be based on similarity to a single other gene or to a group of other genes. is_a: ECO:0000041 ! similarity evidence [Term] id: ECO:0000045 name: spatial pattern of protein expression evidence is_a: ECO:0000010 ! protein expression evidence [Term] id: ECO:0000046 name: protein expression level evidence def: "A type of protein expression evidence resulting from the quantification of protein production in a sample." [NBK:22011, url:http\://www.informatics.jax.org/glossary/gain-of-function] is_a: ECO:0000010 ! protein expression evidence [Term] id: ECO:0000047 name: spatial pattern of transcript expression evidence is_a: ECO:0000009 ! transcript expression evidence [Term] id: ECO:0000049 name: reporter gene assay evidence def: "A type of experimental phenotypic evidence that is based on the expression pattern of a reporter gene." [TAIR:TED] synonym: "IEP: expression of a reporter gene" RELATED [] is_a: ECO:0000059 ! experimental phenotypic evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0002082 ! is_specified_output_of reporter gene assay [Term] id: ECO:0000050 name: voucher specimen analysis evidence def: "A type of phenotypic evidence based on an author's phenotypic description of a species or higher level group explicitly referencing an observation of a voucher specimen, a specimen with a permanent museum catalog." [TAIR:TED] synonym: "IVS" EXACT [] is_a: ECO:0000059 ! experimental phenotypic evidence [Term] id: ECO:0000051 name: genetic similarity evidence def: "A type of similarity based on genotype without respect to expression." [ECO:MCC, PhenoScape:IGTS] comment: A genetic similarity analysis might consider genetic markers, polymorphisms, alleles, or other characteristics sometimes considered as part of the field of traditional genetics. Although an attempt has been made to treat as distinct the concepts of "genetic", "genotypic", "genomic", and "sequence", there is considerable overlap in usage throughout the field of biology. synonym: "IGTS" EXACT [] synonym: "inferred from genetic similarity" RELATED [] is_a: ECO:0000041 ! similarity evidence [Term] id: ECO:0000052 name: suppressor/enhancer interaction evidence def: "A type of genetic interaction evidence resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation." [url:http\://biorxiv.org/content/early/2015/10/03/021592, url:http\://www.wormbook.org/chapters/www\:geneticsuppression/geneticsuppression.html] synonym: "IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)" RELATED [] xref: TAIR:TED is_a: ECO:0000011 ! genetic interaction evidence [Term] id: ECO:0000053 name: computational combinatorial evidence def: "A type of combinatorial analysis where data are combined and evaluated by an algorithm." [ECO:go, ECO:MCC] comment: Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments. xref: TAIR:TED is_a: ECO:0000212 ! combinatorial evidence [Term] id: ECO:0000054 name: double mutant phenotype evidence def: "A type of genetic interaction evidence that is based on the phenotypic outcome of two mutations in unrelated genetic loci." [ECO:RCT] synonym: "IGI: double mutant analysis" RELATED [] is_a: ECO:0000011 ! genetic interaction evidence [Term] id: ECO:0000055 name: array experiment evidence comment: This general 'array experiment' term should not be used - replace with the specific type of array (e.g. ECO:0000097, ECO:0000062, ECO:0000104, etc.) is_obsolete: true [Term] id: ECO:0000056 name: epistatic interaction evidence def: "A type of genetic interaction evidence that is based on the suppression of one allelic effect by an allele at another genetic locus." [PMID:18852697] comment: Epistasis' can be used in different contexts in different areas of genetics. It is sometimes used to mean 'genetic interaction', whereas other times it may be specific to mutations that block the effects of other mutations. synonym: "IGI: epistatic interactions" RELATED [] is_a: ECO:0000011 ! genetic interaction evidence [Term] id: ECO:0000057 name: phenotypic similarity evidence def: "A type of similarity based on the expression of a genotype in an environment." [ECO:MCC, PhenoScape:IPTS] comment: Phenotype is defined as the outcome of the expression of a genotype in a given environment. A comparison might involve whole organisms or sub-parts of organisms. synonym: "inferred from phenotypic similarity" RELATED [] synonym: "IPTS" EXACT [] synonym: "phenotype similarity evidence" EXACT [] is_a: ECO:0000041 ! similarity evidence [Term] id: ECO:0000058 name: expression microarray evidence alt_id: ECO:0000356 def: "A type of transcript expression evidence resulting from simultaneous profiling of the expression levels of thousands of genes in a single experiment allowing analysis of genes and their networks." [url:http\://www.illumina.com/techniques/microarrays/gene-expression-arrays.html, url:http\://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435252/] synonym: "differential gene expression evidence from microarray experiment" NARROW [] is_a: ECO:0000009 ! transcript expression evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0001463 ! is_specified_output_of transcription profiling by array assay [Term] id: ECO:0000059 name: experimental phenotypic evidence alt_id: ECO:0000014 alt_id: ECO:0005017 def: "A type of experimental evidence that is based on the expression of a genotype in an environment." [ECO:SN] synonym: "inferred from phenotype" RELATED [] is_a: ECO:0000006 ! experimental evidence is_a: IAO:0000030 {is_inferred="true"} ! information content entity relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay [Term] id: ECO:0000060 name: positional similarity evidence def: "A type of phenotypic similarity evidence based on the similarity of stucture locations or arrangements." [TAIR:TED] synonym: "IPS" EXACT [] is_a: ECO:0000057 ! phenotypic similarity evidence [Term] id: ECO:0000061 name: quantitative trait analysis evidence def: "A type of phenotypic evidence that is based on a gene product that is associated with a quantitative trait locus, but has not been cloned." [TAIR:TED] synonym: "IGI: quantitative trait analysis" RELATED [] synonym: "QTL analysis evidence" EXACT [] is_a: ECO:0000059 ! experimental phenotypic evidence [Term] id: ECO:0000062 name: cRNA to DNA expression microarray evidence def: "A type of expression microarray evidence where expression level is quantified by sample biotin-labeled cRNA (transcribed from an unknown RNA sample) hybridized to DNA oligonuclotides immoblized on a solid surface." [url:https\://link.springer.com/chapter/10.1007/978-94-017-9716-0_30] synonym: "genomic microarray evidence" EXACT [] is_a: ECO:0000058 ! expression microarray evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression [Term] id: ECO:0000063 name: compositional similarity evidence def: "A type of phenotypic similarity evidence based on the similarity of the histological makeup of structures." [TAIR:TED] synonym: "ICS" EXACT [] is_a: ECO:0000057 ! phenotypic similarity evidence [Term] id: ECO:0000064 name: functional complementation in heterologous system evidence def: "A type of functional complementation evidence that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene." [TAIR:TED] synonym: "IGI: functional complementation in heterologous system" RELATED [] is_a: ECO:0000012 ! functional complementation evidence [Term] id: ECO:0000066 name: yeast one-hybrid evidence def: "A type of hybrid interaction evidence that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors." [ECO:MCC, PSI-MI:MI\:0432, TAIR:TED] comment: The assay involves screening a library of candidate proteins for the ability bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to a yeast reporter gene (TAIR:TED). synonym: "IPI: yeast one-hybrid assay" RELATED [] xref: MI:0432 "one hybrid" is_a: ECO:0000025 ! hybrid interaction evidence [Term] id: ECO:0000067 name: developmental similarity evidence def: "A type of phenotypic similarity evidence based on the similarity of embryological or post-embryonic orgin of structures." [TAIR:TED] synonym: "IDS" EXACT [] is_a: ECO:0000057 ! phenotypic similarity evidence [Term] id: ECO:0000068 name: yeast 2-hybrid evidence def: "A type of hybrid interaction evidence that is based on detection of protein-protein interaction by activation of a yeast reporter gene after a bait protein fused to a DNA-binding domain (which has been transfected into a yeast cell) is used to screen a cDNA library of clones fused to an activation domain." [PMID:12734586] synonym: "IPI: yeast two-hybrid assay" RELATED [] is_a: ECO:0000025 ! hybrid interaction evidence [Term] id: ECO:0000069 name: differential methylation hybridization evidence alt_id: ECO:0000065 def: "A type of in vitro methylation assay evidence where methylation-sensitive restriction enzymes are utilized to compare differential methylation between two samples by first shearing DNA, followed by end-blunting, ligation of linkers, methylation sensitive restriction, PCR using linker primers, dye labeling and relative quantification of methylated DNA fragments by two-colored array hybridization to a CpG island microarray for visual assessment." [PMID:18987809] comment: Color is indicative of methylation status - be it hypo- (pseudo-green), hyper- (pseudo-red), or equal methylation (pseudo-yellow). synonym: "CpG island microarray evidence" EXACT [] is_a: ECO:0001065 ! in vitro methylation assay evidence relationship: IAO:0000136 GO:0044030 ! is about regulation of DNA methylation relationship: OBI:0000312 OBI:0001861 ! is_specified_output_of methylation-sensitive restriction enzyme sequencing assay [Term] id: ECO:0000070 name: co-immunoprecipitation evidence def: "A type of immunoprecipitation evidence that involves precipitating two or more proteins via binding to an antibody specific to a single protein, followed by protein identification." [ECO:MCC] comment: If performing GO annotation, the interacting protein is referenced in the evidence_with column. synonym: "IPI: co-immunoprecipitation" RELATED [] xref: MI:0019 "coimmunoprecipitation" is_a: ECO:0000021 ! physical interaction evidence is_a: ECO:0000085 ! immunoprecipitation evidence [Term] id: ECO:0000071 name: morphological similarity evidence def: "A type of phenotypic similarity evidence based on the similarity of shape, structure, or configuration in structures." [TAIR:TED] synonym: "IMS" EXACT [] is_a: ECO:0000057 ! phenotypic similarity evidence [Term] id: ECO:0000072 name: Sos-recruitment assay evidence is_obsolete: true [Term] id: ECO:0000073 name: experimental genomic evidence def: "A type of experimental evidence that is based on the characterization of an attribute of the genome underlying a gene product." [ECO:MCC] comment: This term has been made obsolete with the clean up of experimental genomic evidence branch. synonym: "inferred from genomic analysis" EXACT [] is_obsolete: true [Term] id: ECO:0000074 name: split-ubiquitin assay evidence def: "A type of physical interaction evidence that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein." [PMID:15064465] comment: The bait protein is fused to the C-terminal ubiquitin (Cub) domain followed by a reporter protein, and the prey protein is fused to a mutated N terminal ubiquitin (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough to reconstitute.TAIR:TED synonym: "IPI: split-ubiquitin assay" RELATED [] xref: MI:0112 "ubiquitin reconstruction" is_a: ECO:0000021 ! physical interaction evidence [Term] id: ECO:0000075 name: gene expression similarity evidence def: "A type of phenotypic similarity evidence that is based on the categorization of genes by the similarity of expression profiles." [PMID:19958477] synonym: "IGES" EXACT [] is_a: ECO:0000057 ! phenotypic similarity evidence [Term] id: ECO:0000076 name: far-Western blotting evidence def: "A type of physical interaction evidence that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes." [PMID:18079728] comment: The interacting protein is referenced in the evidence_with column. synonym: "IPI: far-Western analysis" RELATED [] xref: MI:0047 is_a: ECO:0000021 ! physical interaction evidence [Term] id: ECO:0000077 name: methylation-specific polymerase chain reaction evidence def: "A type of in vitro methylation assay evidence resulting from initial modification of DNA by sodium bisulfite, converting all unmethylated cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA." [PMC:38513, PMID:8790415] comment: The product is the amplification of existing sequences - i.e. more DNA that can be further processed e.g. sequenced, DNA fingerprinting. synonym: "methylation-specific PCR evidence" EXACT [] synonym: "MS-PCR" EXACT [] synonym: "MSP" EXACT [] is_a: ECO:0001065 ! in vitro methylation assay evidence relationship: IAO:0000136 GO:0006306 ! is about DNA methylation relationship: OBI:0000312 OBI:0001684 ! is_specified_output_of methylation-specific polymerase chain reaction [Term] id: ECO:0000078 name: southern hybridization evidence def: "A type of DNA detection assay evidence that is based on detection of a specific DNA sequence by hybridization of labeled probes to any immobilized DNA fragment with sequence similarity." [PMID:18432697] comment: The DNA fragments are prepared through gel electrophoresis then transferred to a filter membrane. synonym: "ISS: Southern blotting" RELATED [] synonym: "Southern blot" EXACT [] is_a: ECO:0005519 ! DNA detection assay evidence relationship: OBI:0000312 OBI:0000892 ! is_specified_output_of Southern blot analysis [Term] id: ECO:0000079 name: affinity chromatography evidence def: "A type of affinity evidence that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound." [ECO:MCC, TAIR:TED] comment: "Used when an annotation is made based on affinity chromatography, which is a selective separation technique by which a compound (e.g., an antibody) is immobilized on a polymeric matrix and used to bind selectively other compounds. Following removal of the unattached components, the bound compound is displaced by changing the concentration of protons, salts, or cofactors in the eluent" (from original definition by TAIR:TED). Types of highly specific interaction might include those of antigen and antibody, enzyme and substrate, or receptor and ligand. synonym: "IDA: affinity chromatography" RELATED [] xref: MI:0004 "affinity chromatography technology" is_a: ECO:0000023 ! affinity evidence relationship: OBI:0000312 OBI:0001630 ! is_specified_output_of analytical chromatography [Term] id: ECO:0000080 name: phylogenetic evidence def: "A type of similarity that indicates common ancestry." [ECO:MCC, PhenoScape:IP] synonym: "IP" EXACT [PhenoScape:IP] is_a: ECO:0000041 ! similarity evidence [Term] id: ECO:0000081 name: targeting sequence prediction evidence def: "A type of motif similarity evidence that is based on detection of a targeting sequence in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence." [ECO:RCT, TAIR:TED] synonym: "ISS: targeting sequence prediction" RELATED [] is_a: ECO:0000028 ! motif similarity evidence [Term] id: ECO:0000082 name: polymerase chain reaction evidence def: "A type of experimental genomic evidence where DNA polymerase is used to synthesize new strand of DNA complementary to the offered template strand." [OBI:0000415] comment: This term has been made obsolete because PCR is not evidence. The children have been appropriately placed under other parents. synonym: "PCR evidence" EXACT [] is_obsolete: true [Term] id: ECO:0000083 name: transmembrane domain prediction evidence def: "A type of motif similarity evidence that is based on detection of one, or more, transmembrane domains in the primary sequence of a protein through computational prediction and/or a manual examination of the sequence." [ECO:RCT, TAIR:TED] synonym: "ISS: transmembrane domain prediction" RELATED [] is_a: ECO:0000028 ! motif similarity evidence [Term] id: ECO:0000084 name: gene neighbors evidence def: "A type of genomic context evidence in which a gene product's identity is supported on the basis of the identity of neighboring genes." [ECO:MCC, GOC:MG] comment: Genomic cluster analyses include synteny and operon structure. synonym: "ICL" RELATED [] synonym: "inferred from genome cluster" EXACT [] xref: GO_REF:0000025 "Operon structure as IGC evidence" is_a: ECO:0000177 ! genomic context evidence created_by: mgiglio creation_date: 2009-03-20T11:55:18Z [Term] id: ECO:0000085 name: immunoprecipitation evidence def: "A type of protein assay evidence that involves precipitation of a multivalent antigen by a bivalent antibody for protein isolation." [ECO:MCC, ECO:SW, TAIR:TED] comment: Transcription factors isolated in this way can be incubated with a radiolabeled probe to demonstrate binding. synonym: "IDA: immunoprecipitation" RELATED [] is_a: ECO:0000039 ! protein assay evidence property_value: IAO:0000234 "CollecTF" xsd:string [Term] id: ECO:0000086 name: amplification of intermethylated sites evidence def: "A type of in vitro methylation assay evidence resulting from a genome-wide estimate of DNA methylation by differential enzymatic digestion of genomic DNA with methylation-sensitive and methylation-insensitive isoschizomers, followed by restrained PCR amplification of sequences methylated at both ends and resolving the PCR products in a denaturing polyacrylamide-sequencing gel to generate fingerprints that consist of multiple anonymous bands that represent the DNA methylome of the cell." [PMID:18987810, url:https\://www.ncbi.nlm.nih.gov/probe/docs/techpcr/] comment: The bands can be individually isolated and characterized which leads to the identification of hypo- and hypermethylation events. synonym: "AIMS" EXACT [] is_a: ECO:0001065 ! in vitro methylation assay evidence relationship: IAO:0000136 GO:0006306 ! is about DNA methylation relationship: OBI:0000312 OBI:0001685 ! is_specified_output_of amplification of intermethylated sites (AIMS) assay [Term] id: ECO:0000087 name: immunolocalization evidence def: "A type of microscopy evidence where antibodies are used to detect the location of molecules or other structures within cells or tissues." [ECO:MCC, ECO:SN] synonym: "IDA: immunolocalization" RELATED [] is_a: ECO:0001098 ! microscopy evidence is_a: ECO:0005593 ! immunodetection assay evidence relationship: IAO:0000136 GO:0033036 ! is about macromolecule localization [Term] id: ECO:0000088 name: biological system reconstruction evidence def: "A type of evidence that is based on a combination of experimental evidences or existing models of that system in a related species used for the reconstruction of a biological system." [ECO:MCC, GOC:mg] comment: The biological system in question might be a multi-step process or pathway or a physical complex comprising several components. The components in the experimental evidence can come from the same species or a mix of species. The experimental evidences may be only partial or weak. synonym: "inferred from system reconstruction" RELATED [] synonym: "ISR" RELATED [] is_a: ECO:0000000 ! evidence created_by: mgiglio creation_date: 2009-03-20T12:00:17Z [Term] id: ECO:0000089 name: restriction landmark genomic scanning evidence alt_id: ECO:0001125 def: "A type of DNA detection assay evidence resulting from the use of restriction enzymes for direct end-labeling of DNA (creating landmarks), followed by high-resolution two-dimensional electrophoresis to visualize the landmarks." [PMID:8388788] synonym: "restriction landmark genome scanning evidence" EXACT [] synonym: "RLGS evidence" EXACT [] is_a: ECO:0005519 ! DNA detection assay evidence property_value: IAO:0000234 SIB:PG xsd:string [Term] id: ECO:0000090 name: immunogold labelling evidence def: "A type of immunolocalization evidence where the antibodies are labeled with colloidal gold particles whose location is then detected via microscopy." [ECO:MCC] synonym: "IDA: immunogold labelling" RELATED [] is_a: ECO:0000087 ! immunolocalization evidence [Term] id: ECO:0000092 name: epitope-tagged protein immunolocalization evidence def: "A type of immunolocalization evidence in which recombinant proteins fused with epitopes are recognized by antibodies." [TAIR:TED] synonym: "IDA: immunolocalization of epitope-tagged protein" RELATED [] is_a: ECO:0000087 ! immunolocalization evidence [Term] id: ECO:0000093 name: array-based sequence capture evidence def: "A type of DNA detection assay evidence evidence where gene sequence or variation is determined or detected by fluorescently-labeled DNA fragments hybridized to sequence-specific oligonucleotides immobilized on an array." [PMID:21049075] synonym: "DNA microarray" BROAD [] synonym: "oligonucleotide microarray evidence" BROAD [] synonym: "single nucleotide polymorphism array evidence" NARROW [] synonym: "SNP array evidence" NARROW [] is_a: ECO:0005519 ! DNA detection assay evidence [Term] id: ECO:0000094 name: biological assay evidence comment: The children of 'biological assay evidence' have been moved under 'direct assay evidence', and this term has been deprecated with no children left. is_a: IAO:0000030 {is_inferred="true"} ! information content entity relationship: IAO:0000136 GO:0008150 ! is about biological_process relationship: OBI:0000312 OBI:0000070 ! is_specified_output_of assay is_obsolete: true [Term] id: ECO:0000095 name: cell growth regulation assay evidence def: "A type of cell growth assay evidence that measures one or more aspects of cell growth over a specified time period to indicate an induced or repressed regulatory effect." [ECO:SW, PomBase:MAH] comment: Cell growth aspects can include growth rate and extent of growth. A cell growth curve acts as a natural reporter. synonym: "growth curve analysis" RELATED [] is_a: ECO:0001563 ! cell growth assay evidence relationship: IAO:0000136 GO:0016049 ! is about cell growth relationship: OBI:0000312 OBI:0000964 ! is_specified_output_of in live cell assay created_by: mchibucos creation_date: 2014-10-15T00:58:50Z [Term] id: ECO:0000096 name: electrophoretic mobility shift assay evidence def: "A type of direct assay evidence based on an electrophoretic mobility shift of macromolecules, compounds, and proteins where solutions of protein and nucleic acid are combined and the resulting mixtures are electrophoresed under native conditions through polyacrylamide or agarose gel to detect protein-nucleic acid interactions." [ECO:KIM, ECO:SW, PMID:17703195, TAIR:TED] comment: EMSA is often used for assessing TF-binding with fluorophore labelling. Protein-nucleic acid complexes generally migrate at a slower rate than the corresponding non-bonded nucleic acid. synonym: "EMSA: electrophoretic mobility shift assay" EXACT [] synonym: "Gel retardation assay" RELATED [PMID:17703195] synonym: "IDA: electrophoretic mobility shift assay" RELATED [] xref: MI:0413 "electrophoretic mobility shift assay" is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "CollecTF" xsd:string [Term] id: ECO:0000097 name: cDNA to DNA expression microarray evidence alt_id: ECO:0001041 alt_id: ECO:0005524 def: "A type of expression microarray evidence where expression level is quantified by fluroescently-labeled cDNA (reverse transcribed from an unknown RNA sample) hybridized to DNA immobilized on a solid surface." [ECO:RCT] synonym: "DNA microarray" RELATED [] synonym: "RNA microarray" RELATED [] is_a: ECO:0000058 ! expression microarray evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression property_value: IAO:0000234 "CollecTF" xsd:string [Term] id: ECO:0000098 name: in situ hybridization evidence def: "A type of nucleic acid hybridization evidence based on localization of a specific segment of DNA or RNA by the application of a complementary strand of nucleic acid to which a reporter molecule is attached." [url:https\://www.ncbi.nlm.nih.gov/probe/docs/techish/] comment: This term has been made obsolete with the clean up of experimental genomic evidence branch. synonym: "IDA: in situ hybridization" RELATED [] is_a: IAO:0000030 {is_inferred="true"} ! information content entity relationship: IAO:0000136 GO:0033036 ! is about macromolecule localization relationship: OBI:0000312 OBI:0001686 ! is_specified_output_of in situ hybridization is_obsolete: true [Term] id: ECO:0000100 name: fractionation evidence def: "A type of direct assay evidence resulting from the separation of various cell components while preserving their individual functions." [NBK:26936, url:https\://www.ncbi.nlm.nih.gov/books/NBK26936/] is_a: ECO:0000002 ! direct assay evidence [Term] id: ECO:0000101 name: Affymetrix GeneChip evidence def: "A type of cRNA to DNA expression microarray evidence resulting from the use of a proprietary Affymetrix GeneChip System for analyzing complex genetic information." [ERO:0001265] synonym: "Affymetrix array experiment evidence" EXACT [] is_a: ECO:0000062 ! cRNA to DNA expression microarray evidence [Term] id: ECO:0000102 name: co-fractionation evidence def: "A type of fractionation evidence resulting from a protein fractionated with other compounds, factors, or macromolecules." [TAIR:TED] synonym: "IDA: co-fractionation" RELATED [] is_a: ECO:0000100 ! fractionation evidence [Term] id: ECO:0000104 name: DNA to cDNA expression microarray evidence def: "A type of expression microarray evidence where expression levels are quantified by hybridization of fluorescently-labeled DNA to cDNA (reverse transcribed from an unknown RNA sample) immobilized on a solid surface." [ECO:RCT, PMID:15329382] comment: REM is a 'reverse-format' microarray, where the unknown sample is immoblized to a surface and known DNA is hybridized to that. {xref="PMID:15329382"} synonym: "IEP: transcript levels (e.g. microarray data)" RELATED [] synonym: "microarray RNA expression level evidence" EXACT [] synonym: "REM evidence" EXACT [] synonym: "RNA expression microarray evidence" EXACT [] is_a: ECO:0000058 ! expression microarray evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression [Term] id: ECO:0000105 name: Nimblegen array evidence def: "A type of cDNA to DNA expression microarray evidence resulting from the use of a proprietary NimbleGen array to measure expression levels." [PMID:15607417, url:https\://roche-biochem.jp/pdf/products/microarray/user_guide/SeqCap/SeqCap_UserGuide_Delivery_ver3.0.pdf] is_a: ECO:0000097 ! cDNA to DNA expression microarray evidence [Term] id: ECO:0000106 name: northern blot evidence def: "A type of transcript expression evidence based on electrophoresis and probing to determine levels of RNA expression using a complementary hybridization probe on the separated RNA samples." [ECO:SW, TAIR:TED] synonym: "IEP: transcript levels (e.g. Northerns)" RELATED [] synonym: "northern assay evidence" EXACT [] synonym: "RNA blot evidence" EXACT [] is_a: ECO:0000009 ! transcript expression evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0000860 ! is_specified_output_of northern blot analysis property_value: IAO:0000234 "CollecTF" xsd:string [Term] id: ECO:0000109 name: reverse transcription polymerase chain reaction evidence alt_id: ECO:0000108 def: "A type of RNA detection assay evidence where an RNA transcript is reverse transcribed into cDNA and amplified to qualitatively detect gene expression." [ECO:SW, PMID:11013345, PMID:12901609] comment: The starting product for PCR, and therefore amplification volume, is directly correlated to the transcription rate. synonym: "IEP: transcript levels (e.g. RT-PCR)" RELATED [] synonym: "reverse transcription polymerase chain reaction transcription evidence" BROAD [] synonym: "RT-PCR" EXACT [] is_a: ECO:0005518 ! RNA detection assay evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0001361 ! is_specified_output_of transcription profiling by RT-PCR assay property_value: IAO:0000234 "CollecTF" xsd:string [Term] id: ECO:0000110 name: RNA protection assay evidence def: "A type of nuclease protection assay evidence where mRNA is hybridized with radiolabeled RNA probes after which RNAse is added to digest the unbound, nonresistant single-stranded overhang regions, later the remaining probe target hybrids are purified and resolved on denaturing polyacrylamide gel, and quantified by autoradiography." [ECO:SW, PMID:23457339, TAIR:TED] synonym: "IEP: RNA protection assay" RELATED [] synonym: "ribonuclease protection assay" EXACT [] synonym: "RNAse protection assay" RELATED [] synonym: "RPA" NARROW [] is_a: ECO:0001106 ! nuclease protection assay evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0001670 ! is_specified_output_of RNA protection assay property_value: IAO:0000234 "CollecTF" xsd:string [Term] id: ECO:0000112 name: western blot evidence def: "A type of gel electrophoresis evidence where proteins are separated using gel electrophoresis and then they are blotted on a nitrocellulose or polyvinylidene difluoride (PVDF) membrane, later an antibody with a dye or an enzyme is added to the solution which is able to bind to its specific protein and this product is detected either by chemiluminescent detection technique or fluorescence imaging technique." [ECO:SW, PMID:23050259, TAIR:TED] comment: Western blot is used for protein detection and analysis. A mixed protein sample is separated through polyacrylamide gel electrophoresis then transferred to a membrane, such as polyvinylidene fluoride (PVDF), and labeled with protein-specific antibodies. synonym: "IEP: protein levels (e.g. Western blots)" RELATED [] synonym: "protein immunoblot" RELATED [] synonym: "Western blot expression analysis" RELATED [] is_a: ECO:0000333 ! sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence is_a: ECO:0005593 ! immunodetection assay evidence property_value: IAO:0000234 "CollecTF" xsd:string [Term] id: ECO:0000114 name: expression library screen evidence def: "A type of protein expression evidence where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein." [ECO:MCC, TAIR:TED] synonym: "IEP: expression library screening" RELATED [] is_a: ECO:0000010 ! protein expression evidence [Term] id: ECO:0000116 name: differential hybridization evidence def: "A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue is compared to another cell type or tissue when mRNA from each sample is reverse transcribed, labeled, and hybridized to a cDNA library to compare hybridization patterns." [PMID:14668817] comment: Differential hybridization identifies differentially expressed cloned genes. Two different mRNA-derived probes are used to demonstrate RNA expression under a specific condition. synonym: "IEP: differential hybridization" RELATED [] is_a: ECO:0000009 ! transcript expression evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0000424 ! is_specified_output_of transcription profiling assay [Term] id: ECO:0000118 name: subtractive hybridization evidence def: "A type of nucleic acid hybridization evidence in which preferential or exclusive expression of genes in one cell type or tissue are compared to another cell type or tissue when denatured ds-cDNA from the two samples are hybridized, and the common sequences are 'subtracted'." [PMID:11298187] comment: Subtractive hybridization is used for isolation and identification of transcripts involving the removal of any sequences present in the control from the test probe to detect only transcripts present in the sample. The method is PCR-based for the comparison of two cDNA libraries. synonym: "IEP: subtractive hybridization" RELATED [] is_a: ECO:0000009 ! transcript expression evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0000424 ! is_specified_output_of transcription profiling assay [Term] id: ECO:0000120 name: over expression analysis evidence def: "A type of experimental phenotypic evidence in which a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product." [PMID:22419077] synonym: "IMP: analysis of overexpression/ectopic expression phenotype" RELATED [] is_a: ECO:0000059 ! experimental phenotypic evidence [Term] id: ECO:0000122 name: protein localization evidence def: "A type of localization evidence where sub-cellular localization of a protein is determined." [GO:0008104, url:http\://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019937] is_a: ECO:0001533 ! localization evidence [Term] id: ECO:0000124 name: fusion protein localization evidence def: "A type of protein localization evidence resulting from the fusion of a protein of interest to a labeling protein which has enzymatic activity or fluorescence properties." [MI:0240] is_a: ECO:0000122 ! protein localization evidence relationship: IAO:0000136 GO:0033036 ! is about macromolecule localization relationship: OBI:0000312 OBI:0002167 ! is_specified_output_of subcellular protein localization assay [Term] id: ECO:0000126 name: green fluorescent protein fusion protein localization evidence def: "A type of fusion protein localization evidence resulting from the labeling of a protein of interest with green fluorescent protein (GFP) from the jellyfish Aequorea victoria." [PMID:9759496] synonym: "GFP fusion protein localization evidence" EXACT [] synonym: "IDA: localization of GFP/YFP fusion protein" RELATED [] is_a: ECO:0000124 ! fusion protein localization evidence [Term] id: ECO:0000128 name: yellow fluorescent protein fusion protein localization evidence def: "A type of fusion protein localization evidence resulting from the labeling of a protein of interest with yellow fluorescent protein (YFP), which was created by mutating green fluorescent protein (GFP) of the Aequorea victoria." [MI:0368, url:http\://www.jbc.org/content/276/31/29188.long] synonym: "IDA: localization of GFP/YFP fusion protein" RELATED [] synonym: "YFP fusion protein localization evidence" EXACT [] is_a: ECO:0000124 ! fusion protein localization evidence [Term] id: ECO:0000130 name: beta-glucuronidase fusion protein localization evidence def: "A type of fusion protein localization evidence resulting from the targeted insertion of the beta-glucuronidase (GUS) coding gene as a reporter gene for the localization of a particular gene product." [ECO:RCT] synonym: "GUS fusion protein localization evidence" EXACT [] synonym: "GUS staining evidence" NARROW [] synonym: "IDA: localization of GUS fusion protein" RELATED [] is_a: ECO:0000124 ! fusion protein localization evidence [Term] id: ECO:0000132 name: beta-galactosidase fusion protein localization evidence def: "A type of fusion protein localization evidence resulting from the targeted insertion of the beta-galactosidase coding gene (lacZ) into a specific gene to create a beta-galactosidase-tagged fusion protein." [PMID:23681629] synonym: "LacZ fusion protein localization evidence" EXACT [] is_a: ECO:0000124 ! fusion protein localization evidence [Term] id: ECO:0000134 name: transport assay evidence def: "A type of direct assay evidence resulting from the activity assessment of transport proteins." [PMID:18401524] synonym: "IDA: transport assay" RELATED [] is_a: ECO:0000002 ! direct assay evidence relationship: IAO:0000136 GO:0015031 ! is about protein transport relationship: OBI:0000312 OBI:0000964 ! is_specified_output_of in live cell assay [Term] id: ECO:0000136 name: nucleic acid binding evidence def: "A type of affinity evidence resulting from the binding of a molecule to a nucleic acid." [GO:0003676] is_a: ECO:0000023 ! affinity evidence [Term] id: ECO:0000138 name: ribohomopolymer binding assay evidence def: "A type of nucleic acid binding evidence resulting from an enzyme displaying binding activity to specific ribohomopolymer." [PMC:102612] synonym: "IDA: ribohomopolymer binding assay" RELATED [] is_a: ECO:0000136 ! nucleic acid binding evidence [Term] id: ECO:0000140 name: thin layer chromatography evidence def: "A type of chromatography evidence that uses a thin layer of adsorbent (such as silica gel, alumina, or cellulose) on a flat, inert substrate." [ECO:MCC] synonym: "IDA: thin layer chromatography" RELATED [] synonym: "TLC evidence" EXACT [] is_a: ECO:0000325 ! chromatography evidence [Term] id: ECO:0000142 name: protein:ion binding evidence def: "A type of protein binding evidence resulting from a metal ion binding to a protein at a specific binding site." [PMID:2377604] is_a: ECO:0000024 ! protein binding evidence [Term] id: ECO:0000144 name: Southwestern blot evidence def: "A type of nucleic acid binding evidence in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins." [ECO:RCT, TAIR:TED] synonym: "IDA: Southwestern analysis" RELATED [] is_a: ECO:0000136 ! nucleic acid binding evidence [Term] id: ECO:0000146 name: Northwestern blot evidence def: "A type of nucleic acid binding evidence in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins." [ECO:RCT, TAIR:TED] synonym: "IDA: Northwestern analysis" RELATED [] is_a: ECO:0000136 ! nucleic acid binding evidence [Term] id: ECO:0000148 name: in vitro binding evidence is_obsolete: true [Term] id: ECO:0000150 name: in vitro transcription reconstitution assay evidence def: "A type of reconstitution assay evidence resulting from the use of reconstituted polymerase transcription systems to investigate RNA synthesis." [PMID:9237163] synonym: "IDA: in vitro reconstitution assay with recombinant protein" RELATED [] is_a: ECO:0000003 ! reconstitution assay evidence [Term] id: ECO:0000152 name: in vitro recombinant protein transcription reconstitution assay evidence def: "A type of in vitro transcription reconstitution assay evidence resulting from the use of recombinant proteins in preparation of a fully-defined transcription system." [PMID:9237165] synonym: "IDA: in vitro reconstitution assay with recombinant protein" RELATED [] is_a: ECO:0000150 ! in vitro transcription reconstitution assay evidence [Term] id: ECO:0000154 name: heterologous protein expression evidence def: "A type of protein expression evidence where a gene from one cell is inserted into a cell that does not typically contain that gene and heterologous protein expression is assessed." [ECO:KAV] synonym: "IDA: protein expression in heterologous system" RELATED [] is_a: ECO:0000010 ! protein expression evidence [Term] id: ECO:0000156 name: protein separation evidence def: "A type of fractionation evidence resulting from the isolation of a single type of protein from a complex mixture." [ERO:0000526] is_a: ECO:0000100 ! fractionation evidence [Term] id: ECO:0000158 name: protein separation followed by direct sequencing evidence synonym: "IDA: protein separation and direct sequencing" RELATED [] is_a: ECO:0000156 ! protein separation evidence [Term] id: ECO:0000160 name: protein separation followed by fragment identification evidence synonym: "IDA: protein separation and fragment identification" RELATED [] is_a: ECO:0000156 ! protein separation evidence [Term] id: ECO:0000162 name: heterologous system uptake evidence def: "A type of transport assay evidence in which the uptake mechanism of a transporter is investigated in a cell that does not normally express that protein." [doi:10.1146/annurev.pp.46.060195.002223, ECO:RCT] comment: The transporter is a recombinant protein. synonym: "IDA: uptake assay in heterologous system" RELATED [] is_a: ECO:0000134 ! transport assay evidence [Term] id: ECO:0000164 name: electrophysiology assay evidence def: "A type of direct assay evidence where electrical properties of cells or tissues are studied." [ECO:KAV] comment: The scale of electrophysiology assays can range from small, e.g. a single ion channel, to large, e.g. an entire organ such as a heart. is_a: ECO:0000002 ! direct assay evidence relationship: OBI:0000312 OBI:0002176 ! is_specified_output_of electrophysiology assay [Term] id: ECO:0000166 name: two-electrode voltage clamp recording evidence def: "A type of voltage clamp recording evidence which involves using two electrodes inserted into a large cell (often a xenopus oocyte) where one electrode is used to measure the internal potential (voltage) of the cell and the other electrode is used to clamp the current." [ECO:SN, PMID:23529422] synonym: "IDA: two-electrode voltage clamp technique" RELATED [] is_a: ECO:0005576 ! voltage clamp recording evidence [Term] id: ECO:0000168 name: transcription assay evidence def: "A type of direct assay evidence resulting from the detection and quantification of transcribed RNA." [MeSH:D014158, url:https\://bmcmolbiol.biomedcentral.com/articles/10.1186/1471-2199-15-7] is_a: ECO:0000002 ! direct assay evidence [Term] id: ECO:0000170 name: transcriptional activation assay evidence def: "A type of transcription assay evidence in which sequence-specific binding proteins that increase transcription of a specific target gene or genes are identified, quantified, and/or analyzed." [url:http\://smcg.ccg.unam.mx/enp-unam/05-TranscripYRegulacion/transcription.pdf] synonym: "IDA: transcriptional activation assay" RELATED [] is_a: ECO:0000168 ! transcription assay evidence relationship: IAO:0000136 GO:0001047 ! is about core promoter binding [Term] id: ECO:0000172 name: biochemical trait analysis evidence def: "A type of experimental phenotypic evidence in which the biochemical aspect of a mutation is analyzed." [ECO:RCT] comment: For example, the accumulation of a biosynthetic intermediate. synonym: "IMP: analysis of biochemical trait" RELATED [] is_a: ECO:0000059 ! experimental phenotypic evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0000366 ! is_specified_output_of metabolite profiling [Term] id: ECO:0000174 name: mutant physiological response evidence def: "A type of mutant phenotype evidence in which the physiological response of a mutant when presented with an external stimulus is determined." [ECO:RCT] comment: Examples include: abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions. synonym: "IMP: analysis of physiological response" RELATED [] is_a: ECO:0000015 ! mutant phenotype evidence relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay [Term] id: ECO:0000176 name: mutant visible phenotype evidence def: "A type of mutant phenotype evidence in which traits arising from a mutation are visually examined." [ECO:RCT] synonym: "IMP: analysis of visible trait" RELATED [] is_a: ECO:0000015 ! mutant phenotype evidence [Term] id: ECO:0000177 name: genomic context evidence def: "A type of evidence in which the location of the gene within the genome provides insight into its function, or provides evolutionary insight." [PMID:21609955] comment: This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis. is_a: ECO:0000000 ! evidence [Term] id: ECO:0000178 name: in vivo assay evidence def: "A type of direct assay evidence resulting from a sample of microorganisms or living tissue grown in a medium." [ECO:RCT, url:https\://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=46352] is_a: ECO:0000002 ! direct assay evidence relationship: OBI:0000312 OBI:0000964 ! is_specified_output_of in live cell assay [Term] id: ECO:0000179 name: animal model system study evidence def: "A type of experimental evidence arising from the investigation of an animal model system." [ECO:MCC] is_a: ECO:0000006 ! experimental evidence is_a: IAO:0000030 {is_inferred="true"} ! information content entity relationship: IAO:0000136 GO:0008150 ! is about biological_process relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay [Term] id: ECO:0000180 name: clinical study evidence def: "A type of experimental evidence arising from a controlled investigation that uses human subjects." [ECO:MCC] is_a: ECO:0000006 ! experimental evidence [Term] id: ECO:0000181 name: in vitro assay evidence alt_id: ECO:0005013 def: "A type of direct assay evidence resulting from a process performed outside the living organism, where the components of an organism have been isolated from their usual biological context, to permit a more detailed or more convenient analysis in an artificial setting." [ECO:RCT, url:https\://www.cancer.gov/publications/dictionaries/cancer-terms?cdrid=45733] is_a: ECO:0000002 ! direct assay evidence relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay [Term] id: ECO:0000182 name: in vitro culture assay evidence comment: Use ECO:0001563 (cell growth assay evidence) in place of this term. is_obsolete: true [Term] id: ECO:0000183 name: cell-free assay evidence def: "A type of direct assay evidence resulting from studies in which cytoplasmic and/or nuclear cellular components from resting, nonstimulated cells, are isolated by ultracentrifugation to provide molecular machinery that can be used in reactions in the absence of many of the other cellular components for the purpose of in vitro protein synthesis, transcription, DNA replication, etc." [PMID:18453125] synonym: "in vitro assay" BROAD [] is_a: ECO:0000002 ! direct assay evidence relationship: IAO:0000136 GO:0008152 ! is about metabolic process relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay [Term] id: ECO:0000184 name: enzyme inhibition evidence def: "A type of specific protein inhibition evidence where the protein under study is an enzyme." [ECO:MCC] is_a: ECO:0000005 ! enzyme assay evidence is_a: ECO:0000020 ! specific protein inhibition evidence [Term] id: ECO:0000200 name: sequence alignment evidence alt_id: ECO:00000057 def: "A type of sequence similarity evidence in which an annotation is made based on a manually-reviewed or published sequence alignment" [url:http\://www.geneontology.org/GO.evidence.shtml] comment: Such alignments may be pairwise alignments or multiple alignments. is_a: ECO:0000044 ! sequence similarity evidence created_by: mchibucos creation_date: 2010-03-18T12:21:31Z [Term] id: ECO:0000201 name: sequence orthology evidence alt_id: ECO:00000060 def: "A type of sequence similarity evidence in which orthology is established by multiple criteria, including amino acid and/or nucleotide sequence comparisons and one or more of the following: phylogenetic analysis, coincident expression, conserved map location, functional complementation, immunological cross-reaction, similarity in subcellular localization, subunit structure, substrate specificity, and response to specific inhibitors." [url:http\://www.geneontology.org/GO.evidence.shtml] comment: Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor. synonym: "ortholog evidence" RELATED [] is_a: ECO:0000044 ! sequence similarity evidence created_by: mchibucos creation_date: 2010-03-18T12:30:06Z [Term] id: ECO:0000202 name: match to sequence model evidence alt_id: ECO:00000063 def: "A type of sequence similarity evidence in which the function of a gene product is predicted based on a sequence-based statistical model." [ECO:MCC] {comment="url:http://www.geneontology.org/GO.evidence.shtml"} comment: Used when evidence from any kind of statistical model of a sequence or group of sequences is used to make a prediction about the function of a protein or RNA. Examples of relevant evidence are: Hidden Markov Models, PROSITE motifs, and tools such as tRNASCAN. is_a: ECO:0000044 ! sequence similarity evidence created_by: mchibucos creation_date: 2010-03-18T12:32:30Z [Term] id: ECO:0000203 name: automatic assertion alt_id: ECO:00000067 def: "An assertion method that does not involve human review." [ECO:MCC] comment: An automatic assertion is based on computationally generated information that is not reviewed by a person prior to making the assertion. For example, one common type of automatic assertion involves creating an association of evidence with an entity based on commonness of attributes of that entity and another entity for which an assertion already exists. The commonness is determined algorithmically. is_a: ECO:0000217 ! assertion method disjoint_from: ECO:0000218 ! manual assertion created_by: mchibucos creation_date: 2010-03-18T12:36:04Z [Term] id: ECO:0000204 name: author statement def: "An evidence type that is based on an assertion by the author of a paper, which is read by a curator." [ECO:MCC] is_a: ECO:0000000 ! evidence union_of: ECO:0000033 ! author statement supported by traceable reference union_of: ECO:0000034 ! author statement without traceable support created_by: mchibucos creation_date: 2010-06-21T11:17:21Z [Term] id: ECO:0000205 name: curator inference def: "A type of inferential evidence that is based on a conclusion drawn by a curator." [ECO:MCC] is_a: ECO:0000361 ! inferential evidence created_by: mchibucos creation_date: 2010-08-18T05:55:12Z [Term] id: ECO:0000206 name: BLAST evidence def: "A type of pairwise sequence alignment evidence obtained with basic local alignment search tool (BLAST)." [ECO:MCC] is_a: ECO:0005554 ! pairwise sequence alignment evidence created_by: mchibucos creation_date: 2010-08-06T04:48:24Z [Term] id: ECO:0000207 name: nucleotide BLAST evidence def: "A type of BLAST evidence in which nucleotide sequences are aligned." [ECO:MCC] is_a: ECO:0000206 ! BLAST evidence created_by: mchibucos creation_date: 2010-08-06T04:49:58Z [Term] id: ECO:0000208 name: protein BLAST evidence def: "A type of BLAST evidence in which amino acid or translated nucleotide sequences are aligned." [ECO:MCC] is_a: ECO:0000206 ! BLAST evidence created_by: mchibucos creation_date: 2010-08-06T04:50:45Z [Term] id: ECO:0000209 name: BLAST evidence used in automatic assertion def: "A type of BLAST evidence that is used in an automatic assertion." [ECO:MCC] is_a: ECO:0000206 ! BLAST evidence is_a: ECO:0005561 {is_inferred="true"} ! pairwise sequence alignment evidence used in automatic assertion intersection_of: ECO:0000206 ! BLAST evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-08-06T04:55:21Z [Term] id: ECO:0000210 name: nucleotide BLAST evidence used in automatic assertion def: "A type of nucleotide BLAST evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000207 ! nucleotide BLAST evidence is_a: ECO:0000209 {is_inferred="true"} ! BLAST evidence used in automatic assertion intersection_of: ECO:0000207 ! nucleotide BLAST evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-08-06T05:09:51Z [Term] id: ECO:0000211 name: protein BLAST evidence used in automatic assertion def: "A type of protein BLAST evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000208 ! protein BLAST evidence is_a: ECO:0000209 {is_inferred="true"} ! BLAST evidence used in automatic assertion intersection_of: ECO:0000208 ! protein BLAST evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-08-06T05:11:04Z [Term] id: ECO:0000212 name: combinatorial evidence alt_id: ECO:0000036 alt_id: ECO:0000043 def: "A type of evidence that arises out of the integration of more than one line of evidence." [ECO:MCC] comment: A key aspect of this type of evidence is that two or more pieces of information are combined to generate an emergent type of evidence not possible with the constituent pieces of evidence alone. A combinatorial analysis typically involves incorporation of different types of evidence. synonym: "inferred from in-silico analysis" RELATED [] is_a: ECO:0000000 ! evidence created_by: mchibucos creation_date: 2010-08-06T05:24:57Z [Term] id: ECO:0000213 name: combinatorial evidence used in automatic assertion def: "A type of combinatorial analysis that is used in an automatic assertion." [ECO:MCC] comment: Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments. synonym: "inferred from in-silico analysis" RELATED [] is_a: ECO:0000212 ! combinatorial evidence is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion intersection_of: ECO:0000212 ! combinatorial evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-08-06T05:28:33Z [Term] id: ECO:0000214 name: biological aspect of descendant evidence def: "A type of phylogenetic evidence whereby an aspect of an ancestral gene is inferred through the characterization of an aspect of a descendant gene." [ECO:MCC] comment: This type of evidence can be used in support of both positive and "not" GO annotations. It should be used to annotate ancestral genes but not extant ones. is_a: ECO:0000080 ! phylogenetic evidence created_by: mchibucos creation_date: 2010-10-05T11:16:50Z [Term] id: ECO:0000215 name: rapid divergence from ancestral sequence evidence def: "A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event." [ECO:MCC] comment: Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence. is_a: ECO:0000080 ! phylogenetic evidence created_by: mchibucos creation_date: 2010-10-05T03:41:34Z [Term] id: ECO:0000216 name: phylogenetic determination of loss of key residues evidence def: "A type of phylogenetic evidence characterized by the absence of key sequence residues." [ECO:MCC] comment: The loss of certain residues important for function can indicate that a sequence lacks a particular function. is_a: ECO:0000080 ! phylogenetic evidence created_by: mchibucos creation_date: 2010-10-05T03:43:17Z [Term] id: ECO:0000217 name: assertion method def: "A means by which a statement is made about an entity." [ECO:MCC] union_of: ECO:0000203 ! automatic assertion union_of: ECO:0000218 ! manual assertion created_by: mchibucos creation_date: 2010-11-12T04:17:37Z [Term] id: ECO:0000218 name: manual assertion def: "An assertion method that involves human review." [ECO:MCC] comment: A manual assertion could be based on evidence that is generated by and interpreted by a human or it could involve human review of computationally generated information. is_a: ECO:0000217 ! assertion method created_by: mchibucos creation_date: 2010-11-12T04:20:02Z [Term] id: ECO:0000219 name: nucleotide sequencing assay evidence def: "A type of sequencing assay that determines the sequence of a biopolymer comprised of nucleotides." [ECO:MCC] synonym: "DNA sequencing" RELATED [OBI:0000626] is_a: ECO:0000220 ! sequencing assay evidence created_by: mchibucos creation_date: 2010-11-15T12:22:40Z [Term] id: ECO:0000220 name: sequencing assay evidence def: "A type of experimental evidence where the order of molecules that constitute a biopolymer is determined." [ECO:MCC, OBI:0600047] is_a: ECO:0000006 ! experimental evidence created_by: mchibucos creation_date: 2010-11-15T01:44:45Z [Term] id: ECO:0000221 name: high throughput nucleotide sequencing assay evidence def: "A type of nucleotide sequencing assay evidence in which a sequence is derived from a parallelized sequencing technique." [ECO:MCC] comment: Typically thousands to millions of reads are produced in parallel. synonym: "next generation sequencing evidence" RELATED [] is_a: ECO:0000219 ! nucleotide sequencing assay evidence relationship: OBI:0000312 OBI:0001247 ! is_specified_output_of genotyping by high throughput sequencing assay created_by: mchibucos creation_date: 2010-11-15T02:19:34Z [Term] id: ECO:0000222 name: Illumina sequencing evidence def: "A type of high throughput nucleotide sequencing evidence in which sequence is determined through hybridization of adaptor-ligated DNA to a glass slide on which each fragment is simultaneously clonally amplified, followed by progressive rounds of base incorporation with fluorescently-tagged nucleotides, washing, imaging, and cleavage." [OBI:0000724, PMID:26000844] comment: In Illumina sequencing technology, adapters are ligated onto the ends of randomly fragmented DNA. After single-stranded fragments are bound to the inside surface of a flow cell channel, they undergo in-place bridge PCR amplification. To begin the sequencing cycle, labeled reversible terminators, primers and DNA polymerase are added, followed by laser excitation of the fluorescent label and high resolution scanning. After non-incorporated nucleotides are washed away and the dye is chemically removed, the next cycle repeats with four labeled reversible terminators, primers and DNA polymerase, again followed by imaging. synonym: "Solexa sequencing result" RELATED [OBI:0000724] is_a: ECO:0000221 ! high throughput nucleotide sequencing assay evidence created_by: mchibucos creation_date: 2010-11-15T02:38:03Z [Term] id: ECO:0000223 name: 454 pyrosequencing evidence def: "A type of high throughput nucleotide sequencing evidence in which the sequence for a ssDNA is determined by addition of primers and then nucleotides, one base pair at a time (which generate a specific fluorescence), to the target strand." [EFO:0005016] comment: 454 pyrosequencing technology amplifies individual DNA fragments inside water droplets within an oil solution (emulsion PCR). Within each droplet, a single DNA template is attached to a single primer-coated bead. Each bead is subsequently captured in a picolitre well within the sequencing machine. A luciferase-based readout system is used to identify individual nucleotides added to the nascent DNA.\n\nThe target strand is usually prepared by fragmentation, adaptor ligation, and amplification by emulsion PCR. synonym: "pyrosequencing" BROAD [OBI:0000730] is_a: ECO:0000221 ! high throughput nucleotide sequencing assay evidence created_by: mchibucos creation_date: 2010-11-15T03:50:14Z [Term] id: ECO:0000224 name: SOLiD sequencing evidence def: "A type of high throughput nucleotide sequencing evidence in which sequence is determined through rounds of ligation-based sequencing with fluorescently-labeled Di-base probes and cleavage, after which the template is reset, with a primer offset by one base, for subsequent rounds of ligation." [OBI:0000706] comment: SOLiD sequencing technology is based on sequencing by ligation. After library preparation, emulsion PCR and bead enrichment are performed, including 3' modification of templates on selected beads to allow covalent bonding to a slide. 3' modified beads are attached to a glass slide and primers are added. Four fluorescently labeled di-base probes are added and multiple cycles of ligation, detection and cleavage are performed. The number of cycles determines read length. After a number of ligation cycles, the extension product is removed and another round of ligation cycles is performed with a new primer complimentary to the n-1 position of the template. Five rounds of primer reset are performed for each sequence tag.\n\nSamples are prepared by fragmentation of a sample library, adaptor ligation, emulsion PCR, and attachment of resultant beads to glass slides. is_a: ECO:0000221 ! high throughput nucleotide sequencing assay evidence created_by: mchibucos creation_date: 2010-11-15T04:17:41Z [Term] id: ECO:0000225 name: chain termination sequencing evidence def: "A type of nucleotide sequencing assay in which DNA sequence is determined by addition of a primed DNA template to a reaction mixture, followed by addition of DNA polymerase, deoxynucleosidetriphosphates (dNTPs - one of which may be radiolabeled), and one of four di-deoxynucleotidetriphosphates (ddNTPs), after which DNA elongation is terminated and the DNA is separated by size and imaged." [OBI:0000695] comment: Chain termination sequencing, also called Sanger sequencing after its developer, uses dideoxynucleotide triphosphates (ddNTPs) as DNA chain terminators. Single-stranded DNA template, DNA primer, DNA polymerase, fluorescently or radioactively labeled nucleotides, and one of four ddNTPs are added together in each of four separate sequencing reactions. The synthesized and labeled DNA fragments from each of the four reactions are denatured, separated by size by gel electrophoresis, and visualized by autoradiography or UV light.\n\nThe ddNTPs lack an OH group so the next dNTP cannot be attached, causing chain termination. synonym: "dye terminator sequencing" EXACT [] synonym: "Sanger sequencing" EXACT [] is_a: ECO:0000219 ! nucleotide sequencing assay evidence created_by: mchibucos creation_date: 2010-11-15T04:46:31Z [Term] id: ECO:0000226 name: chromatin immunoprecipitation evidence def: "A type of immunoprecipitation evidence that is used to identify a protein binding site on a genomic DNA sequence." [ECO:MCC] comment: Chromatin immunoprecipitation (ChIP) is used to investigate protein-DNA interactions in vivo. DNA and proteins are chemically cross-linked in vivo to form chromatin complexes, followed by cell lysis and DNA shearing. Fragmented DNA-protein complexes are selectively enriched for a protein of interest using a specific antibody (immunoprecipitation). Protein digestion and DNA purification are performed prior to DNA detection via molecular cloning and sequencing, polymerase chain reaction (PCR), microarray analysis (ChIP-on-chip), or direct high-throughput sequencing (ChIP-seq). synonym: "ChIP evidence" EXACT [] xref: MI:0402 "chromatin immunoprecipitation assay" is_a: ECO:0000085 ! immunoprecipitation evidence relationship: IAO:0000136 GO:0043565 ! is about sequence-specific DNA binding relationship: OBI:0000312 OBI:0001956 ! is_specified_output_of assay using chromatin immunoprecipitation created_by: mchibucos creation_date: 2010-11-16T01:29:08Z [Term] id: ECO:0000227 name: chromatin immunoprecipitation-PCR evidence def: "A type of chromatin immunoprecipitation evidence that uses polymerase chain reaction (PCR) where specific primers are used on the pulled-down DNA for DNA detection." [ECO:MCC, ECO:SW, PMID:18388953] comment: ChIP-PCR is often used to validate ChIP-chip results and less frequently,ChIP-Seq results. synonym: "ChIP-PCR evidence" EXACT [] is_a: ECO:0000226 ! chromatin immunoprecipitation evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: mchibucos creation_date: 2010-11-16T05:02:00Z [Term] id: ECO:0000228 name: chromatin immunoprecipitation-qPCR evidence def: "A type of chromatin immunoprecipitation evidence in which protein-DNA interactions are investigated at known genomic binding sites through a process of ChIP, DNA purification, and finally quantitative polymerase chain reaction (qPCR) for DNA detection." [url:https\://www.diagenode.com/applications/chip-qpcr] synonym: "ChIP-qPCR evidence" EXACT [] is_a: ECO:0000226 ! chromatin immunoprecipitation evidence relationship: OBI:0000312 OBI:0002169 ! is_specified_output_of ChIP-qPCR assay created_by: mchibucos creation_date: 2010-11-16T05:26:47Z [Term] id: ECO:0000229 name: chromatin immunoprecipitation-seq evidence def: "A type of chromatin immunoprecipitation evidence that uses high-throughput sequencing where immunoprecipitated DNA fragments are funnelled into a massively parallel sequencer to produce multiple short reads for locating binding sites of DNA-associated proteins." [ECO:MCC, ECO:SW, OBI:0000716, PMID:22955991] comment: ChIP-Seq experiments often use the input as a control to eliminate biases. To obtain similar results, ChIP-chip with high-density tiling arrays can be used. synonym: "ChIP-SEQ evidence" EXACT [OBI:0000716] synonym: "ChIP-seq evidence" EXACT [PMID:22955991] is_a: ECO:0000226 ! chromatin immunoprecipitation evidence relationship: IAO:0000136 GO:0043565 ! is about sequence-specific DNA binding relationship: OBI:0000312 OBI:0000716 ! is_specified_output_of ChIP-seq assay property_value: IAO:0000234 "CollecTF" xsd:string created_by: mchibucos creation_date: 2010-11-16T05:30:41Z [Term] id: ECO:0000230 name: chromatin immunoprecipitation-chip evidence def: "A type of chromatin immunoprecipitation evidence that uses a tiling microarray for the detection of protein-bound DNA regions where chromatin is immunoprecipitated for protein tagging and DNA is sheared from the cross-linked protein-DNA complex to be arrayed revealing the protein-bound genomic regions." [ECO:MCC, ECO:SW, PMID:18388953, PMID:19381927] comment: A fixating agent such as formaldehyde is used to cross link proteins and DNA. Sonication is applied for DNA shearing. For transcription factor tagging, an antibody or epitope is employed. After cross-linking is reversed, the DNA is amplified and labeled with a flourophore for microarray which produces a resolution of aproximately 500 bp. synonym: "ChIP-chip evidence" EXACT [] synonym: "ChIP-on-chip evidence" EXACT [] xref: MI:0225 "chromatin immunoprecipitation array" is_a: ECO:0000226 ! chromatin immunoprecipitation evidence relationship: IAO:0000136 GO:0043565 ! is about sequence-specific DNA binding relationship: OBI:0000312 OBI:0001248 ! is_specified_output_of ChIP-chip assay property_value: IAO:0000234 "CollecTF" xsd:string created_by: mchibucos creation_date: 2010-11-16T05:43:55Z [Term] id: ECO:0000231 name: quantitative polymerase chain reaction evidence def: "A type of DNA detection assay evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes or fluorescent probes for detection and quantification of specific sequences in a DNA sample." [ECO:MCC, ECO:SW] comment: Quantitative PCR 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. The dye is activated upon binding double-stranded DNA.\n\nAlthough qRT-PCR is commonly found in literature synonymous to qPCR, it is preferable not to use this synonym as it is the accepted abbreviation for reverse transcription PCR. qPCR should be used instead (ISBN 978-0-470-68386-6 page 173).\n\nqPCR can be used to quantitatively determine levels of gene expression. synonym: "Q-PCR evidence" EXACT [] synonym: "qPCR evidence" EXACT [] synonym: "qRT-PCR evidence" RELATED [] synonym: "quantitative PCR evidence" EXACT [] synonym: "quantitative real-time PCR evidence" EXACT [] synonym: "real time polymerase chain reaction evidence" EXACT [] synonym: "real-time PCR evidence" EXACT [] synonym: "real-time quantitative PCR" EXACT [] is_a: ECO:0005519 ! DNA detection assay evidence relationship: OBI:0000312 OBI:0000893 ! is_specified_output_of real time polymerase chain reaction assay property_value: IAO:0000234 "CollecTF" xsd:string created_by: mchibucos creation_date: 2010-11-16T05:57:20Z [Term] id: ECO:0000232 name: chromosome conformation-based evidence def: "A type of experimental evidence that is based on a five-step technique of cross-linking DNA in vivo, restriction digestion, intramolecular ligation, reversing DNA cross-links, DNA processing, and quantitation that serves to analyze the spatial organization of chromatin in a cell and quantify the number of interactions between genomic loci that are nearby in 3-D space." [ECO:MCC] comment: Chromosome conformation capture technologies are used to study the structural properties and spatial organization of chromosomes inside cells. All types of chromosome conformation capture technology involve five primary steps: cross-linking of DNA in vivo, restriction digestion, intramolecular ligation, reversing cross-linkages, and DNA enrichment and quantitation. The last step is different for each type of chromosome conformation capture technology, and may include PCR (3C), inverse PCR (4C), or ligation-mediated amplification (5C). Methods for product quantitation can include agarose gel detection or real-time quantitative PCR in the case of 3C, or high-throughput sequencing or microarray analysis for 4C and 5C. synonym: "3C" NARROW [] synonym: "chromosome conformation capture" NARROW [] synonym: "chromosome conformation capture-based evidence" EXACT [] is_a: ECO:0000006 ! experimental evidence relationship: OBI:0000312 OBI:0002438 ! is_specified_output_of nuclear ligation assay created_by: mchibucos creation_date: 2010-11-17T12:27:14Z [Term] id: ECO:0000233 name: 3C evidence def: "A type of chromosome conformation-based evidence that is derived by 1) quantifying interactions between a single pair of genomic loci and not multiple interactions and 2) performing polymerase chain reaction (PCR) in the final product quantitation step." [ECO:MCC] comment: 3C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C differs only in the fifth step, which involves performing either standard polymerase chain reaction (PCR) or quantitative PCR (qPCR) for product quantitation. synonym: "3C" EXACT [] synonym: "chromosome conformation capture evidence" EXACT [] synonym: "chromosome conformation capture-PCR evidence" NARROW [] is_a: ECO:0000232 ! chromosome conformation-based evidence relationship: OBI:0000312 OBI:0002439 ! is_specified_output_of chromosome conformation capture assay created_by: mchibucos creation_date: 2010-11-17T12:46:15Z [Term] id: ECO:0000234 name: 4C evidence def: "A type of chromosome conformation-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a prior circularized 3C library followed by product quantitation with a microarray." [ECO:MCC, PMID:17033624] comment: 4C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 4C differs only in the fifth step, which involves inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation. synonym: "chromosome conformation capture on chip" EXACT [] synonym: "circularized 3C" EXACT [] synonym: "circularized chromosome conformation capture evidence" EXACT [] is_a: ECO:0000232 ! chromosome conformation-based evidence created_by: mchibucos creation_date: 2010-11-19T01:20:28Z [Term] id: ECO:0000235 name: 5C evidence def: "A type of chromosome conformation-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation." [ECO:MCC] comment: 5C is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 5C differs only in the fifth step, which involves ligation-mediated amplification (LMA) followed by product quantitation. synonym: "5C" EXACT [] synonym: "carbon-copy 3C" EXACT [] synonym: "carbon-copy chromosome conformation capture evidence" EXACT [] is_a: ECO:0000232 ! chromosome conformation-based evidence relationship: OBI:0000312 OBI:0001919 ! is_specified_output_of Carbon-copy chromosome conformation capture assay created_by: mchibucos creation_date: 2010-11-19T01:22:20Z [Term] id: ECO:0000236 name: chromosome conformation capture-PCR evidence def: "A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step." [ECO:MCC] comment: See 3C evidence. 3C evidence was initially developed using PCR. synonym: "3C" BROAD [] synonym: "3C-PCR" EXACT [] is_obsolete: true created_by: mchibucos creation_date: 2010-11-19T03:00:47Z [Term] id: ECO:0000237 name: 3C-qPCR evidence def: "A type of 3C evidence evidence that 1) quantifies interactions between a single pair of genomic loci (not multiple interactions) and 2) performs quantitative polymerase chain reaction (qPCR) in the quantitation step." [ECO:MCC, PMID:17641637, PMID:26025624] synonym: "3C-quantitative PCR" EXACT [] synonym: "3C-real-time PCR" EXACT [] synonym: "chromosome conformation capture-qPCR evidence" EXACT [] is_a: ECO:0000233 ! 3C evidence created_by: mchibucos creation_date: 2010-11-19T03:06:47Z [Term] id: ECO:0000238 name: Hi-C evidence def: "A type of chromosome conformation-based evidence that is derived by performing immunoprecipitation enrichment of the biotin labelled ligated fragments events prior to sequencing of the library and mapping it to the genome." [ECO:MCC] comment: Hi-C is used to study the structural properties and spatial organization of chromosomes inside cells. Hi-C is similar to other types of chromosome conformation capture technology, but involves the addition of biotinylated nucleotides during the second or fourth step and enrichment for ligated fragments using immunoprecipitation after the fourth step. is_a: ECO:0000232 ! chromosome conformation-based evidence relationship: OBI:0000312 OBI:0002440 ! is_specified_output_of Hi-C assay created_by: mchibucos creation_date: 2010-11-19T04:24:03Z [Term] id: ECO:0000239 name: 3C-seq evidence def: "A type of chromosome conformation-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with multiplexed high-throughput (HT) sequencing." [ECO:MCC, PMID:23411633] comment: 3C-seq is used to study the structural properties and spatial organization of chromosomes inside cells. Like other types of chromosome conformation capture technology, 3C-seq differs only in the fifth step, which involves inverse polymerase chain reaction (PCR) on a circularized 3C library prior to product quantitation. synonym: "3C sequencing" EXACT [] synonym: "chromosome conformation capture sequencing evidence" RELATED [] synonym: "circularized 3C sequencing" EXACT [] synonym: "circularized 3C-seq" EXACT [] is_a: ECO:0000232 ! chromosome conformation-based evidence created_by: mchibucos creation_date: 2010-11-30T03:22:25Z [Term] id: ECO:0000240 name: anatomical perturbation evidence def: "A type of experimental phenotypic evidence in which the phenotype of an organism is observed after the disruption of a structural feature." [ECO:MCC] is_a: ECO:0000059 ! experimental phenotypic evidence created_by: mchibucos creation_date: 2010-12-06T12:24:16Z [Term] id: ECO:0000241 name: environmental perturbation evidence def: "A type of experimental phenotypic evidence in which the phenotype of an organism is observed after modification of the extra-organismal context." [ECO:MCC] comment: Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth. synonym: "mechanical constraint evidence" RELATED [] is_a: ECO:0000059 ! experimental phenotypic evidence created_by: mchibucos creation_date: 2010-12-06T12:33:58Z [Term] id: ECO:0000242 name: tissue ablation evidence def: "A type of anatomical perturbation that is based on disruption of tissue." [ECO:MCC] comment: A tissue ablation experiment involves observing the phenotype of an entity whose tissues have been disrupted through genetic or biochemical manipulation, physical destruction, or some other means. synonym: "ablated tissue evidence" EXACT [] is_a: ECO:0000240 ! anatomical perturbation evidence created_by: mchibucos creation_date: 2010-12-06T12:33:58Z [Term] id: ECO:0000243 name: tissue grafting evidence def: "A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure." [ECO:MCC] is_a: ECO:0000240 ! anatomical perturbation evidence relationship: IAO:0000136 GO:0008150 ! is about biological_process relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay created_by: mchibucos creation_date: 2010-12-06T12:33:58Z [Term] id: ECO:0000244 name: combinatorial evidence used in manual assertion def: "A type of combinatorial analysis that is used in a manual assertion." [ECO:MCC] comment: Combinatorial analyses could include experimental or computational results. Examples include: (i) large-scale experiment such as a genome-wide two-hybrid or genome-wide synthetic interactions; (ii) integration of large-scale data sets of various types; and (iii) text-based-computation, e.g. text-mining. For simple sequence comparisons, one should use the sequence similarity analysis evidence type. For microarray results alone, expression pattern analysis is appropriate; whereas, large-scale computational analysis should be used when microarray results are combined with the results of other types of large-scale experiments. synonym: "inferred from in-silico analysis" RELATED [] is_a: ECO:0000212 ! combinatorial evidence is_a: ECO:0000352 {is_inferred="true"} ! evidence used in manual assertion intersection_of: ECO:0000212 ! combinatorial evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-09T02:02:12Z [Term] id: ECO:0000245 name: computational combinatorial evidence used in manual assertion def: "A type of computational combinatorial analysis that is used in a manual assertion." [ECO:MCC] subset: valid_with_gene subset: valid_with_protein subset: valid_with_protein_complex synonym: "inferred from reviewed computational analysis" EXACT [GOECO:RCA] synonym: "RCA" EXACT [GOECO:RCA] xref: GOECO:RCA "inferred from reviewed computational analysis" is_a: ECO:0000053 ! computational combinatorial evidence is_a: ECO:0000244 {is_inferred="true"} ! combinatorial evidence used in manual assertion intersection_of: ECO:0000053 ! computational combinatorial evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/rca-inferred-reviewed-computational-analysis xsd:string created_by: mchibucos creation_date: 2010-12-09T02:37:54Z [Term] id: ECO:0000246 name: computational combinatorial evidence used in automatic assertion def: "A type of computational combinatorial analysis that is used in an automatic assertion." [ECO:MCC] is_a: ECO:0000053 ! computational combinatorial evidence is_a: ECO:0000213 {is_inferred="true"} ! combinatorial evidence used in automatic assertion intersection_of: ECO:0000053 ! computational combinatorial evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-12-09T02:37:54Z [Term] id: ECO:0000247 name: sequence alignment evidence used in manual assertion def: "A type of sequence alignment evidence that is used in a manual assertion." [ECO:RCT] subset: valid_with_gene subset: valid_with_protein synonym: "inferred from sequence alignment" EXACT [GOECO:ISA] synonym: "ISA" EXACT [GOECO:ISA] xref: GOECO:ISA "inferred from sequence alignment" is_a: ECO:0000200 ! sequence alignment evidence is_a: ECO:0000250 {is_inferred="true"} ! sequence similarity evidence used in manual assertion intersection_of: ECO:0000200 ! sequence alignment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/isa-inferred-sequence-alignment xsd:string created_by: mchibucos creation_date: 2010-12-09T05:12:27Z [Term] id: ECO:0000248 name: sequence alignment evidence used in automatic assertion def: "A type of sequence alignment evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000200 ! sequence alignment evidence is_a: ECO:0000249 {is_inferred="true"} ! sequence similarity evidence used in automatic assertion intersection_of: ECO:0000200 ! sequence alignment evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-12-09T05:12:27Z [Term] id: ECO:0000249 name: sequence similarity evidence used in automatic assertion def: "A type of sequence similarity evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000044 ! sequence similarity evidence is_a: ECO:0000251 {is_inferred="true"} ! similarity evidence used in automatic assertion intersection_of: ECO:0000044 ! sequence similarity evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-12-09T05:22:30Z [Term] id: ECO:0000250 name: sequence similarity evidence used in manual assertion def: "A type of sequence similarity evidence that is used in a manual assertion." [ECO:MCC] subset: valid_with_gene subset: valid_with_protein subset: valid_with_protein_complex synonym: "inferred from sequence or structural similarity" EXACT [GOECO:ISS] synonym: "ISS" EXACT [GOECO:ISS] xref: GOECO:ISS "inferred from sequence or structural similarity" is_a: ECO:0000044 ! sequence similarity evidence is_a: ECO:0000252 {is_inferred="true"} ! similarity evidence used in manual assertion intersection_of: ECO:0000044 ! sequence similarity evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/iss-inferred-sequence-or-structural-similarity xsd:string created_by: mchibucos creation_date: 2010-12-09T05:22:30Z [Term] id: ECO:0000251 name: similarity evidence used in automatic assertion def: "A type of similarity evidence that is used in an automatic assertion." [ECO:RCT] synonym: "inferred from similarity" RELATED [] synonym: "IS" BROAD [] is_a: ECO:0000041 ! similarity evidence is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion intersection_of: ECO:0000041 ! similarity evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-12-09T05:28:12Z [Term] id: ECO:0000252 name: similarity evidence used in manual assertion def: "A type of similarity evidence that is used in a manual assertion." [ECO:RCT] subset: go_groupings synonym: "inferred from similarity" RELATED [] synonym: "IS" BROAD [] is_a: ECO:0000041 ! similarity evidence is_a: ECO:0000352 {is_inferred="true"} ! evidence used in manual assertion intersection_of: ECO:0000041 ! similarity evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-09T05:28:12Z [Term] id: ECO:0000253 name: genetic similarity evidence used in manual assertion def: "A type of genetic similarity evidence that is used in a manual assertion." [ECO:RCT] synonym: "IGTS" BROAD [] synonym: "inferred from genetic similarity" RELATED [] is_a: ECO:0000051 ! genetic similarity evidence is_a: ECO:0000252 {is_inferred="true"} ! similarity evidence used in manual assertion intersection_of: ECO:0000051 ! genetic similarity evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-10T01:42:44Z [Term] id: ECO:0000254 name: genetic similarity evidence used in automatic assertion def: "A type of genetic similarity evidence that is used in an automatic assertion." [ECO:RCT] synonym: "IGTS" BROAD [] synonym: "inferred from genetic similarity" RELATED [] is_a: ECO:0000051 ! genetic similarity evidence is_a: ECO:0000251 {is_inferred="true"} ! similarity evidence used in automatic assertion intersection_of: ECO:0000051 ! genetic similarity evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-12-10T01:42:44Z [Term] id: ECO:0000255 name: match to sequence model evidence used in manual assertion def: "A type of match to sequence model evidence that is used in a manual assertion." [ECO:RCT] synonym: "inferred from sequence model" EXACT [GOECO:ISM] synonym: "ISM" EXACT [GOECO:ISM] xref: GO_REF:0000011 "Hidden Markov Models (TIGR)" xref: GOECO:ISM "inferred from sequence model" is_a: ECO:0000202 ! match to sequence model evidence is_a: ECO:0000250 {is_inferred="true"} ! sequence similarity evidence used in manual assertion intersection_of: ECO:0000202 ! match to sequence model evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/ism-inferred-sequence-model xsd:string created_by: mchibucos creation_date: 2010-12-10T02:26:35Z [Term] id: ECO:0000256 name: match to sequence model evidence used in automatic assertion def: "A type of match to sequence model evidence that is used in an automatic assertion." [ECO:RCT] xref: GO_REF:0000002 "Gene Ontology annotation through association of InterPro records with GO terms." xref: GO_REF:0000107 "Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl" is_a: ECO:0000202 ! match to sequence model evidence is_a: ECO:0000249 {is_inferred="true"} ! sequence similarity evidence used in automatic assertion intersection_of: ECO:0000202 ! match to sequence model evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-12-10T02:26:35Z [Term] id: ECO:0000257 name: motif similarity evidence used in manual assertion def: "A type of motif similarity evidence that is used in a manual assertion." [ECO:RCT] synonym: "ISS: recognized domains" RELATED [] is_a: ECO:0000028 ! motif similarity evidence is_a: ECO:0000255 {is_inferred="true"} ! match to sequence model evidence used in manual assertion intersection_of: ECO:0000028 ! motif similarity evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-10T02:44:34Z [Term] id: ECO:0000258 name: motif similarity evidence used in automatic assertion def: "A type of motif similarity evidence that is used in an automatic assertion." [ECO:RCT] synonym: "ISS: recognized domains" RELATED [] is_a: ECO:0000028 ! motif similarity evidence is_a: ECO:0000256 {is_inferred="true"} ! match to sequence model evidence used in automatic assertion intersection_of: ECO:0000028 ! motif similarity evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-12-10T02:44:34Z [Term] id: ECO:0000259 name: match to InterPro member signature evidence used in automatic assertion def: "A type of match to InterPro member signature evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000029 ! match to InterPro member signature evidence is_a: ECO:0000256 {is_inferred="true"} ! match to sequence model evidence used in automatic assertion intersection_of: ECO:0000029 ! match to InterPro member signature evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-12-10T02:54:51Z [Term] id: ECO:0000260 name: match to InterPro member signature evidence used in manual assertion def: "A type of match to InterPro member signature evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000029 ! match to InterPro member signature evidence is_a: ECO:0000255 {is_inferred="true"} ! match to sequence model evidence used in manual assertion intersection_of: ECO:0000029 ! match to InterPro member signature evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-10T02:54:51Z [Term] id: ECO:0000261 name: targeting sequence prediction evidence used in automatic assertion def: "A type of targeting sequence prediction that is used in an automatic assertion." [ECO:RCT] synonym: "ISS: targeting sequence prediction" RELATED [] is_a: ECO:0000081 ! targeting sequence prediction evidence is_a: ECO:0000258 {is_inferred="true"} ! motif similarity evidence used in automatic assertion intersection_of: ECO:0000081 ! targeting sequence prediction evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-12-10T03:02:49Z [Term] id: ECO:0000262 name: targeting sequence prediction evidence used in manual assertion def: "A type of targeting sequence prediction that is used in a manual assertion." [ECO:RCT] synonym: "ISS: targeting sequence prediction" RELATED [] is_a: ECO:0000081 ! targeting sequence prediction evidence is_a: ECO:0000257 {is_inferred="true"} ! motif similarity evidence used in manual assertion intersection_of: ECO:0000081 ! targeting sequence prediction evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-10T03:02:49Z [Term] id: ECO:0000263 name: transmembrane domain prediction evidence used in automatic assertion def: "A type of transmembrane domain prediction that is used in an automatic assertion." [ECO:RCT] synonym: "ISS: transmembrane domain prediction" RELATED [] is_a: ECO:0000083 ! transmembrane domain prediction evidence is_a: ECO:0000258 {is_inferred="true"} ! motif similarity evidence used in automatic assertion intersection_of: ECO:0000083 ! transmembrane domain prediction evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-12-10T03:28:35Z [Term] id: ECO:0000264 name: transmembrane domain prediction evidence used in manual assertion def: "A type of transmembrane domain prediction that is used in a manual assertion." [ECO:RCT] synonym: "ISS: transmembrane domain prediction" RELATED [] is_a: ECO:0000083 ! transmembrane domain prediction evidence is_a: ECO:0000257 {is_inferred="true"} ! motif similarity evidence used in manual assertion intersection_of: ECO:0000083 ! transmembrane domain prediction evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-10T03:28:35Z [Term] id: ECO:0000265 name: sequence orthology evidence used in automatic assertion def: "A type of sequence orthology evidence that is used in an automatic assertion." [ECO:RCT] synonym: "Ortholog evidence" RELATED [] synonym: "ortholog evidence" RELATED [] xref: GO_REF:0000019 "Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara" xref: GO_REF:0000020 "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins." xref: GO_REF:0000035 "Automatic transfer of experimentally verified manual GO annotation data to plant orthologs using Ensembl Compara" xref: GO_REF:0000049 "Automatic transfer of experimentally verified manual GO annotation data to fungal orthologs using Ensembl Compara" is_a: ECO:0000201 ! sequence orthology evidence is_a: ECO:0000249 {is_inferred="true"} ! sequence similarity evidence used in automatic assertion intersection_of: ECO:0000201 ! sequence orthology evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2010-12-10T03:39:41Z [Term] id: ECO:0000266 name: sequence orthology evidence used in manual assertion def: "A type of sequence orthology evidence that is used in a manual assertion." [ECO:MCC] subset: valid_with_gene subset: valid_with_protein subset: valid_with_protein_complex synonym: "inferred from sequence orthology" EXACT [] {name="GOECO:ISO"} synonym: "ISO" EXACT [GOECO:ISO] synonym: "Ortholog evidence" RELATED [] synonym: "ortholog evidence" RELATED [] xref: GOECO:ISO "inferred from sequence orthology" is_a: ECO:0000201 ! sequence orthology evidence is_a: ECO:0000250 {is_inferred="true"} ! sequence similarity evidence used in manual assertion intersection_of: ECO:0000201 ! sequence orthology evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/iso-inferred-sequence-orthology xsd:string created_by: mchibucos creation_date: 2010-12-10T03:39:41Z [Term] id: ECO:0000267 name: enzyme-linked immunoabsorbent assay evidence def: "A type of protein detection assay evidence where an antigen is bound to a substrate, and an antibody directly or indirectly linked to an enzyme is utilized to determine the amount of bound antigen which is visualized with a color change in the substrate." [ECO:MCC, ECO:SW, PMID:23949770] comment: ELISA is sometimes used in the study of transcriptional regulation to identify a produced protein, especially secreted protein. synonym: "ELISA evidence" EXACT [] synonym: "enzyme-linked immunosorbent assay" NARROW [] xref: MI:0411 "enzyme linked immunosorbent assay" is_a: ECO:0005517 ! protein detection assay evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: mchibucos creation_date: 2010-12-14T01:57:13Z [Term] id: ECO:0000268 name: flow cytometry evidence def: "A type of direct assay evidence in which cells or particles are characterized by passing them through a light source and monitoring the resultant light scatter or fluorochrome excitation." [ECO:MCC] synonym: "FCM" EXACT [] is_a: ECO:0000002 ! direct assay evidence relationship: OBI:0000312 OBI:0000916 ! is_specified_output_of flow cytometry assay created_by: mchibucos creation_date: 2010-12-14T02:07:08Z [Term] id: ECO:0000269 name: experimental evidence used in manual assertion def: "A type of experimental evidence that is used in a manual assertion." [ECO:MCC] synonym: "EXP" EXACT [GOECO:EXP] synonym: "inferred from experiment" EXACT [GOECO:EXP] xref: GOECO:EXP "inferred from experiment" is_a: ECO:0000006 ! experimental evidence is_a: ECO:0000352 {is_inferred="true"} ! evidence used in manual assertion intersection_of: ECO:0000006 ! experimental evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/exp-inferred-experiment xsd:string created_by: mchibucos creation_date: 2010-12-20T05:36:49Z [Term] id: ECO:0000270 name: expression evidence used in manual assertion def: "A type of expression pattern evidence that is used in a manual assertion." [ECO:MCC] synonym: "IEP" EXACT [GOECO:IEP] synonym: "inferred from expression pattern" EXACT [GOECO:IEP] xref: GOECO:IEP "inferred from expression pattern" is_a: ECO:0000008 ! expression pattern evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000008 ! expression pattern evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/iep-inferred-expression-pattern xsd:string created_by: mchibucos creation_date: 2010-12-20T05:46:39Z [Term] id: ECO:0000271 name: array experiment evidence used in manual assertion comment: This general 'array experiment' term should not be used - replace with the specific type of array (e.g. ECO:0000273, ECO:0000276, ECO:0000285, etc.) is_obsolete: true created_by: mchibucos creation_date: 2010-12-20T05:51:58Z [Term] id: ECO:0000272 name: Affymetrix GeneChip evidence used in manual assertion def: "A type of Affymetrix GeneChip evidence that is used in a manual assertion." [ECO:MCC] synonym: "Affymetrix array experiment evidence" BROAD [] is_a: ECO:0000101 ! Affymetrix GeneChip evidence is_a: ECO:0000276 {is_inferred="true"} ! cRNA to DNA expression microarray evidence used in manual assertion intersection_of: ECO:0000101 ! Affymetrix GeneChip evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T05:53:36Z [Term] id: ECO:0000273 name: cDNA to DNA expression microarray evidence used in manual assertion alt_id: ECO:0001178 alt_id: ECO:0005525 def: "A type of cDNA to DNA expression microarray evidence that is used in a manual assertion." [ECO:MCC] synonym: "DNA microarray|RNA microarray" RELATED [] is_a: ECO:0000097 ! cDNA to DNA expression microarray evidence is_a: ECO:0000275 {is_inferred="true"} ! expression microarray evidence used in manual assertion intersection_of: ECO:0000097 ! cDNA to DNA expression microarray evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T05:55:49Z [Term] id: ECO:0000274 name: differential methylation hybridization evidence used in manual assertion def: "A type of differential methylation hybridization evidence that is used in a manual assertion." [ECO:RCT] synonym: "CpG island microarray evidence" BROAD [] synonym: "CpG island microarray evidence used in manual assertion" EXACT [] is_a: ECO:0000069 ! differential methylation hybridization evidence is_a: ECO:0001198 {is_inferred="true"} ! in vitro methylation assay evidence used in manual assertion intersection_of: ECO:0000069 ! differential methylation hybridization evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T05:58:44Z [Term] id: ECO:0000275 name: expression microarray evidence used in manual assertion def: "A type of expression microarray evidence that is used in a manual assertion." [ECO:MCC] synonym: "differential gene expression evidence from microarray experiment" RELATED [] is_a: ECO:0000058 ! expression microarray evidence is_a: ECO:0000291 {is_inferred="true"} ! transcript expression evidence used in manual assertion intersection_of: ECO:0000058 ! expression microarray evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:01:26Z [Term] id: ECO:0000276 name: cRNA to DNA expression microarray evidence used in manual assertion def: "A type of cRNA to DNA expression microarray evidence that is used in a manual assertion." [ECO:RCT] synonym: "genomic microarray evidence" BROAD [] synonym: "genomic microarray evidence used in manual assertion" EXACT [] is_a: ECO:0000062 ! cRNA to DNA expression microarray evidence is_a: ECO:0000275 {is_inferred="true"} ! expression microarray evidence used in manual assertion intersection_of: ECO:0000062 ! cRNA to DNA expression microarray evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:03:28Z [Term] id: ECO:0000277 name: Nimblegen array evidence used in manual assertion def: "A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000105 ! Nimblegen array evidence is_a: ECO:0000273 {is_inferred="true"} ! cDNA to DNA expression microarray evidence used in manual assertion intersection_of: ECO:0000105 ! Nimblegen array evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:05:20Z [Term] id: ECO:0000278 name: array-based sequence capture evidence used in manual assertion def: "A type of array-based sequence capture evidence that is used in a manual assertion." [ECO:MCC] synonym: "DNA microarray" BROAD [] synonym: "oligonucleotide microarray evidence" BROAD [] synonym: "oligonucleotide microarray evidence used in manual assertion" BROAD [] synonym: "single nucleotide polymorphism array evidence" RELATED [] synonym: "SNP array evidence" RELATED [] is_a: ECO:0000093 ! array-based sequence capture evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000093 ! array-based sequence capture evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:09:45Z [Term] id: ECO:0000279 name: western blot evidence used in manual assertion def: "A type of Western blot assay that is used in a manual assertion." [ECO:MCC] synonym: "IEP: protein levels (e.g. Western blots)" RELATED [] synonym: "protein immunoblot" RELATED [] synonym: "Western blot expression analysis" RELATED [] is_a: ECO:0000112 ! western blot evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000112 ! western blot evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:20:01Z [Term] id: ECO:0000280 name: protein expression level evidence used in manual assertion def: "A type of protein expression level analysis that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000046 ! protein expression level evidence is_a: ECO:0000284 {is_inferred="true"} ! protein expression evidence used in manual assertion intersection_of: ECO:0000046 ! protein expression level evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:21:54Z [Term] id: ECO:0000281 name: expression library screen evidence used in manual assertion def: "A type of expression library screen evidence that is used in a manual assertion." [ECO:MCC] synonym: "IEP: expression library screening" RELATED [] is_a: ECO:0000114 ! expression library screen evidence is_a: ECO:0000284 {is_inferred="true"} ! protein expression evidence used in manual assertion intersection_of: ECO:0000114 ! expression library screen evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:24:05Z [Term] id: ECO:0000282 name: heterologous protein expression evidence used in manual assertion def: "A type of heterologous protein expression analysis that is used in a manual assertion." [ECO:MCC] synonym: "IDA: protein expression in heterologous system" RELATED [] is_a: ECO:0000154 ! heterologous protein expression evidence is_a: ECO:0000284 {is_inferred="true"} ! protein expression evidence used in manual assertion intersection_of: ECO:0000154 ! heterologous protein expression evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:27:04Z [Term] id: ECO:0000283 name: spatial pattern of protein expression evidence used in manual assertion def: "A type of protein expression spatial pattern analysis that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000045 ! spatial pattern of protein expression evidence is_a: ECO:0000284 {is_inferred="true"} ! protein expression evidence used in manual assertion intersection_of: ECO:0000045 ! spatial pattern of protein expression evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:31:44Z [Term] id: ECO:0000284 name: protein expression evidence used in manual assertion def: "A type of protein expression analysis that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000010 ! protein expression evidence is_a: ECO:0000270 {is_inferred="true"} ! expression evidence used in manual assertion is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000010 ! protein expression evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:33:46Z [Term] id: ECO:0000285 name: DNA to cDNA expression microarray evidence used in manual assertion def: "A type of DNA to cDNA expression microarray evidence that is used in a manual assertion." [ECO:MCC] synonym: "IEP: transcript levels (e.g. microarray data)" RELATED [] synonym: "microarray RNA expression level evidence" BROAD [] synonym: "REM evidence" BROAD [] synonym: "RNA expression microarray evidence" BROAD [] is_a: ECO:0000104 ! DNA to cDNA expression microarray evidence is_a: ECO:0000275 {is_inferred="true"} ! expression microarray evidence used in manual assertion intersection_of: ECO:0000104 ! DNA to cDNA expression microarray evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:41:33Z [Term] id: ECO:0000287 name: differential hybridization evidence used in manual assertion def: "A type of differential hybridization experiment that is used in a manual assertion." [ECO:MCC] synonym: "IEP: differential hybridization" RELATED [] is_a: ECO:0000116 ! differential hybridization evidence is_a: ECO:0000291 {is_inferred="true"} ! transcript expression evidence used in manual assertion intersection_of: ECO:0000116 ! differential hybridization evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:55:14Z [Term] id: ECO:0000288 name: RNA protection assay evidence used in manual assertion def: "A type of RNA protection assay that is used in a manual assertion." [ECO:MCC] synonym: "IEP: RNA protection assay|RPA" RELATED [] synonym: "ribonuclease protection assay" BROAD [] synonym: "RNAse protection assay" RELATED [] is_a: ECO:0000110 ! RNA protection assay evidence is_a: ECO:0001240 {is_inferred="true"} ! nuclease protection assay evidence used in manual assertion intersection_of: ECO:0000110 ! RNA protection assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:57:33Z [Term] id: ECO:0000289 name: spatial pattern of transcript expression evidence used in manual assertion def: "A type of spatial pattern of transcript expression analysis that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000047 ! spatial pattern of transcript expression evidence is_a: ECO:0000291 {is_inferred="true"} ! transcript expression evidence used in manual assertion intersection_of: ECO:0000047 ! spatial pattern of transcript expression evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T06:59:18Z [Term] id: ECO:0000290 name: subtractive hybridization evidence used in manual assertion def: "A type of subtractive hybridization experiment that is used in a manual assertion." [ECO:MCC] synonym: "IEP: subtractive hybridization" RELATED [] is_a: ECO:0000118 ! subtractive hybridization evidence is_a: ECO:0000291 {is_inferred="true"} ! transcript expression evidence used in manual assertion intersection_of: ECO:0000118 ! subtractive hybridization evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T07:00:48Z [Term] id: ECO:0000291 name: transcript expression evidence used in manual assertion alt_id: ECO:0000286 def: "A type of transcript expression evidence that is used in a manual assertion." [ECO:MCC] synonym: "transcript expression level evidence" BROAD [] is_a: ECO:0000009 ! transcript expression evidence is_a: ECO:0000270 {is_inferred="true"} ! expression evidence used in manual assertion intersection_of: ECO:0000009 ! transcript expression evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2010-12-20T07:02:08Z [Term] id: ECO:0000292 name: morpholino experiment evidence def: "A type of mutant phenotype evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell." [ECO:MCC] comment: Morpholino oligonucleotides modify gene expression by blocking access of other molecules to specific, approximately 25-base-long regions of the base-pairing surfaces of ribonucleic acid (RNA). To achieve this anti-sense knockdown technique, delivery of the morpholino can be achieved via microinjection, electroporation, or another method. synonym: "anti-sense" BROAD [] is_a: ECO:0000015 ! mutant phenotype evidence created_by: mchibucos creation_date: 2011-01-10T03:36:25Z [Term] id: ECO:0000293 name: systematic evolution of ligands by exponential amplification evidence def: "A type of evidence arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand." [ECO:MCC, url:http\://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment] comment: SELEX begins with the synthesis of a large oligonucleotide library, either single-stranded DNA or RNA, which consists of random fixed-length sequences flanked by constant 5' and 3' ends that serve as primers. The library is exposed to a target ligand, typically a protein or small organic compound. Unbound sequences are removed, typically with affinity chromatography. Bound sequences are eluted and the nucleic acid is extracted, followed by PCR amplification (RNA is first reverse transcribed). PCR product is converted to single stranded (DNA) or transcribed (RNA). Oligonucleotides are bound to the ligand again and the process is repeated with increasing elution stringency. After several rounds of the process, recovered oligonucleotides are sequenced and analyzed to reveal the binding specificity of the protein. synonym: "in vitro evolution evidence" RELATED [] synonym: "in vitro selection evidence" EXACT [] synonym: "SELEX evidence" EXACT [] xref: MI:0657 "systematic evolution of ligands by exponential enrichment" is_a: ECO:0000021 ! physical interaction evidence created_by: mchibucos creation_date: 2011-01-10T04:23:50Z [Term] id: ECO:0000294 name: bacterial one-hybrid evidence def: "A type of hybrid interaction evidence that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey)." [ECO:MCC] comment: Bacterial one-hybrid assay is a method for screening a library of candidate proteins (prey plasmid) for the ability to bind to a target, cis-regulatory element or any other short, DNA binding sequence placed 5' to reporter genes (bait plasmid). Transformation of a bacterial host with two different plasmids is required: One is designed to express the "bait". The other plasmid contains a "prey" which, if bound to by the chimeric fusion product, drives expression of downstream reporter genes. synonym: "B1H evidence" EXACT [] is_a: ECO:0000025 ! hybrid interaction evidence created_by: mchibucos creation_date: 2011-01-10T06:16:20Z [Term] id: ECO:0000295 name: RNA-seq evidence alt_id: ECO:0000357 def: "A type of transcript evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules." [ECO:MCC] comment: Total RNA is isolated from cells and mRNA is purified by targeting the 3' polyadenylated (poly(A)) tail with poly(T) oligos covalently attached to a substrate. Next, cDNA fragments are generated either by hydrolysis of RNA into 200-300 base oligonucleotides, preceded by reverse transcription, or by reverse transcription initiated by random primers. The cDNA second strand is synthesized, fragments are adapter ligated and high-throughput sequencing is performed by Roche 454, Illumina, ABI-SOLiD, or another HT sequencing technology. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed. synonym: "differential gene expression evidence from RNA-seq experiment" NARROW [] synonym: "RNA sequencing" RELATED [] synonym: "whole transcriptome shotgun sequencing" EXACT [PMID:18611170] synonym: "WTSS" EXACT [] is_a: ECO:0000009 ! transcript expression evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0001271 ! is_specified_output_of RNA-seq assay created_by: mchibucos creation_date: 2011-01-11T12:54:50Z [Term] id: ECO:0000298 name: cleavage arrested development evidence def: "A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked." [ECO:MCC] comment: In the embryos of some organisms, inhibition of cytokinesis blocks neither the cell cycle nor the unfolding of the developmental program. As such, embryonic morphology can be frozen, allowing analysis of the developmental fate of each cell present at the time of cleavage arrest. is_a: ECO:0000059 ! experimental phenotypic evidence created_by: mchibucos creation_date: 2011-01-11T03:28:49Z [Term] id: ECO:0000299 name: cytochalasin experiment evidence def: "A type of cleavage arrested development that arises after treatment with cytochalasin." [ECO:MCC] comment: Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments. is_a: ECO:0000298 ! cleavage arrested development evidence relationship: IAO:0000136 GO:0072749 ! is about cellular response to cytochalasin B relationship: OBI:0000312 OBI:0001689 ! is_specified_output_of cytochalasin-induced inhibition of actin polymerization assay created_by: mchibucos creation_date: 2011-01-11T03:30:29Z [Term] id: ECO:0000300 name: green fluorescent protein immunolocalization evidence def: "A type of immunolocalization evidence data that was generated using green fluorescent protein (GFP) as a marker." [ECO:MCC] comment: This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript". synonym: "GFP immunolocalization evidence" EXACT [] is_a: ECO:0000087 ! immunolocalization evidence created_by: mchibucos creation_date: 2011-01-11T03:48:50Z [Term] id: ECO:0000301 name: beta-galactosidase protein immunolocalization evidence def: "A type of immunolocalization evidence that was generated using LacZ protein as a marker." [ECO:MCC] comment: This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript". synonym: "LacZ protein immunolocalization evidence" EXACT [] is_a: ECO:0000087 ! immunolocalization evidence created_by: mchibucos creation_date: 2011-01-11T04:06:40Z [Term] id: ECO:0000302 name: author statement used in manual assertion def: "A type of author statement that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000204 ! author statement is_a: ECO:0000352 {is_inferred="true"} ! evidence used in manual assertion intersection_of: ECO:0000204 ! author statement intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2011-01-20T02:26:47Z [Term] id: ECO:0000303 name: author statement without traceable support used in manual assertion def: "A type of author statement without traceable support that is used in a manual assertion." [ECO:MCC] synonym: "NAS" EXACT [GOECO:NAS] synonym: "non-traceable author statement" RELATED [GOECO:NAS] xref: GOECO:NAS "non-traceable author statement" is_a: ECO:0000034 ! author statement without traceable support is_a: ECO:0000302 {is_inferred="true"} ! author statement used in manual assertion intersection_of: ECO:0000034 ! author statement without traceable support intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/nas-non-traceable-author-statement xsd:string created_by: mchibucos creation_date: 2011-01-20T02:29:50Z [Term] id: ECO:0000304 name: author statement supported by traceable reference used in manual assertion def: "A type of author statement supported by traceable reference that is used in a manual assertion." [ECO:MCC] synonym: "TAS" EXACT [GOECO:TAS] synonym: "traceable author statement" RELATED [GOECO:TAS] xref: GOECO:TAS "traceable author statement" is_a: ECO:0000033 ! author statement supported by traceable reference is_a: ECO:0000302 {is_inferred="true"} ! author statement used in manual assertion intersection_of: ECO:0000033 ! author statement supported by traceable reference intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/tas-traceable-author-statement xsd:string created_by: mchibucos creation_date: 2011-01-20T02:31:03Z [Term] id: ECO:0000305 name: curator inference used in manual assertion def: "A type of curator inference that is used in a manual assertion." [ECO:MCC] subset: valid_with_biological_process subset: valid_with_cellular_component subset: valid_with_molecular_function synonym: "IC" EXACT [GOECO:IC] synonym: "inferred by curator" EXACT [GOECO:IC] xref: GOECO:IC "inferred by curator" is_a: ECO:0000205 ! curator inference is_a: ECO:0000352 {is_inferred="true"} ! evidence used in manual assertion intersection_of: ECO:0000205 ! curator inference intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/ic-inferred-curator xsd:string created_by: mchibucos creation_date: 2011-01-20T02:33:32Z [Term] id: ECO:0000306 name: inference from background scientific knowledge used in manual assertion def: "A type of inference from background scientific knowledge that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000001 ! inference from background scientific knowledge is_a: ECO:0000305 {is_inferred="true"} ! curator inference used in manual assertion intersection_of: ECO:0000001 ! inference from background scientific knowledge intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2011-01-20T02:35:11Z [Term] id: ECO:0000307 name: no biological data found used in manual assertion def: "A type of no biological data found that is used in a manual assertion." [ECO:MCC] synonym: "ND" EXACT [GOECO:ND] synonym: "no biological data available" EXACT [GOECO:ND] xref: GOECO:ND "no biological data available" is_a: ECO:0000035 ! no biological data found is_a: ECO:0000305 {is_inferred="true"} ! curator inference used in manual assertion intersection_of: ECO:0000035 ! no biological data found intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/nd-no-biological-data-available xsd:string created_by: mchibucos creation_date: 2011-01-20T02:43:18Z [Term] id: ECO:0000308 name: biological aspect of ancestor evidence def: "A type of phylogenetic evidence whereby an aspect of a descendant gene is inferred through the characterization of an aspect of an ancestral gene." [ECO:MCC] comment: First, a characteristic of the most recent common ancestor (MRCA) is inferred from experimental evidence in descendants; this is followed by inferring a characteristic of a descendant of the MRCA. This type of evidence can be used in support of both positive and "not" GO annotations. is_a: ECO:0000080 ! phylogenetic evidence created_by: mchibucos creation_date: 2011-02-04T05:41:26Z [Term] id: ECO:0000309 name: cap analysis of gene expression evidence def: "A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by a cap-trapper system." [ECO:MCC] comment: Complementary DNA (cDNA) is synthesized from microgram quantities of mRNA using first-strand cDNA primer (oligo dT12-18) and reverse transcriptase in the presence of trehalose and sorbitol, followed by selection of full-length cDNA with biotinylated cap-trapper. Linkers are attached to the 5' ends of full-length enriched cDNAs to introduce a recognition site for the restriction endonuclease MmeI, which creates a two base overhang. After amplification, sequencing tags are concatenated for high-throughput sequencing. Resulting sort reads are aligned against a reference genome, and downstream analysis is performed. synonym: "CAGE" EXACT [PMID:16489339] is_a: ECO:0000009 ! transcript expression evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0001674 ! is_specified_output_of cap analysis of gene expression created_by: mchibucos creation_date: 2011-02-17T01:33:09Z [Term] id: ECO:0000310 name: nano-cap analysis of gene expression evidence def: "A type of transcript expression evidence based on high-throughput (HT) sequencing of the 5' ends of cDNA molecules that are selected by reverse transcriptase template switching." [ECO:MCC] comment: NanoCAGE captures the 5' ends of molecules by template switching. When polymerizing the cDNA of a capped mRNA, the reverse transcriptase adds extra cytosines that are complementary to the cap. Each 5' full length cDNAs is extended upon hybridization of the riboguanosine-tailed template switching oligonucleotides to these extra cytosines. In semisuppressive PCR, the short templates fold intramolecularly and prevent the binding of primers, which precludes amplification; longer molecules are less likely to fold and are thus amplified. Templates derived from reaction artifacts form stable homoduplexes, also precluding amplification. After template switching, semisuppressive PCR, and EcoP151 cleavage, 25-bp tags are ligated to bar code-containing oligonucleotide adaptors. After PCR amplification, the nanoCAGE tags are sequenced by synthesis. NanoCAGE requires as little as 10 nanograms of total RNA. synonym: "nanoCAGE" RELATED [PMID:20543846] is_a: ECO:0000009 ! transcript expression evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0001673 ! is_specified_output_of nano-cap analysis of gene expression created_by: mchibucos creation_date: 2011-02-17T01:33:34Z [Term] id: ECO:0000311 name: imported information def: "A type of evidence that is based on work performed by a person or group prior to a use by a different person or group." [ECO:MCC] is_a: ECO:0000000 ! evidence created_by: mchibucos creation_date: 2011-03-02T05:24:13Z [Term] id: ECO:0000312 name: imported information used in manual assertion def: "A type of imported information that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000311 ! imported information is_a: ECO:0000352 {is_inferred="true"} ! evidence used in manual assertion intersection_of: ECO:0000311 ! imported information intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2011-03-02T05:29:44Z [Term] id: ECO:0000313 name: imported information used in automatic assertion def: "A type of imported information that is used in an automatic assertion." [ECO:MCC] is_a: ECO:0000311 ! imported information is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion intersection_of: ECO:0000311 ! imported information intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2011-03-02T05:33:43Z [Term] id: ECO:0000314 name: direct assay evidence used in manual assertion def: "A type of direct assay evidence that is used in a manual assertion." [ECO:MCC] subset: valid_with_chemical_entity synonym: "IDA" RELATED [GOECO:IDA] synonym: "inferred from direct assay" EXACT [GOECO:IDA] xref: GOECO:IDA "inferred from direct assay" is_a: ECO:0000002 ! direct assay evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000002 ! direct assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/ida-inferred-direct-assay xsd:string created_by: mchibucos creation_date: 2011-10-28T04:59:31Z [Term] id: ECO:0000315 name: mutant phenotype evidence used in manual assertion def: "A type of mutant phenotype evidence that is used in a manual assertion." [ECO:MCC] subset: valid_with_chemical_entity subset: valid_with_gene subset: valid_with_protein subset: valid_with_protein_complex synonym: "IMP" RELATED [GOECO:IMP] synonym: "inferred from mutant phenotype" RELATED [GOECO:IMP] xref: GOECO:IMP "inferred from mutant phenotype" is_a: ECO:0000015 ! mutant phenotype evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0000015 ! mutant phenotype evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/imp-inferred-mutant-phenotype xsd:string created_by: mchibucos creation_date: 2011-10-28T05:12:49Z [Term] id: ECO:0000316 name: genetic interaction evidence used in manual assertion def: "A type of genetic interaction experiment evidence that is used in a manual assertion." [ECO:MCC] subset: valid_with_gene subset: valid_with_protein subset: valid_with_protein_complex synonym: "IGI" EXACT [GOECO:IGI] synonym: "inferred from genetic interaction" EXACT [GOECO:IGI] xref: GOECO:IGI "inferred from genetic interaction" is_a: ECO:0000011 ! genetic interaction evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0000011 ! genetic interaction evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/igi-inferred-genetic-interaction xsd:string created_by: mchibucos creation_date: 2011-10-28T05:14:42Z [Term] id: ECO:0000317 name: genomic context evidence used in manual assertion def: "A type of genomic context evidence that is used in a manual assertion." [ECO:MCC] subset: valid_with_gene subset: valid_with_protein synonym: "IGC" EXACT [GOECO:IGC] synonym: "inferred from genomic context" EXACT [GOECO:IGC] xref: GOECO:IGC "inferred from genomic context" is_a: ECO:0000177 ! genomic context evidence is_a: ECO:0000352 {is_inferred="true"} ! evidence used in manual assertion intersection_of: ECO:0000177 ! genomic context evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/igc-inferred-genomic-context xsd:string created_by: mchibucos creation_date: 2011-10-28T05:22:53Z [Term] id: ECO:0000318 name: biological aspect of ancestor evidence used in manual assertion def: "A type of biological aspect of ancestor evidence that is used in a manual assertion." [ECO:MCC] subset: valid_with_gene subset: valid_with_protein synonym: "IBA" EXACT [GOECO:IBA] synonym: "inferred from biological aspect of ancestor" EXACT [GOECO:IBA] xref: GOECO:IBA "inferred from biological aspect of ancestor" is_a: ECO:0000252 {is_inferred="true"} ! similarity evidence used in manual assertion is_a: ECO:0000308 ! biological aspect of ancestor evidence intersection_of: ECO:0000308 ! biological aspect of ancestor evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/iba-inferred-biological-aspect-ancestor xsd:string created_by: mchibucos creation_date: 2011-10-28T05:23:51Z [Term] id: ECO:0000319 name: biological aspect of descendant evidence used in manual assertion def: "A type of biological aspect of descendant evidence that is used in a manual assertion." [ECO:MCC] subset: valid_with_gene subset: valid_with_protein synonym: "IBD" EXACT [GOECO:IBD] synonym: "inferred from biological aspect of descendant" EXACT [GOECO:IBD] xref: GOECO:IBD "inferred from biological aspect of descendant" is_a: ECO:0000214 ! biological aspect of descendant evidence is_a: ECO:0000252 {is_inferred="true"} ! similarity evidence used in manual assertion intersection_of: ECO:0000214 ! biological aspect of descendant evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/ibd-inferred-biological-aspect-descendent xsd:string created_by: mchibucos creation_date: 2011-10-28T05:25:09Z [Term] id: ECO:0000320 name: phylogenetic determination of loss of key residues evidence used in manual assertion def: "A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion." [ECO:MCC] synonym: "IKR" EXACT [GOECO:IKR] synonym: "IMR" EXACT [GOECO:IKR] synonym: "inferred from key residues" EXACT [GOECO:IKR] synonym: "inferred from missing residues" EXACT [GOECO:IKR] xref: GOECO:IKR "inferred from key residues" xref: GOECO:IMR "inferred from missing residues" is_a: ECO:0000216 ! phylogenetic determination of loss of key residues evidence is_a: ECO:0000252 {is_inferred="true"} ! similarity evidence used in manual assertion intersection_of: ECO:0000216 ! phylogenetic determination of loss of key residues evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/ikr-inferred-key-residues xsd:string created_by: mchibucos creation_date: 2011-10-28T05:25:48Z [Term] id: ECO:0000321 name: rapid divergence from ancestral sequence evidence used in manual assertion def: "A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion." [ECO:MCC] subset: valid_with_gene subset: valid_with_protein synonym: "inferred from rapid divergence" EXACT [GOECO:IRD] synonym: "IRD" EXACT [GOECO:IRD] xref: GOECO:IRD "inferred from rapid divergence" is_a: ECO:0000215 ! rapid divergence from ancestral sequence evidence is_a: ECO:0000252 {is_inferred="true"} ! similarity evidence used in manual assertion intersection_of: ECO:0000215 ! rapid divergence from ancestral sequence evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/ird-inferred-rapid-divergence xsd:string created_by: mchibucos creation_date: 2011-10-28T05:26:42Z [Term] id: ECO:0000322 name: imported manually asserted information used in automatic assertion def: "Evidence that was initially used in manual assertion by one person or group, which is imported by a second person or group and used in automatic assertion." [ECO:MCC] xref: GO_REF:0000037 "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries." xref: GO_REF:0000039 "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries." xref: GO_REF:0000041 "IEA (UniProt UniPathway)" is_a: ECO:0000313 ! imported information used in automatic assertion created_by: mchibucos creation_date: 2011-12-13T12:04:48Z [Term] id: ECO:0000323 name: imported automatically asserted information used in automatic assertion def: "A type of imported information used in automatic assertion that was initially used in automatic assertion by one person or group, which is imported by a second person or group and used in automatic assertion." [ECO:MCC] xref: GO_REF:0000038 "Gene Ontology annotation based on automatic assignment of UniProtKB keywords in UniProtKB/TrEMBL entries." xref: GO_REF:0000040 "Gene Ontology annotation based on the automatic assignment of UniProtKB Subcellular Location terms in UniProtKB/TrEMBL entries." is_a: ECO:0000313 ! imported information used in automatic assertion created_by: mchibucos creation_date: 2011-12-13T02:06:25Z [Term] id: ECO:0000324 name: imaging assay evidence alt_id: ECO:0001122 alt_id: ECO:0005024 def: "A type of direct assay evidence in which an image is created and analyzed." [] synonym: "radiologic test evidence" NARROW [] xref: ECO:MCC is_a: ECO:0000002 ! direct assay evidence relationship: OBI:0000312 OBI:0000185 ! is_specified_output_of imaging assay created_by: mchibucos creation_date: 2012-02-23T12:01:43Z [Term] id: ECO:0000325 name: chromatography evidence def: "A type of experimental evidence that is based on separation of constituent parts of a mixture (the mobile phase) as they pass differentially through a stationary phase due to differences in partition coefficient and retention on the stationary phase." [ECO:MCC] synonym: "chromatographic evidence" EXACT [] is_a: ECO:0000006 ! experimental evidence relationship: OBI:0000312 OBI:0001630 ! is_specified_output_of analytical chromatography created_by: mchibucos creation_date: 2012-05-16T11:46:27Z [Term] id: ECO:0000326 name: transcript splice pattern evidence def: "A type of sequence alignment evidence that is based on comparing the position of exon junctions, relative to a reference genome, for a transcript annotation and a supporting transcript." [ECO:MCC] is_a: ECO:0000200 ! sequence alignment evidence created_by: mchibucos creation_date: 2012-06-08T11:03:59Z [Term] id: ECO:0000327 name: whole transcript splice pattern evidence def: "A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features." [ECO:MCC] comment: This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child. is_a: ECO:0000326 ! transcript splice pattern evidence created_by: mchibucos creation_date: 2012-06-08T11:11:24Z [Term] id: ECO:0000328 name: coding sequence splice pattern evidence def: "A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript." [ECO:MCC] comment: This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child. is_a: ECO:0000326 ! transcript splice pattern evidence created_by: mchibucos creation_date: 2012-06-08T11:21:57Z [Term] id: ECO:0000329 name: whole transcript splice pattern evidence used in manual assertion def: "A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in manual assertion." [ECO:MCC] comment: This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child. is_a: ECO:0000247 {is_inferred="true"} ! sequence alignment evidence used in manual assertion is_a: ECO:0000327 ! whole transcript splice pattern evidence intersection_of: ECO:0000327 ! whole transcript splice pattern evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2012-06-08T11:40:03Z [Term] id: ECO:0000330 name: coding sequence splice pattern evidence used in manual assertion def: "A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in manual assertion." [ECO:MCC] comment: This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child. is_a: ECO:0000247 {is_inferred="true"} ! sequence alignment evidence used in manual assertion is_a: ECO:0000328 ! coding sequence splice pattern evidence intersection_of: ECO:0000328 ! coding sequence splice pattern evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2012-06-08T11:43:47Z [Term] id: ECO:0000331 name: coding sequence splice pattern evidence used in automatic assertion def: "A type of transcript splice pattern evidence that is based on the exon combination of a coding sequence (CDS), a sub-feature of a whole transcript, and is used in automatic assertion." [ECO:MCC] comment: This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, but for which full transcript information is unavailable. For sequences that have the same splice pattern as a whole RefSeq transcript, use the evidence term ECO:0000327 or a child. is_a: ECO:0000248 {is_inferred="true"} ! sequence alignment evidence used in automatic assertion is_a: ECO:0000328 ! coding sequence splice pattern evidence intersection_of: ECO:0000328 ! coding sequence splice pattern evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2012-06-08T11:48:09Z [Term] id: ECO:0000332 name: whole transcript splice pattern evidence used in automatic assertion def: "A type of transcript splice pattern evidence that is based on the exon combination of a whole transcript, rather than its constituent features, and is used in automatic assertion." [ECO:MCC] comment: This term is used by the NCBI Reference Sequences (RefSeq) in support of sequences that have the same splice pattern as a RefSeq transcript. If such full transcript information is not available, RefSeq reports sequences that match the splice pattern of a coding sequence (CDS) annotated on a RefSeq, supported by the evidence term ECO:0000328 or a child. is_a: ECO:0000248 {is_inferred="true"} ! sequence alignment evidence used in automatic assertion is_a: ECO:0000327 ! whole transcript splice pattern evidence intersection_of: ECO:0000327 ! whole transcript splice pattern evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2012-06-08T11:49:17Z [Term] id: ECO:0000333 name: sodium dodecyl sulfate polyacrylamide gel electrophoresis evidence def: "A type of gel electrophoresis evidence where proteins are separated according to their electrophoretic mobility." [ECO:MCC, PubMed:4861258, url:http\://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html, url:http\://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Protein/protein18.html] comment: Electrophoretic mobility is a function of both the length and charge of a protein. The protein sample is linearized with sodium dodecyl sulfate (SDS), an anionic detergent. Typically, polypeptides bound with SDS possess an even distribution of charge per unit mass, and subsequent fractionation is by size. synonym: "SDS-PAGE evidence" EXACT [] is_a: ECO:0000337 ! gel electrophoresis evidence created_by: mchibucos creation_date: 2012-07-31T02:56:43Z [Term] id: ECO:0000334 name: particle size and count assay evidence def: "A type of direct assay evidence resulting from an assay where both the size of and number of particles in a sample are determined." [ECO:MCC] comment: An example of an instrument used to analyze particle sizes and counts is the Beckman Coulter® Z Series system. is_a: ECO:0000002 ! direct assay evidence created_by: mchibucos creation_date: 2012-07-31T03:19:32Z [Term] id: ECO:0000335 name: substance quantification evidence def: "A type of direct assay evidence where the quantity of a substance used as part of an assay is measured." [ECO:MCC] comment: Two examples of substance quantification assay are (i) measuring how much of a radiolabelled compound is taken up by a cell and (ii) measuring how much of a substrate is turned over by a given enzyme. is_a: ECO:0000002 ! direct assay evidence created_by: mchibucos creation_date: 2012-07-31T03:52:46Z [Term] id: ECO:0000336 name: competitive growth assay evidence def: "A type of cell proliferation assay evidence in which a mutated strain of a microorganism, such as a yeast or bacterium, is grown competitively with wild-type cells and the relative fitness of the strains is assessed usually by means of a fluorescent marker and flow cytometric analysis." [GOC:MAH, PMID:14718172, PMID:20537132] synonym: "fitness profiling" EXACT [GOC:MAH, PMID:20537132] is_a: ECO:0005007 ! cell proliferation assay evidence relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay created_by: mchibucos creation_date: 2012-08-24T12:03:58Z [Term] id: ECO:0000337 name: gel electrophoresis evidence alt_id: ECO:0005026 def: "A type of direct assay evidence where molecules have been sorted according to their size and charge by moving through a gel in the presence of an electric field." [ECO:MCC, wikipedia:Gel_electrophoresis] comment: Molecules typically separated include DNA, RNA, or protein. The gel is typically made of agarose, polyacrylamide, or starch. is_a: ECO:0000002 ! direct assay evidence relationship: IAO:0000136 OBI:0600051 ! is about gradient separation created_by: mchibucos creation_date: 2012-08-24T12:11:51Z [Term] id: ECO:0000338 name: pulsed-field gel electrophoresis evidence def: "A type of gel electrophoresis evidence in which large DNA molecules are separated on agarose gel by alternately pulsed, perpendicularly oriented electrical fields, at least one of which is inhomogeneous." [PMID:6373014] synonym: "PFGE" EXACT [] is_a: ECO:0000337 ! gel electrophoresis evidence created_by: mchibucos creation_date: 2012-08-24T12:34:01Z [Term] id: ECO:0000339 name: two-dimensional agarose gel electrophoresis evidence def: "A type of gel electrophoresis evidence where DNA molecules are electrophoresed on a low percentage agarose gel followed by high voltage electrophoresis on a higher percentage agarose gel in the presence of ethidium bromide." [PMID:16118435, PMID:8594382] comment: The first dimension gel is intentionally run at low voltage in low percentage agarose to separate DNA molecules in proportion to their mass. The second dimension is run at high voltage in a gel of higher agarose concentration in the presence of ethidium bromide so that the mobility of a non-linear molecule is drastically influenced by its shape. synonym: "2-D agarose gel electrophoresis" EXACT [] is_a: ECO:0000337 ! gel electrophoresis evidence created_by: mchibucos creation_date: 2012-08-24T12:42:37Z [Term] id: ECO:0000340 name: plasmid maintenance assay evidence def: "A type of experimental evidence in which retention of an introduced plasmid is determined when a mitotically stable plasmid (or minichromosome) is introduced into cells, which are grown without selection for several generations." [] {comment="ECO:MCC", comment="PMID:6323245"} comment: Loss per generation is determined by comparing colony numbers on selective and non-selective media. synonym: "minichromosome maintenance assay evidence" EXACT [PMID:6323245] is_a: ECO:0000006 ! experimental evidence is_a: IAO:0000030 {is_inferred="true"} ! information content entity relationship: IAO:0000136 GO:0006276 ! is about plasmid maintenance relationship: OBI:0000312 OBI:0000964 ! is_specified_output_of in live cell assay created_by: mchibucos creation_date: 2012-08-24T01:27:58Z [Term] id: ECO:0000341 name: specific protein inhibition by antibody evidence def: "A type of specific protein inhibition evidence where the molecular function of a protein is inhibited by an antibody." [ECO:MCC] is_a: ECO:0000020 ! specific protein inhibition evidence created_by: mchibucos creation_date: 2012-08-24T01:48:24Z [Term] id: ECO:0000342 name: Support of intron position by RNA-seq alignment evidence def: "A type of RNA-seq evidence where intron locations in predicted transcripts are compared to intron locations supported by RNA-seq evidence." [ECO:MCC] comment: RNA-seq alignment intron location evidence is used by NCBI RefSeq (http://www.ncbi.nlm.nih.gov/refseq). Exon-exon boundaries (or intron locations) of a RefSeq transcript, as determined by aligning the transcript to a reference chromosome, are compared to intron locations supported by RNAseq data. is_a: ECO:0000295 ! RNA-seq evidence created_by: mchibucos creation_date: 2013-04-03T04:22:05Z [Term] id: ECO:0000343 name: Full support of intron position by RNA-seq alignment evidence def: "A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment from a single sample supports all of the intron positions (exon pairs) predicted for a transcript." [ECO:MCC] comment: Full support entails that all exon pairs represented in the transcript are supported. For example, for a transcript containing five exons, if liver RNA-seq reads support all four introns but brain RNA-seq supports only three introns, then the liver data fully support the transcript exons whereas the brain data do not. is_a: ECO:0000342 ! Support of intron position by RNA-seq alignment evidence created_by: mchibucos creation_date: 2013-04-03T04:41:48Z [Term] id: ECO:0000344 name: Partial support of intron position by RNA-seq alignment evidence def: "A type of support of intron position by RNA-seq alignment evidence where RNA-seq alignment to a genome supports only some of the intron positions (exon pairs) predicted for a transcript." [ECO:MCC] comment: Partial support can occur in two ways. First, one or more exon-exon pair (intron) is not supported by any RNA-seq sample included in the analysis. Second, no single RNA-seq sample provides support for all exon-exon pairs (introns) represented in a transcript, but all represented exons are supported by at least one sample. is_a: ECO:0000342 ! Support of intron position by RNA-seq alignment evidence created_by: mchibucos creation_date: 2013-04-03T04:50:46Z [Term] id: ECO:0000345 name: single exon transcript confirmation via alignment evidence is_a: ECO:0000200 ! sequence alignment evidence created_by: mchibucos creation_date: 2013-04-03T05:10:34Z [Term] id: ECO:0000346 name: Support of intron position by RNA-seq alignment evidence used in manual assertion def: "A type of support of intron position by RNA-seq alignment evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000342 ! Support of intron position by RNA-seq alignment evidence is_a: ECO:0006068 {is_inferred="true"} ! RNA-seq evidence used in manual assertion intersection_of: ECO:0000342 ! Support of intron position by RNA-seq alignment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2013-04-04T04:37:35Z [Term] id: ECO:0000347 name: Support of intron position by RNA-seq alignment evidence used in automatic assertion def: "A type of support of intron position by RNA-seq alignment evidence that is used in an automatic assertion." [ECO:MCC] is_a: ECO:0000342 ! Support of intron position by RNA-seq alignment evidence is_a: ECO:0006069 {is_inferred="true"} ! RNA-seq evidence used in automatic assertion intersection_of: ECO:0000342 ! Support of intron position by RNA-seq alignment evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2013-04-04T04:38:45Z [Term] id: ECO:0000348 name: Full support of intron position by RNA-seq alignment evidence used in automatic assertion def: "A type of full support of intron position by RNA-seq alignment evidence that is used in an automatic assertion." [ECO:MCC] is_a: ECO:0000343 ! Full support of intron position by RNA-seq alignment evidence is_a: ECO:0000347 {is_inferred="true"} ! Support of intron position by RNA-seq alignment evidence used in automatic assertion intersection_of: ECO:0000343 ! Full support of intron position by RNA-seq alignment evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2013-04-04T04:40:19Z [Term] id: ECO:0000349 name: Full support of intron position by RNA-seq alignment evidence used in manual assertion def: "A type of full support of intron position by RNA-seq alignment evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000343 ! Full support of intron position by RNA-seq alignment evidence is_a: ECO:0000346 {is_inferred="true"} ! Support of intron position by RNA-seq alignment evidence used in manual assertion intersection_of: ECO:0000343 ! Full support of intron position by RNA-seq alignment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2013-04-04T04:41:34Z [Term] id: ECO:0000350 name: Partial support of intron position by RNA-seq alignment evidence used in automatic assertion def: "A type of partial support of intron position by RNA-seq alignment evidence that is used in an automatic assertion." [ECO:MCC] is_a: ECO:0000344 ! Partial support of intron position by RNA-seq alignment evidence is_a: ECO:0000347 {is_inferred="true"} ! Support of intron position by RNA-seq alignment evidence used in automatic assertion intersection_of: ECO:0000344 ! Partial support of intron position by RNA-seq alignment evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2013-04-04T04:42:53Z [Term] id: ECO:0000351 name: Partial support of intron position by RNA-seq alignment evidence used in manual assertion def: "A type of partial support of intron position by RNA-seq alignment evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000344 ! Partial support of intron position by RNA-seq alignment evidence is_a: ECO:0000346 {is_inferred="true"} ! Support of intron position by RNA-seq alignment evidence used in manual assertion intersection_of: ECO:0000344 ! Partial support of intron position by RNA-seq alignment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2013-04-04T04:43:56Z [Term] id: ECO:0000352 name: evidence used in manual assertion def: "A type of evidence that is used in an manual assertion." [ECO:MCC] is_a: ECO:0000000 {is_inferred="true"} ! evidence intersection_of: ECO:0000000 ! evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos [Term] id: ECO:0000353 name: physical interaction evidence used in manual assertion def: "A type of physical interaction evidence that is used in a manual assertion." [ECO:MCC] subset: valid_with_chemical_entity subset: valid_with_gene subset: valid_with_protein subset: valid_with_protein_complex synonym: "inferred from physical interaction" EXACT [GOECO:IPI] synonym: "IPI" EXACT [GOECO:IPI] xref: GOECO:IPI "inferred from physical interaction" is_a: ECO:0000021 ! physical interaction evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000021 ! physical interaction evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: seeAlso http://geneontology.org/page/ipi-inferred-physical-interaction xsd:string created_by: mchibucos creation_date: 2013-10-31T21:01:27Z [Term] id: ECO:0000354 name: gene neighbors evidence used in manual assertion def: "A type of gene neighbors evidence that is used in a manual assertion." [ECO:MCC] synonym: "ICL" RELATED [] synonym: "inferred from genome cluster" BROAD [] xref: GO_REF:0000025 "operon structure as IGC evidence" is_a: ECO:0000084 ! gene neighbors evidence is_a: ECO:0000317 {is_inferred="true"} ! genomic context evidence used in manual assertion intersection_of: ECO:0000084 ! gene neighbors evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2013-11-19T13:37:24Z [Term] id: ECO:0000355 name: phylogenetic distribution evidence def: "A type of phylogenetic evidence characterized by the mapping of the character states of living organisms onto phylogenies using the method of maximum parsimony." [ECO:MCC, PMID:21238344] comment: Example of use: "The presence of paired evaginated hemispheres and olfactory bulbs in both agnathan and gnathostome radiations suggests that such hemispheres were also present in the common ancestor." PMID: 7013637. Northcutt RG. (1981) Evolution of the telencephalon in nonmammals. Ann. Rev. Neurosci. is_a: ECO:0000080 ! phylogenetic evidence created_by: mchibucos creation_date: 2014-04-22T17:02:31Z [Term] id: ECO:0000358 name: differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) def: "A type of transcript expression evidence resulting from a microarray analysis with the use of the Gene Set Enrichment Analysis (GSEA) method or the Fisher's-Exact (FE) method to assess the differential expression." [PMID:19725948] is_a: ECO:0000009 ! transcript expression evidence created_by: mchibucos creation_date: 2014-09-26T16:25:47Z [Term] id: ECO:0000359 name: differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) def: "A type of transcript expression evidence resulting from the use of the Gene Set Enrichment Analysis (GSEA) method or Fisher's-Exact (FE) method to assess an RNA-seq dataset for differential gene expression." [PMC:2881125] is_a: ECO:0000009 ! transcript expression evidence created_by: mchibucos creation_date: 2014-09-26T16:26:48Z [Term] id: ECO:0000360 name: biological target-disease association via drug is_a: ECO:0000006 ! experimental evidence created_by: mchibucos creation_date: 2014-09-26T16:39:11Z [Term] id: ECO:0000361 name: inferential evidence def: "A type of evidence where an assertion is derived from another assertion via logical inference or some non-logical but rational means." [ECO:MCC] comment: Inference is the process of deriving logical conclusions from premises known or assumed to be true, or alternatively, arriving at conclusions via some non-logical means of observation of patterns of facts, which can result in identifying new meanings and contexts for understanding. Given the evidence provided by a set of premises, deductive reasoning involves drawing conclusions that necessarily follow, i.e. are certain, whereas inductive reasoning generates conclusions that are likely to be, but are not necessarily, true. is_a: ECO:0000000 ! evidence created_by: mchibucos creation_date: 2015-07-14T11:19:37Z [Term] id: ECO:0000362 name: evidence based on computational logical inference def: "A type of inferential evidence based on a computationally derived unary inference or an inference chain in which at least one step is \ncomputationally derived." [ECO:MCC, GOC:MC] is_a: ECO:0000361 ! inferential evidence created_by: mchibucos creation_date: 2015-07-14T11:24:27Z [Term] id: ECO:0000363 name: evidence based on computational logical inference used in automatic assertion def: "A type of evidence based on computational logical inference that is used in automatic assertion." [ECO:MCC] xref: GO_REF:0000108 "Automatic assignment of GO terms using logical inference, based on on inter-ontology links" is_a: ECO:0000362 ! evidence based on computational logical inference is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion intersection_of: ECO:0000362 ! evidence based on computational logical inference intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: mchibucos creation_date: 2015-07-14T11:35:08Z [Term] id: ECO:0000364 name: evidence based on logical inference from manual annotation used in automatic assertion def: "A type of evidence based on logical inference from a manually curated annotation that is used in an automatic assertion." [ECO:MCC] is_a: ECO:0000363 ! evidence based on computational logical inference used in automatic assertion created_by: mchibucos creation_date: 2015-07-14T11:44:19Z [Term] id: ECO:0000366 name: evidence based on logical inference from automatic annotation used in automatic assertion def: "A type of evidence based on logical inference from an automatically curated annotation that is used in an automatic assertion." [ECO:MCC] is_a: ECO:0000363 ! evidence based on computational logical inference used in automatic assertion created_by: mchibucos creation_date: 2015-07-14T11:45:25Z [Term] id: ECO:0000501 name: evidence used in automatic assertion def: "A type of evidence that is used in an automatic assertion." [ECO:cjm] subset: valid_with_gene subset: valid_with_protein subset: valid_with_protein_complex synonym: "IEA" EXACT [GOECO:IEA] synonym: "inferred from electronic annotation" EXACT [GOECO:IEA] xref: GO_REF:0000003 "Gene Ontology annotation based on Enzyme Commission mapping." xref: GO_REF:0000004 "Gene Ontology annotation based on Swiss-Prot keyword mapping." xref: GO_REF:0000023 "Gene Ontology annotation based on Swiss-Prot Subcellular Location vocabulary mapping." xref: GOECO:IEA "inferred from electronic annotation" is_a: ECO:0000000 {is_inferred="true"} ! evidence intersection_of: ECO:0000000 ! evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion property_value: seeAlso http://geneontology.org/page/automatically-assigned-evidence-codes xsd:string created_by: cjm [Term] id: ECO:0001001 name: 3D cell culture evidence def: "A type of cell proliferation assay evidence resulting from the growth of cells in a micro-environment that mimics real tissue and establishes physiological cell-cell and cell-substrate interactions that regulate proliferation and differentiation." [PMID:21042962, url:http\://volttecnologia.com.br/wp-content/uploads/2016/03/Drug-discovery.pdf] is_a: ECO:0005007 ! cell proliferation assay evidence relationship: IAO:0000136 GO:0008283 ! is about cell proliferation relationship: OBI:0000312 OBI:0000891 ! is_specified_output_of cell proliferation assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001002 name: [3H]arachidonic acid release assay evidence def: "A type of cell-based assay evidence resulting from labeling cells with [3H]arachidonic acid and subsequently determining the release of the arachidonic acid by the cells." [ISBN:0323152295, PMID:20693009] is_a: ECO:0001565 ! cell-based assay evidence relationship: IAO:0000136 GO:0050482 ! is about arachidonic acid secretion relationship: OBI:0000312 OBI:0000366 ! is_specified_output_of metabolite profiling property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001003 name: [3H]-thymidine incorporation assay evidence def: "A type of DNA synthesis cell proliferation assay evidence resulting from the measurement of cell proliferation rate by determining the incorporation of [3H]-thymidine into cellular nucleic acids." [OBI:0000669, url:http\://www.scientistsolutions.com/forum/cell-culture-and-tissue-culture-proliferationapoptosis/3h-thymidine-incorporation-assay-rat-1a] is_a: ECO:0005008 ! DNA synthesis cell proliferation assay evidence relationship: IAO:0000136 GO:0008283 ! is about cell proliferation relationship: OBI:0000312 OBI:0000669 ! is_specified_output_of tritiated thymidine incorporation assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001004 name: 51Cr release assay evidence def: "A type of cytotoxicity assay evidence resulting from the measurement of the amount of radioactive 51Cr released in the supernatant of a sample of 51Cr pre-labeled cells via cytolysis by effector cells (cytotoxic T-cells)." [PMC:3929704, url:http\://www4.mpbio.com/ecom/docs/proddata.nsf/5f64ffd4f38c2fda8525645d00769d68/53d2a75653615bab852568cb00572ff3?OpenDocument] is_a: ECO:0005012 ! cytotoxicity assay evidence relationship: IAO:0000136 GO:0001906 ! is about cell killing relationship: OBI:0000312 OBI:9999994 ! is_specified_output_of chromium release assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001005 name: 7-aminoactinomycin staining evidence def: "A type of apoptotic assay evidence resulting from the use of 7-aminoactinomycin D (7-AAD) to distinguish viable, apoptotic, and dead cells, using the fact that permeability of the cell membrane, and fluorescence intensity, is low in early apoptotic cells and high in late apoptotic and dead cells." [ECO:RCT] synonym: "7-AAD staining evidence" EXACT [] synonym: "7-amino-actinomycin D staining evidence" EXACT [] is_a: ECO:0005019 ! staining evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001006 name: adhesion assay evidence def: "A type of cell-based assay evidence resulting from the analysis of cell binding either to extracellular matrix proteins or other cells." [PMID:15576904, PMID:21909903] is_a: ECO:0001565 ! cell-based assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001007 name: adoptive cell transfer evidence def: "A type of ex vivo assay evidence derived by ex vivo selection of tumor-reactive lymphocytes, and their activation and numerical expansion before re-infusion to the autologous tumor-bearing host." [ECO:SN, url:http\://jco.ascopubs.org/content/23/10/2346.full.pdf+html, url:http\://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf] synonym: "Adoptive immunotherapy" EXACT [] synonym: "passive immunization" EXACT [] is_a: ECO:0005502 ! ex vivo assay evidence relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001008 name: alamarBlue assay evidence def: "A type of cell viability assay evidence resulting from the continuous measurement of fluorescence intensity from the viable cells, where a cell permeable compound, resazurin (the active ingredient of alamarBlue), is reduced to fluorescent resorufin." [PMC:3478843, url:https\://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/cell-profilteration-assay-protocols/cell-viability-with-alamarblue.html] is_a: ECO:0005004 ! cell viability assay evidence relationship: OBI:0000312 OBI:0000443 ! is_specified_output_of analyte assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001009 name: allograft transplantation experiment evidence def: "A type of anatomical perturbation evidence where an organ or tissue is transplanted from one individual to another of the same species with a different genotype." [ECO:SN, url:http\://www.nature.com/subjects/allograft, url:http\://www.organdonor.gov/about/terms_and_topics/] synonym: "allografting" EXACT [] synonym: "Allotransplantation" EXACT [] synonym: "tissue grafting" NARROW [] is_a: ECO:0000240 ! anatomical perturbation evidence relationship: IAO:0000136 GO:0008150 ! is about biological_process relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001010 name: anion-exchange chromatography evidence def: "A type of chromatography evidence where a positively charged ion exchange resin with an affinity for molecules having net negative surface charges is used to separate the molecules." [ECO:SN, PMID:20978968, url:http\://www.bio-rad.com/en-us/applications-technologies/anion-exchange-chromatography, url:http\://www.uta.edu/faculty/sawasthi/Enzymology-4351-5324/Class%20Syllabus%20Enzymology/Ion%20Exchange%20Chromatography-1.pdf] is_a: ECO:0000325 ! chromatography evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001011 name: annexin-V staining evidence def: "A type of apoptotic assay evidence resulting from the addition and subsequent binding of Annexin V to phosphatidylserine in cells to detect if they are viable, apoptotic, or necrotic." [PMC:3169266] is_a: ECO:0005034 ! apoptotic assay evidence relationship: IAO:0000136 GO:0006915 ! is about apoptotic process relationship: OBI:0000312 OBI:0001977 ! is_specified_output_of cytometry assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001012 name: behavioral assay evidence def: "A type of experimental phenotypic evidence resulting from behavioral phenotyping and analysis to assess cognitive functioning." [PMID:24462904] is_a: ECO:0000059 ! experimental phenotypic evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001013 name: blocking monoclonal antibody evidence def: "A type of immunological assay evidence resulting from inhibitory effect of monoclonal antibody combining with an antigen over other antibodies." [PMID:11292349, url:http\://www.sciencedirect.com/science/article/pii/S0140673600034966] is_a: ECO:0000040 ! immunological assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001014 name: blocking peptide evidence def: "A type of immunological assay evidence resulting from the use of peptides to block antibodies from binding to their targets." [ECO:RCT] is_a: ECO:0000040 ! immunological assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001015 name: blocking polyclonal antibody evidence is_a: ECO:0000040 ! immunological assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001016 name: blood test evidence def: "A type of direct assay evidence where a blood sample is extracted from an organism to analyze different blood components." [ECO:SN, url:https\://www.nhlbi.nih.gov/health/health-topics/topics/bdt] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001017 name: Boyden chamber assay evidence def: "A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the number of cells that migrate from the upper compartment of a chamber (separated by a micro-porous membrane) to the lower compartment, in which chemotactic agents are present." [PMID:13872176, PMID:15576901] is_a: ECO:0005021 ! chemotaxis assay evidence relationship: IAO:0000136 GO:0060326 ! is about cell chemotaxis relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001018 name: bromodeoxyuridine incorporation assay evidence alt_id: ECO:0005010 def: "A type of nucleotide analog incorporation evidence resulting from the incorporation of bromodeoxyuridine (BrdU) as a thymidine analog into nuclear DNA, resulting in a label that can be tracked using antibody probes." [PMID:23690005] synonym: "5-bromo-2'-deoxyuridine incorporation assay evidence" EXACT [] synonym: "BrdU incorporation assay evidence" EXACT [] synonym: "BrdUrd incorporation assay evidence" EXACT [] synonym: "BUdR incorporation assay evidence" EXACT [] synonym: "cell proliferation marker detection assay evidence" BROAD [] is_a: ECO:0001107 ! nucleotide analog incorporation assay evidence relationship: IAO:0000136 GO:0008283 ! is about cell proliferation relationship: OBI:0000312 OBI:0000664 ! is_specified_output_of BrdU incorporation assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001019 name: caspase assay evidence def: "A type of apoptotic assay evidence resulting from the detection of caspase activation, which results in the cleaving of intracellular substrates during apoptosis." [PMID:18314058, PMID:25086023] is_a: ECO:0005034 ! apoptotic assay evidence relationship: IAO:0000136 GO:0006915 ! is about apoptotic process relationship: OBI:0000312 OBI:0001977 ! is_specified_output_of cytometry assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001020 name: cell counting evidence def: "A type of cell-based assay evidence resulting from the quantification of a sample of cells." [ECO:RCT] is_a: ECO:0001565 ! cell-based assay evidence relationship: IAO:0000136 GO:0008283 ! is about cell proliferation relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001021 name: cell permeability assay evidence def: "A type of cell-based assay evidence resulting from the quantification of cell permeability." [PMID:16962665] is_a: ECO:0001565 ! cell-based assay evidence relationship: IAO:0000136 GO:0009987 ! is about cellular process relationship: OBI:0000312 OBI:0001977 ! is_specified_output_of cytometry assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001022 name: carboxyfluorescein diacetate succinimidyl ester staining evidence def: "A type of staining evidence resulting from monitoring division by the use of carboxyfluorescein diacetate succinimidyl ester (CFSE) to label intracellular molecules with carboxyfluorescein; when a labeled cell divides, the number of carboxyfluorescein-tagged molecules is split." [PMC:3185625] synonym: "CFDA-SE staining evidence" EXACT [] synonym: "CFSE-staining evidence" EXACT [] is_a: ECO:0005019 ! staining evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001023 name: chemiluminescence-linked immunoassay evidence def: "A type of protein detection assay evidence resulting from a complex (a chemiluminescent compound, protein and a steroidal hapten) utilized as a labeled antigen, which emits light when treated with hydrogen peroxide and copper acetate at a high pH." [PMID:659901] synonym: "CLIA evidence" EXACT [] is_a: ECO:0005517 ! protein detection assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001024 name: chimeric protein evidence def: "A type of mutant phenotype evidence resulting from the fusion of two or more different genes to create one protein product." [PMID:22588898, PMID:25832756] is_a: ECO:0000015 ! mutant phenotype evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001025 name: co-electrophoresis evidence def: "A type of gel electrophoresis evidence resulting from the electrophoresis of two substances together, allowing for the characterization of ligand/nucleic acid binding interactions." [PMID:7668395] is_a: ECO:0000337 ! gel electrophoresis evidence relationship: IAO:0000136 OBI:0001588 ! is about binding property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001026 name: co-localization evidence def: "A type of imaging assay evidence resulting from the limited observation of the co-occurrence of molecules in a subcellular location." [PMC:3074624] is_a: ECO:0000324 ! imaging assay evidence relationship: IAO:0000136 GO:0033036 ! is about macromolecule localization relationship: OBI:0000312 OBI:0000185 ! is_specified_output_of imaging assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001027 name: colony counting evidence def: "A type of direct assay evidence resulting from the counting of microbial colonies that arise from viable cells grown on a plate or dish." [PMID:16558698, PMID:23457446] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001028 name: co-sedimentation assay evidence def: "A type of physical interaction evidence resulting from the separation of a mixture of molecules under the influence of a force such as artificial gravity, where molecules sedimenting together are assumed to interact." [MI:0027] is_a: ECO:0000021 ! physical interaction evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001029 name: comet assay evidence def: "A type of gel electrophoresis evidence resulting in the assessment of DNA breakage in a cell, based on size and shape of DNA migration." [OBI:0302736, PMID:10737956] is_a: ECO:0000337 ! gel electrophoresis evidence relationship: IAO:0000136 GO:0006974 ! is about cellular response to DNA damage stimulus relationship: OBI:0000312 OBI:0302736 ! is_specified_output_of comet assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001030 name: conditional knockout evidence def: "A type of knockout evidence resulting from a temporally-restricted and/or tissue-specific targeted gene removal." [PMC:3572410] is_a: ECO:0001091 ! knockout evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001031 name: conditional knockin evidence def: "A type of knockin evidence resulting from the targeted introduction of a temporally-restricted and/or tissue-specific mutation." [PMID:16832820] is_a: ECO:0001090 ! knockin evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001032 name: constitutively active mutant evidence def: "A type of experimental phenotypic evidence resulting from a constitutively active mutant (CAM), resulting in mutant proteins that remain active in the absence of upstream signals." [PMID:12217490] is_a: ECO:0000059 ! experimental phenotypic evidence relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001033 name: cross-linking evidence def: "A type of protein binding evidence resulting from the identification of two interacting proteins (that exist in close proximity) by linking through covalent bonds followed by identification" [PMID:15530987, PMID:19241040] is_a: ECO:0000024 ! protein binding evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001034 name: crystallography evidence def: "A type of structure determination evidence resulting from the use of a narrow beam of x-rays to identify molecular structures by creating a diffraction pattern." [MI:0114] is_a: ECO:0005031 ! structure determination evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001035 name: cytochemistry evidence def: "A type of histochemistry evidence resulting from localizing chemical components of cells and organelles on histological sections." [PMID:11597006] is_a: ECO:0001050 ! histochemistry evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001036 name: cytochrome C release assay evidence def: "A type of apoptotic assay evidence resulting from the identification of an accumulation of cytochrome C in the cytoplasm after its release from the mitochondria, an early event in apoptosis." [PMID:10914021, PMID:12815469] is_a: ECO:0005034 ! apoptotic assay evidence relationship: IAO:0000136 GO:0006915 ! is about apoptotic process property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001037 name: 4',6-diamidino-2-phenylindole staining evidence def: "A type of staining evidence resulting from 4',6-diamidino-2-phenylindole (DAPI) binding to AT regions of DNA and emitting a blue fluorescence." [PMID:8580206, url:https\://www.thermofisher.com/us/en/home/references/protocols/cell-and-tissue-analysis/protocols/dapi-imaging-protocol.html] synonym: "DAPI staining evidence" EXACT [] synonym: "diaminophenylindole staining" EXACT [] is_a: ECO:0005019 ! staining evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001038 name: deletion mutation evidence alt_id: ECO:0005510 def: "A type of experimental phenotypic evidence resulting from a mutation in which there is a removal of one or more contiguous nucleotides." [SO:0000159] is_a: ECO:0000059 ! experimental phenotypic evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001039 name: DNA laddering assay evidence def: "A type of apoptotic assay evidence resulting from the visualization via gel electrophoresis of the fragmented DNA (DNA ladder) which is the result of apoptotic DNA fragmentation." [PMC:4401164] is_a: ECO:0005034 ! apoptotic assay evidence relationship: IAO:0000136 GO:0006309 ! is about apoptotic DNA fragmentation property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001040 name: RNA dot blot assay evidence def: "A type of RNA detection assay evidence based on the direct application of a RNA mixture in a circular motion on a matrix for hybridization with labeled DNA fragments." [ECO:SW, PMID:21424648] synonym: "RNA dot blot" RELATED [] is_a: ECO:0005518 ! RNA detection assay evidence property_value: IAO:0000234 "CollecTF" xsd:string property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001042 name: dominant-negative mutant evidence def: "A type of experimental phenotypic evidence resulting from the analysis of a mutated gene producing mutant polypeptides that disrupt the activity of the wild-type genes." [PMC:2217636, PMID:8018332] is_a: ECO:0000059 ! experimental phenotypic evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001043 name: Edman degradation evidence used in manual assertion def: "A type of Edman degradation evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001044 ! Edman degradation evidence intersection_of: ECO:0001044 ! Edman degradation evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:59:00Z [Term] id: ECO:0001044 name: Edman degradation evidence def: "A type of protein detection assay evidence resulting from labeling a termonal amino acid residue and cleaving it from a peptide by sequentially removing one residue at a time from the amino end of the peptide, without disrupting the bonds." [doi:10.3891/acta.chem.scand.04-0283, OBI:0000705] is_a: ECO:0005517 ! protein detection assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001045 name: eTag assay evidence def: "A type of affinity evidence resulting from the quantitative analysis of gene and protein expression monitored by proprietary eTag reporters." [PMID:15137949] is_a: ECO:0000023 ! affinity evidence is_a: IAO:0000030 {is_inferred="true"} ! information content entity relationship: IAO:0000136 GO:0010467 ! is about gene expression property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001046 name: filter binding assay evidence def: "A type of physical interaction evidence resulting from a mixture of two molecules passed through a nitrocellulose filter, where one may be immobilized on the filter, and if the immobilized molecule is capable of binding to the other, it will be retained on the filter as well." [PMID:23028069] is_a: ECO:0000021 ! physical interaction evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001047 name: fluorescence in situ hybridization evidence def: "A type of nucleic acid localization evidence and in situ hybridization evidence resulting from the use of fluorescent probes to detect complementary sequences of nucleic acids." [PMC:346675, PMID:6812046] is_a: ECO:0000008 ! expression pattern evidence is_a: ECO:0001534 ! nucleic acid localization evidence relationship: IAO:0000136 GO:0051276 ! is about chromosome organization relationship: OBI:0000312 OBI:0001683 ! is_specified_output_of chromosome organization assay by fluorescence in situ hybridization property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001048 name: fluorescence resonance energy transfer evidence def: "A type of physical interaction evidence resulting from the measurement of the proximity of two fluorophores, where the energy from an excited molecular fluorophore to another fluorophore can only occur within ~10nm." [PMID:11516318, PMID:15696158] synonym: "FRET" EXACT [] is_a: ECO:0000021 ! physical interaction evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001049 name: gel-filtration evidence def: "A type of chromatography evidence resulting from the exclusion of proteins based on molecular size by filtration through a porous matrix (swollen gel), from which larger molecules are excluded." [CHMO:0001011, doi:10.1038/nmeth0506-410] is_a: ECO:0000325 ! chromatography evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001050 name: histochemistry evidence def: "A type of histology evidence resulting from the identification of chemical components in cells and tissues." [MMO:0000497] is_a: ECO:0001051 ! histology evidence relationship: OBI:0000312 OBI:0600020 ! is_specified_output_of histology assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001051 name: histology evidence def: "A type of imaging assay evidence resulting from the qualitative microscopic examination of cells or tissues." [OBI:0600020] is_a: ECO:0000324 ! imaging assay evidence relationship: IAO:0000136 GO:0048532 ! is about anatomical structure arrangement relationship: OBI:0000312 OBI:0600020 ! is_specified_output_of histology assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001052 name: high-performance liquid chromatography evidence def: "A type of chromatography evidence resulting from the separation of molecules in a solute by forcing the solvent containing the sample through a column packed with nonporous particles at high pressure." [PMID:16376355] synonym: "HPLC evidence" EXACT [] is_a: ECO:0000325 ! chromatography evidence relationship: OBI:0000312 OBI:0002116 ! is_specified_output_of high performance liquid chromotography assay created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001053 name: immunocytochemistry evidence def: "A type of protein detection assay evidence resulting from the use of antibodies linked to coloring agents to localize structures in cell cultures to identify proteins." [MI:1200, OBI:0001986] is_a: ECO:0005517 ! protein detection assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001054 name: immunodepletion evidence def: "A type of immunological assay evidence resulting from the use of antibodies to remove specific proteins from a sample." [BAO:0002505] is_a: ECO:0000040 ! immunological assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001055 name: immunohistochemistry evidence def: "A type of protein detection assay evidence resulting from the use of antibodies to detect proteins in localized cells of tissue sections." [OBI:0001986] is_a: ECO:0005517 ! protein detection assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001056 name: induced mutation evidence def: "A type of genetic transformation evidence resulting from a mutation induced by a mutagenic compounds or irradiation." [OBI:0001154] is_a: ECO:0005027 ! genetic transformation evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001057 name: in vitro acetylation assay evidence def: "A type of acetylation assay evidence used in an in vitro experiment." [ECO:SN, SIB:PG, url:http\://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml] is_a: ECO:0001546 ! acetylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001058 name: in vitro cleavage assay evidence def: "A type of cleavage assay evidence used in an in vitro experiment." [PMID:21121091] is_a: ECO:0001547 ! cleavage assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001059 name: in vitro deubiquitination assay evidence def: "A type of deubiquitination assay evidence used in an in vitro experiment." [ECO:SN, PMID:19692941, SIB:PG] is_a: ECO:0001552 ! deubiquitination assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001060 name: in vitro deacetylation assay evidence def: "A type of deacetylation assay evidence used in an in vitro experiment." [ECO:SN, SIB:PG, url:http\://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml] is_a: ECO:0001548 ! deacetylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001061 name: in vitro defarnesylation assay evidence def: "A type of defarnesylation assay evidence used in an in vitro experiment." [ECO:SN, PMID:16126733, SIB:PG] is_a: ECO:0001549 ! defarnesylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001062 name: in vitro demethylation assay evidence def: "A type of demethylation assay evidence used in an in vitro experiment." [ECO:SN, SIB:PG, url:http\://en.wikipedia.org/wiki/Demethylation] is_a: ECO:0001550 ! demethylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001063 name: in vitro desumoylation assay evidence def: "A type of desumoylation assay evidence used in an in vitro experiment." [ECO:SN, SIB:PG, url:http\://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/] is_a: ECO:0001551 ! desumoylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001064 name: in vitro farnesylation assay evidence def: "A type of farnesylation assay evidence used in an in vitro experiment." [ECO:SN, SIB:PG, url:http\://en.wikipedia.org/wiki/Farnesyltransferase] is_a: ECO:0001553 ! farnesylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001065 name: in vitro methylation assay evidence def: "A type of methylation assay evidence used in an in vitro experiment." [ECO:SN, SIB:PG, url:http\://en.wikipedia.org/wiki/Methylation] is_a: ECO:0001554 ! methylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001066 name: in vitro palmitoylation assay evidence def: "A type of palmitoylation assay evidence used in an in vitro experiment." [ECO:SN, PMID:17077383, SIB:PG] is_a: ECO:0001555 ! palmitoylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001067 name: in vitro phosphatase assay evidence def: "A type of phosphatase assay evidence used in an in vitro experiment." [ECO:SN, SIB:PG, url:http\://en.wikipedia.org/wiki/Phosphatase] is_a: ECO:0001556 ! phosphatase assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001068 name: in vitro protein kinase assay evidence def: "A type of protein kinase assay evidence used in an in vitro experiment." [ECO:SN, SIB:PG, url:http\://en.wikipedia.org/wiki/Protein_kinase, url:http\://en.wikipedia.org/wiki/Protein_phosphorylation] is_a: ECO:0001558 ! protein kinase assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001069 name: in vitro polyADP-ribosylation assay evidence def: "A type of polyADP-ribosylation assay evidence used in an in vitro experiment." [ECO:SN, PMID:21870253, SIB:PG] is_a: ECO:0001557 ! polyADP-ribosylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001070 name: in vitro sumoylation assay evidence def: "A type of sumoylation assay evidence used in an in vitro experiment." [ECO:SN, SIB:PG, url:http\://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/] is_a: ECO:0001559 ! sumoylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001071 name: in vitro transcription assay evidence def: "A type of transcription assay evidence used in an in vitro experiment." [ECO:SN, ECO:SW, PMID:21125481, SIB:PG] is_a: ECO:0000168 ! transcription assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001072 name: in vitro translation assay evidence def: "A type of translation assay evidence used in an in vitro experiment." [ECO:SN, PMID:18230759, SIB:PG] is_a: ECO:0001561 ! translation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001073 name: in vitro ubiquitination assay evidence def: "A type of ubiquitination assay evidenceused in an in vitro experiment." [ECO:SN, PMID:19692941, SIB:PG] is_a: ECO:0001562 ! ubiquitination assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001074 name: in vivo acetylation assay evidence def: "A type of acetylation assay evidence used in an in vivo experiment." [ECO:SN, SIB:PG, url:http\://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml] is_a: ECO:0001546 ! acetylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001075 name: in vivo cleavage assay evidence def: "A type of cleavage assay evidence used in an in vivo experiment." [ECO:SN, PMID:22154596] is_a: ECO:0001547 ! cleavage assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001076 name: in vivo deacetylation assay evidence def: "A type of deacetylation assay evidence used in an in vivo experiment." [ECO:SN, SIB:PG, url:http\://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml] is_a: ECO:0001548 ! deacetylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001077 name: in vivo defarnesylation assay evidence def: "A type of defarnesylation assay evidence used in an in vivo experiment." [ECO:SN, PMID:15556768, PMID:16507103, SIB:PG] is_a: ECO:0001549 ! defarnesylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001078 name: in vivo demethylation assay evidence def: "A type of demethylation assay evidence used in an in vivo experiment." [ECO:SN, SIB:PG, url:http\://en.wikipedia.org/wiki/Demethylation] is_a: ECO:0001550 ! demethylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001079 name: in vivo deubiquitination assay evidence def: "A type of deubiquitination assay evidence used in an in vivo experiment." [ECO:SN, PMID:19692941, SIB:PG] is_a: ECO:0001552 ! deubiquitination assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001080 name: in vivo desumoylation assay evidence def: "A type of desumoylation assay evidence used in an in vivo experiment." [ECO:SN, SIB:PG, url:http\://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/] is_a: ECO:0001551 ! desumoylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001081 name: in vivo farnesylation assay evidence def: "A type of farnesylation assay evidence used in an in vivo experiment." [ECO:SN, PMID:9030603, SIB:PG] is_a: ECO:0001553 ! farnesylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001082 name: in vivo methylation assay evidence def: "A type of methylation assay evidence used in an in vivo experiment." [ECO:SN, SIB:PG, url:http\://en.wikipedia.org/wiki/Methylation] is_a: ECO:0001554 ! methylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001083 name: in vivo palmitoylation assay evidence def: "A type of palmitoylation assay evidence used in an in vivo experiment." [ECO:SN, PMID:10329400, SIB:PG] is_a: ECO:0001555 ! palmitoylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001084 name: in vivo phosphatase assay evidence def: "A type of phosphatase assay evidence used in an in vivo experiment." [ECO:SN, SIB:PG, url:http\://en.wikipedia.org/wiki/Phosphatase] is_a: ECO:0001556 ! phosphatase assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001085 name: in vivo protein kinase assay evidence def: "A type of protein kinase assay evidence used in an in vivo experiment." [ECO:SN, SIB:PG, url:http\://en.wikipedia.org/wiki/Protein_kinase, url:http\://en.wikipedia.org/wiki/Protein_phosphorylation] is_a: ECO:0001558 ! protein kinase assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001086 name: in vivo sumoylation assay evidence def: "A type of sumoylation assay evidence used in an in vivo experiment." [ECO:SN, SIB:PG, url:http\://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/] is_a: ECO:0001559 ! sumoylation assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001087 name: in vivo transcription assay evidence def: "A type of transcription assay evidence used in an in vivo experiment." [ECO:SN, PMID:12181418, SIB:PG] is_a: ECO:0000168 ! transcription assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001088 name: in vivo translation assay evidence def: "A type of translation assay evidence used in an in vivo experiment." [ECO:SN, PMID:24901308, SIB:PG] is_a: ECO:0001561 ! translation assay evidence relationship: IAO:0000136 GO:0006412 ! is about translation relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001089 name: in vivo ubiquitination assay evidence def: "A type of ubiquitination assay evidence used in an in vivo experiment." [ECO:SN, PMID:19692941, SIB:PG] is_a: ECO:0001562 ! ubiquitination assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001090 name: knockin evidence def: "A type of genetic transformation evidence resulting from the targetted replacement of a wild-type DNA sequence with a different sequence." [PMID:18077807, PMID:21800101] is_a: ECO:0005027 ! genetic transformation evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001091 name: knockout evidence def: "A type of genetic transformation evidence resulting from the removal of a particular gene (or genes), disrupting the function and allowing for functional analysis." [PMC:2782548] is_a: ECO:0005027 ! genetic transformation evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001092 name: lipid binding assay evidence def: "A type of physical interaction evidence resulting from the qualitative and quantitative analysis of the affinity with which a protein binds to a lipid." [PMID:22848065, PMID:23681540] is_a: ECO:0000021 ! physical interaction evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001093 name: luminescence-based mammalian interactome mapping assay evidence def: "A type of physical interaction evidence resulting from the analysis of protein-protein interactions by use of a luciferase enzyme fused to a particular protein (or proteins), which are coexpressed with epitope-tagged partners in mammalian cells." [MI:0729, PMID:15761153] synonym: "LUMIER assay" EXACT [] is_a: ECO:0000021 ! physical interaction evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001094 name: macroscopy evidence is_a: ECO:0000006 ! experimental evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001095 name: mammalian 2-hybrid assay evidence def: "A type of hybrid interaction evidence resulting from the analysis of proteins of interest attached to two portions of the transcriptional activator, and in interaction bring the two portions together to increase expression of the reporter gene." [ECO:RCT, PMID:9043710] is_a: ECO:0000025 ! hybrid interaction evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001096 name: mass spectrometry evidence def: "A type of spectrometry evidence resulting from identifying the amount and type of material entities present in a sample by fragmenting it and measuring the mass-to-charge ratio of the resulting particles." [OBI:0000470] is_a: ECO:0005504 ! spectrometry evidence relationship: OBI:0000312 OBI:0000470 ! is_specified_output_of mass spectrometry assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001097 name: medical imaging evidence def: "A type of imaging assay evidence resulting from the use of technology to visualize and provide information about the body to diagnose, treat, or monitor medical conditions." [url:http\://www.fda.gov/Radiation-EmittingProducts/RadiationEmittingProductsandProcedures/MedicalImaging/ucm2005914.htm] is_a: ECO:0000324 ! imaging assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001098 name: microscopy evidence def: "A type of direct assay evidence where a microscope was used to view a sample." [ECO:MCC] is_a: ECO:0000324 ! imaging assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001099 name: motility wound healing assay evidence alt_id: ECO:0001135 def: "A type of cell-based assay evidence to measure cell motility in which a \"wound\" is created in a cell monolayer and the migration of the cells is captured by imaging at regular intervals during cell migration to close the wound." [] synonym: "wound healing assay evidence" BROAD [] is_a: ECO:0001565 ! cell-based assay evidence relationship: IAO:0000136 GO:0042060 ! is about wound healing relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001100 name: MTS assay evidence def: "A type of apoptotic assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) in combination with phenazine methyl sulfate (PMS) as an intermediate electron acceptor reagent to produce a soluble formazan dye in viable cells." [NBK:144065, PMID:1867954] synonym: "3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium" NARROW [] is_a: ECO:0005034 ! apoptotic assay evidence relationship: IAO:0000136 GO:0008283 ! is about cell proliferation relationship: OBI:0000312 OBI:0000443 ! is_specified_output_of analyte assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001101 name: MTT assay evidence def: "A type of apoptotic assay evidence resulting from the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to its insoluble purple formazan dye in viable cells and measures cell viability / metabolic activity." [NBK:144065, PMID:6606682] synonym: "3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide" NARROW [] is_a: ECO:0005034 ! apoptotic assay evidence relationship: IAO:0000136 GO:0008283 ! is about cell proliferation relationship: OBI:0000312 OBI:0000443 ! is_specified_output_of analyte assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001102 name: multiplex bead-based immunoassay evidence def: "A type of protein detection assay evidence resulting from determination of analyte concentration by fluorescent bead sets attached to an antibody (to a specific analyte) with a fluorescent reporter dye label attached to a second antibody (to a specific analyte)." [PMC:1534009] is_a: ECO:0005517 ! protein detection assay evidence relationship: OBI:0000312 OBI:0000443 ! is_specified_output_of analyte assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001103 name: natural variation mutant evidence def: "A type of experimental phenotypic evidence resulting from the observation of the impact of a natural mutation on the expressed traits." [ECO:RCT] is_a: ECO:0000059 ! experimental phenotypic evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001104 name: nuclear fragmentation evidence def: "A type of apoptotic assay evidence resulting from the nuclei fragmenting into smaller pieces during programmed cell death." [PMID:16738861] is_a: ECO:0005034 ! apoptotic assay evidence relationship: IAO:0000136 GO:0007576 ! is about nucleolar fragmentation property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001105 name: nuclear magnetic resonance spectroscopy evidence def: "A type of structure determination evidence resulting from the use of an MRI to provide chemical information about tissue metabolites." [PMID:16428685] synonym: "NMR spectroscopy" EXACT [] is_a: ECO:0005031 ! structure determination evidence relationship: OBI:0000312 OBI:0000623 ! is_specified_output_of NMR spectroscopy property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001106 name: nuclease protection assay evidence def: "A type of RNA detection assay evidence resulting from the detection and quantitation of specific RNAs (from a sample of total cellular RNA) that are bound by antisense RNA or DNA probes and therefore protected from nucleases." [PMID:17486122, PMID:18428580] is_a: ECO:0005518 ! RNA detection assay evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001107 name: nucleotide analog incorporation assay evidence def: "A type of DNA synthesis cell proliferation assay evidence resulting from the analysis and measurement of the incorporation of fluorescently labeled nucleotide analog(s) into the DNA." [PMC:3149870] is_a: ECO:0005008 ! DNA synthesis cell proliferation assay evidence relationship: IAO:0000136 GO:0090592 ! is about DNA synthesis involved in DNA replication relationship: OBI:0000312 OBI:0000891 ! is_specified_output_of cell proliferation assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001108 name: phage display evidence def: "A type of protein binding evidence resulting from the panning of a phage library where the individual phage displayed a different peptide or protein by fusion to coat proteins on the capsid." [MI:0084, PMID:11680867] is_a: ECO:0000024 ! protein binding evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001109 name: phosphoamino acid analysis evidence def: "A type of protein assay evidence resulting from the identification of the phosphorylated residue in a protein by amino acid analysis." [PMID:11680867, PMID:18429115] is_a: ECO:0000039 ! protein assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001110 name: peptide affinity enrichment evidence synonym: "phosphopeptide affinity enrichment evidence" NARROW [] is_a: ECO:0000023 ! affinity evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001111 name: physical examination evidence def: "A type of direct assay evidence resulting from the physical examination and measurement of the feature of a subject or sample." [ECO:RCT] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001112 name: peptide array evidence def: "A type of protein assay evidence resulting from protein-bound peptides detected from a collection of peptides arranged as an array and incubated with the partner protein in order to map protein-protein interaction sites." [PMID:21243154] synonym: "phosphopeptide array evidence" NARROW [] is_a: ECO:0000039 ! protein assay evidence relationship: OBI:0000312 OBI:0000288 ! is_specified_output_of protein-protein interaction detection property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001113 name: point mutation evidence def: "A type of experimental phenotypic evidence resulting from the change in a single nucleotide." [SO:1000008] is_a: ECO:0000059 ! experimental phenotypic evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001114 name: propidium iodide staining evidence def: "A type of staining evidence resulting from the binding and labeling of DNA (during apoptosis, when there is a loss of nuclear DNA content) with propidium iodide (PI) to identify the cells from which it originated." [PMID:17406435] is_a: ECO:0005019 ! staining evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001115 name: fluorescence evidence def: "A type of direct assay evidence resulting from the analysis of a molecule by its intrinsic fluorescence, or by attaching it with a fluorophore." [url:http\://www.nature.com/subjects/biological-fluorescence] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001116 name: protein dot blot assay evidence def: "A type of protein detection assay evidence resulting from protein samples immobilized on a membrane, then subsequently incubated and imaged." [doi:10.1007/978-94-009-0951-9_24] is_a: ECO:0005517 ! protein detection assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001117 name: protein microarray evidence def: "A type of protein detection assay evidence resulting from proteins immobilized to prepare protein chips, or microwells, that can be utilized to determine presence of proteins, monitor differential expression profiles, and/or study protein interactions." [PMC:1828913] is_a: ECO:0005517 ! protein detection assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001118 name: protein sequencing assay evidence def: "A type of sequencing assay evidence resulting from determining the sequence of amino acids in a protein." [ERO:0001287] is_a: ECO:0000220 ! sequencing assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001119 name: quantitative mass spectrometry evidence def: "A type of mass spectrometry evidence resulting from quantitative analysis of peptides, proteins, and proteomes." [PMID:22665296] is_a: ECO:0001096 ! mass spectrometry evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001120 name: radioisotope assay evidence def: "A type of direct assay evidence resulting from the assessment of biological reactions by use of a radioactive isotope to label the reactant." [ISBN:978-3-642-50036-7] synonym: "radioassay" EXACT [] synonym: "radioisotopic assay" EXACT [] is_a: ECO:0000002 ! direct assay evidence relationship: IAO:0000136 GO:0008150 ! is about biological_process property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001121 name: radioimmunoassay evidence def: "A type of protein detection assay evidence resulting from the use of a radioligand to measure the binding of a substance to a specific antibody or other receptor system." [MeSH:D011863] is_a: ECO:0005517 ! protein detection assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001123 name: resonant mirror biosensor evidence def: "A type of direct assay evidence from the analysis of the real-time interaction between an analyte in solution and its interactant linked to the surface of the resonant mirror." [PMID:19151938] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001124 name: restriction fragment detection evidence def: "A type of DNA detection assay evidence resulting from homologous DNA fragments digested by restriction enzymes, and the resulting restriction fragments are sorted by length to illustrate differences." [doi:10.1007/978-94-009-0951-9_24, url:http\://www.ncbi.nlm.nih.gov/probe/docs/techrflp/] is_a: ECO:0005519 ! DNA detection assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001126 name: spectrophotometry evidence def: "A type of spectrometry evidence resulting from the evaluation of a molecule in a fluid by its ability to alter the transmission of light at specific wavelengths." [MMO:0000173] is_a: ECO:0005504 ! spectrometry evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001127 name: surface plasmon resonance evidence def: "A type of physical interaction evidence based on real-time, rapid plasmon generation on the interface between a planar surface and vacuum that measures changes in refractive index close to the sensor surface when an analyte and its immobilized ligand bind to observe and characterize molecular interaction." [ECO:SW, PMID:11578932, PMID:19151937, PMID:8574707] comment: Plasmons are generated by an incident light beam. synonym: "SPR evidence" EXACT [PMID:11578932] is_a: ECO:0000021 ! physical interaction evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001128 name: syngeneic transplantation experiment evidence def: "A type of experimental phenotypic evidence resulting from a transplantation in which the transplanted material (stem cells) is from an individual's identical twin." [PMID:18469352] is_a: ECO:0000059 ! experimental phenotypic evidence relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001129 name: TACE activity assay evidence def: "A type of enzyme assay evidence resulting from the analysis of tumor necrosis factor (TNF)-a converting enzyme (TACE), which releases a soluble TNF-a from the membrane-bound precursor protein." [PMC:1808921] synonym: "Tumor necrosis factor - alpha converting enzyme activity assay" EXACT [] is_a: ECO:0000005 ! enzyme assay evidence relationship: IAO:0000136 GO:1990774 ! is about tumor necrosis factor secretion relationship: OBI:0000312 OBI:0000443 ! is_specified_output_of analyte assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001130 name: tissue microarray evidence def: "A type of cytochemistry evidence resulting from the analysis of section(s) of a paraffin block containing embedded tissues cores arranged in an array pattern." [PMID:11770905] is_a: ECO:0001035 ! cytochemistry evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001131 name: transgenic organism evidence def: "A type of genetic transformation evidence resulting from an organism that has had its expressed phenotype altered by modification." [OBI:1000048] is_a: ECO:0005027 ! genetic transformation evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001132 name: tryptic phosphopeptide mapping assay evidence def: "A type of mass spectrometry evidence resulting from the analysis of prepared phosphopeptides separated in two dimensions on a TLC plate." [PMID:18429120] is_a: ECO:0001096 ! mass spectrometry evidence relationship: OBI:0000312 OBI:0002035 ! is_specified_output_of peptide mass fingerprinting property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001133 name: terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence def: "A type of apoptotic assay evidence resulting from the visualization of DNA fragmentation by detection of exposed 3'-OH ends, localized by terminal deoxynucleotidyl transferase (TdT) which then catalyzes the addition of labeled dUTPs." [PMID:22566045] synonym: "TdT-mediated dUTP-biotin nick end labeling assay" EXACT [] synonym: "terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence" EXACT [] synonym: "TUNEL assay evidence" EXACT [] is_a: ECO:0005034 ! apoptotic assay evidence property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001134 name: urine test evidence def: "A type of direct assay evidence resulting from the analysis of a urine sample." [ECO:RCT] is_a: ECO:0000002 ! direct assay evidence relationship: OBI:0000312 OBI:0000443 ! is_specified_output_of analyte assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001136 name: WST-1 assay evidence alt_id: ECO:0005009 def: "A type of cell proliferation assay evidence resulting from the assessment of metabolic activity from a water-soluble tetrazolium salt WST-1 being reduced outside the cell (by reacting with mitochondrial succinate-tetrazolium reductase) to form a formazan dye." [PMID:18417231] synonym: "metabolic cell proliferation assay evidence" BROAD [] is_a: ECO:0005007 ! cell proliferation assay evidence relationship: IAO:0000136 GO:0008283 ! is about cell proliferation property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001137 name: xenotransplantation experiment evidence def: "A type of anatomical perturbation evidence where live cells, tissues, or organs from a non-human animal source are transplanted, implanted or infused into a human recipient." [ECO:SN, url:http\://ilarjournal.oxfordjournals.org/content/37/1/16.full.pdf+html, url:http\://www.fda.gov/BiologicsBloodVaccines/Xenotransplantation/] synonym: "tissue grafting" NARROW [] synonym: "Xenograft transplantation" EXACT [] synonym: "Xenografting" EXACT [] synonym: "Xenotransplantation" EXACT [] is_a: ECO:0000240 ! anatomical perturbation evidence relationship: IAO:0000136 GO:0008150 ! is about biological_process relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-16T11:30:54Z [Term] id: ECO:0001138 name: 3D cell culture evidence used in manual assertion def: "A type of 3D cell culture evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001001 ! 3D cell culture evidence intersection_of: ECO:0001001 ! 3D cell culture evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:18:35Z [Term] id: ECO:0001139 name: 51Cr release assay evidence used in manual assertion def: "A type of 51Cr release assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001004 ! 51Cr release assay evidence intersection_of: ECO:0001004 ! 51Cr release assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:20:55Z [Term] id: ECO:0001140 name: 7-aminoactinomycin staining evidence used in manual assertion def: "A type of 7-aminoactinomycin staining evidence that is used in a manual assertion." [ECO:MCC] synonym: "7-AAD staining evidence" BROAD [] synonym: "7-amino-actinomycin D staining evidence" BROAD [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001005 ! 7-aminoactinomycin staining evidence intersection_of: ECO:0001005 ! 7-aminoactinomycin staining evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:22:01Z [Term] id: ECO:0001141 name: [3H]-thymidine incorporation assay evidence used in manual assertion def: "A type of [3H]-thymidine incorporation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001003 ! [3H]-thymidine incorporation assay evidence intersection_of: ECO:0001003 ! [3H]-thymidine incorporation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:31:52Z [Term] id: ECO:0001142 name: [3H]arachidonic acid release assay evidence used in manual assertion def: "A type of [3H]arachidonic acid release assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001002 ! [3H]arachidonic acid release assay evidence intersection_of: ECO:0001002 ! [3H]arachidonic acid release assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:32:44Z [Term] id: ECO:0001143 name: adhesion assay evidence used in manual assertion def: "A type of adhesion assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001006 ! adhesion assay evidence intersection_of: ECO:0001006 ! adhesion assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:33:38Z [Term] id: ECO:0001144 name: adoptive cell transfer evidence used in manual assertion def: "A type of adoptive cell transfer evidence that is used in a manual assertion." [ECO:MCC] synonym: "Adoptive immunotherapy" BROAD [] synonym: "passive immunization" BROAD [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001007 ! adoptive cell transfer evidence intersection_of: ECO:0001007 ! adoptive cell transfer evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:36:19Z [Term] id: ECO:0001145 name: alamarBlue assay evidence used in manual assertion def: "A type of alamarBlue assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001008 ! alamarBlue assay evidence intersection_of: ECO:0001008 ! alamarBlue assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:37:21Z [Term] id: ECO:0001146 name: allograft transplantation experiment evidence used in manual assertion def: "A type of allograft transplantation experiment evidence that is used in a manual assertion." [ECO:MCC] synonym: "allografting" BROAD [] synonym: "Allotransplantation" BROAD [] synonym: "tissue grafting" RELATED [] is_a: ECO:0001009 ! allograft transplantation experiment evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001009 ! allograft transplantation experiment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:38:22Z [Term] id: ECO:0001147 name: anion-exchange chromatography evidence used in manual assertion def: "A type of anion-exchange chromatography evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001010 ! anion-exchange chromatography evidence intersection_of: ECO:0001010 ! anion-exchange chromatography evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:44:30Z [Term] id: ECO:0001148 name: annexin-V staining evidence used in manual assertion def: "A type of annexin-V staining evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001011 ! annexin-V staining evidence intersection_of: ECO:0001011 ! annexin-V staining evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:52:01Z [Term] id: ECO:0001149 name: behavioral assay evidence used in manual assertion def: "A type of behavioral assay evidence used that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001012 ! behavioral assay evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001012 ! behavioral assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:53:38Z [Term] id: ECO:0001150 name: blocking monoclonal antibody evidence used in manual assertion def: "A type of blocking monoclonal antibody evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001013 ! blocking monoclonal antibody evidence is_a: ECO:0006078 {is_inferred="true"} ! immunological assay evidence used in manual assertion intersection_of: ECO:0001013 ! blocking monoclonal antibody evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:54:44Z [Term] id: ECO:0001151 name: blocking peptide evidence used in manual assertion def: "A type of blocking peptide evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001014 ! blocking peptide evidence is_a: ECO:0006078 {is_inferred="true"} ! immunological assay evidence used in manual assertion intersection_of: ECO:0001014 ! blocking peptide evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T15:55:33Z [Term] id: ECO:0001152 name: blocking polyclonal antibody evidence used in manual assertion def: "A type of blocking polyclonal antibody evidence tthat is used in a manual assertion." [ECO:MCC] is_a: ECO:0001015 ! blocking polyclonal antibody evidence is_a: ECO:0006078 {is_inferred="true"} ! immunological assay evidence used in manual assertion intersection_of: ECO:0001015 ! blocking polyclonal antibody evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:01:39Z [Term] id: ECO:0001153 name: blood test evidence used in manual assertion def: "A type of blood test evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001016 ! blood test evidence intersection_of: ECO:0001016 ! blood test evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:02:47Z [Term] id: ECO:0001154 name: Boyden chamber assay evidence used in manual assertion def: "A type of Boyden chamber assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001017 ! Boyden chamber assay evidence intersection_of: ECO:0001017 ! Boyden chamber assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:03:53Z [Term] id: ECO:0001155 name: bromodeoxyuridine incorporation assay evidence used in manual assertion def: "A type of bromodeoxyuridine incorporation assay evidence used in manual assertion." [ECO:MCC] synonym: "5-bromo-2'-deoxyuridine incorporation assay evidence" BROAD [] synonym: "BrdU incorporation assay evidence" BROAD [] synonym: "BrdUrd incorporation assay evidence" BROAD [] synonym: "BUdR incorporation assay evidence" BROAD [] is_a: ECO:0001018 ! bromodeoxyuridine incorporation assay evidence is_a: ECO:0001241 {is_inferred="true"} ! nucleotide analog incorporation assay evidence used in manual assertion intersection_of: ECO:0001018 ! bromodeoxyuridine incorporation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:04:49Z [Term] id: ECO:0001156 name: caspase assay evidence used in manual assertion def: "A type of caspase assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001019 ! caspase assay evidence intersection_of: ECO:0001019 ! caspase assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:06:06Z [Term] id: ECO:0001157 name: cell counting evidence used in manual assertion def: "A type of cell counting evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001020 ! cell counting evidence intersection_of: ECO:0001020 ! cell counting evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:07:13Z [Term] id: ECO:0001158 name: cell permeability assay evidence used in manual assertion def: "A type of cell permeability assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001021 ! cell permeability assay evidence intersection_of: ECO:0001021 ! cell permeability assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:07:58Z [Term] id: ECO:0001159 name: carboxyfluorescein diacetate succinimidyl ester staining evidence used in manual assertion def: "A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in a manual assertion." [ECO:MCC] synonym: "CFDA-SE staining evidence" BROAD [] synonym: "CFSE-staining evidence" BROAD [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001022 ! carboxyfluorescein diacetate succinimidyl ester staining evidence intersection_of: ECO:0001022 ! carboxyfluorescein diacetate succinimidyl ester staining evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:08:54Z [Term] id: ECO:0001160 name: chemiluminescence-linked immunoassay evidence used in manual assertion def: "A type of chemiluminescence-linked immunoassay evidence that is used in a manual assertion." [ECO:MCC] synonym: "CLIA evidence" BROAD [] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001023 ! chemiluminescence-linked immunoassay evidence intersection_of: ECO:0001023 ! chemiluminescence-linked immunoassay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:09:55Z [Term] id: ECO:0001161 name: chimeric protein evidence used in manual assertion def: "A type of chimeric protein evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion is_a: ECO:0001024 ! chimeric protein evidence intersection_of: ECO:0001024 ! chimeric protein evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:10:40Z [Term] id: ECO:0001162 name: co-electrophoresis evidence used in manual assertion def: "A type of co-electrophoresis evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001025 ! co-electrophoresis evidence intersection_of: ECO:0001025 ! co-electrophoresis evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:11:22Z [Term] id: ECO:0001163 name: co-localization evidence used in manual assertion def: "A type of co-localization evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001026 ! co-localization evidence is_a: ECO:0001256 {is_inferred="true"} ! imaging assay evidence used in manual assertion intersection_of: ECO:0001026 ! co-localization evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:12:04Z [Term] id: ECO:0001164 name: co-sedimentation assay evidence used in manual assertion def: "A type of co-sedimentation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000353 {is_inferred="true"} ! physical interaction evidence used in manual assertion is_a: ECO:0001028 ! co-sedimentation assay evidence intersection_of: ECO:0001028 ! co-sedimentation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:12:55Z [Term] id: ECO:0001165 name: colony counting evidence used in manual assertion def: "A type of colony counting evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001027 ! colony counting evidence intersection_of: ECO:0001027 ! colony counting evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:14:57Z [Term] id: ECO:0001166 name: comet assay evidence used in manual assertion def: "A type of comet assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001029 ! comet assay evidence intersection_of: ECO:0001029 ! comet assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:16:01Z [Term] id: ECO:0001167 name: conditional knockin evidence used in manual assertion def: "A type of conditional knockin evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001031 ! conditional knockin evidence is_a: ECO:0001224 {is_inferred="true"} ! knockin evidence used in manual assertion intersection_of: ECO:0001031 ! conditional knockin evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:17:22Z [Term] id: ECO:0001168 name: conditional knockout evidence used in manual assertion def: "A type of conditional knockout evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001030 ! conditional knockout evidence is_a: ECO:0001225 {is_inferred="true"} ! knockout evidence used in manual assertion intersection_of: ECO:0001030 ! conditional knockout evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:17:58Z [Term] id: ECO:0001169 name: constitutively active mutant evidence used in manual assertion def: "A type of constitutively active mutant evidence that is used a in manual assertion." [ECO:MCC] is_a: ECO:0001032 ! constitutively active mutant evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001032 ! constitutively active mutant evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:20:23Z [Term] id: ECO:0001170 name: cross-linking evidence used in manual assertion def: "A type of cross-linking evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001033 ! cross-linking evidence is_a: ECO:0006076 {is_inferred="true"} ! protein binding evidence used in manual assertion intersection_of: ECO:0001033 ! cross-linking evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:21:29Z [Term] id: ECO:0001171 name: crystallography evidence used in manual assertion def: "A type of crystallography evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001034 ! crystallography evidence intersection_of: ECO:0001034 ! crystallography evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:22:20Z [Term] id: ECO:0001172 name: cytochemistry evidence used in manual assertion def: "A type of cytochemistry evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001035 ! cytochemistry evidence is_a: ECO:0001185 {is_inferred="true"} ! histochemistry evidence used in manual assertion intersection_of: ECO:0001035 ! cytochemistry evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:23:10Z [Term] id: ECO:0001173 name: cytochrome C release assay evidence used in manual assertion def: "A type of cytochrome C release assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001036 ! cytochrome C release assay evidence intersection_of: ECO:0001036 ! cytochrome C release assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:23:53Z [Term] id: ECO:0001174 name: 4',6-diamidino-2-phenylindole staining evidence used in manual assertion def: "A type of 4',6-diamidino-2-phenylindole staining evidence that is used in a manual assertion." [ECO:MCC] synonym: "DAPI staining evidence" BROAD [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001037 ! 4',6-diamidino-2-phenylindole staining evidence intersection_of: ECO:0001037 ! 4',6-diamidino-2-phenylindole staining evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:25:03Z [Term] id: ECO:0001175 name: deletion mutation evidence used in manual assertion def: "A type of deletion evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001038 ! deletion mutation evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001038 ! deletion mutation evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:25:54Z [Term] id: ECO:0001176 name: DNA laddering assay evidence used in manual assertion def: "A type of DNA laddering assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001039 ! DNA laddering assay evidence intersection_of: ECO:0001039 ! DNA laddering assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:26:46Z [Term] id: ECO:0001177 name: RNA dot blot assay evidence used in manual assertion def: "A type of RNA dot blot assay evidence that is used in a manual assertion." [ECO:MCC] synonym: "RNA dot blot evidence" BROAD [] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001040 ! RNA dot blot assay evidence intersection_of: ECO:0001040 ! RNA dot blot assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:45:52Z [Term] id: ECO:0001179 name: dominant-negative mutant evidence used in manual assertion def: "A type of dominant-negative mutant evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001042 ! dominant-negative mutant evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001042 ! dominant-negative mutant evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:47:44Z [Term] id: ECO:0001180 name: eTag assay evidence used in manual assertion def: "A type of eTag assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001045 ! eTag assay evidence is_a: ECO:0006075 {is_inferred="true"} ! affinity evidence used in manual assertion intersection_of: ECO:0001045 ! eTag assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T16:59:39Z [Term] id: ECO:0001181 name: filter binding assay evidence used in manual assertion def: "A type of filter binding assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000353 {is_inferred="true"} ! physical interaction evidence used in manual assertion is_a: ECO:0001046 ! filter binding assay evidence intersection_of: ECO:0001046 ! filter binding assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:03:28Z [Term] id: ECO:0001182 name: fluorescence in situ hybridization evidence used in manual assertion def: "A type of fluorescence in situ hybridization evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000270 {is_inferred="true"} ! expression evidence used in manual assertion is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001047 ! fluorescence in situ hybridization evidence intersection_of: ECO:0001047 ! fluorescence in situ hybridization evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:04:20Z [Term] id: ECO:0001183 name: fluorescence resonance energy transfer evidence used in manual assertion def: "A type of fluorescence resonance energy transfer evidence that is used in a manual assertion." [ECO:MCC] synonym: "FRET evidence" BROAD [] is_a: ECO:0000353 {is_inferred="true"} ! physical interaction evidence used in manual assertion is_a: ECO:0001048 ! fluorescence resonance energy transfer evidence intersection_of: ECO:0001048 ! fluorescence resonance energy transfer evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:05:22Z [Term] id: ECO:0001184 name: gel-filtration evidence used in manual assertion def: "A type of gel-filtration evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001049 ! gel-filtration evidence intersection_of: ECO:0001049 ! gel-filtration evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:06:14Z [Term] id: ECO:0001185 name: histochemistry evidence used in manual assertion def: "A type of histochemistry evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001050 ! histochemistry evidence is_a: ECO:0001187 {is_inferred="true"} ! histology evidence used in manual assertion intersection_of: ECO:0001050 ! histochemistry evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:07:19Z [Term] id: ECO:0001186 name: immunocytochemistry evidence used in manual assertion def: "A type of immunocytochemistry evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001053 ! immunocytochemistry evidence intersection_of: ECO:0001053 ! immunocytochemistry evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:12:39Z [Term] id: ECO:0001187 name: histology evidence used in manual assertion def: "A type of histology evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001051 ! histology evidence is_a: ECO:0001256 {is_inferred="true"} ! imaging assay evidence used in manual assertion intersection_of: ECO:0001051 ! histology evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:09:50Z [Term] id: ECO:0001188 name: immunodepletion evidence used in manual assertion def: "A type of immunodepletion evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001054 ! immunodepletion evidence is_a: ECO:0006078 {is_inferred="true"} ! immunological assay evidence used in manual assertion intersection_of: ECO:0001054 ! immunodepletion evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:16:19Z [Term] id: ECO:0001189 name: immunohistochemistry evidence used in manual assertion def: "A type of immunohistochemistry evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001055 ! immunohistochemistry evidence intersection_of: ECO:0001055 ! immunohistochemistry evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:17:22Z [Term] id: ECO:0001190 name: in vitro acetylation assay evidence used in manual assertion def: "A type of in vitro acetylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001057 ! in vitro acetylation assay evidence intersection_of: ECO:0001057 ! in vitro acetylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:19:24Z [Term] id: ECO:0001191 name: in vitro cleavage assay evidence used in manual assertion def: "A type of in vitro cleavage assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001058 ! in vitro cleavage assay evidence intersection_of: ECO:0001058 ! in vitro cleavage assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:21:22Z [Term] id: ECO:0001192 name: in vitro deacetylation assay evidence used in manual assertion def: "A type of in vitro deacetylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001060 ! in vitro deacetylation assay evidence intersection_of: ECO:0001060 ! in vitro deacetylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:23:42Z [Term] id: ECO:0001193 name: in vitro defarnesylation assay evidence used in manual assertion def: "A type of in vitro defarnesylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001061 ! in vitro defarnesylation assay evidence intersection_of: ECO:0001061 ! in vitro defarnesylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:25:45Z [Term] id: ECO:0001194 name: in vitro demethylation assay evidence used in manual assertion def: "A type of in vitro demethylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001062 ! in vitro demethylation assay evidence intersection_of: ECO:0001062 ! in vitro demethylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:27:00Z [Term] id: ECO:0001195 name: in vitro desumoylation assay evidence used in manual assertion def: "A type of in vitro desumoylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001063 ! in vitro desumoylation assay evidence intersection_of: ECO:0001063 ! in vitro desumoylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:29:01Z [Term] id: ECO:0001196 name: in vitro deubiquitination assay evidence used in manual assertion def: "A type of in vitro deubiquitination assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001059 ! in vitro deubiquitination assay evidence intersection_of: ECO:0001059 ! in vitro deubiquitination assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:29:48Z [Term] id: ECO:0001197 name: in vitro farnesylation assay evidence used in manual assertion def: "A type of in vitro farnesylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001064 ! in vitro farnesylation assay evidence intersection_of: ECO:0001064 ! in vitro farnesylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:30:50Z [Term] id: ECO:0001198 name: in vitro methylation assay evidence used in manual assertion def: "A type of in vitro methylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001065 ! in vitro methylation assay evidence intersection_of: ECO:0001065 ! in vitro methylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:31:54Z [Term] id: ECO:0001199 name: in vitro palmitoylation assay evidence used in manual assertion def: "A type of in vitro palmitoylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001066 ! in vitro palmitoylation assay evidence intersection_of: ECO:0001066 ! in vitro palmitoylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:32:57Z [Term] id: ECO:0001200 name: in vitro phosphatase assay evidence used in manual assertion def: "A type of in vitro phosphatase assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001067 ! in vitro phosphatase assay evidence intersection_of: ECO:0001067 ! in vitro phosphatase assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:34:16Z [Term] id: ECO:0001201 name: in vitro polyADP-ribosylation assay evidence used in manual assertion def: "A type of in vitro polyADP-ribosylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001069 ! in vitro polyADP-ribosylation assay evidence intersection_of: ECO:0001069 ! in vitro polyADP-ribosylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:34:57Z [Term] id: ECO:0001202 name: in vitro protein kinase assay evidence used in manual assertion def: "A type of in vitro protein kinase assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001068 ! in vitro protein kinase assay evidence intersection_of: ECO:0001068 ! in vitro protein kinase assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:39:57Z [Term] id: ECO:0001203 name: in vitro sumoylation assay evidence used in manual assertion def: "A type of in vitro sumoylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001070 ! in vitro sumoylation assay evidence intersection_of: ECO:0001070 ! in vitro sumoylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:41:25Z [Term] id: ECO:0001204 name: in vitro transcription assay evidence used in manual assertion def: "A type of in vitro transcription assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001071 ! in vitro transcription assay evidence intersection_of: ECO:0001071 ! in vitro transcription assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:44:40Z [Term] id: ECO:0001205 name: in vitro translation assay evidence used in manual assertion def: "A type of in vitro translation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001072 ! in vitro translation assay evidence intersection_of: ECO:0001072 ! in vitro translation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:46:30Z [Term] id: ECO:0001206 name: in vitro ubiquitination assay evidence used in manual assertion def: "A type of in vitro ubiquitination assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001073 ! in vitro ubiquitination assay evidence intersection_of: ECO:0001073 ! in vitro ubiquitination assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:47:18Z [Term] id: ECO:0001207 name: in vivo acetylation assay evidence used in manual assertion def: "A type of in vivo acetylation assay evidence that is used in manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001074 ! in vivo acetylation assay evidence intersection_of: ECO:0001074 ! in vivo acetylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:48:56Z [Term] id: ECO:0001208 name: in vivo cleavage assay evidence used in manual assertion def: "A type of in vivo cleavage assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001075 ! in vivo cleavage assay evidence intersection_of: ECO:0001075 ! in vivo cleavage assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:49:43Z [Term] id: ECO:0001209 name: in vivo deacetylation assay evidence used in manual assertion def: "A type of in vivo deacetylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001076 ! in vivo deacetylation assay evidence intersection_of: ECO:0001076 ! in vivo deacetylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:50:47Z [Term] id: ECO:0001210 name: in vivo defarnesylation assay evidence used in manual assertion def: "A type of in vivo defarnesylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001077 ! in vivo defarnesylation assay evidence intersection_of: ECO:0001077 ! in vivo defarnesylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:52:41Z [Term] id: ECO:0001211 name: in vivo demethylation assay evidence used in manual assertion def: "A type of in vivo demethylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001078 ! in vivo demethylation assay evidence intersection_of: ECO:0001078 ! in vivo demethylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:53:40Z [Term] id: ECO:0001212 name: in vivo desumoylation assay evidence used in manual assertion def: "A type of in vivo desumoylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001080 ! in vivo desumoylation assay evidence intersection_of: ECO:0001080 ! in vivo desumoylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:54:36Z [Term] id: ECO:0001213 name: in vivo deubiquitination assay evidence used in manual assertion def: "A type of in vivo deubiquitination assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001079 ! in vivo deubiquitination assay evidence intersection_of: ECO:0001079 ! in vivo deubiquitination assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:56:28Z [Term] id: ECO:0001214 name: in vivo farnesylation assay evidence used in manual assertion def: "A type of in vivo farnesylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001081 ! in vivo farnesylation assay evidence intersection_of: ECO:0001081 ! in vivo farnesylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T17:57:18Z [Term] id: ECO:0001215 name: in vivo methylation assay evidence used in manual assertion def: "A type of in vivo methylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001082 ! in vivo methylation assay evidence intersection_of: ECO:0001082 ! in vivo methylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:03:16Z [Term] id: ECO:0001216 name: in vivo palmitoylation assay evidence used in manual assertion def: "A type of in vivo palmitoylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001083 ! in vivo palmitoylation assay evidence intersection_of: ECO:0001083 ! in vivo palmitoylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:04:07Z [Term] id: ECO:0001217 name: in vivo phosphatase assay evidence used in manual assertion def: "A type of in vivo phosphatase assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001084 ! in vivo phosphatase assay evidence intersection_of: ECO:0001084 ! in vivo phosphatase assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:06:08Z [Term] id: ECO:0001218 name: in vivo protein kinase assay evidence used in manual assertion def: "A type of in vivo protein kinase assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001085 ! in vivo protein kinase assay evidence intersection_of: ECO:0001085 ! in vivo protein kinase assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:07:58Z [Term] id: ECO:0001219 name: in vivo sumoylation assay evidence used in manual assertion def: "A type of in vivo sumoylation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001086 ! in vivo sumoylation assay evidence intersection_of: ECO:0001086 ! in vivo sumoylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:09:49Z [Term] id: ECO:0001220 name: in vivo transcription assay evidence used in manual assertion def: "A type of in vivo transcription assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001087 ! in vivo transcription assay evidence intersection_of: ECO:0001087 ! in vivo transcription assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:11:20Z [Term] id: ECO:0001221 name: in vivo translation assay evidence used in manual assertion def: "A type of in vivo translation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001088 ! in vivo translation assay evidence intersection_of: ECO:0001088 ! in vivo translation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:42:50Z [Term] id: ECO:0001222 name: in vivo ubiquitination assay evidence used in manual assertion def: "A type of in vivo ubiquitination assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001089 ! in vivo ubiquitination assay evidence intersection_of: ECO:0001089 ! in vivo ubiquitination assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:44:11Z [Term] id: ECO:0001223 name: induced mutation evidence used in manual assertion def: "A type of induced mutation evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001056 ! induced mutation evidence is_a: ECO:0006049 {is_inferred="true"} ! genetic transformation evidence used in manual assertion intersection_of: ECO:0001056 ! induced mutation evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:45:56Z [Term] id: ECO:0001224 name: knockin evidence used in manual assertion def: "A type of knockin evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001090 ! knockin evidence is_a: ECO:0006049 {is_inferred="true"} ! genetic transformation evidence used in manual assertion intersection_of: ECO:0001090 ! knockin evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:49:35Z [Term] id: ECO:0001225 name: knockout evidence used in manual assertion def: "A type of knockout evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001091 ! knockout evidence is_a: ECO:0006049 {is_inferred="true"} ! genetic transformation evidence used in manual assertion intersection_of: ECO:0001091 ! knockout evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:51:31Z [Term] id: ECO:0001226 name: lipid binding assay evidence used in manual assertion def: "A type of lipid binding assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000353 {is_inferred="true"} ! physical interaction evidence used in manual assertion is_a: ECO:0001092 ! lipid binding assay evidence intersection_of: ECO:0001092 ! lipid binding assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:52:19Z [Term] id: ECO:0001227 name: luminescence-based mammalian interactome mapping assay evidence used in manual assertion def: "A type of LUMIER assay evidence that is used in a manual assertion." [ECO:MCC] synonym: "LUMIER assay evidence" BROAD [] is_a: ECO:0000353 {is_inferred="true"} ! physical interaction evidence used in manual assertion is_a: ECO:0001093 ! luminescence-based mammalian interactome mapping assay evidence intersection_of: ECO:0001093 ! luminescence-based mammalian interactome mapping assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:55:16Z [Term] id: ECO:0001228 name: macroscopy evidence used in manual assertion def: "A type of macroscopy evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001094 ! macroscopy evidence intersection_of: ECO:0001094 ! macroscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:56:21Z [Term] id: ECO:0001229 name: mammalian 2-hybrid assay evidence used in manual assertion def: "A type of mammalian 2-hybrid assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001095 ! mammalian 2-hybrid assay evidence is_a: ECO:0006077 {is_inferred="true"} ! hybrid interaction evidence used in manual assertion intersection_of: ECO:0001095 ! mammalian 2-hybrid assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:57:25Z [Term] id: ECO:0001230 name: mass spectrometry evidence used in manual assertion def: "A type of mass spectrometry evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001096 ! mass spectrometry evidence intersection_of: ECO:0001096 ! mass spectrometry evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T18:59:50Z [Term] id: ECO:0001231 name: medical imaging evidence used in manual assertion def: "A type of medical imaging evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001097 ! medical imaging evidence is_a: ECO:0001256 {is_inferred="true"} ! imaging assay evidence used in manual assertion intersection_of: ECO:0001097 ! medical imaging evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:04:43Z [Term] id: ECO:0001232 name: microscopy evidence used in manual assertion def: "A type of microscopy evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001098 ! microscopy evidence is_a: ECO:0001256 {is_inferred="true"} ! imaging assay evidence used in manual assertion intersection_of: ECO:0001098 ! microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:05:37Z [Term] id: ECO:0001233 name: motility wound healing assay evidence used in manual assertion alt_id: ECO:0001262 def: "A type of motility wound healing assay evidence that is used in a manual assertion." [ECO:MCC] synonym: "wound healing assay evidence used in manual assertion" BROAD [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001099 ! motility wound healing assay evidence intersection_of: ECO:0001099 ! motility wound healing assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:08:13Z [Term] id: ECO:0001234 name: MTS assay evidence used in manual assertion def: "A type of MTS assay evidence that is used in a manual assertion." [ECO:MCC] synonym: "3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium" RELATED [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001100 ! MTS assay evidence intersection_of: ECO:0001100 ! MTS assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:08:51Z [Term] id: ECO:0001235 name: MTT assay evidence used in manual assertion def: "A type of MTT assay evidence that is used in a manual assertion." [ECO:MCC] synonym: "3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide" RELATED [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001101 ! MTT assay evidence intersection_of: ECO:0001101 ! MTT assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:13:17Z [Term] id: ECO:0001236 name: multiplex bead-based immunoassay evidence used in manual assertion def: "A type of multiplex bead-based immunoassay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001102 ! multiplex bead-based immunoassay evidence intersection_of: ECO:0001102 ! multiplex bead-based immunoassay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:14:03Z [Term] id: ECO:0001237 name: natural variation mutant evidence used in manual assertion def: "A type of natural variation mutant evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001103 ! natural variation mutant evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001103 ! natural variation mutant evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:15:48Z [Term] id: ECO:0001238 name: nuclear magnetic resonance spectroscopy evidence used in manual assertion def: "A type of nuclear magnetic resonance spectroscopy evidence that is used in a manual assertion." [ECO:MCC] synonym: "NMR spectroscopy evidence" BROAD [] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001105 ! nuclear magnetic resonance spectroscopy evidence intersection_of: ECO:0001105 ! nuclear magnetic resonance spectroscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:18:50Z [Term] id: ECO:0001239 name: nuclear fragmentation evidence used in manual assertion def: "A type of nuclear fragmentation evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001104 ! nuclear fragmentation evidence intersection_of: ECO:0001104 ! nuclear fragmentation evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:19:55Z [Term] id: ECO:0001240 name: nuclease protection assay evidence used in manual assertion def: "A type of nuclease protection assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001106 ! nuclease protection assay evidence intersection_of: ECO:0001106 ! nuclease protection assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:23:41Z [Term] id: ECO:0001241 name: nucleotide analog incorporation assay evidence used in manual assertion def: "A type of nucleotide analog incorporation assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001107 ! nucleotide analog incorporation assay evidence intersection_of: ECO:0001107 ! nucleotide analog incorporation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:25:17Z [Term] id: ECO:0001242 name: phage display evidence used in manual assertion def: "A type of phage display evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001108 ! phage display evidence is_a: ECO:0006076 {is_inferred="true"} ! protein binding evidence used in manual assertion intersection_of: ECO:0001108 ! phage display evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:27:17Z [Term] id: ECO:0001243 name: phosphoamino acid analysis evidence used in manual assertion def: "A type of phosphoamino acid analysis evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001109 ! phosphoamino acid analysis evidence intersection_of: ECO:0001109 ! phosphoamino acid analysis evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:28:59Z [Term] id: ECO:0001244 name: peptide affinity enrichment evidence used in manual assertion def: "A type of peptide affinity enrichment evidence that is used in a manual assertion." [ECO:MCC] synonym: "phosphopeptide affinity enrichment evidence" RELATED [] is_a: ECO:0001110 ! peptide affinity enrichment evidence is_a: ECO:0006075 {is_inferred="true"} ! affinity evidence used in manual assertion intersection_of: ECO:0001110 ! peptide affinity enrichment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T19:30:13Z [Term] id: ECO:0001245 name: peptide array evidence used in manual assertion def: "A type of peptide array evidence that is used in a manual assertion." [ECO:MCC] synonym: "phosphopeptide array evidence" RELATED [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001112 ! peptide array evidence intersection_of: ECO:0001112 ! peptide array evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:16:45Z [Term] id: ECO:0001246 name: physical examination evidence used in manual assertion def: "A type of physical examination evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001111 ! physical examination evidence intersection_of: ECO:0001111 ! physical examination evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:17:27Z [Term] id: ECO:0001247 name: point mutation evidence used in manual assertion def: "A type of point mutation evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001113 ! point mutation evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001113 ! point mutation evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:18:10Z [Term] id: ECO:0001248 name: propidium iodide staining evidence used in manual assertion def: "A type of propidium iodide staining evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001114 ! propidium iodide staining evidence intersection_of: ECO:0001114 ! propidium iodide staining evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:18:58Z [Term] id: ECO:0001249 name: fluorescence evidence used in manual assertion def: "A type of protein detection by fluorescence evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001115 ! fluorescence evidence intersection_of: ECO:0001115 ! fluorescence evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:19:35Z [Term] id: ECO:0001250 name: protein dot blot assay evidence used in manual assertion def: "A type of protein dot blot assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001116 ! protein dot blot assay evidence intersection_of: ECO:0001116 ! protein dot blot assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:20:30Z [Term] id: ECO:0001251 name: protein microarray evidence used in manual assertion def: "A type of protein microarray evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001117 ! protein microarray evidence intersection_of: ECO:0001117 ! protein microarray evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:21:11Z [Term] id: ECO:0001252 name: protein sequencing assay evidence used in manual assertion def: "A type of protein sequencing assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001118 ! protein sequencing assay evidence intersection_of: ECO:0001118 ! protein sequencing assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:22:08Z [Term] id: ECO:0001253 name: quantitative mass spectrometry evidence used in manual assertion def: "A type of quantitative mass spectrometry evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001119 ! quantitative mass spectrometry evidence is_a: ECO:0001230 {is_inferred="true"} ! mass spectrometry evidence used in manual assertion intersection_of: ECO:0001119 ! quantitative mass spectrometry evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:23:15Z [Term] id: ECO:0001254 name: radioisotope assay evidence used in manual assertion def: "A type of radioisotope assay evidence that is used in a manual assertion." [ECO:MCC] synonym: "radioassay evidence" BROAD [] synonym: "radioisotopic assay evidence" BROAD [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001120 ! radioisotope assay evidence intersection_of: ECO:0001120 ! radioisotope assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:27:05Z [Term] id: ECO:0001255 name: radioimmunoassay evidence used in manual assertion def: "A type of radioimmunoassay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001121 ! radioimmunoassay evidence intersection_of: ECO:0001121 ! radioimmunoassay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:28:04Z [Term] id: ECO:0001256 name: imaging assay evidence used in manual assertion def: "A type of imaging assay evidence that is used in a manual assertion." [ECO:MCC] synonym: "radiologic test evidence" RELATED [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0000324 ! imaging assay evidence intersection_of: ECO:0000324 ! imaging assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:00Z [Term] id: ECO:0001257 name: restriction fragment detection evidence used in manual assertion def: "A type of restriction fragment detection evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001124 ! restriction fragment detection evidence intersection_of: ECO:0001124 ! restriction fragment detection evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:05Z [Term] id: ECO:0001258 name: spectrophotometry evidence used in manual assertion def: "A type of spectrophotometry evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001126 ! spectrophotometry evidence intersection_of: ECO:0001126 ! spectrophotometry evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:09Z [Term] id: ECO:0001259 name: syngeneic transplantation experiment evidence used in manual assertion def: "A type of syngeneic transplantation experiment evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001128 ! syngeneic transplantation experiment evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001128 ! syngeneic transplantation experiment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:13Z [Term] id: ECO:0001260 name: xenotransplantation experiment evidence used in manual assertion def: "A type of xenotransplantation experiment evidence that is used in a manual assertion." [ECO:MCC] synonym: "tissue grafting" RELATED [] synonym: "xenograft transplantation evidence" BROAD [] synonym: "xenografting evidence" BROAD [] synonym: "xenotransplantation evidence" BROAD [] is_a: ECO:0001137 ! xenotransplantation experiment evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001137 ! xenotransplantation experiment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:18Z [Term] id: ECO:0001261 name: WST-1 assay evidence used in manual assertion def: "A type of WST-1 assay evidence that is used in a manual assertion." [ECO:MCC] synonym: "metabolic cell proliferation assay evidence" BROAD [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001136 ! WST-1 assay evidence intersection_of: ECO:0001136 ! WST-1 assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:22Z [Term] id: ECO:0001263 name: urine test evidence used in manual assertion def: "A type of urine test evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001134 ! urine test evidence intersection_of: ECO:0001134 ! urine test evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:30Z [Term] id: ECO:0001264 name: terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in manual assertion def: "A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence assay evidence that is used in a manual assertion." [ECO:MCC] synonym: "TdT-mediated dUTP-biotin nick end labeling assay evidence" BROAD [] synonym: "terminal deoxynucleotidyl transferase-dUTP nick end labeling assay evidence" BROAD [] synonym: "TUNEL assay evidence" BROAD [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001133 ! terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence intersection_of: ECO:0001133 ! terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:34Z [Term] id: ECO:0001265 name: tryptic phosphopeptide mapping assay evidence used in manual assertion def: "A type of tryptic phosphopeptide mapping assay evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001132 ! tryptic phosphopeptide mapping assay evidence is_a: ECO:0001230 {is_inferred="true"} ! mass spectrometry evidence used in manual assertion intersection_of: ECO:0001132 ! tryptic phosphopeptide mapping assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:38Z [Term] id: ECO:0001266 name: transgenic organism evidence used in manual assertion def: "A type of transgenic organism evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001131 ! transgenic organism evidence is_a: ECO:0006049 {is_inferred="true"} ! genetic transformation evidence used in manual assertion intersection_of: ECO:0001131 ! transgenic organism evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:41Z [Term] id: ECO:0001267 name: tissue microarray evidence used in manual assertion def: "A type of tissue microarray evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0001130 ! tissue microarray evidence is_a: ECO:0001172 {is_inferred="true"} ! cytochemistry evidence used in manual assertion intersection_of: ECO:0001130 ! tissue microarray evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:45Z [Term] id: ECO:0001268 name: TACE activity assay evidence used in manual assertion def: "A type of TACE activity assay evidence that is used in a manual assertion." [ECO:MCC] synonym: "Tumor necrosis factor - alpha converting enzyme activity assay evidence" BROAD [] is_a: ECO:0001129 ! TACE activity assay evidence is_a: ECO:0005801 {is_inferred="true"} ! enzyme assay evidence used in manual assertion intersection_of: ECO:0001129 ! TACE activity assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:49Z [Term] id: ECO:0001269 name: surface plasmon resonance evidence used in manual assertion def: "A type of surface plasmon resonance evidence that is used in a manual assertion." [ECO:MCC] synonym: "SPR evidence" BROAD [] is_a: ECO:0000353 {is_inferred="true"} ! physical interaction evidence used in manual assertion is_a: ECO:0001127 ! surface plasmon resonance evidence intersection_of: ECO:0001127 ! surface plasmon resonance evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:54Z [Term] id: ECO:0001270 name: restriction landmark genomic scanning evidence used in manual assertion def: "A type of restriction landmark genome scanning evidence that is used in a manual assertion." [ECO:MCC] synonym: "restriction landmark genome scanning evidence" BROAD [] synonym: "RLGS evidence" BROAD [] is_a: ECO:0000089 ! restriction landmark genomic scanning evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000089 ! restriction landmark genomic scanning evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:29:58Z [Term] id: ECO:0001271 name: resonant mirror biosensor evidence used in manual assertion def: "A type of resonant mirror biosensor evidence that is used in a manual assertion." [ECO:MCC] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001123 ! resonant mirror biosensor evidence intersection_of: ECO:0001123 ! resonant mirror biosensor evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T20:30:02Z [Term] id: ECO:0001272 name: high-performance liquid chromatography evidence used in manual assertion def: "A type of high-performance liquid chromatography evidence that is used in a manual assertion." [ECO:MCC] synonym: "HPLC evidence" BROAD [] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001052 ! high-performance liquid chromatography evidence intersection_of: ECO:0001052 ! high-performance liquid chromatography evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: mchibucos creation_date: 2014-03-16T20:49:54Z [Term] id: ECO:0001273 name: ectopic expression evidence used in manual assertion def: "A type of ectopic expression evidence that is used in a manual assertion." [ECO:MCC] synonym: "IMP: analysis of overexpression/ectopic expression phenotype" RELATED [] is_a: ECO:0000017 ! ectopic expression evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0000017 ! ectopic expression evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion property_value: IAO:0000234 SIB:PG xsd:string created_by: mchibucos creation_date: 2014-03-17T22:34:56Z [Term] id: ECO:0001533 name: localization evidence def: "A type of direct assay evidence in which the sub-cellular location of a protein or nucleic acid sequence is determined." [] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_ExpGenomicCleanup" xsd:string created_by: jbmunro creation_date: 2018-05-17T12:00:00Z [Term] id: ECO:0001534 name: nucleic acid localization evidence def: "A type of localization evidence based on localization of a specific segment of DNA or RNA within tissue by the application of a complementary strand of nucleic acid to which a reporter molecule (i.e. either radio-, fluorescent- or antigen-labeled probe) is attached and quantified using either autoradiography, fluorescence microscopy, or immunohistochemistry." [] is_a: ECO:0001533 ! localization evidence property_value: IAO:0000234 "ECO_ExpGenomicCleanup" xsd:string created_by: jbmunro creation_date: 2018-05-17T12:00:00Z [Term] id: ECO:0001546 name: acetylation assay evidence def: "A type of direct assay evidence where acetylated residues are detected in a protein." [SIB:PG, url:http\://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001547 name: cleavage assay evidence def: "A type of direct assay evidence where the cleavage of a protein into protein fragments by a protease is detected." [PMID:21121091, PMID:22154596] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001548 name: deacetylation assay evidence def: "A type of direct assay evidence where the removal of acetyl groups are detected in a protein." [SIB:PG, url:http\://www.perkinelmer.com/resources/technicalresources/applicationsupportknowledgebase/radiometric/acetylation.xhtml] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001549 name: defarnesylation assay evidence def: "A type of direct assay evidence where the removal of farnesyl groups from a protein is detected." [PMID:15556768, PMID:16126733, PMID:16507103, SIB:PG] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001550 name: demethylation assay evidence def: "A type of direct assay evidence where the removal of methyl groups from a substrate (RNA/DNA or protein) is detected." [SIB:PG, url:http\://en.wikipedia.org/wiki/Demethylation] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001551 name: desumoylation assay evidence def: "A type of direct assay evidence where the removal of sumo groups from a protein is detected." [SIB:PG, url:http\://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001552 name: deubiquitination assay evidence def: "A type of direct assay evidence where the removal of ubiquitin groups from a protein is detected." [PMID:19692941, SIB:PG] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001553 name: farnesylation assay evidence def: "A type of direct assay evidence where farnesylated residues in proteins are detected." [PMID:9030603, SIB:PG, url:http\://en.wikipedia.org/wiki/Farnesyltransferase] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001554 name: methylation assay evidence def: "A type of direct assay evidence where methylated residues of a substarte (RNA/DNA or protein) are detected." [SIB:PG, url:http\://en.wikipedia.org/wiki/Methylation] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001555 name: palmitoylation assay evidence def: "A type of direct assay evidence where palmitoylated residues in a protein are detected." [PMID:10329400, PMID:17077383, SIB:PG] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001556 name: phosphatase assay evidence def: "A type of direct assay evidence where the removal of phosphatase groups from a protein is detected." [SIB:PG, url:http\://en.wikipedia.org/wiki/Phosphatase] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001557 name: polyADP-ribosylation assay evidence def: "A type of direct assay evidence where ADP-ribosylated residues in proteins are detected." [PMID:21870253, PMID:2820766, SIB:PG] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001558 name: protein kinase assay evidence def: "A type of direct assay evidence where phosphorylated residues in proteins are detected." [SIB:PG, url:http\://en.wikipedia.org/wiki/Protein_kinase, url:http\://en.wikipedia.org/wiki/Protein_phosphorylation] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001559 name: sumoylation assay evidence def: "A type of direct assay evidence where sumoylated residues on a protein are detected." [SIB:PG, url:http\://www.enzolifesciences.com/BML-UW8955/sumoylation-kit/] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001561 name: translation assay evidence def: "A type of direct assay evidence where de novo protein synthesis is detected." [PMID:18230759, PMID:24901308, SIB:PG] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001562 name: ubiquitination assay evidence def: "A type of direct assay evidence where ubiquitinated residues on a protein are detected." [PMID:19692941, SIB:PG] is_a: ECO:0000002 ! direct assay evidence property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001563 name: cell growth assay evidence def: "A type of direct assay evidence where biological cell development, i.e. an increase in cell mass and size are measured." [GO:0016049, PMID:11057898] is_a: ECO:0001565 ! cell-based assay evidence relationship: IAO:0000136 GO:0016049 ! is about cell growth property_value: IAO:0000234 "ECO_AssayCleanup" xsd:string created_by: mchibucos / jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001565 name: cell-based assay evidence def: "A type of direct assay evidence resulting from the study of cells." [] is_a: ECO:0000002 ! direct assay evidence created_by: jbmunro creation_date: 2017-11-30T14:00:00Z [Term] id: ECO:0001601 name: protein-binding microarray evidence def: "A type of protein-binding evidence that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites." [PMID:22146299] synonym: "PBM evidence" EXACT [] is_a: ECO:0000024 ! protein binding evidence is_a: ECO:0000136 ! nucleic acid binding evidence relationship: OBI:0000312 OBI:0001318 ! is_specified_output_of proteomic profiling by array assay created_by: swolfish creation_date: 2015-06-05T14:36:00Z [Term] id: ECO:0001603 name: cell staining evidence def: "A type of cell-based assay evidence in which living cells are stained with a vital stain, i.e. dye that can be used on living cells without causing cell death." [GOC:MAH] synonym: "vital staining evidence" RELATED [GOC:MAH] is_a: ECO:0001565 ! cell-based assay evidence created_by: swolfish creation_date: 2015-06-08T11:51:37Z [Term] id: ECO:0001801 name: alkaline phosphatase reporter gene assay evidence def: "A type of reporter gene assay evidence based on the fusion of selected genes with the phoA gene to express alkaline phosphatase in periplasmic space for protein tracing." [ECO:SW, PMID:11823238] comment: Alkaline phosphatase reporter assay produces a hybrid protein with alkaline phosphatase activity following transportation across the cellular membrane. synonym: "SEAP reporter assay" RELATED [] synonym: "Secreted Embryonic Alkaline Phosphatase reporter assay" RELATED [] is_a: ECO:0000049 ! reporter gene assay evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-10-29T15:53:45Z [Term] id: ECO:0001802 name: beta-galactosidase reporter gene assay evidence alt_id: ECO:0000297 def: "A type of reporter gene assay evidence based on the fusion of the lacZ gene to a specific promoter for the expression of beta-galactosidase which will appear blue when grown on a X-gal medium." [ECO:SW, PMID:20439410] comment: The assay is often performed using a plasmid borne construction on a lacZ strain. synonym: "beta-gal reporter gene assay" EXACT [] synonym: "beta-galactosidase assay evidence" EXACT [] synonym: "lacZ reporter gene assay" RELATED [] synonym: "LacZ transcript localization evidence" EXACT [] is_a: ECO:0000049 ! reporter gene assay evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-10-29T15:57:10Z [Term] id: ECO:0001803 name: chloramphenicol acetyltransferase reporter gene assay evidence def: "A type of reporter gene assay evidence based on the fusion of the CAT gene to a specific promoter for the expression of chloramphenicol acetyltransferase which confers resistance to the chloramphenicol antibiotic." [ECO:SW, PMID:1630936] comment: The amount of acetylated chloramphenicol is directly proportional to the amount of CAT enzyme present. synonym: "CAT reporter gene assay" EXACT [PMID:1630936] is_a: ECO:0000049 ! reporter gene assay evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-10-29T16:06:42Z [Term] id: ECO:0001804 name: beta-glucuronidase reporter gene assay evidence def: "A type of reporter gene assay evidence where the beta-glucuronidase enzyme from Escherichia coli is used as the reporter to transform non-fluorescent substrates into fluorescents for detection." [ECO:SW] synonym: "GUS reporter gene assay" EXACT [] is_a: ECO:0000049 ! reporter gene assay evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-10-29T16:11:02Z [Term] id: ECO:0001805 name: luciferase reporter gene assay evidence def: "A type of reporter gene assay evidence where luciferase, an oxidative enzyme, is used as the reporter to detect a gene product with bioluminescence." [ECO:SW, PMID:17623934] is_a: ECO:0000049 ! reporter gene assay evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-10-29T16:15:39Z [Term] id: ECO:0001806 name: chromatin immunoprecipitation- exonuclease evidence def: "A type of chromatin immunoprecipitation evidence that uses gama-exonuclease to digest TF-unbound DNA after ChIP for the identification of transcription factor binding site locations with high-resolution data." [ECO:SW, PMID:25249628] synonym: "ChIP-exo" EXACT [PMID:25249628] is_a: ECO:0000226 ! chromatin immunoprecipitation evidence relationship: IAO:0000136 GO:0043565 ! is about sequence-specific DNA binding relationship: OBI:0000312 OBI:0001925 ! is_specified_output_of chromatin immunoprecipitation with exonuclease sequencing assay property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-10-29T16:37:36Z [Term] id: ECO:0001807 name: electrophoretic mobility shift assay evidence used in manual assertion def: "A type of electrophoretic mobility shift that is used in a manual assertion." [ECO:SW] synonym: "EMSA evidence" BROAD [] synonym: "gel retardation assay" RELATED [] synonym: "IDA: electrophoretic mobility shift assay" BROAD [] is_a: ECO:0000096 ! electrophoretic mobility shift assay evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000096 ! electrophoretic mobility shift assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: swolfish creation_date: 2015-11-03T12:13:17Z [Term] id: ECO:0001808 name: reverse transcription polymerase chain reaction evidence used in manual assertion def: "A type of reverse transcription polymerase chain reaction evidence that is used in a manual assertion." [ECO:SW] is_a: ECO:0000109 ! reverse transcription polymerase chain reaction evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000109 ! reverse transcription polymerase chain reaction evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: swolfish creation_date: 2015-11-03T12:22:46Z [Term] id: ECO:0001809 name: DNA affinity chromatography evidence def: "A type of chromatography evidence where immobilized promoter DNA is labeled and bound to a matrix through which a protein mixture is poured and then eluted to purify specific DNA binding proteins." [ECO:SW, PMID:11694305, PMID:11725488] comment: Biotinylation is commonly used for labeling and beads are commonly used as the matrix. Bound protein will remain attached to the beads. Results can be detected through gel electrophoresis and then sequenced by mass-spectrometry. This technique can be used to demonstrate binding of a purified protein, or to purify the binding protein from crude extract or protein mixture. synonym: "DNA affinity purification" RELATED [] is_a: ECO:0000325 ! chromatography evidence relationship: OBI:0000312 OBI:0001630 ! is_specified_output_of analytical chromatography property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-03T13:48:49Z [Term] id: ECO:0001810 name: DNAse footprinting evidence def: "A type of nucleic acid binding evidence where proteins that have been bound to DNA protect a binding site from enzymatic cleavage with DNAse, thereby detecting protein-DNA interactions." [ECO:SW, PMID:212715, PMID:22194258] comment: In DNAse footingprinting amplified DNA combined with TF and DNAse is electrophoresed for fragment comparison with a non-TF control sample. TF-bound fragments do not appear in the gel. Such fragments can be isolated, purified, and sequenced. This technique is often used to identify the binding motif of a TF resolving the protected region to 50-100 bp which can be further examined for TF-binding sites. synonym: "DNase protection" RELATED [] is_a: ECO:0000136 ! nucleic acid binding evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-03T13:55:15Z [Term] id: ECO:0001811 name: fluorescence anisotropy evidence def: "A type of fluorescence evidence based on rapid and quantitative analysis of diverse molecular interactions, enzyme activities, and nucleic acid hybridization which uses a fluorophore to measure the binding constants and kinetics of reactions that cause a change in the rotational time of the molecules." [ECO:SW, PMID:20232898] comment: The degree of polarization of a fluorophore is inversely related to its molecular rotation. When the fluorophore is bound to a small molecule, the rate at which it tumbles can decrease significantly from when it is bound tightly to a large protein. If the fluorophore is attached to the larger protein in a binding pair, the difference in polarization between bound and unbound states will be smaller and less accurate. The degree of binding is calculated by using the difference in anisotropy of the partially bound, free, and fully bound states measured by titrating the two binding partners. Fluorescence polarixation assays are homogeneous. synonym: "FA" EXACT [] synonym: "Fluorescence polarization" RELATED [PMCID:3277431, PMID:20232898] synonym: "FP" RELATED [PMCID:3277431, PMID:20232898] is_a: ECO:0001115 ! fluorescence evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-03T14:01:36Z [Term] id: ECO:0001812 name: genomic systematic evolution of ligands by exponential amplification evidence def: "A type of systematic evolution of ligands by exponential amplification evidence based on a restricted genomic DNA library to identify naturally occurring genomic aptamers and RNA-protein interaction networks with RNA-binding protein as bait and high-throughput sequencing." [ECO:SW, PMID:20541015, PMID:21720957] comment: The reported sequences should always be verified for presence in the genome sequence. synonym: "genomic SELEX" EXACT [PMID:20541015] is_a: ECO:0000293 ! systematic evolution of ligands by exponential amplification evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-03T14:05:37Z [Term] id: ECO:0001813 name: heteronuclear single quantum coherence spectroscopy evidence def: "A type of nuclear magnetic resonance spectroscopy evidence based on two-dimensional NMR for elucidation of the chemical structure of an isolated or synthesized chemical compound where the characteristic transfer magnetization of a proton to a nitrogen or carbon isotope is monitored by NMR, generating a specific peak in the spectrum." [ECO:SW, PMID:19856946] comment: Chemical shifts in the spectrum indicating binding can be detected from analysis of a protein spectrum in the presence or absence of its cognate DNA binding site. synonym: "HSQC" EXACT [PMID:19856946] is_a: ECO:0001105 ! nuclear magnetic resonance spectroscopy evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-03T14:11:06Z [Term] id: ECO:0001814 name: methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence def: "A type of nucleic acid binding evidence where the synthetic molecule methidiumpropyl-EDTA (MPE) is used to cleave ligand-protected DNA, followed by analysis of the restriction fragments to generate a footprint (i.e. size and location) of small molecule binding sites on the DNA." [ECO:SW, PMID:6225070] synonym: "Methidiumpropyl-EDTA Fe(II) footprinting" RELATED [PMID:6225070] synonym: "MPE Fe(II) footprinting" RELATED [PMID:6225070] synonym: "MPE-EDTA Fe(II) footprinting" RELATED [PMID:6225070] is_a: ECO:0000136 ! nucleic acid binding evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-03T14:24:04Z [Term] id: ECO:0001815 name: copper-phenanthroline footprinting evidence def: "A type of nucleic acid binding evidence where nucleic acid that has been bound to protein is cleaved with 1,10-phenanthroline-copper complex resulting in a high-resolution footprint of sequence-specific protein-DNA contacts." [ECO:SW, PMID:11691942] synonym: "1,10-Phenanthroline-copper footprinting" EXACT [PMID:1384472] synonym: "OP-Cu Complex" RELATED [PMID:1384472] is_a: ECO:0000136 ! nucleic acid binding evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-04T08:37:51Z [Term] id: ECO:0001816 name: green fluorescent protein reporter gene assay evidence alt_id: ECO:0000296 def: "A type of reporter gene assay evidence based on the fusion of select genes with the green fluorescent protein (GFP) gene for detection with bioluminescence of the gene product when exposed to blue ultraviolet light." [ECO:SW, PMID:11989662] synonym: "GFP promoter fusion" RELATED [] synonym: "GFP reporter gene assay" EXACT [PMID:11989662] synonym: "green fluorescent protein promoter fusion" RELATED [] synonym: "green fluorescent protein transcript localization evidence" EXACT [] is_a: ECO:0000049 ! reporter gene assay evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-04T08:58:42Z [Term] id: ECO:0001817 name: glutathione S-transferase pull-down assay evidence def: "A type of protein binding evidence where a gene is fused with the GST gene and the resulting recombinant bait protein is captured on an immobilized Glutathione affinity ligand and incubated with prey protein to identify and characterize protein-protein interactions." [ECO:SW, PMID:26096507] comment: The recombinant protein can also be eluted following the pull-down and analyzed further with qPCR or sequencing. synonym: "GST pull-down assay" EXACT [PMID:26096507] is_a: ECO:0000024 ! protein binding evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-04T09:05:56Z [Term] id: ECO:0001818 name: hydroxyl-radical footprinting evidence def: "A type of nucleic acid binding evidence used to identify protein-binding sites on the DNA molecule where DNA that has been bound to protein is digested with hydroxyl radical produced by reduction of hydrogen peroxide with iron (II), followed by separating the cleavage products on a denaturing electrophoresis gel." [ECO:SW, PMID:18546600, PMID:19378159, PMID:3090544] is_a: ECO:0000136 ! nucleic acid binding evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-04T09:20:26Z [Term] id: ECO:0001819 name: primer extension assay evidence def: "A type of transcript expression evidence used to determine expression levels of mRNA where a radiolabeled synthetic oligonucleotide primer is annealed to mRNA at the transcription start site of a gene and the mRNA is extended with reverse transcriptase producing cDNA which is electrophoresed on a polyacrylamide gel and autoradiographed, and the band size is proportional to the initial RNA." [ECO:SW, PMID:23378648] comment: The most commonly used radiolabel is 32P. is_a: ECO:0000009 ! transcript expression evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-04T09:33:18Z [Term] id: ECO:0001820 name: rapid amplification of cDNA ends polymerase chain reaction evidence def: "A type of nucleotide sequencing assay evidence in which RT-PCR (cDNA synthesis) is first used to produce a cDNA copy of a region of the RNA transcript being investigated followed by PCR to capture either the unknown 5' or 3' end of the transcript for sequencing, depending on whether 5' RACE-PCR or 3' RACE-PCR are being undertaken." [ECO:SW, PMID:17498297, PMID:7685466] comment: 5' and 3' RACE-PCR utilize different protocols to amplify an unknown end using the known sequence of the center of the transcript. For cDNA synthesis, 5' RACE-PCR uses an anti-sense oligonucleotide primer (gene specific primer (GSP)) that recognizes a known sequence in the middle of the gene of interest and the reverse transcriptase to add base pairs to the 3' end of the primer. Next, terminal deoxynucleotidyl transferase (TdT) is used to add a string of identical nucleotides to the 3' end of the cDNA. A PCR reaction is then carried out, using a second anti-sense gene specific primer (GSP2) that binds to the known sequence, and a sense (forward) universal primer (UP) that binds the homopolymeric tail added to the 3' ends of the cDNAs to amplify a cDNA product from the 5' end. In contrast, 3' RACE-PCR utilizes the naturally occurring 3' polyA tail of the transcript and uses an Oligo-dT-adaptor primer (a primer with a short sequence of deoxy-thymine nucleotides) that complements the polyA tail and adds a special adaptor sequence to the 5' end of each cDNA. PCR is then used to amplify 3' cDNA from a known region using a sense GSP, and an anti-sense primer complementary to the adaptor sequence. comment: RACE PCR is frequently used to verify transcription start sites relevant to the function of transcription factor binding sites such as repression. synonym: "3’ RACE-PCR" EXACT [] synonym: "5’ RACE-PCR" EXACT [] synonym: "RACE PCR" EXACT [PMI:17498297] is_a: ECO:0000219 ! nucleotide sequencing assay evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-04T09:48:38Z [Term] id: ECO:0001821 name: RNA sequencing assay evidence comment: Use ECO:0000295 (RNA-seq evidence) in place of this term. property_value: IAO:0000234 "CollecTF" xsd:string is_obsolete: true created_by: swolfish creation_date: 2015-11-04T10:15:57Z [Term] id: ECO:0001822 name: survival rate analysis evidence def: "A type of knockout evidence based on the survival of an organism in a particular environment where a gene for an enzyme or regulator is knocked out and results are used as a natural reporter." [ECO:SW] is_a: ECO:0001091 ! knockout evidence relationship: IAO:0000136 OBI:0600054 ! is about selection by survival relationship: OBI:0000312 OBI:0000699 ! is_specified_output_of survival assessment property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-04T10:48:59Z [Term] id: ECO:0001823 name: x-ray crystallography evidence def: "A type of crystallography evidence where a purified sample at high concentration is crystallised and the crystals are exposed to an x ray beam to obtain three dimensional molecular structure of proteins and biological macromolecules." [ECO:SW, PMID:23135450, PMID:24648090] comment: X-ray crystallography can be used for a crystal used to probe at the tridimensional structure of proteins. In some cases, it is possible to co-crystallize the protein bound to its DNA binding site, providing detail on the particular arrangement of the two components. is_a: ECO:0001034 ! crystallography evidence relationship: OBI:0000312 OBI:0000912 ! is_specified_output_of X-ray crystallography assay property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-04T10:56:22Z [Term] id: ECO:0001824 name: DNA adenine methyltransferase identification evidence def: "A type of affinity evidence used to identify DNA binding sites in eukaryotes where Escherichia coli DNA adenine methyltransferase (Dam) is fused to a transcription factor, co-factor, chromatin-associated protein, or nuclear-associated protein, followed by a methyl-dependent PCR to localize methyltransferase in the region of the binding site." [ECO:SW, PMID:16938559, PMID:17545983, PMID:19588092] comment: The methylation tag is detected with methylation-sensitive restriction enzymes, DpnI and DpnII. synonym: "DamID" EXACT [PMID:19588092] is_a: ECO:0000023 ! affinity evidence is_a: IAO:0000030 {is_inferred="true"} ! information content entity relationship: IAO:0000136 GO:0008104 ! is about protein localization property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-05T15:56:13Z [Term] id: ECO:0001825 name: isothermal titration calorimetry evidence def: "A type of affinity evidence where the absorbed or released heat of a biomolecular binding event is directly measured in a reference cell and sample cell after the addition of a ligand using a microcalorimeter for a complete thermodynamic profile of the molecular interaction." [ECO:SW, PMID:10527727] comment: When ITC is used to study TF, the temperature of two identical cells containing a known concentration of TF is monitored. After the ligand is added to the cells in precisely measured aliquots, the temperature difference in each cell is observed to determine target binding. This value can be used to compute the energetics of the reaction and hence, binding affinity of the TF for the DNA fragment. The thermodynamic profile that is measured includes the values of binding constant (K(a)), stoichiometry (n), and the enthalpy of binding (DeltaH(b)). synonym: "ITC" EXACT [PMID:10527727] is_a: ECO:0000023 ! affinity evidence is_a: IAO:0000030 {is_inferred="true"} ! information content entity relationship: IAO:0000136 OBI:0001588 ! is about binding relationship: OBI:0000312 OBI:0001634 ! is_specified_output_of calorimetric binding assay property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-05T16:06:20Z [Term] id: ECO:0001826 name: ultraviolet light footprinting evidence def: "A type of nucleic acid binding evidence where DNA is non-specifically fragmented with ultraviolet light while protein-bound regions are protected from UV damage and strand breakage patterns are analyzed by PAGE and sequenced to detect protein-DNA contacts." [ECO:SW, PMID:2842760, PMID:7602584] synonym: "ultraviolet footprinting" RELATED [] synonym: "UV footprinting" RELATED [] is_a: ECO:0000136 ! nucleic acid binding evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-05T16:13:36Z [Term] id: ECO:0001827 name: methylation interference footprinting evidence def: "A type of nucleic acid binding evidence used to identify protein binding sites on the DNA molecule where multiple copies of a DNA fragment containing a putative TF-binding site are randomly methylated with dimethyl sulfate (DMS) and cleaved at the methyl group, followed by separating the cleavage products on a denaturing electrophoresis gel." [ECO:SW, PMID:1583685] synonym: "methylation interference footprinting evidence" EXACT [] is_a: ECO:0000136 ! nucleic acid binding evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-05T16:16:27Z [Term] id: ECO:0001828 name: visual sequence inspection evidence def: "A type of inference from background scientific knowledge used in manual assertion where a visual inspection of promoter region is made to identify putative binding sites." [ECO:SW] is_a: ECO:0000306 ! inference from background scientific knowledge used in manual assertion created_by: swolfish creation_date: 2015-11-10T14:40:16Z [Term] id: ECO:0001829 name: ferric uptake regulator titration assay evidence def: "A type of reporter gene assay evidence used to locate and isolate Fur sites where a plasmid library is created and cloned into a cell line with a ferric uptake regulator (Fur)-repressed reporter and the Fur protein is titrated away from its binding site on the reporter, after which the cell is isolated and plasmid extracted for further sequence analysis." [ECO:SW, PMID:10713425, PMID:7642488, PMID:8107138] synonym: "Fluorescence polarization" RELATED [PMID:15689115] synonym: "FURTA" EXACT [PMID:10713425] is_a: ECO:0000049 ! reporter gene assay evidence relationship: OBI:0000312 OBI:0000913 ! is_specified_output_of promoter activity detection by reporter gene assay property_value: IAO:0000234 "CollecTF" xsd:string created_by: swolfish creation_date: 2015-11-10T14:55:36Z [Term] id: ECO:0005004 name: cell viability assay evidence def: "A type of cell-based assay evidence resulting from analyzing the ability of cells to survive or live successfully." [NBK:144065] is_a: ECO:0001565 ! cell-based assay evidence relationship: IAO:0000136 GO:0009987 ! is about cellular process relationship: OBI:0000312 OBI:0001977 ! is_specified_output_of cytometry assay created_by: snadendla creation_date: 2015-02-13T12:08:01Z [Term] id: ECO:0005007 name: cell proliferation assay evidence def: "A type of cell-based assay evidence resulting from the measurement of the number of cells, which is a reflection of the balance between cell division and cell loss through cell differentiation or cell death." [ECO:RCT] {comment="PMID:11057898", comment="GO:0008283"} is_a: ECO:0001565 ! cell-based assay evidence relationship: IAO:0000136 GO:0008283 ! is about cell proliferation relationship: OBI:0000312 OBI:0000891 ! is_specified_output_of cell proliferation assay created_by: snadendla creation_date: 2015-02-11T16:27:13Z [Term] id: ECO:0005008 name: DNA synthesis cell proliferation assay evidence def: "A type of cell proliferation assay evidence resulting from the measure of DNA synthesis in the presece of a label." [PMC:3908118] is_a: ECO:0005007 ! cell proliferation assay evidence relationship: IAO:0000136 GO:0090592 ! is about DNA synthesis involved in DNA replication relationship: OBI:0000312 OBI:0000891 ! is_specified_output_of cell proliferation assay created_by: snadendla creation_date: 2015-02-11T16:30:10Z [Term] id: ECO:0005011 name: ATP bioluminescence assay evidence def: "A type of cell viability assay evidence resulting from the analysis of ATP concentration (by measuring light intensity) when luciferase catalyzes the oxidation of luciferin in the presence of ATP, magnesium ions and molecular oxygen." [PMID:15344559] is_a: ECO:0005004 ! cell viability assay evidence relationship: OBI:0000312 OBI:0002175 ! is_specified_output_of ATP bioluminescence assay created_by: snadendla creation_date: 2015-02-11T16:47:30Z [Term] id: ECO:0005012 name: cytotoxicity assay evidence def: "A type of cell-based assay evidence resulting from the ability of an agent to induce cellular necrosis or apoptosis and the subsequent analysis of cell death mechanism." [] is_a: ECO:0001565 ! cell-based assay evidence relationship: IAO:0000136 GO:0009636 ! is about response to toxic substance relationship: OBI:0000312 OBI:0001977 ! is_specified_output_of cytometry assay created_by: snadendla creation_date: 2015-02-12T11:39:35Z [Term] id: ECO:0005014 name: in vitro cell based assay evidence comment: Use children of ECO:0001565 (cell-based assay evidence) in place of this term. is_obsolete: true created_by: snadendla creation_date: 2015-02-12T13:26:55Z [Term] id: ECO:0005019 name: staining evidence def: "A type of direct assay evidence resulting from the use of stains or dyes to aid in analysis of a microscopic image." [ECO:RCT] is_a: ECO:0000002 ! direct assay evidence created_by: snadendla creation_date: 2015-02-19T11:48:57Z [Term] id: ECO:0005021 name: chemotaxis assay evidence def: "A type of cell-based assay evidence resulting from the evaluation of chemotactic ability (i.e. the movement, or lack of movement, in response to a chemical stimulus) of prokaryotic or eukaryotic cells." [PMC:3667641] is_a: ECO:0001565 ! cell-based assay evidence relationship: IAO:0000136 GO:0006935 ! is about chemotaxis relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay created_by: snadendla creation_date: 2015-02-19T13:10:20Z [Term] id: ECO:0005027 name: genetic transformation evidence def: "A type of mutant phenotype evidence resulting from the conversion of one genotype into another by the introduction of exogenous DNA." [ECO:RCT] is_a: ECO:0000015 ! mutant phenotype evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay created_by: snadendla creation_date: 2015-03-16T15:33:50Z [Term] id: ECO:0005031 name: structure determination evidence def: "A type of experimental evidence resulting from the visualization and examination of chemical and/or molecular structures." [ECO:RCT] is_a: ECO:0000006 ! experimental evidence created_by: snadendla creation_date: 2015-03-20T12:16:17Z [Term] id: ECO:0005033 name: electron microscopy evidence def: "A type of microscopy evidence and structure determination evidence resulting from an electron beam utilized to create an image." [ECO:RCT] is_a: ECO:0001098 ! microscopy evidence is_a: ECO:0005031 ! structure determination evidence relationship: OBI:0000312 OBI:0001631 ! is_specified_output_of electron microscopy imaging assay created_by: snadendla creation_date: 2015-03-20T12:21:48Z [Term] id: ECO:0005034 name: apoptotic assay evidence def: "A type of cell-based assay evidence resulting from the occurrence, visualization, and/or analysis of apoptosis." [ECO:RCT] is_a: ECO:0001565 ! cell-based assay evidence relationship: IAO:0000136 GO:0006915 ! is about apoptotic process relationship: OBI:0000312 OBI:0001977 ! is_specified_output_of cytometry assay created_by: snadendla creation_date: 2015-04-07T21:58:24Z [Term] id: ECO:0005500 name: in vivo polyADP-ribosylation assay evidence def: "A type of polyADP-ribosylation assay evidence used in an in vivo experiment." [ECO:SN, PMID:2820766, SIB:PG] is_a: ECO:0001557 ! polyADP-ribosylation assay evidence created_by: snadendla creation_date: 2015-06-15T15:35:05Z [Term] id: ECO:0005501 name: in vivo polyADP-ribosylation assay evidence used in manual assertion def: "A type of in vivo polyADP-ribosylation assay evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0005500 ! in vivo polyADP-ribosylation assay evidence intersection_of: ECO:0005500 ! in vivo polyADP-ribosylation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2015-06-15T15:37:23Z [Term] id: ECO:0005502 name: ex vivo assay evidence def: "A type of direct assay evidence derived by studying an organ, tissues, or cells taken from an organism and studied in an external environment with the minimum alteration of natural conditions." [ECO:SN, PMID:16305312, url:http\://www.ncbi.nlm.nih.gov/pmc/articles/PMC2305722/pdf/nihms42807.pdf] is_a: ECO:0000002 ! direct assay evidence relationship: OBI:0000312 OBI:0000964 ! is_specified_output_of in live cell assay created_by: snadendla creation_date: 2015-06-26T11:46:15Z [Term] id: ECO:0005503 name: two-dimensional polyacrylamide gel electrophoresis evidence def: "A type of gel electrophoresis evidence that involves one dimension electrophoresis where biomolecules are electrophoresed on a low percentage polyacrylamide gel to be separated in proportion to their mass or isoelectric point, followed by high voltage electrophoresis on a higher percentage gel in the presence of ethidium bromide to alter non-linear molecular shape." [ECO:SW, url:http\://www.nature.com/nmeth/journal/v2/n1/full/nmeth0105-83.html] comment: Two-dimensional polyacrylamide gel electrophoresis is commonly employed to establish a proteome for an organism and demonstrate expression changes. synonym: "2D PAGE" EXACT [] synonym: "2D-PAGE" EXACT [] is_a: ECO:0000337 ! gel electrophoresis evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-10-01T16:23:20Z [Term] id: ECO:0005504 name: spectrometry evidence def: "A type of experimental evidence resulting from the use of a spectrometer." [ECO:RCT] is_a: ECO:0000006 ! experimental evidence created_by: snadendla creation_date: 2015-08-14T15:48:08Z [Term] id: ECO:0005505 name: regular expression motif search evidence def: "A type of motif similarity evidence where the motif, a local alignment of sequences, is represented by a regular expression, which captures the variability of nucleotides at each position in a discrete form and can then be used to search genetic sequences by identifying matches to the regular expression." [ECO:SW, PMID:17337630] comment: Regular expression is a computational tool used for determining whether a given genome contains a DNA region resembling a transcription factor binding motif. For example A/T=W indicates A or T may be present in a column of the alignment. (PMID: 20708667). is_a: ECO:0000028 ! motif similarity evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-10-09T13:51:52Z [Term] id: ECO:0005506 name: missense mutation evidence def: "A type of point mutation evidence resulting from a change in a base (or bases) causing the substitution of one amino acid for another." [SO:0001583] is_a: ECO:0001113 ! point mutation evidence created_by: snadendla creation_date: 2015-09-18T16:52:34Z [Term] id: ECO:0005507 name: nonsense mutation evidence def: "A type of point mutation evidence resulting in an incomplete and usually nonfunctional protein product because of a premature stop codon." [url:https\://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations] is_a: ECO:0001113 ! point mutation evidence created_by: snadendla creation_date: 2015-09-18T16:55:32Z [Term] id: ECO:0005508 name: silent mutation evidence def: "A type of point mutation evidence resulting from the change of a DNA nucleotide that does not cause any changes in the amino acid sequence." [url:http\://www.sciencemag.org/news/2006/12/sound-silent-mutation] is_a: ECO:0001113 ! point mutation evidence created_by: snadendla creation_date: 2015-09-18T17:01:12Z [Term] id: ECO:0005509 name: insertion mutation evidence def: "A type of experimental phenotypic evidence resulting from a mutation in which there is an insertion of an additional nucleotide, or nucleotides." [GO:0070705] is_a: ECO:0000059 ! experimental phenotypic evidence created_by: snadendla creation_date: 2015-09-18T17:02:03Z [Term] id: ECO:0005511 name: duplication mutation evidence def: "A type of experimental phenotypic evidence resulting from a mutation in which inserted nucleotide(s) have a sequence identical to, or derived from, adjacent nucleotides." [SO:1000035] is_a: ECO:0000059 ! experimental phenotypic evidence created_by: snadendla creation_date: 2015-09-18T17:03:25Z [Term] id: ECO:0005512 name: frameshift mutation evidence def: "A type of experimental phenotypic evidence resulting from any mutation that causes a shift in bases and therefore changes the code for the amino acids." [url:https\://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations] is_a: ECO:0000059 ! experimental phenotypic evidence created_by: snadendla creation_date: 2015-09-18T17:05:49Z [Term] id: ECO:0005513 name: repeat expansion mutation evidence def: "A type of experimental phenotypic evidence resulting from a mutation that increases the number of times that a DNA sequence is repeated." [PMID:9397685, url:https\://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations] is_a: ECO:0000059 ! experimental phenotypic evidence created_by: snadendla creation_date: 2015-09-18T17:06:34Z [Term] id: ECO:0005514 name: splice site mutation evidence def: "A type of experimental phenotypic evidence resulting from a mutation in which there is a change in nucleotides at a splice site" [ECO:RCT] is_a: ECO:0000059 ! experimental phenotypic evidence created_by: snadendla creation_date: 2015-09-18T17:07:29Z [Term] id: ECO:0005515 name: translocation mutation evidence def: "A type of experimental phenotypic evidence resulting from a mutation in which a region of a chromosome is transferred to a nonhomologous chromosome" [ECO:RCT] is_a: ECO:0000059 ! experimental phenotypic evidence created_by: snadendla creation_date: 2015-09-18T17:08:01Z [Term] id: ECO:0005516 name: molecule detection assay evidence def: "A type of experimental evidence resulting from the detection and analysis of molecular markers." [ECO:RCT] is_a: ECO:0000006 ! experimental evidence relationship: OBI:0000312 OBI:0600017 ! is_specified_output_of detection of molecular label created_by: snadendla creation_date: 2015-09-24T15:54:21Z [Term] id: ECO:0005517 name: protein detection assay evidence def: "A type of molecule detection assay evidence resulting from the detection and quantification of a protein, or multiple proteins." [ECO:RCT] is_a: ECO:0005516 ! molecule detection assay evidence created_by: snadendla creation_date: 2015-09-25T14:27:40Z [Term] id: ECO:0005518 name: RNA detection assay evidence def: "A type of molecule detection assay evidence resulting from the detection of specific RNAs." [ECO:RCT] is_a: ECO:0005516 ! molecule detection assay evidence is_a: IAO:0000030 {is_inferred="true"} ! information content entity relationship: IAO:0000136 GO:0010467 ! is about gene expression created_by: snadendla creation_date: 2015-09-25T14:43:53Z [Term] id: ECO:0005519 name: DNA detection assay evidence def: "A type of molecule detection assay evidence resulting from the detection and visualization of a sequence of DNA." [ECO:RCT] is_a: ECO:0005516 ! molecule detection assay evidence created_by: snadendla creation_date: 2015-09-25T19:33:25Z [Term] id: ECO:0005520 name: interferometric reflectance imaging sensor evidence def: "A type of molecule detection assay evidence based on changes in surface-reflected light due to ligand binding on the surface of a semi-transparent substrate to detect proteins, DNA, and other biological material in a multiplexed, high-throughput microarray format without labels." [ECO:SW, PMID:21587155, PMID:24271115] comment: Differences in the optical path lengths between a surface layer and a buried silica layer can be measured very precisely allowing optical height information to be converted to accumulated mass on the surface. For the purpose of TF-binding site identification, IRIS is coupled with DNA-arrays with immobilized potential binding regions exposed to the protein of interest and eluted. Protein-bound fragments exhibit changes in reflectance that can be used to gauge binding quantitatively. synonym: "IRIS" EXACT [] synonym: "Spectral Reflectance Imaging Biosensor" EXACT [] synonym: "SRIB" EXACT [] is_a: ECO:0005516 ! molecule detection assay evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-09-28T16:01:01Z [Term] id: ECO:0005521 name: S1 nuclease protection assay evidence def: "A type of nuclease protection assay evidence where RNA is hybridized with complementary DNA probes and exposed to S1 nuclease for unbound RNA degradation after which the intact RNA is run on a gel for probe size determination and RNA identification to detect and map specific RNAs in a complex mixture of total cellular RNA." [ECO:SW, PMID:21390683] is_a: ECO:0001106 ! nuclease protection assay evidence relationship: IAO:0000136 GO:0010467 ! is about gene expression property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-09-28T17:16:56Z [Term] id: ECO:0005522 name: DNA dot blot assay evidence def: "A type of DNA detection assay evidence resulting from evaluation of the relative abundance of target sequences hybridizing to DNA samples that are immobilized on a nitrocellulose or nylon membrane." [PMID:18265189] is_a: ECO:0005519 ! DNA detection assay evidence created_by: snadendla creation_date: 2015-09-30T10:03:03Z [Term] id: ECO:0005523 name: DNA dot blot assay evidence used in manual assertion def: "A type of DNA dot blot assay evidence that is used in a manual assertion." [ECO:SN, ECO:SW] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0005522 ! DNA dot blot assay evidence intersection_of: ECO:0005522 ! DNA dot blot assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2015-09-30T10:04:00Z [Term] id: ECO:0005526 name: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence def: "A type of protein detection assay evidence where soft ionization is used for the analysis of biomolecules for mass determination in a three step process of plate preparation, radiation, and ionization with high throughput technology." [ECO:SW, PMID:21964792, PMID:25354905] comment: MALDI-TOF MS is commonly used for protein identification in constructing a proteome where protein fingerprints obtained by microbial cells are compared with a database of reference spectra by means of various algorithms integrated in systems recently made commercially available. synonym: "MALDI-TOF Mass Spectrometry" EXACT [] synonym: "MALDI-TOF-MS" EXACT [] is_a: ECO:0005517 ! protein detection assay evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-09-30T10:51:56Z [Term] id: ECO:0005527 name: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in manual assertion def: "A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in a manual assertion." [ECO:SN, ECO:SW] synonym: "MALDI-TOF mass spectrometry evidence" BROAD [] synonym: "MALDI-TOF-MS evidence" BROAD [] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0005526 ! matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence intersection_of: ECO:0005526 ! matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2015-09-30T10:58:51Z [Term] id: ECO:0005528 name: site-directed mutagenesis evidence def: "A type of experimental phenotypic evidence based on target-specified mutagenesis for the characterization of various gene and protein interactions, structures, and functions where oligonucleotide primers are used to alter a nucleotide sequence." [ECO:SW, PMID:21204030, PMID:24011050, PMID:3541892] comment: Site-directed mutagenesis is often performed in tandem with EMSA. It is often implemented only in conserved motif positions or serially through all positions of a site. synonym: "site directed mutagenesis" EXACT [] is_a: ECO:0000059 ! experimental phenotypic evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-09-30T11:34:41Z [Term] id: ECO:0005529 name: random mutagenesis evidence def: "A type of experimental phenotypic evidence where radiation or a DNA-damaging agent in vivo, or PCR with degenerate primers in vitro are used for non-targeted mutagenesis." [ECO:SW, PMID:15153637, PMID:18265275] comment: Random mutagenesis is not often used in TF-binding site determination; however, it is sometimes used to investigate the effect of mutations in TF binding domains in conjunction with expression assays. Random mutations can also be introduced via chemicals, error-prone PCR (EP-PCR), degenerate oligonucleotides-Pfu(DOP), UV irradiation, mutator strains, nucleotide analogs, or DNA recombination. is_a: ECO:0000059 ! experimental phenotypic evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-09-30T11:55:03Z [Term] id: ECO:0005530 name: random mutagenesis evidence used in manual assertion def: "A type of random mutagenesis evidence that is used in a manual assertion." [] is_a: ECO:0005529 ! random mutagenesis evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0005529 ! random mutagenesis evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2015-09-30T11:57:00Z [Term] id: ECO:0005531 name: motif discovery evidence def: "A type of multiple sequence alignment evidence based on a set of algorithms that infer over-represented motifs from a set of biological sequences returning one or more local multiple sequence alignment defining the inferred motifs." [ECO:SW, PMID:10812473, PMID:16845028, PMID:8211139] comment: Relationship type between sequences (e.g. orthologs from multiple genomes or co-expressed genes in the same genome) is not necessarily assumed. The local multiple sequence alignment is typically ungapped. A common application of motif discovery is to infer the binding motif of a given transcription factor (TF). This can be based on the results of a whole-genome expression analysis, assuming that co-expressed genes are co-regulated by the same TF, from peaks in ChIP-seq experiments with the TF, or from the comparative genomics analysis of the promoter regions of orthologs. {xref="PMID:19892760", xref="PMID:23032607"} is_a: ECO:0005555 ! multiple sequence alignment evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-09-30T15:04:45Z [Term] id: ECO:0005532 name: consensus search evidence def: "A type of motif similarity evidence where the motif is represented by a consensus sequence which incorporates the most frequent nucleotide at each position acting as a generic representative for the sequences in the alignment, and is compared to the genetic sequence for a perfect or imperfect match." [ECO:SW, PMID:15130839] comment: This technique is used to identify transcription factor binding sites by searching a bacterial genome for DNA regions resembling a given TF-binding motif. PMID: 17085555. is_a: ECO:0000028 ! motif similarity evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-10-09T14:12:54Z [Term] id: ECO:0005533 name: phylogenetic footprinting evidence def: "A type of motif discovery evidence based on a set of algorithms that infer motifs in non-coding DNA sequences from the conservation of functional regulatory sites through evolution at a higher rate than their local surroundings for the identification of an evolutionary 'footprint'." [ECO:SW, PMID:16477324, PMID:3199442] comment: The name derives to experimental footprinting techniques where transcription factor (TF)-binding sites are identified by sequencing the region of DNA protected from biochemical agents by the bound TF. This technique is used to identify or verify transcription factor-binding motifs, most commonly in the Eukaryota (PMID: 11997340). is_a: ECO:0005531 ! motif discovery evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-09-30T16:23:02Z [Term] id: ECO:0005534 name: comparative genomics motif search evidence def: "A type of motif similarity evidence based on comparative genomics which uses a search method to scan a set of genomes for instances of a specific motif, and then applies a comparative criterion to analyze the collective strength of these predictions, based on the assumption that functional instances of the motif will be preserved by natural selection and their prediction will therefore be consistent across genomes." [ECO:SW, PMID:10854408] comment: This technique is used to predict transcription factor binding sites in gene promoter regions by identifying conserved DNA regions across multiple genomes. PMID: 22305460. Orthology is a typical comparative criterion used. is_a: ECO:0000028 ! motif similarity evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-10-09T14:30:38Z [Term] id: ECO:0005535 name: machine learning prediction of motif instance evidence def: "A type of match to sequence model evidence which captures the application of a broad suite of supervised and unsupervised machine learning algorithms trained on known motif instances and applied to the prediction of novel putative instances of a motif in a set of biological sequences." [ECO:SW, PMID:17117497, PMID:2014171] comment: Machine learning algorithms include, but are not limited to artificial neural networks, random-forest, k-means clustering, hidden Markov models. This suite of methods can be used to identify or verify transcription factor-binding sites in genomic sequences (PMID: 15703297). is_a: ECO:0000202 ! match to sequence model evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-10-01T11:58:36Z [Term] id: ECO:0005536 name: position-specific scoring matrix motif search evidence def: "A type of motif similarity evidence where the motif is represented by a position-specific frequency matrix (PSFM) that specifies the frequency of each base at each position of the motif, from which a position-specific scoring matrix (PSSM) can be derived under the framework of a log-likelihood ratio providing a scoring system based on the likelihood of a sequence given the motif, versus a genomic-frequency based null hypothesis." [ECO:SW, PMID:10812473] comment: This technique is used to predict transcription factor binding sites in gene promoter regions by using a position weight matrix approach. (PMID: 15604457). synonym: "PSSM" NARROW [] synonym: "PSSM motif search" EXACT [] is_a: ECO:0000028 ! motif similarity evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-10-09T15:04:35Z [Term] id: ECO:0005537 name: xylE reporter gene assay evidence def: "A type of reporter gene assay evidence based on the fusion of the xylE gene to a specific promoter for the expression of catechol 2,3-dioxygenase that converts the colorless catechol substrate to yellow 2-hydroxymuconic semialdehyde for identification of the expression of a particular gene." [ECO:SW, PMID:2592344] is_a: ECO:0000049 ! reporter gene assay evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2015-10-28T15:31:28Z [Term] id: ECO:0005538 name: computationally derived logical inference is_obsolete: true created_by: snadendla creation_date: 2015-11-17T15:15:50Z [Term] id: ECO:0005539 name: computationally derived logical inference used in automatic assertion is_obsolete: true created_by: snadendla creation_date: 2015-11-17T15:17:47Z [Term] id: ECO:0005540 name: computationally derived logical inference from automatic assertion used in automatic assertion is_obsolete: true created_by: snadendla creation_date: 2015-11-17T15:24:42Z [Term] id: ECO:0005541 name: computationally derived logical inference from manual assertion used in automatic assertion is_obsolete: true created_by: snadendla creation_date: 2015-11-17T15:32:03Z [Term] id: ECO:0005542 name: biological system reconstruction evidence by experimental evidence from single species used in manual assertion def: "A type of biological system reconstruction evidence by experimental evidence from single species that is used in a manual assertion." [ECO:SN, PMID:19450514] comment: Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof. is_a: ECO:0000352 {is_inferred="true"} ! evidence used in manual assertion is_a: ECO:0005553 ! biological system reconstruction evidence by experimental evidence from single species intersection_of: ECO:0005553 ! biological system reconstruction evidence by experimental evidence from single species intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2015-12-16T15:32:41Z [Term] id: ECO:0005543 name: biological system reconstruction evidence by experimental evidence from mixed species used in manual assertion def: "A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in a manual assertion." [ECO:SN, PMID:22232657] comment: Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. The evidence may originate from a combination of several experiments. is_a: ECO:0000352 {is_inferred="true"} ! evidence used in manual assertion is_a: ECO:0005552 ! biological system reconstruction evidence by experimental evidence from mixed species intersection_of: ECO:0005552 ! biological system reconstruction evidence by experimental evidence from mixed species intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2015-12-16T15:45:01Z [Term] id: ECO:0005544 name: biological system reconstruction evidence based on orthology evidence used in manual assertion def: "A type of biological system reconstruction evidence based on orthology evidence that is used in a manual assertion." [ECO:SN] comment: Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments. is_a: ECO:0005545 ! biological system reconstruction evidence based on orthology evidence is_a: ECO:0005610 ! biological system reconstruction evidence based on homology evidence used in manual assertion intersection_of: ECO:0005545 ! biological system reconstruction evidence based on orthology evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2015-12-18T16:20:49Z [Term] id: ECO:0005545 name: biological system reconstruction evidence based on orthology evidence def: "A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by orthology from an existing experimentally supported model to a process, pathway or complex in another species." [ECO:SN, PMID:15660128] comment: Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments. is_a: ECO:0005549 ! biological system reconstruction evidence based on homology evidence created_by: snadendla creation_date: 2015-12-16T15:57:37Z [Term] id: ECO:0005546 name: biological system reconstruction evidence based on paralogy evidence used in manual assertion def: "A type of biological system reconstruction evidence based on paralogy evidence that is used in a manual assertion." [ECO:SN, PMID:15660128] comment: Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments. is_a: ECO:0005550 ! biological system reconstruction evidence based on paralogy evidence is_a: ECO:0005610 ! biological system reconstruction evidence based on homology evidence used in manual assertion intersection_of: ECO:0005550 ! biological system reconstruction evidence based on paralogy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2015-12-16T16:05:15Z [Term] id: ECO:0005547 name: biological system reconstruction evidence based on inference from background scientific knowledge used in manual assertion def: "A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in a manual assertion." [ECO:SN, PMID:17876790] comment: Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components. is_a: ECO:0000352 {is_inferred="true"} ! evidence used in manual assertion is_a: ECO:0005548 ! biological system reconstruction evidence based on inference from background scientific knowledge intersection_of: ECO:0005548 ! biological system reconstruction evidence based on inference from background scientific knowledge intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2015-12-16T16:07:42Z [Term] id: ECO:0005548 name: biological system reconstruction evidence based on inference from background scientific knowledge def: "A type of biological system reconstruction based solely on background scientific knowledge of that biological system." [ECO:SN, PMID:17876790] comment: The available knowledge is usually a combination of partial or weak experimental evidence where either some components are missing or no physical interaction evidence can be found but the system is inferred by similarity to related systems in taxonomically-disparate organisms with experimental evidence. Functional studies or ligand binding evidence are often used for the reconstruction of biological systems. It does not provide physical interaction evidence but uses proxies such a ligand binding evidences to infer the presence or absence of the complex components. is_a: ECO:0000088 ! biological system reconstruction evidence created_by: snadendla creation_date: 2015-12-18T15:32:15Z [Term] id: ECO:0005549 name: biological system reconstruction evidence based on homology evidence def: "A type of biological system reconstruction where the evidence is inferred by homology based on conservation of sequence, function, and composition from an existing experimentally supported model to a process, pathway, or complex." [ECO:SN, PMID:15660128] comment: Inference may be based on paralogy and/or orthology of the genome-encoded components and is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments in the same or another species. is_a: ECO:0000088 ! biological system reconstruction evidence created_by: snadendla creation_date: 2015-12-18T15:49:46Z [Term] id: ECO:0005550 name: biological system reconstruction evidence based on paralogy evidence def: "A type of biological system reconstruction evidence based on homology evidence where the evidence is inferred by paralogy from an existing experimentally supported model to a process, pathway, or complex in the same species." [ECO:SN, PMID:15660128] comment: Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments. is_a: ECO:0005549 ! biological system reconstruction evidence based on homology evidence created_by: snadendla creation_date: 2015-12-18T16:24:08Z [Term] id: ECO:0005551 name: biological system reconstruction evidence by experimental evidence def: "A type of biological system reconstruction evidence that uses experimental evidence as support." [ECO:SN, PMID:19450514, PMID:22232657] is_a: ECO:0000088 ! biological system reconstruction evidence created_by: snadendla creation_date: 2015-12-18T16:34:13Z [Term] id: ECO:0005552 name: biological system reconstruction evidence by experimental evidence from mixed species def: "A type of biological system reconstruction evidence where the experimental evidence is derived by using a mix of species used in the same experiment." [ECO:SN, PMID:22232657] comment: Inference is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. The evidence may originate from a combination of several experiments. is_a: ECO:0005551 ! biological system reconstruction evidence by experimental evidence created_by: snadendla creation_date: 2015-12-18T16:35:13Z [Term] id: ECO:0005553 name: biological system reconstruction evidence by experimental evidence from single species def: "A type of biological system reconstruction where the experimental evidence is derived by using multiple experiments in a single species." [ECO:SN] comment: Processes, pathways and complexes shown by a single experiment should not be annotated with this term but with ECO:0000353 or a child thereof. is_a: ECO:0005551 ! biological system reconstruction evidence by experimental evidence created_by: snadendla creation_date: 2015-12-18T16:36:44Z [Term] id: ECO:0005554 name: pairwise sequence alignment evidence def: "A type of sequence alignment evidence where two sequences are aligned to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid)." [ECO:SN, url:http\://www.ebi.ac.uk/Tools/psa/] is_a: ECO:0000200 ! sequence alignment evidence created_by: snadendla creation_date: 2016-02-08T14:30:46Z [Term] id: ECO:0005555 name: multiple sequence alignment evidence def: "A type of sequence alignment evidence where three or more biological sequences (protein or nucleic acid) of similar length are aligned to infer homology and the evolutionary relationships between the sequences studied." [ECO:SN, url:http\://www.ebi.ac.uk/Tools/msa/] is_a: ECO:0000200 ! sequence alignment evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2016-02-08T14:31:24Z [Term] id: ECO:0005556 name: multiple sequence alignment evidence used in manual assertion def: "A type of multiple sequence alignment evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0000247 {is_inferred="true"} ! sequence alignment evidence used in manual assertion is_a: ECO:0005555 ! multiple sequence alignment evidence intersection_of: ECO:0005555 ! multiple sequence alignment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-02-08T14:59:18Z [Term] id: ECO:0005557 name: multiple sequence alignment evidence used in automatic assertion def: "A type of multiple sequence alignment evidence that is used in an automatic assertion." [ECO:SN] is_a: ECO:0000248 {is_inferred="true"} ! sequence alignment evidence used in automatic assertion is_a: ECO:0005555 ! multiple sequence alignment evidence intersection_of: ECO:0005555 ! multiple sequence alignment evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-02-08T15:00:50Z [Term] id: ECO:0005558 name: motif discovery evidence used in manual assertion def: "A type of motif discovery evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0005531 ! motif discovery evidence is_a: ECO:0005556 {is_inferred="true"} ! multiple sequence alignment evidence used in manual assertion intersection_of: ECO:0005531 ! motif discovery evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-02-08T15:07:47Z [Term] id: ECO:0005559 name: motif discovery evidence used in automatic assertion def: "A type of motif discovery evidence that is used in an automatic assertion." [ECO:SN] is_a: ECO:0005531 ! motif discovery evidence is_a: ECO:0005557 {is_inferred="true"} ! multiple sequence alignment evidence used in automatic assertion intersection_of: ECO:0005531 ! motif discovery evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-02-08T15:08:19Z [Term] id: ECO:0005560 name: pairwise sequence alignment evidence used in manual assertion def: "A type of pairwise sequence alignment evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0000247 {is_inferred="true"} ! sequence alignment evidence used in manual assertion is_a: ECO:0005554 ! pairwise sequence alignment evidence intersection_of: ECO:0005554 ! pairwise sequence alignment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-02-08T15:17:05Z [Term] id: ECO:0005561 name: pairwise sequence alignment evidence used in automatic assertion def: "A type of pairwise sequence alignment evidence that is used in an automatic evidence." [ECO:SN] is_a: ECO:0000248 {is_inferred="true"} ! sequence alignment evidence used in automatic assertion is_a: ECO:0005554 ! pairwise sequence alignment evidence intersection_of: ECO:0005554 ! pairwise sequence alignment evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-02-08T15:17:52Z [Term] id: ECO:0005562 name: in-gel protein kinase assay evidence def: "A type of protein kinase assay evidence resulting from the evaluation of the phosphorylation activity of kinase on a gel-incorporated kinase substrate." [PMID:12372853] is_a: ECO:0001558 ! protein kinase assay evidence created_by: snadendla creation_date: 2016-02-09T12:05:29Z [Term] id: ECO:0005563 name: macroscopic current trace evidence def: "A type of voltage clamp recording evidence that involves recording trace of the current (pA) going through the analyzed ion channels determined from voltage clamp current recording." [ECO:SN, PMID:17938230, url:http\://www.utdallas.edu/~tres/microelectrode/microelectrodes_ch03.pdf] is_a: ECO:0005576 ! voltage clamp recording evidence relationship: IAO:0000136 GO:0005216 ! is about ion channel activity relationship: OBI:0000312 OBI:0000447 ! is_specified_output_of intra cellular electrophysiology recording created_by: snadendla creation_date: 2016-02-09T12:40:03Z [Term] id: ECO:0005564 name: current density evidence def: "A type of electrophysiology assay evidence that involves measuring the amount of current (pA) going through the ion channels per unit of membrane." [ECO:SN, url:http\://circres.ahajournals.org/content/102/11/1298.full, url:http\://www.bem.fi/book/04/04.htm] is_a: ECO:0000164 ! electrophysiology assay evidence relationship: IAO:0000136 GO:0005216 ! is about ion channel activity relationship: OBI:0000312 OBI:0000447 ! is_specified_output_of intra cellular electrophysiology recording created_by: snadendla creation_date: 2016-02-09T12:43:07Z [Term] id: ECO:0005565 name: single channel conductance evidence is_obsolete: true created_by: snadendla creation_date: 2016-02-09T12:45:42Z [Term] id: ECO:0005566 name: sustained current evidence def: "A type of electrophysiology assay evidence that involves the measurement of the current that persists after the fast and slow inactivation of the analyzed channels." [ECO:SN, url:http\://www.nature.com/ncomms/journal/v3/n2/full/ncomms1717.html] is_a: ECO:0000164 ! electrophysiology assay evidence relationship: IAO:0000136 GO:0005216 ! is about ion channel activity relationship: OBI:0000312 OBI:0000447 ! is_specified_output_of intra cellular electrophysiology recording created_by: snadendla creation_date: 2016-02-09T12:46:54Z [Term] id: ECO:0005567 name: steady state activation curve evidence is_obsolete: true created_by: snadendla creation_date: 2016-02-09T12:48:17Z [Term] id: ECO:0005568 name: steady state inactivation curve evidence is_obsolete: true created_by: snadendla creation_date: 2016-02-09T12:50:45Z [Term] id: ECO:0005569 name: window current trace evidence is_obsolete: true created_by: snadendla creation_date: 2016-02-09T12:57:16Z [Term] id: ECO:0005570 name: use dependence of inactivation evidence def: "A type of electrophysiology assay evidence in which the amount of current remaining after a series of depolarization at different frequencies described as the normalized current related to the time course." [ECO:SN, url:http\://circres.ahajournals.org/content/89/8/700.full] is_a: ECO:0000164 ! electrophysiology assay evidence created_by: snadendla creation_date: 2016-02-09T12:58:18Z [Term] id: ECO:0005571 name: current clamp recording evidence def: "A type of electrophysiology assay evidence that involves recording the change in membrane potential caused by applying specific current to the cell." [ECO:SN, url:http\://www.nature.com/nprot/journal/v4/n8/full/nprot.2009.91.html] synonym: "current clamp voltage recording evidence" EXACT [] xref: birnlex:2278 "current clamp voltage recording protocol" is_a: ECO:0000164 ! electrophysiology assay evidence created_by: snadendla creation_date: 2016-02-12T13:58:32Z [Term] id: ECO:0005572 name: whole-cell voltage clamp recording evidence def: "A type of voltage clamp recording evidence that involves direct measurement of ionic current across a membrane while controlling the membrane potential by maintaining the voltage." [ECO:SN, url:http\://circres.ahajournals.org/content/72/1/91.full.pdf] xref: birnlex:2281 "whole-cell voltage clamp recording protocol" is_a: ECO:0005576 ! voltage clamp recording evidence relationship: IAO:0000136 GO:0005216 ! is about ion channel activity created_by: snadendla creation_date: 2016-02-12T14:06:40Z [Term] id: ECO:0005573 name: cell-attached single-channel recording evidence def: "A type of patch-clamp recording evidence that involves isolation of a patch of membrane electrically from the external solution and to record current flowing into the patch and this is achieved by pressing a fire-polished glass pipette, which has been filled with a suitable electrolyte solution, against the surface of a cell and applying light suction." [ECO:SN, url:http\://www.utdallas.edu/~tres/microelectrode/microelectrodes_ch04.pdf] synonym: "cell-attached patch-clamp recording evidence" EXACT [] xref: birnlex:2283 "cell-attached single-channel recording protocol" is_a: ECO:0006012 ! patch-clamp recording evidence relationship: IAO:0000136 GO:0005216 ! is about ion channel activity relationship: OBI:0000312 OBI:0002179 ! is_specified_output_of cell-attached patch clamp assay created_by: snadendla creation_date: 2016-02-12T14:07:39Z [Term] id: ECO:0005574 name: cell-detached inside-out single-channel recording evidence def: "A type of patch-clamp recording evidence that involves study of individual ion channels by gently pulling the patch of membrane away from the cell, and the patch remains attached to the pipette with its cytoplasmic surface exposed to the bathing solution." [ECO:SN, url:http\://www.acnp.org/g4/GN401000005/CH005.html] synonym: "cell-detached inside-out patch-clamp recording evidence" EXACT [] xref: birnlex:2286 "cell-detached inside-out single-channel recording protocol" is_a: ECO:0006012 ! patch-clamp recording evidence relationship: IAO:0000136 GO:0005216 ! is about ion channel activity relationship: OBI:0000312 OBI:0002180 ! is_specified_output_of inside-out patch clamp assay created_by: snadendla creation_date: 2016-02-12T14:16:53Z [Term] id: ECO:0005575 name: reconstituted bilayer single-channel patch recording evidence def: "A type of patch-clamp reocrding evidence that involves ion channel analysis by incorporating the ion channels into liposomes suitable for patch-clamping which allows isolation and study of a specific population of channels into that bilayer membrane." [ECO:SN, url:http\://nanion.de/images/stories/papers/Bilayers_lab-on-a-chip08.pdf] xref: birnlex:2287 "reconstituted bilayer single-channel patch recording protocol" is_a: ECO:0006012 ! patch-clamp recording evidence relationship: IAO:0000136 GO:0005216 ! is about ion channel activity relationship: OBI:0000312 OBI:0000447 ! is_specified_output_of intra cellular electrophysiology recording created_by: snadendla creation_date: 2016-02-12T14:17:46Z [Term] id: ECO:0005576 name: voltage clamp recording evidence def: "A type of electrophysiology assay evidence that involves recording membrane potential by controlling the membrane voltage and measuring the transmembrane current required to maintain that voltage." [ECO:SN, url:http\://neurobio.drexelmed.edu/GaoWeb/Resources/Recording%20_Techniques.pdf, url:http\://www.acnp.org/g4/GN401000005/CH005.html] synonym: "voltage clamp current recording evidence" EXACT [] xref: birnlex:2279 "voltage clamp current recording protocol" is_a: ECO:0000164 ! electrophysiology assay evidence created_by: snadendla creation_date: 2016-02-12T14:18:36Z [Term] id: ECO:0005577 name: electroencephalography recording evidence def: "A type of electrophysiology assay evidence that involves recording the electrical activity of the brain by means of electrodes placed on the surface of the head." [ECO:SN, url:http\://www.jove.com/science-education/5420/electro-encephalography-eeg] xref: birnlex:2293 "electroencephalography recording protocol" is_a: ECO:0000164 ! electrophysiology assay evidence relationship: IAO:0000136 GO:0005216 ! is about ion channel activity relationship: OBI:0000312 OBI:0002186 ! is_specified_output_of electroencephalography created_by: snadendla creation_date: 2016-02-12T14:19:21Z [Term] id: ECO:0005578 name: super-resolution microscopy evidence def: "A type of microscopy evidence where the images are taken with a higher resolution than the diffraction limit that help in studying nanoscopic sub-cellular structures." [ECO:SN, url:http\://journal.frontiersin.org/article/10.3389/fncel.2015.00007/full] is_a: ECO:0001098 ! microscopy evidence relationship: OBI:0000312 CHMO:0000102 ! is_specified_output_of light microscopy created_by: snadendla creation_date: 2016-02-12T15:20:47Z [Term] id: ECO:0005579 name: immunogold labelling evidence used in manual assertion def: "A type of immunogold labelling evidence that is used in a manual assertion." [ECO:SN] synonym: "IDA: immunogold labelling" BROAD [] is_a: ECO:0000090 ! immunogold labelling evidence is_a: ECO:0006031 {is_inferred="true"} ! immunolocalization evidence used in manual assertion intersection_of: ECO:0000090 ! immunogold labelling evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-02-12T15:38:03Z [Term] id: ECO:0005580 name: flow cytometry evidence used in manual assertion def: "A type of flow cytometry evidence that is used in a manual assertion." [ECO:SN] synonym: "FCM" BROAD [] is_a: ECO:0000268 ! flow cytometry evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000268 ! flow cytometry evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-02-12T16:04:23Z [Term] id: ECO:0005581 name: enzyme-linked immunoabsorbent assay evidence used in manual assertion def: "A type of enzyme-linked immunoabsorbent assay evidence that is used in a manual assertion." [ECO:SN] synonym: "ELISA evidence|enzyme-linked immunosorbent assay evidence" BROAD [] is_a: ECO:0000267 ! enzyme-linked immunoabsorbent assay evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000267 ! enzyme-linked immunoabsorbent assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-02-12T16:23:38Z [Term] id: ECO:0005582 name: cell-detached outside-out single-channel recording evidence def: "A type of patch-clamp recording evidence where a part of cellular membrane is detached from the cell and whose external face is exposed to the extracellular medium which allows isolating and studying a single or at least a small number of channels into that fragment (patch)." [ECO:SN, url:http\://www.nature.com/nprot/journal/v2/n11/full/nprot.2007.403.html] synonym: "cell-detached outside-out patch-clamp evidence" EXACT [] is_a: ECO:0006012 ! patch-clamp recording evidence relationship: IAO:0000136 GO:0005216 ! is about ion channel activity relationship: OBI:0000312 OBI:0002181 ! is_specified_output_of outside-out patch clamp assay created_by: snadendla creation_date: 2016-03-02T10:47:25Z [Term] id: ECO:0005583 name: cut-open oocyte voltage clamp recording evidence def: "A type of voltage clamp recording evidence that involves inserting the oocyte in a chamber that separates the surface into 3 regions where the top portion of the oocyte membrane is the region that is clamped from which currents are actually recorded while the bottom portion is the region of the oocyte that is cut-open, making it possible to inject current intracellularly through a low resistance pathway." [ECO:SN, PMID:9711615] is_a: ECO:0005576 ! voltage clamp recording evidence created_by: snadendla creation_date: 2016-03-02T11:29:32Z [Term] id: ECO:0005584 name: macropatch voltage clamp recording evidence def: "A type of voltage clamp recording evidence where recording is done on a fragment of the cell membrane (attached to or detached from the cell) using a large tip diameter pipette that allows isolating and studying a small number of channels into that fragment (patch)." [ECO:SN, url:http\://jxb.oxfordjournals.org/content/50/Special_Issue/1037.full.pdf] is_a: ECO:0005576 ! voltage clamp recording evidence relationship: IAO:0000136 GO:0005216 ! is about ion channel activity created_by: snadendla creation_date: 2016-03-02T11:33:48Z [Term] id: ECO:0005585 name: high throughput mass spectrometry evidence def: "A type of mass spectrometry evidence where mass-to-charge ratio (m/z) of gas-phase ions is measured which is used to identify and quantify molecules in complex solutions within the framework of high throughput studies." [ECO:SN, PMID:20805795] comment: There are significant differences in data analysis and data evaluation if to compare a HTP mass-spec and a regular mass-spec. The regular mass spec method is quite a reliable technique for identifying a protein molecular weight and analysing its post-modifications, other mass-spec applications might require the additional quality controls and more stringent data evaluation. More complex sample mixture is processed, more quality questions should be addressed, such as a sample contamination and sensitivity of the mass spectrometer while using HTP mass-spec.\nFor HTP mass-spec, the analysis of the small data sets allows to manually assign the spectra to proteins or peptides, but for large data sets only the statistical tools can be used instead. is_a: ECO:0001096 ! mass spectrometry evidence created_by: snadendla creation_date: 2016-03-02T12:33:07Z [Term] id: ECO:0005586 name: high throughput mass spectrometry evidence used in manual assertion def: "A type of high throughput mass spectrometry evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0001230 {is_inferred="true"} ! mass spectrometry evidence used in manual assertion is_a: ECO:0005585 ! high throughput mass spectrometry evidence intersection_of: ECO:0005585 ! high throughput mass spectrometry evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: snadendla creation_date: 2016-03-02T12:50:02Z [Term] id: ECO:0005587 name: confocal microscopy evidence def: "A type of microscopy evidence where sharp images are taken by excluding most of the light from the specimen that is not from the microscope's focal plane, thus allowing better contrast and less haze, which makes it possible to build three-dimensional reconstructions of a volume of the specimen by assembling a series of thin slices taken along the vertical axis." [ECO:SN, url:http\://www.physics.emory.edu/faculty/weeks//lab/papers/ebbe05.pdf] is_a: ECO:0001098 ! microscopy evidence created_by: snadendla creation_date: 2016-03-17T12:29:45Z [Term] id: ECO:0005588 name: wide-field microscopy evidence def: "A type of microscopy evidence where imaging of a thin cell or a tissue specimen is performed by full aperture emission of light gathered by the microscope's objective, which maximizes the recorded signal and simultaneously minimizes the required exposure times." [ECO:SN, url:http\://jcb.rupress.org/content/172/1/9.full, url:http\://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048960/, url:http\://zeiss-campus.magnet.fsu.edu/articles/livecellimaging/techniques.html] is_a: ECO:0001098 ! microscopy evidence created_by: snadendla creation_date: 2016-03-17T12:30:27Z [Term] id: ECO:0005589 name: confocal microscopy evidence used in manual assertion def: "A type confocal microscopy evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0001232 {is_inferred="true"} ! microscopy evidence used in manual assertion is_a: ECO:0005587 ! confocal microscopy evidence intersection_of: ECO:0005587 ! confocal microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-03-17T12:32:24Z [Term] id: ECO:0005590 name: wide-field microscopy evidence used in manual assertion def: "A type of wide-field microscopy evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0001232 {is_inferred="true"} ! microscopy evidence used in manual assertion is_a: ECO:0005588 ! wide-field microscopy evidence intersection_of: ECO:0005588 ! wide-field microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-03-17T12:34:42Z [Term] id: ECO:0005591 name: immunogold labelling electron microscopy assay evidence def: "A type of immunogold labelling evidence where electron microscopy technique is used to detect the location of the antibodies labeled with colloidal gold particles." [ECO:SN, PMID:4110101] is_a: ECO:0000090 ! immunogold labelling evidence is_a: ECO:0005033 ! electron microscopy evidence relationship: IAO:0000136 GO:0033036 ! is about macromolecule localization created_by: snadendla creation_date: 2016-03-17T15:43:00Z [Term] id: ECO:0005592 name: immunogold labelling electron microscopy assay evidence used in manual assertion def: "A type of immunogold labelling electron microscopy assay evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0005579 {is_inferred="true"} ! immunogold labelling evidence used in manual assertion is_a: ECO:0005591 ! immunogold labelling electron microscopy assay evidence is_a: ECO:0006003 {is_inferred="true"} ! electron microscopy evidence used in manual assertion intersection_of: ECO:0005591 ! immunogold labelling electron microscopy assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-03-17T16:39:37Z [Term] id: ECO:0005593 name: immunodetection assay evidence def: "A type of direct assay evidence that involves the use of antibodies to detect biomolecules." [ECO:SN] is_a: ECO:0000002 ! direct assay evidence relationship: IAO:0000136 GO:0003823 ! is about antigen binding relationship: OBI:0000312 OBI:0600025 ! is_specified_output_of substance detection created_by: snadendla creation_date: 2016-03-17T17:07:33Z [Term] id: ECO:0005594 name: immunoperoxidase immunolocalization evidence def: "A type of immunolocalization evidence involving enzymatic detection of a peroxidase tagged antibody." [ECO:SN] is_a: ECO:0000087 ! immunolocalization evidence created_by: snadendla creation_date: 2016-03-17T17:11:34Z [Term] id: ECO:0005595 name: immunoperoxidase immunolocalization evidence used in manual assertion def: "A type of immunoperoxidase immunolocalization evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0005594 ! immunoperoxidase immunolocalization evidence is_a: ECO:0006031 {is_inferred="true"} ! immunolocalization evidence used in manual assertion intersection_of: ECO:0005594 ! immunoperoxidase immunolocalization evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-03-17T17:14:05Z [Term] id: ECO:0005596 name: immunoperoxidase immunolocalization electron microscopy evidence def: "A type of immunoperoxidase immunolocalization evidence where electron microscopy technique is used for enzymatic detection of a peroxidase tagged antibody." [ECO:SN] synonym: "Immunoperoxidase labelling electron microscopy" EXACT [] is_a: ECO:0005033 ! electron microscopy evidence is_a: ECO:0005594 ! immunoperoxidase immunolocalization evidence relationship: IAO:0000136 GO:0033036 ! is about macromolecule localization created_by: snadendla creation_date: 2016-03-17T17:16:38Z [Term] id: ECO:0005597 name: immunoperoxidase immunolocalization electron microscopy evidence used in manual assertion def: "A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in a manual assertion." [ECO:SN] synonym: "immunoperoxidase labelling electron microscopy evidence" BROAD [] is_a: ECO:0005595 {is_inferred="true"} ! immunoperoxidase immunolocalization evidence used in manual assertion is_a: ECO:0005596 ! immunoperoxidase immunolocalization electron microscopy evidence is_a: ECO:0006003 {is_inferred="true"} ! electron microscopy evidence used in manual assertion intersection_of: ECO:0005596 ! immunoperoxidase immunolocalization electron microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-03-17T17:23:56Z [Term] id: ECO:0005598 name: wide-field fluorescence microscopy evidence def: "A type of wide-field microscopy evidence where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter." [ECO:SN, url:http\://www.bristol.ac.uk/synaptic/research/techniques/widefield.html] comment: The optical filter is used to select the wavelength of excitation light. The detection camera is typically a CCD camera. Both topographical and dynamic information of a sample are obtained. is_a: ECO:0005588 ! wide-field microscopy evidence created_by: snadendla creation_date: 2016-03-18T11:53:56Z [Term] id: ECO:0005599 name: immunofluorescence wide-field microscopy evidence def: "A type of wide-field fluorescence microscopy evidence where fluorescently tagged antibodies are imaged that are used to bind to their antigens." [ECO:SN, url:http\://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057135] synonym: "wide-field epifluorescence microscopy" EXACT [] is_a: ECO:0000007 ! immunofluorescence evidence is_a: ECO:0005598 ! wide-field fluorescence microscopy evidence created_by: snadendla creation_date: 2016-03-18T11:55:40Z [Term] id: ECO:0005600 name: immunofluorescence confocal microscopy evidence def: "A type of confocal microscopy evidence where light passes through immunofluorescent-stained tissue sections or cells and then the emitted light passes through the dichroic mirror and is focused onto the pinhole for subsequent detection." [ECO:SN, url:http\://www.physics.emory.edu/faculty/weeks/confocal/, url:https\://www.hycultbiotech.com/media/wysiwyg/protocol_Immunofluorescence.pdf] comment: This allows visualization of sub cellular distribution of biomolecules of interest. is_a: ECO:0000007 ! immunofluorescence evidence is_a: ECO:0005587 ! confocal microscopy evidence created_by: snadendla creation_date: 2016-03-18T12:48:42Z [Term] id: ECO:0005601 name: immunofluorescence confocal microscopy evidence used in manual assertion def: "A type of immunofluorescence confocal microscopy evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0005589 {is_inferred="true"} ! confocal microscopy evidence used in manual assertion is_a: ECO:0005600 ! immunofluorescence confocal microscopy evidence is_a: ECO:0005804 {is_inferred="true"} ! immunofluorescence evidence used in manual assertion intersection_of: ECO:0005600 ! immunofluorescence confocal microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-03-18T12:52:04Z [Term] id: ECO:0005602 name: protein expression level evidence based on western blot def: "A type of protein expression level evidence where the level of expression of a protein is determined in a cell or tissue extract by western blot technique." [ECO:SN] is_a: ECO:0000046 ! protein expression level evidence is_a: ECO:0000112 ! western blot evidence created_by: snadendla creation_date: 2016-03-18T13:02:29Z [Term] id: ECO:0005603 name: protein mass spectrometry evidence def: "A type of mass spectrometry evidence where one or more protein analyses are performed." [ECO:SN] is_a: ECO:0000039 ! protein assay evidence is_a: ECO:0001096 ! mass spectrometry evidence created_by: snadendla creation_date: 2016-03-18T13:11:37Z [Term] id: ECO:0005604 name: cross-streak test evidence def: "A type of cell proliferation assay evidence where the investigated organism or a potential antagonist is inoculated so as to grow along the diameter line of the agar medium in a Petri dish, then, potentially susceptible microbes (usually bacteria) are streaked perpendicularly to the growth line and inhibition of growth of a test microbe in the vicinity of that line suggests that the antagonist secretes one or more diffusible antibiotics." [ECO:SN, url:www.jstor.org/stable/3792785] is_a: ECO:0005007 ! cell proliferation assay evidence relationship: IAO:0000136 GO:0009607 ! is about response to biotic stimulus relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay created_by: snadendla creation_date: 2016-03-29T15:40:54Z [Term] id: ECO:0005605 name: disk diffusion test evidence def: "A type of zone of inhibition evidence where sensitivity/resistance to an antimicrobial agent is tested by impregnating small filter disks with a known concentration of antimicrobial agent which is then placed on a Mueller-Hinton agar plate inoculated with the test organism." [ECO:SN, url:http\://www.cdc.gov/nczved/resources/cholera/ch9.pdf] is_a: ECO:0007083 ! zone of inhibition evidence relationship: IAO:0000136 GO:0046677 ! is about response to antibiotic relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay created_by: snadendla creation_date: 2016-03-29T16:02:22Z [Term] id: ECO:0005606 name: cell transfection experiment evidence def: "A type of experimental evidence where a foreign genetic material is introduced into the cell for study of gene function and regulation and protein function." [ECO:SN, url:http\://ch.promega.com/resources/product-guides-and-selectors/protocols-and-applications-guide/transfection/, url:http\://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911531/] is_a: ECO:0000006 ! experimental evidence is_a: IAO:0000030 {is_inferred="true"} ! information content entity relationship: IAO:0000136 GO:0050789 ! is about regulation of biological process created_by: snadendla creation_date: 2016-03-29T16:59:17Z [Term] id: ECO:0005607 name: tethered cell assay evidence def: "A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by observing the rotational behavior of the cells tethered to a coverslip by their flagella." [ECO:SN, PMID:1103143] is_a: ECO:0005021 ! chemotaxis assay evidence relationship: IAO:0000136 GO:0060326 ! is about cell chemotaxis relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay created_by: snadendla creation_date: 2016-03-31T15:51:10Z [Term] id: ECO:0005608 name: tumble frequency assay evidence def: "A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis in swimming organisms is determined by measuring chemotaxis in response to sudden concentration changes from one uniform spatial environment to another." [ECO:SN, PMID:4576832] synonym: "Temporal assay" EXACT [] is_a: ECO:0005021 ! chemotaxis assay evidence relationship: IAO:0000136 GO:0060326 ! is about cell chemotaxis relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay created_by: snadendla creation_date: 2016-03-31T16:42:35Z [Term] id: ECO:0005609 name: capillary assay evidence def: "A type of chemotaxis assay evidence where the presence or absence of positive or negative chemotaxis is determined by measuring the rate of accumulation of the cells into a capillary." [ECO:SN, PMID:4632978] comment: To determine the presence of negative chemotaxis, a repellent is added to the organismal suspension (but not in the capillary) and the organisms that fled into the capillary are measured. comment: To determine the presence of positive chemotaxis, an attractant is placed in the capillary and the presence of positive chemotaxis is determined based on the amount of organism that accumulated in the capillary. is_a: ECO:0005021 ! chemotaxis assay evidence relationship: IAO:0000136 GO:0060326 ! is about cell chemotaxis relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay created_by: snadendla creation_date: 2016-03-31T16:45:29Z [Term] id: ECO:0005610 name: biological system reconstruction evidence based on homology evidence used in manual assertion def: "A type of biological system reconstruction evidence based on homology evidence that is used in a manual assertion." [ECO:SN] comment: Inference may be based on paralogy and/or orthology of the genome-encoded components and is made primarily on functional conservation between the two systems. The sequences and number of genome-encoded components are fairly conserved but some divergence is observed. Evidence may originate from a combination of several experiments in the same or another species. is_a: ECO:0000352 {is_inferred="true"} ! evidence used in manual assertion is_a: ECO:0005549 ! biological system reconstruction evidence based on homology evidence intersection_of: ECO:0005549 ! biological system reconstruction evidence based on homology evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-03-31T17:00:03Z [Term] id: ECO:0005611 name: inference from experimental data evidence def: "A type of direct assay evidence used in manual assertion where phenotype or disease association is made with the gene because of involvement in the molecular mechanism of disease or involvement in a pathway known to contribute to a disease." [ECO:SN] synonym: "IED" EXACT [] synonym: "inferred from experimental data" EXACT [] is_a: ECO:0000314 ! direct assay evidence used in manual assertion created_by: snadendla creation_date: 2016-04-12T16:55:16Z [Term] id: ECO:0005612 name: inference from phenotype manipulation evidence def: "A type of mutant phenotype evidence used in manual assertion where variations or changes, such as mutations or abnormal levels of the product(s) of a single gene of interest, including non-mutational changes such as inhibition with antibodies or other inhibitors are determined." [ECO:SN] comment: Changes can include any gene mutation/knockout, over-expression or ectopic expression of wild-type or mutant genes, anti-sense experiments, RNAi experiments, specific protein inhibitors. synonym: "inferred from phenotype manipulation" EXACT [] synonym: "IPM" EXACT [] is_a: ECO:0000315 ! mutant phenotype evidence used in manual assertion created_by: snadendla creation_date: 2016-04-12T17:09:43Z [Term] id: ECO:0005613 name: inference by association of genotype from phenotype def: "A type of natural variation mutant evidence used in manual assertion where alleles are directly linked to phenotype and Mendelian diseases as a result of various experiments." [ECO:SN] comment: Used for 1) polymorphism or segregation of genetic markers (SNPs, mutations, RFLPs, microsatellites); 2) polymorphism or segregation of physical markers (FISH, centromeric or heterochromatic regions, chromosomal banding patterns); 3) detection of polymorphisms in inbred stock. synonym: "IAGP" EXACT [] synonym: "inferred by association of genotype from phenotype" EXACT [] is_a: ECO:0001237 ! natural variation mutant evidence used in manual assertion created_by: snadendla creation_date: 2016-04-12T17:24:00Z [Term] id: ECO:0005614 name: two-dimensional polyacrylamide gel electrophoresis evidence used in manual assertion def: "A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in a manual assertion." [ECO:SN] synonym: "2D-PAGE evidence" BROAD [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0005503 ! two-dimensional polyacrylamide gel electrophoresis evidence intersection_of: ECO:0005503 ! two-dimensional polyacrylamide gel electrophoresis evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T11:03:08Z [Term] id: ECO:0005615 name: alkaline phosphatase reporter gene assay evidence used in manual assertion def: "A type of alkaline phosphatase reporter gene assay evidence that is used in a manual assertion." [ECO:SN] synonym: "SEAP reporter assay" RELATED [] synonym: "secreted embryonic alkaline phosphatase reporter assay" RELATED [] is_a: ECO:0001801 ! alkaline phosphatase reporter gene assay evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001801 ! alkaline phosphatase reporter gene assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T11:05:59Z [Term] id: ECO:0005616 name: beta-galactosidase reporter gene assay evidence used in manual assertion def: "A type of beta-galactosidase reporter gene assay evidence that is used in a manual assertion." [ECO:SN] synonym: "beta-gal reporter gene assay evidence" BROAD [] synonym: "lacZ reporter gene assay" RELATED [] synonym: "LacZ transcript localization evidence used in manual assertion" EXACT [] is_a: ECO:0001802 ! beta-galactosidase reporter gene assay evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001802 ! beta-galactosidase reporter gene assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T11:08:57Z [Term] id: ECO:0005617 name: chloramphenicol acetyltransferase reporter gene assay evidence used in manual assertion def: "A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in a manual assertion." [ECO:SN] synonym: "CAT reporter gene assay evidence" BROAD [] is_a: ECO:0001803 ! chloramphenicol acetyltransferase reporter gene assay evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001803 ! chloramphenicol acetyltransferase reporter gene assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T11:11:07Z [Term] id: ECO:0005618 name: chromatin immunoprecipitation-chip evidence used in automatic assertion def: "A type of chromatin immunoprecipitation-chip evidence that is used in an automatic assertion." [ECO:SN] synonym: "ChIP-chip evidence" BROAD [] synonym: "ChIP-on-chip evidence" BROAD [] is_a: ECO:0000230 ! chromatin immunoprecipitation-chip evidence is_a: ECO:0007503 {is_inferred="true"} ! immunoprecipitation evidence used in automatic assertion intersection_of: ECO:0000230 ! chromatin immunoprecipitation-chip evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-06T11:17:04Z [Term] id: ECO:0005619 name: chromatin immunoprecipitation- exonuclease evidence used in automatic assertion def: "A type of chromatin immunoprecipitation- exonuclease evidence that is used in an automatic assertion." [ECO:SN] synonym: "ChIP-exo evidence" BROAD [] is_a: ECO:0001806 ! chromatin immunoprecipitation- exonuclease evidence is_a: ECO:0007503 {is_inferred="true"} ! immunoprecipitation evidence used in automatic assertion intersection_of: ECO:0001806 ! chromatin immunoprecipitation- exonuclease evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-06T11:22:25Z [Term] id: ECO:0005620 name: chromatin immunoprecipitation-PCR evidence used in manual assertion def: "A type of chromatin immunoprecipitation-PCR evidence that is used in a manual assertion." [ECO:SN] synonym: "ChIP-PCR evidence" BROAD [] is_a: ECO:0000227 ! chromatin immunoprecipitation-PCR evidence is_a: ECO:0005644 {is_inferred="true"} ! immunoprecipitation evidence used in manual assertion intersection_of: ECO:0000227 ! chromatin immunoprecipitation-PCR evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T11:25:01Z [Term] id: ECO:0005621 name: chromatin immunoprecipitation-seq evidence used in automatic assertion def: "A type of chromatin immunoprecipitation-seq evidence that is used in an automatic assertion." [ECO:SN] synonym: "ChIP-SEQ evidence" BROAD [] synonym: "ChIP-seq evidence" BROAD [] is_a: ECO:0000229 ! chromatin immunoprecipitation-seq evidence is_a: ECO:0007503 {is_inferred="true"} ! immunoprecipitation evidence used in automatic assertion intersection_of: ECO:0000229 ! chromatin immunoprecipitation-seq evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-06T11:29:13Z [Term] id: ECO:0005622 name: comparative genomics motif search evidence used in manual assertion def: "A type of comparative genomics motif search evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0000257 {is_inferred="true"} ! motif similarity evidence used in manual assertion is_a: ECO:0005534 ! comparative genomics motif search evidence intersection_of: ECO:0005534 ! comparative genomics motif search evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T14:49:36Z [Term] id: ECO:0005623 name: comparative genomics motif search evidence used in automatic assertion def: "A type of comparative genomics motif search evidence that is used in an automatic assertion." [ECO:SN] is_a: ECO:0000258 {is_inferred="true"} ! motif similarity evidence used in automatic assertion is_a: ECO:0005534 ! comparative genomics motif search evidence intersection_of: ECO:0005534 ! comparative genomics motif search evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-06T14:52:21Z [Term] id: ECO:0005624 name: consensus search evidence used in manual assertion def: "A type of consensus search evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0000257 {is_inferred="true"} ! motif similarity evidence used in manual assertion is_a: ECO:0005532 ! consensus search evidence intersection_of: ECO:0005532 ! consensus search evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T14:54:53Z [Term] id: ECO:0005625 name: consensus search evidence used in automatic assertion def: "A type of consensus search evidence that is used in an automatic assertion." [ECO:SN] is_a: ECO:0000258 {is_inferred="true"} ! motif similarity evidence used in automatic assertion is_a: ECO:0005532 ! consensus search evidence intersection_of: ECO:0005532 ! consensus search evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-06T14:58:22Z [Term] id: ECO:0005626 name: copper-phenanthroline footprinting evidence used in manual assertion def: "A type of copper-phenanthroline footprinting evidence that is used in a manual assertion." [ECO:SN] synonym: "1,10-phenanthroline-copper footprinting evidence" BROAD [] synonym: "OP-Cu Complex" RELATED [] is_a: ECO:0001815 ! copper-phenanthroline footprinting evidence is_a: ECO:0006083 {is_inferred="true"} ! nucleic acid binding evidence used in manual assertion intersection_of: ECO:0001815 ! copper-phenanthroline footprinting evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T15:01:25Z [Term] id: ECO:0005627 name: DNA adenine methyltransferase identification evidence used in manual assertion def: "A type of DNA adenine methyltransferase identification evidence that is used in a manual assertion." [ECO:SN] synonym: "DamID evidence" BROAD [] is_a: ECO:0001824 ! DNA adenine methyltransferase identification evidence is_a: ECO:0006075 {is_inferred="true"} ! affinity evidence used in manual assertion intersection_of: ECO:0001824 ! DNA adenine methyltransferase identification evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T15:05:14Z [Term] id: ECO:0005628 name: DNA adenine methyltransferase identification evidence used in automatic assertion def: "A type of DNA adenine methyltransferase identification evidence that is used in an automatic assertion." [ECO:SN] synonym: "DamID evidence" BROAD [] is_a: ECO:0001824 ! DNA adenine methyltransferase identification evidence is_a: ECO:0007384 {is_inferred="true"} ! affinity evidence used in automatic assertion intersection_of: ECO:0001824 ! DNA adenine methyltransferase identification evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-06T15:06:46Z [Term] id: ECO:0005629 name: DNA affinity chromatography evidence used in manual assertion def: "A type of DNA affinity chromatography evidence that is used in a manual assertion." [ECO:SN] synonym: "DNA affinity purification evidence" BROAD [] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001809 ! DNA affinity chromatography evidence intersection_of: ECO:0001809 ! DNA affinity chromatography evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T15:08:40Z [Term] id: ECO:0005630 name: cDNA to DNA expression microarray evidence used in automatic assertion def: "A type of cDNA to DNA expression microarray evidence that is used in an automatic assertion." [ECO:SN] synonym: "DNA microarray evidence" BROAD [] synonym: "RNA microarray evidence" BROAD [] is_a: ECO:0000097 ! cDNA to DNA expression microarray evidence is_a: ECO:0007301 {is_inferred="true"} ! expression microarray evidence used in automatic assertion intersection_of: ECO:0000097 ! cDNA to DNA expression microarray evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-06T15:31:51Z [Term] id: ECO:0005631 name: DNAse footprinting evidence used in manual assertion def: "A type of DNAse footprinting evidence that is used in a manual assertion." [ECO:SN] synonym: "DNase protection evidence" BROAD [] is_a: ECO:0001810 ! DNAse footprinting evidence is_a: ECO:0006083 {is_inferred="true"} ! nucleic acid binding evidence used in manual assertion intersection_of: ECO:0001810 ! DNAse footprinting evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T15:35:41Z [Term] id: ECO:0005632 name: fluorescence anisotropy evidence used in manual assertion def: "A type of fluorescence anisotropy evidence that is used in a manual assertion." [ECO:SN] synonym: "FA evidence" BROAD [] synonym: "fluorescence polarization" RELATED [] synonym: "FP" RELATED [] is_a: ECO:0001249 {is_inferred="true"} ! fluorescence evidence used in manual assertion is_a: ECO:0001811 ! fluorescence anisotropy evidence intersection_of: ECO:0001811 ! fluorescence anisotropy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T15:45:40Z [Term] id: ECO:0005633 name: ferric uptake regulator titration assay evidence used in manual assertion def: "A type of ferric uptake regulator titration assay evidence that is used in a manual assertion." [ECO:SN] synonym: "FURTA evidence" BROAD [] is_a: ECO:0001829 ! ferric uptake regulator titration assay evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001829 ! ferric uptake regulator titration assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T15:49:18Z [Term] id: ECO:0005634 name: genomic systematic evolution of ligands by exponential amplification evidence used in manual assertion def: "A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in a manual assertion." [ECO:SN] synonym: "genomic SELEX evidence" BROAD [] is_a: ECO:0001812 ! genomic systematic evolution of ligands by exponential amplification evidence is_a: ECO:0006088 {is_inferred="true"} ! systematic evolution of ligands by exponential amplification evidence used in manual assertion intersection_of: ECO:0001812 ! genomic systematic evolution of ligands by exponential amplification evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T16:41:30Z [Term] id: ECO:0005635 name: genomic systematic evolution of ligands by exponential amplification evidence used in automatic assertion def: "A type of genomic systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion." [ECO:SN] synonym: "genomic SELEX evidence" BROAD [] is_a: ECO:0001812 ! genomic systematic evolution of ligands by exponential amplification evidence is_a: ECO:0007510 {is_inferred="true"} ! systematic evolution of ligands by exponential amplification evidence used in automatic assertion intersection_of: ECO:0001812 ! genomic systematic evolution of ligands by exponential amplification evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-06T16:43:03Z [Term] id: ECO:0005636 name: green fluorescent protein reporter gene assay evidence used in manual assertion def: "A type of green fluorescent protein reporter gene assay evidence that is used in a manual assertion." [ECO:SN] synonym: "GFP promoter fusion" RELATED [] synonym: "GFP reporter gene assay evidence" BROAD [] synonym: "green fluorescent protein promoter fusion" RELATED [] synonym: "green fluorescent protein transcript localization evidence used in manual assertion" EXACT [] is_a: ECO:0001816 ! green fluorescent protein reporter gene assay evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001816 ! green fluorescent protein reporter gene assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T16:46:32Z [Term] id: ECO:0005637 name: green fluorescent protein reporter gene assay evidence used in automatic assertion def: "A type of green fluorescent protein reporter gene assay evidence that is used in an automatic assertion." [ECO:SN] synonym: "GFP promoter fusion" RELATED [] synonym: "GFP reporter gene assay evidence" BROAD [] synonym: "green fluorescent protein promoter fusion" RELATED [] synonym: "green fluorescent protein transcript localization evidence used in automatic assertion" EXACT [] is_a: ECO:0001816 ! green fluorescent protein reporter gene assay evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001816 ! green fluorescent protein reporter gene assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-06T16:48:29Z [Term] id: ECO:0005638 name: cell growth regulation assay evidence used in manual assertion def: "A type of cell growth regulation assay evidence that is used in a manual assertion." [ECO:SN] synonym: "growth curve analysis" RELATED [] is_a: ECO:0000095 ! cell growth regulation assay evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000095 ! cell growth regulation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T16:52:15Z [Term] id: ECO:0005639 name: cell growth regulation assay evidence used in automatic assertion def: "A type of cell growth regulation assay evidence that is used in an automatic assertion." [ECO:SN] synonym: "growth curve analysis" RELATED [] is_a: ECO:0000095 ! cell growth regulation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000095 ! cell growth regulation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-06T16:53:28Z [Term] id: ECO:0005640 name: glutathione S-transferase pull-down assay evidence used in manual assertion def: "A type of glutathione S-transferase pull-down assay evidence that is used in a manual assertion." [ECO:SN] synonym: "GST pull-down assay evidence" BROAD [] is_a: ECO:0001817 ! glutathione S-transferase pull-down assay evidence is_a: ECO:0006076 {is_inferred="true"} ! protein binding evidence used in manual assertion intersection_of: ECO:0001817 ! glutathione S-transferase pull-down assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T16:56:39Z [Term] id: ECO:0005641 name: beta-glucuronidase reporter gene assay evidence used in manual assertion def: "A type of beta-glucuronidase reporter gene assay evidence that is used in a manual assertion." [ECO:SN] synonym: "GUS reporter gene assay evidence" BROAD [] is_a: ECO:0001804 ! beta-glucuronidase reporter gene assay evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001804 ! beta-glucuronidase reporter gene assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T16:58:29Z [Term] id: ECO:0005642 name: heteronuclear single quantum coherence spectroscopy evidence used in manual assertion def: "A type of heteronuclear single quantum coherence spectroscopy evidence that is used in a manual assertion." [ECO:SN] synonym: "HSQC evidence" BROAD [] is_a: ECO:0001238 {is_inferred="true"} ! nuclear magnetic resonance spectroscopy evidence used in manual assertion is_a: ECO:0001813 ! heteronuclear single quantum coherence spectroscopy evidence intersection_of: ECO:0001813 ! heteronuclear single quantum coherence spectroscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T23:10:13Z [Term] id: ECO:0005643 name: hydroxyl-radical footprinting evidence used in manual assertion def: "A type of hydroxyl-radical footprinting evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0001818 ! hydroxyl-radical footprinting evidence is_a: ECO:0006083 {is_inferred="true"} ! nucleic acid binding evidence used in manual assertion intersection_of: ECO:0001818 ! hydroxyl-radical footprinting evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T23:14:48Z [Term] id: ECO:0005644 name: immunoprecipitation evidence used in manual assertion def: "A type of immunoprecipitation evidence that is used in a manual assertion." [ECO:SN] synonym: "IDA: immunoprecipitation" BROAD [] is_a: ECO:0000085 ! immunoprecipitation evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000085 ! immunoprecipitation evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T23:20:49Z [Term] id: ECO:0005645 name: interferometric reflectance imaging sensor evidence used in manual assertion def: "A type of interferometric reflectance imaging sensor evidence that is used in a manual assertion." [ECO:SN] synonym: "IRIS evidence" BROAD [] synonym: "spectral reflectance imaging biosensor evidence" BROAD [] synonym: "SRIB evidence" BROAD [] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0005520 ! interferometric reflectance imaging sensor evidence intersection_of: ECO:0005520 ! interferometric reflectance imaging sensor evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T23:27:58Z [Term] id: ECO:0005646 name: interferometric reflectance imaging sensor evidence used in automatic assertion def: "A type of interferometric reflectance imaging sensor evidence that is used in an automatic assertion." [ECO:SN] synonym: "IRIS evidence" BROAD [] synonym: "spectral reflectance imaging biosensor evidence" BROAD [] synonym: "SRIB evidence" BROAD [] is_a: ECO:0005520 ! interferometric reflectance imaging sensor evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0005520 ! interferometric reflectance imaging sensor evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-06T23:29:23Z [Term] id: ECO:0005647 name: isothermal titration calorimetry evidence used in manual assertion def: "A type of isothermal titration calorimetry evidence that is used in a manual assertion." [ECO:SN] synonym: "ITC evidence" BROAD [] is_a: ECO:0001825 ! isothermal titration calorimetry evidence is_a: ECO:0006075 {is_inferred="true"} ! affinity evidence used in manual assertion intersection_of: ECO:0001825 ! isothermal titration calorimetry evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T23:36:26Z [Term] id: ECO:0005648 name: luciferase reporter gene assay evidence used in manual assertion def: "A type of luciferase reporter gene assay evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0001805 ! luciferase reporter gene assay evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0001805 ! luciferase reporter gene assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T23:44:52Z [Term] id: ECO:0005649 name: machine learning prediction of motif instance evidence used in manual assertion def: "A type of machine learning prediction of motif instance evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0000255 {is_inferred="true"} ! match to sequence model evidence used in manual assertion is_a: ECO:0005535 ! machine learning prediction of motif instance evidence intersection_of: ECO:0005535 ! machine learning prediction of motif instance evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-06T23:51:30Z [Term] id: ECO:0005650 name: machine learning prediction of motif instance evidence used in automatic assertion def: "A type of machine learning prediction of motif instance evidence that is used in an automatic assertion." [ECO:SN] is_a: ECO:0000256 {is_inferred="true"} ! match to sequence model evidence used in automatic assertion is_a: ECO:0005535 ! machine learning prediction of motif instance evidence intersection_of: ECO:0005535 ! machine learning prediction of motif instance evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-06T23:54:00Z [Term] id: ECO:0005651 name: matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence used in automatic assertion def: "A type of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence that is used in an automatic assertion." [ECO:SN] synonym: "MALDI-TOF mass spectrometry evidence" BROAD [] synonym: "MALDI-TOF-MS evidence" BROAD [] is_a: ECO:0005526 ! matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0005526 ! matrix-assisted laser desorption/ionization time-of-flight mass spectrometry evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-06T23:57:30Z [Term] id: ECO:0005652 name: methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in manual assertion def: "A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in a manual assertion." [ECO:SN] synonym: "Methidiumpropyl-EDTA Fe(II) footprinting evidence" BROAD [] synonym: "MPE Fe(II) footprinting" RELATED [] synonym: "MPE-EDTA Fe(II) footprinting evidence" BROAD [] is_a: ECO:0001814 ! methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence is_a: ECO:0006083 {is_inferred="true"} ! nucleic acid binding evidence used in manual assertion intersection_of: ECO:0001814 ! methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-09T14:42:28Z [Term] id: ECO:0005653 name: northern assay evidence used in manual assertion def: "A type of northern assay evidence that is used in a manual assertion." [ECO:SN] synonym: "IEP: transcript levels (e.g. Northerns)" RELATED [] synonym: "northern assay evidence" BROAD [] synonym: "RNA blot evidence" BROAD [] is_a: ECO:0000106 ! northern blot evidence is_a: ECO:0000291 {is_inferred="true"} ! transcript expression evidence used in manual assertion intersection_of: ECO:0000106 ! northern blot evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-09T14:48:03Z [Term] id: ECO:0005654 name: phylogenetic footprinting evidence used in manual assertion def: "A type of phylogenetic footprinting evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0005533 ! phylogenetic footprinting evidence is_a: ECO:0005558 {is_inferred="true"} ! motif discovery evidence used in manual assertion intersection_of: ECO:0005533 ! phylogenetic footprinting evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-09T14:50:52Z [Term] id: ECO:0005655 name: phylogenetic footprinting evidence used in automatic assertion def: "A type of phylogenetic footprinting evidence that is used in an automatic assertion." [ECO:SN] is_a: ECO:0005533 ! phylogenetic footprinting evidence is_a: ECO:0005559 {is_inferred="true"} ! motif discovery evidence used in automatic assertion intersection_of: ECO:0005533 ! phylogenetic footprinting evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-09T14:51:55Z [Term] id: ECO:0005656 name: methylation interference footprinting evidence used in manual assertion def: "A type of methylation interference footprinting evidence that is used in a manual assertion." [ECO:SN] synonym: "premethylation interference footprinting evidence used in manual assertion" EXACT [] is_a: ECO:0001827 ! methylation interference footprinting evidence is_a: ECO:0006083 {is_inferred="true"} ! nucleic acid binding evidence used in manual assertion intersection_of: ECO:0001827 ! methylation interference footprinting evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-09T14:55:25Z [Term] id: ECO:0005657 name: primer extension assay evidence used in manual assertion def: "A type of primer extension assay evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0000291 {is_inferred="true"} ! transcript expression evidence used in manual assertion is_a: ECO:0001819 ! primer extension assay evidence intersection_of: ECO:0001819 ! primer extension assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-09T14:58:38Z [Term] id: ECO:0005658 name: position-specific scoring matrix motif search evidence used in manual assertion def: "A type of position-specific scoring matrix motif search evidence that is used in a manual assertion." [ECO:SN] synonym: "PSSM motif search evidence" BROAD [] is_a: ECO:0000257 {is_inferred="true"} ! motif similarity evidence used in manual assertion is_a: ECO:0005536 ! position-specific scoring matrix motif search evidence intersection_of: ECO:0005536 ! position-specific scoring matrix motif search evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-09T15:01:31Z [Term] id: ECO:0005659 name: position-specific scoring matrix motif search evidence used in automatic assertion def: "A type of position-specific scoring matrix motif search evidence that is used in an automatic assertion." [ECO:SN] synonym: "PSSM motif search evidence" BROAD [] is_a: ECO:0000258 {is_inferred="true"} ! motif similarity evidence used in automatic assertion is_a: ECO:0005536 ! position-specific scoring matrix motif search evidence intersection_of: ECO:0005536 ! position-specific scoring matrix motif search evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-09T15:02:31Z [Term] id: ECO:0005660 name: quantitative polymerase chain reaction evidence used in manual assertion def: "A type of quantitative polymerase chain reaction evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0000231 ! quantitative polymerase chain reaction evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000231 ! quantitative polymerase chain reaction evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-09T15:09:01Z [Term] id: ECO:0005661 name: rapid amplification of cDNA ends polymerase chain reaction evidence used in manual assertion def: "A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in a manual assertion." [ECO:SN] synonym: "RACE PCR evidence" BROAD [] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001820 ! rapid amplification of cDNA ends polymerase chain reaction evidence intersection_of: ECO:0001820 ! rapid amplification of cDNA ends polymerase chain reaction evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-09T15:19:20Z [Term] id: ECO:0005662 name: regular expression motif search evidence used in manual assertion def: "A type of regular expression motif search evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0000257 {is_inferred="true"} ! motif similarity evidence used in manual assertion is_a: ECO:0005505 ! regular expression motif search evidence intersection_of: ECO:0005505 ! regular expression motif search evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-09T16:13:55Z [Term] id: ECO:0005663 name: regular expression motif search evidence used in automatic assertion def: "A type of regular expression motif search evidence that is used in an automatic assertion." [ECO:SN] is_a: ECO:0000258 {is_inferred="true"} ! motif similarity evidence used in automatic assertion is_a: ECO:0005505 ! regular expression motif search evidence intersection_of: ECO:0005505 ! regular expression motif search evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-09T16:15:03Z [Term] id: ECO:0005664 name: RNA sequencing assay evidence used in manual assertion comment: Use ECO:0006068 (RNA-seq evidence used in manual assertion) in place of this term. is_obsolete: true created_by: snadendla creation_date: 2016-05-09T16:18:35Z [Term] id: ECO:0005665 name: RNA sequencing assay evidence used in automatic assertion comment: Use ECO:0006069 (RNA-seq evidence used in automatic assertion) in place of this term. is_obsolete: true created_by: snadendla creation_date: 2016-05-09T16:19:38Z [Term] id: ECO:0005666 name: S1 nuclease protection assay evidence used in manual assertion def: "A type of S1 nuclease protection assay evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0001240 {is_inferred="true"} ! nuclease protection assay evidence used in manual assertion is_a: ECO:0005521 ! S1 nuclease protection assay evidence intersection_of: ECO:0005521 ! S1 nuclease protection assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-09T16:22:58Z [Term] id: ECO:0005667 name: site-directed mutagenesis evidence used in manual assertion def: "A type of site-directed mutagenesis evidence that is used in a manual assertion." [ECO:SN] synonym: "site directed mutagenesis evidence" BROAD [] is_a: ECO:0005528 ! site-directed mutagenesis evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0005528 ! site-directed mutagenesis evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-09T16:29:13Z [Term] id: ECO:0005668 name: survival rate analysis evidence used in manual assertion def: "A type of survival rate analysis evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0001225 {is_inferred="true"} ! knockout evidence used in manual assertion is_a: ECO:0001822 ! survival rate analysis evidence intersection_of: ECO:0001822 ! survival rate analysis evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-09T16:31:08Z [Term] id: ECO:0005669 name: ultraviolet light footprinting evidence used in manual assertion def: "A type of ultraviolet light footprinting evidence that is used in a manual assertion." [ECO:SN] synonym: "UV footprinting" RELATED [] is_a: ECO:0001826 ! ultraviolet light footprinting evidence is_a: ECO:0006083 {is_inferred="true"} ! nucleic acid binding evidence used in manual assertion intersection_of: ECO:0001826 ! ultraviolet light footprinting evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-09T16:33:44Z [Term] id: ECO:0005670 name: x-ray crystallography evidence used in manual assertion def: "A type of x-ray crystallography evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0001171 {is_inferred="true"} ! crystallography evidence used in manual assertion is_a: ECO:0001823 ! x-ray crystallography evidence intersection_of: ECO:0001823 ! x-ray crystallography evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-10T11:53:00Z [Term] id: ECO:0005671 name: x-ray crystallography evidence used in automatic assertion def: "A type of x-ray crystallography evidence that is used in an automatic assertion." [ECO:SN] is_a: ECO:0001823 ! x-ray crystallography evidence is_a: ECO:0007374 {is_inferred="true"} ! crystallography evidence used in automatic assertion intersection_of: ECO:0001823 ! x-ray crystallography evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 {is_inferred="true"} ! automatic assertion created_by: snadendla creation_date: 2016-05-10T11:54:03Z [Term] id: ECO:0005672 name: xylE reporter gene assay evidence used in manual assertion def: "A type of xylE reporter gene assay evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0005537 ! xylE reporter gene assay evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0005537 ! xylE reporter gene assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-10T11:57:15Z [Term] id: ECO:0005673 name: ad-hoc qualitative phenotype observation evidence def: "A type of experimental phenotypic evidence where a non-standard trait (e.g. natural competence) is assessed qualitatively (e.g. presence/absence) and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor." [ECO:SN, PMID:15150239] is_a: ECO:0000059 ! experimental phenotypic evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2016-05-10T12:57:41Z [Term] id: ECO:0005674 name: ad-hoc qualitative phenotype observation evidence used in manual assertion def: "A type of ad-hoc qualitative phenotype observation that is used in a manual assertion." [ECO:SN] is_a: ECO:0005673 ! ad-hoc qualitative phenotype observation evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0005673 ! ad-hoc qualitative phenotype observation evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-10T14:28:47Z [Term] id: ECO:0005675 name: ad-hoc quantitative phenotype observation evidence def: "A type of experimental phenotypic evidence where a quantifiable phenotypic trait (e.g. glucose intake) is assessed in a quantitative manner after induction of the regulatory mechanism and used as a natural reporter to conclude that some genes or pathways are regulated by the transcription factor." [ECO:SN, PMID:15150239] is_a: ECO:0000059 ! experimental phenotypic evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: snadendla creation_date: 2016-05-10T14:30:50Z [Term] id: ECO:0005676 name: ad-hoc quantitative phenotype observation evidence used in manual assertion def: "A type of ad-hoc quantitative phenotype observation evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0005675 ! ad-hoc quantitative phenotype observation evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0005675 ! ad-hoc quantitative phenotype observation evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 {is_inferred="true"} ! manual assertion created_by: snadendla creation_date: 2016-05-10T14:34:50Z [Term] id: ECO:0005800 name: dilution assay evidence def: "A direct assay evidence where the activity of a solution is determined by exposing an indicator culture or organism to a series of dilutions and determining the lowest concentration that elicits a biological response." [http://www.sciencedirect.com/science/article/pii/016770129400068I] comment: For chemicals, bacteriocins, or phage, the indicator culture is typically present in a soft-agar layer on top of nutrient agar and a small quantity of each dilution is spotted onto the soft agar overlay. synonym: "critical dilution assay" EXACT [] synonym: "spot assay" EXACT [] is_a: ECO:0000002 ! direct assay evidence [Term] id: ECO:0005801 name: enzyme assay evidence used in manual assertion def: "A type of enzyme assay evidence that is used in a manual assertion." [ECO:SN] synonym: "IDA: enzyme assays" BROAD [] is_a: ECO:0000005 ! enzyme assay evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000005 ! enzyme assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion [Term] id: ECO:0005802 name: cell transfection experiment evidence used in manual assertion def: "A type of cell transfection experiment evidence that is used in a manual assertion." [ECO:SN] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0005606 ! cell transfection experiment evidence intersection_of: ECO:0005606 ! cell transfection experiment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion [Term] id: ECO:0005803 name: motility assay evidence def: "A type of direct assay evidence where the motility of a cell or cells is determined." [ECO:SN] is_a: ECO:0000002 ! direct assay evidence [Term] id: ECO:0005804 name: immunofluorescence evidence used in manual assertion def: "A type of immunofluorescence evidence that is used in a manual assertion." [ECO:SN] synonym: "IDA: immunofluorescence" BROAD [] is_a: ECO:0000007 ! immunofluorescence evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000007 ! immunofluorescence evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion [Term] id: ECO:0005805 name: yeast 2-hybrid evidence used in manual assertion def: "A type of yeast 2-hybrid evidence that is used in a manual assertion." [ECO:SN] synonym: "IPI: yeast two-hybrid assay" BROAD [] is_a: ECO:0000068 ! yeast 2-hybrid evidence is_a: ECO:0006077 {is_inferred="true"} ! hybrid interaction evidence used in manual assertion intersection_of: ECO:0000068 ! yeast 2-hybrid evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion [Term] id: ECO:0006001 name: Cya fusion reporter assay evidence def: "A type of evidence derived from exploiting the CyaA (calmodulin-activated adenylate cyclase toxin) secreted by Bordatella pertussis to synthesize cAMP and alter cellular physiology in a host cell for various biological applications." [PMID:10217833, PMID:14702323] is_a: ECO:0000017 ! ectopic expression evidence is_a: ECO:0000049 ! reporter gene assay evidence created_by: rctauber creation_date: 2016-06-15T08:42:16Z [Term] id: ECO:0006002 name: Cya fusion reporter assay evidence used in manual assertion def: "A type of Cya fusion reporter assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001273 {is_inferred="true"} ! ectopic expression evidence used in manual assertion is_a: ECO:0006001 ! Cya fusion reporter assay evidence intersection_of: ECO:0006001 ! Cya fusion reporter assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "CollecTF" xsd:string created_by: rctauber creation_date: 2010-06-15T08:44:10Z [Term] id: ECO:0006003 name: electron microscopy evidence used in manual assertion def: "A type of electron microscopy evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001232 {is_inferred="true"} ! microscopy evidence used in manual assertion is_a: ECO:0005033 ! electron microscopy evidence intersection_of: ECO:0005033 ! electron microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-10-12T12:32:29Z [Term] id: ECO:0006004 name: super-resolution microscopy evidence used in manual assertion def: "A type of super-resolution microscopy evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001232 {is_inferred="true"} ! microscopy evidence used in manual assertion is_a: ECO:0005578 ! super-resolution microscopy evidence intersection_of: ECO:0005578 ! super-resolution microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-10-12T12:32:29Z [Term] id: ECO:0006005 name: fractionation evidence used in manual assertion def: "A type of fractionation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000100 ! fractionation evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000100 ! fractionation evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-10-12T12:32:29Z [Term] id: ECO:0006006 name: electrophysiology assay evidence used in manual assertion def: "A type of electrophysiology assay evidence that is used in a manual assertion." [] {comment="ECO:RCT"} is_a: ECO:0000164 ! electrophysiology assay evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000164 ! electrophysiology assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-10-12T12:32:29Z [Term] id: ECO:0006007 name: chromatin immunoprecipitation-chip evidence used in manual assertion def: "A type of chromatin immunoprecipitation-chip evidence that is used in a manual assertion." [ECO:RCT] synonym: "ChIP-chip evidence" BROAD [] synonym: "ChIP-on-chip evidence" BROAD [] is_a: ECO:0000230 ! chromatin immunoprecipitation-chip evidence is_a: ECO:0005644 {is_inferred="true"} ! immunoprecipitation evidence used in manual assertion intersection_of: ECO:0000230 ! chromatin immunoprecipitation-chip evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-10-21T11:55:53Z [Term] id: ECO:0006008 name: chromatin immunoprecipitation- exonuclease evidence used in manual assertion def: "A type of chromatin immunoprecipitation- exonuclease evidence that is used in a manual assertion." [ECO:RCT] synonym: "ChIP-exo" BROAD [] is_a: ECO:0001806 ! chromatin immunoprecipitation- exonuclease evidence is_a: ECO:0005644 {is_inferred="true"} ! immunoprecipitation evidence used in manual assertion intersection_of: ECO:0001806 ! chromatin immunoprecipitation- exonuclease evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-10-21T11:55:53Z [Term] id: ECO:0006009 name: chromatin immunoprecipitation-seq evidence used in manual assertion def: "A type of chromatin immunoprecipitation-seq evidence that is used in a manual assertion." [ECO:RCT] synonym: "ChIP-SEQ evidence" BROAD [] synonym: "ChIP-seq evidence" BROAD [] is_a: ECO:0000229 ! chromatin immunoprecipitation-seq evidence is_a: ECO:0005644 {is_inferred="true"} ! immunoprecipitation evidence used in manual assertion intersection_of: ECO:0000229 ! chromatin immunoprecipitation-seq evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-10-21T11:55:53Z [Term] id: ECO:0006010 name: mRNA interactome capture evidence def: "A type of nucleic acid binding evidence in which RNA-binding proteins are identified through cross-linking RNA and proteins by UV light, capturing RNA-protein complexes on oligo(dT) beads, and finally identifying by mass spectrometry." [PMID:27729395] synonym: "ultraviolet light cross-linking RNA binding evidence" EXACT [] is_a: ECO:0000136 ! nucleic acid binding evidence created_by: rctauber creation_date: 2016-10-21T12:28:17Z [Term] id: ECO:0006011 name: mRNA interactome capture evidence used in manual assertion def: "A type of mRNA interactome capture evidence that is used in a manual assertion." [ECO:RCT] synonym: "ultraviolet light cross-linking RNA binding evidence" BROAD [] is_a: ECO:0006010 ! mRNA interactome capture evidence is_a: ECO:0006083 {is_inferred="true"} ! nucleic acid binding evidence used in manual assertion intersection_of: ECO:0006010 ! mRNA interactome capture evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-10-21T12:28:17Z [Term] id: ECO:0006012 name: patch-clamp recording evidence def: "A type of electrophysiology assay evidence in which a glass micropipette is sealed to the surface of a cell membrane (patch) to study ion channels." [ECO:RCT] is_a: ECO:0000164 ! electrophysiology assay evidence relationship: IAO:0000136 GO:0005216 ! is about ion channel activity relationship: OBI:0000312 OBI:0002177 ! is_specified_output_of patch clamp assay created_by: rctauber creation_date: 2016-11-28T11:44:05Z [Term] id: ECO:0006013 name: patch-clamp recording evidence used in manual assertion def: "A type of patch-clamp recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0006006 ! electrophysiology assay evidence used in manual assertion is_a: ECO:0006012 ! patch-clamp recording evidence intersection_of: ECO:0006012 ! patch-clamp recording evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-11-28T11:44:05Z [Term] id: ECO:0006014 name: whole-cell patch-clamp recording evidence def: "A type of patch-clamp recording evidence in which a glass micropipette filled with a prepared solution is used to form a seal with the cell membrane followed by rupture of membrane to provide accurate and high resolution electrical property measurements of the whole cell." [PMID:27341060] is_a: ECO:0006012 ! patch-clamp recording evidence relationship: IAO:0000136 GO:0005216 ! is about ion channel activity relationship: OBI:0000312 OBI:0002178 ! is_specified_output_of whole-cell patch clamp assay created_by: rctauber creation_date: 2016-11-28T11:44:05Z [Term] id: ECO:0006015 name: whole-cell patch-clamp recording evidence used in manual assertion def: "A type of whole-cell patch-clamp recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0006013 ! patch-clamp recording evidence used in manual assertion is_a: ECO:0006014 ! whole-cell patch-clamp recording evidence intersection_of: ECO:0006014 ! whole-cell patch-clamp recording evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-11-28T11:44:05Z [Term] id: ECO:0006016 name: author statement from published clinical study def: "A type of traceable author statement that is based on a publication about a clinical study." [] synonym: "published clinical study evidence" EXACT [] synonym: "traceable author statement from published clinical study" RELATED [] is_a: ECO:0000204 ! author statement created_by: rctauber creation_date: 2016-11-30T09:44:47Z [Term] id: ECO:0006017 name: author statement from published clinical study used in manual assertion def: "A type of author statement from published clinical study that is used in a manual assertion." [] comment: Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used when evidence for an HPO annotation is information extracted from articles in the medical literature. synonym: "PCS" EXACT [HPO:PCS] synonym: "published clinical study evidence" BROAD [] is_a: ECO:0000302 {is_inferred="true"} ! author statement used in manual assertion is_a: ECO:0006016 ! author statement from published clinical study intersection_of: ECO:0006016 ! author statement from published clinical study intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: seeAlso http://human-phenotype-ontology.github.io/documentation.html#annot xsd:string created_by: rctauber creation_date: 2016-11-30T09:44:47Z [Term] id: ECO:0006018 name: inference based on individual clinical experience def: "A type of curator inference that is based on the individual clinical experience of a clinician" [] synonym: "individual clinical experience evidence" EXACT [] is_a: ECO:0000205 ! curator inference created_by: rctauber creation_date: 2016-11-30T09:44:47Z [Term] id: ECO:0006019 name: inference based on individual clinical experience used in manual assertion def: "A type of inference based on individual clinical experience that is used in a manual assertion." [] comment: Created and used by the Human Phenotype Ontology (HPO) Annotations group. Here it is used for annotating disorders with a limited amount of published data, and is accompanied by a reference to the individual or center performing the annotation. synonym: "ICE" EXACT [HPO:ICE] synonym: "individual clinical experience evidence" BROAD [] is_a: ECO:0000305 {is_inferred="true"} ! curator inference used in manual assertion is_a: ECO:0006018 ! inference based on individual clinical experience intersection_of: ECO:0006018 ! inference based on individual clinical experience intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: seeAlso http://human-phenotype-ontology.github.io/documentation.html#annot xsd:string created_by: rctauber creation_date: 2016-11-30T09:44:47Z [Term] id: ECO:0006020 name: biofilm formation assay evidence def: "A type of cell proliferation assay evidence in which biofilm growth is monitored and detected from attachment to development." [PMID:10547784] synonym: "biofilm assay evidence" EXACT [] is_a: ECO:0005007 ! cell proliferation assay evidence relationship: IAO:0000136 GO:0042710 ! is about biofilm formation relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay created_by: rctauber creation_date: 2016-12-05T09:33:18Z [Term] id: ECO:0006021 name: biofilm formation assay evidence used in manual assertion def: "A type of biofilm formation assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0006020 ! biofilm formation assay evidence intersection_of: ECO:0006020 ! biofilm formation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-12-05T09:33:18Z [Term] id: ECO:0006022 name: microtiter plate biofilm assay evidence def: "A type of biofilm formation assay evidence in which microtiter dishes or tubes are inoculated and incubated to promote biofilm formation, and then biofilms are detected by staining with crystal violet or safranin to observe phenotypes." [PMID:10547784] synonym: "96-well biofilm assay evidence" EXACT [] is_a: ECO:0006020 ! biofilm formation assay evidence relationship: IAO:0000136 GO:0042710 ! is about biofilm formation created_by: rctauber creation_date: 2016-12-05T09:33:18Z [Term] id: ECO:0006023 name: microtiter plate biofilm assay evidence used in manual assertion def: "A type of microtiter plate biofilm assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0006021 {is_inferred="true"} ! biofilm formation assay evidence used in manual assertion is_a: ECO:0006022 ! microtiter plate biofilm assay evidence intersection_of: ECO:0006022 ! microtiter plate biofilm assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-12-05T09:33:18Z [Term] id: ECO:0006024 name: air-liquid interface assay evidence def: "A type of biofilm formation assay evidence in which biofilm formation is analyzed, without staining, over 4 to 48 hours by growth on a tilted multiwell plate." [PMID:18770545] comment: Tilting of the plate positions the air-liquid interface on a clear portion to improve visability. synonym: "ALI biofilm assay evidence" EXACT [] is_a: ECO:0006020 ! biofilm formation assay evidence relationship: IAO:0000136 GO:0042710 ! is about biofilm formation relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay created_by: rctauber creation_date: 2016-12-05T09:33:18Z [Term] id: ECO:0006025 name: air-liquid interface assay evidence used in manual assertion def: "A type of air-liquid interface assay evidence that is used in a manual assertion." [ECO:RCT] synonym: "ALI biofilm assay evidence" BROAD [] is_a: ECO:0006021 {is_inferred="true"} ! biofilm formation assay evidence used in manual assertion is_a: ECO:0006024 ! air-liquid interface assay evidence intersection_of: ECO:0006024 ! air-liquid interface assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-12-05T09:33:18Z [Term] id: ECO:0006026 name: colony biofilm assay evidence def: "A type of biofilm formation assay evidence in which a colony is grown on a semipermeable membrane on an agar plate. The plate serves to supply nutrients and the semipermeable membrane can be relocated to fresh plates." [PMID:18770545] comment: The plates commonly contain different carbon sources or antibiotic treatments to observe properties of the cells. is_a: ECO:0006020 ! biofilm formation assay evidence relationship: IAO:0000136 GO:0042710 ! is about biofilm formation relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay created_by: rctauber creation_date: 2016-12-05T09:33:18Z [Term] id: ECO:0006027 name: colony biofilm assay evidence used in manual assertion def: "A type of colony biofilm assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0006021 {is_inferred="true"} ! biofilm formation assay evidence used in manual assertion is_a: ECO:0006026 ! colony biofilm assay evidence intersection_of: ECO:0006026 ! colony biofilm assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-12-05T09:33:18Z [Term] id: ECO:0006028 name: Kadouri drip-fed biofilm assay evidence def: "A type of biofilm formation assay evidence in which mature bacterial biofilms are grown in a multiwell plate that has a growth medium continually pumped through the wells while waste is continually pumped out." [PMID:18770545] is_a: ECO:0006020 ! biofilm formation assay evidence relationship: IAO:0000136 GO:0042710 ! is about biofilm formation relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay created_by: rctauber creation_date: 2016-12-05T09:33:18Z [Term] id: ECO:0006029 name: Kadouri drip-fed biofilm assay evidence used in manual assertion def: "A type of Kadouri drip-fed biofilm assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0006021 {is_inferred="true"} ! biofilm formation assay evidence used in manual assertion is_a: ECO:0006028 ! Kadouri drip-fed biofilm assay evidence intersection_of: ECO:0006028 ! Kadouri drip-fed biofilm assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-12-05T09:33:18Z [Term] id: ECO:0006030 name: co-immunoprecipitation evidence used in manual assertion def: "A type of co-immunoprecipitation evidence that is used in a manual assertion." [ECO:RCT] synonym: "IPI: co-immunoprecipitation" BROAD [] is_a: ECO:0000070 ! co-immunoprecipitation evidence is_a: ECO:0000353 {is_inferred="true"} ! physical interaction evidence used in manual assertion is_a: ECO:0005644 {is_inferred="true"} ! immunoprecipitation evidence used in manual assertion intersection_of: ECO:0000070 ! co-immunoprecipitation evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2016-01-13T11:32:26Z [Term] id: ECO:0006031 name: immunolocalization evidence used in manual assertion def: "A type of immunolocalization evidence that is used in a manual assertion." [ECO:RCT] synonym: "IDA: immunolocalization" BROAD [] is_a: ECO:0000087 ! immunolocalization evidence is_a: ECO:0001232 {is_inferred="true"} ! microscopy evidence used in manual assertion intersection_of: ECO:0000087 ! immunolocalization evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-01-23T07:54:37Z [Term] id: ECO:0006032 name: optogenetic evidence def: "A type of experimental phenotypic evidence arising from experiment in which neuronal activity is manipulated using genetically encoded, optically activated neuronal actuators." [GOC:DOS, PMID:17035522] synonym: "optogenetic actuator evidence" EXACT [] is_a: ECO:0000059 ! experimental phenotypic evidence created_by: rctauber creation_date: 2017-01-23T11:58:48Z [Term] id: ECO:0006033 name: optogenetic evidence used in manual assertion def: "A type of optogenetic evidence that is used in a manual assertion." [ECO:RCT] synonym: "optogenetic actuator evidence" BROAD [] is_a: ECO:0006032 ! optogenetic evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0006032 ! optogenetic evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-01-23T11:58:48Z [Term] id: ECO:0006034 name: fluorescent sensor evidence def: "A type of fluorescence evidence that is based on direct, quantitative measurement of some cellular property using a fluorescent sensor." [GOC:DOS] comment: Examples include sensors for ion concentration and potential difference across a membrane. is_a: ECO:0001115 ! fluorescence evidence created_by: rctauber creation_date: 2017-01-23T11:58:48Z [Term] id: ECO:0006035 name: fluorescent sensor evidence used in manual assertion def: "A type of fluorescent sensor evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001249 {is_inferred="true"} ! fluorescence evidence used in manual assertion is_a: ECO:0006034 ! fluorescent sensor evidence intersection_of: ECO:0006034 ! fluorescent sensor evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-01-23T11:58:48Z [Term] id: ECO:0006036 name: genetically encoded fluorescent sensor evidence def: "A type of fluorescent sensor evidence that is based on direct, quantitative measurement of some cellular property using a genetically encoded fluorescent sensor." [GOC:DOS] synonym: "optogenetic sensor evidence" EXACT [] is_a: ECO:0006034 ! fluorescent sensor evidence created_by: rctauber creation_date: 2017-01-23T11:58:48Z [Term] id: ECO:0006037 name: genetically encoded fluorescent sensor evidence used in manual assertion def: "A type of genetically encoded fluorescent sensor evidence that is used in a manual assertion." [ECO:RCT] synonym: "optogenetic sensor evidence" BROAD [] is_a: ECO:0006035 {is_inferred="true"} ! fluorescent sensor evidence used in manual assertion is_a: ECO:0006036 ! genetically encoded fluorescent sensor evidence intersection_of: ECO:0006036 ! genetically encoded fluorescent sensor evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-01-23T11:58:48Z [Term] id: ECO:0006038 name: genetically encoded fluorescent electrophysiology assay evidence def: "A type of fluorescent sensor evidence and electrophysiology assay evidence where the electrical properties of cells or tissues are studied using fluorescent sensors." [GOC:DOS] comment: Examples include genetically encoded sensors that detect potential difference across plasma membrane. synonym: "electrophysiology - optical assay evidence" EXACT [] is_a: ECO:0000164 ! electrophysiology assay evidence is_a: ECO:0006034 ! fluorescent sensor evidence created_by: rctauber creation_date: 2017-01-23T11:58:48Z [Term] id: ECO:0006039 name: genetically encoded fluorescent electrophysiology assay evidence used in manual assertion def: "A type of genetically encoded fluorescent electrophysiology assay evidence that is used in a manual assertion." [ECO:RCT] synonym: "electrophysiology - optical assay evidence" BROAD [] is_a: ECO:0006006 {is_inferred="true"} ! electrophysiology assay evidence used in manual assertion is_a: ECO:0006035 {is_inferred="true"} ! fluorescent sensor evidence used in manual assertion is_a: ECO:0006038 ! genetically encoded fluorescent electrophysiology assay evidence intersection_of: ECO:0006038 ! genetically encoded fluorescent electrophysiology assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-01-23T11:58:48Z [Term] id: ECO:0006040 name: genetically encoded fluorescent ion concentration sensor assay evidence def: "A type of genetically encoded fluorescent electrophysiology assay evidence that is based on direct, quantitative measurement of ion concentration using a genetically encoded fluorescent sensor." [GOC:DOS] comment: Examples include the genetically encoded calcium indicator GCaMP. is_a: ECO:0006038 ! genetically encoded fluorescent electrophysiology assay evidence created_by: rctauber creation_date: 2017-01-23T11:58:48Z [Term] id: ECO:0006041 name: genetically encoded fluorescent ion concentration sensor assay evidence used in manual assertion def: "A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0006039 {is_inferred="true"} ! genetically encoded fluorescent electrophysiology assay evidence used in manual assertion is_a: ECO:0006040 ! genetically encoded fluorescent ion concentration sensor assay evidence intersection_of: ECO:0006040 ! genetically encoded fluorescent ion concentration sensor assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-01-23T11:58:48Z [Term] id: ECO:0006042 name: cell fractionation evidence used in manual assertion def: "A type of cell fractionation evidence that is used in a manual assertion." [ECO:RCT] synonym: "IDA: cell fractionation" BROAD [] is_a: ECO:0000004 ! cell fractionation evidence is_a: ECO:0006005 {is_inferred="true"} ! fractionation evidence used in manual assertion intersection_of: ECO:0000004 ! cell fractionation evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-02-21T07:26:28Z [Term] id: ECO:0006043 name: extracellular recording evidence def: "A type of electrophysiology assay evidence resulting from the use of electrodes to measure in vivo electrical activity coming from adjacent neurons." [url:http\://www.nature.com/subjects/extracellular-recording] is_a: ECO:0000164 ! electrophysiology assay evidence relationship: IAO:0000136 GO:0001508 ! is about action potential relationship: OBI:0000312 OBI:0000454 ! is_specified_output_of extracellular electrophysiology recording created_by: rctauber creation_date: 2017-02-21T07:26:28Z [Term] id: ECO:0006044 name: extracellular recording evidence used in manual assertion def: "A type of extracellular recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0006006 {is_inferred="true"} ! electrophysiology assay evidence used in manual assertion is_a: ECO:0006043 ! extracellular recording evidence intersection_of: ECO:0006043 ! extracellular recording evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-02-21T07:26:28Z [Term] id: ECO:0006045 name: single-unit extracellular recording evidence def: "A type of extracellular recording evidence in which an extracellular microelectrode is used to measure the electrical activity of a single neuron." [doi:10.1385/0-89603-185-3\:1] is_a: ECO:0006043 ! extracellular recording evidence relationship: IAO:0000136 GO:0001508 ! is about action potential relationship: OBI:0000312 OBI:0002187 ! is_specified_output_of single-unit recording created_by: rctauber creation_date: 2017-02-21T07:26:28Z [Term] id: ECO:0006046 name: single-unit extracellular recording evidence used in manual assertion def: "A type of single-unit extracellular recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0006044 {is_inferred="true"} ! extracellular recording evidence used in manual assertion is_a: ECO:0006045 ! single-unit extracellular recording evidence intersection_of: ECO:0006045 ! single-unit extracellular recording evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-02-21T07:26:28Z [Term] id: ECO:0006047 name: field potential recording evidence def: "A type of extracellular recording evidence in which electrical activity is measured in either tissue or at a cellular level with microelectrodes." [ECO:RCT] synonym: "local field potential recording evidence" NARROW [] is_a: ECO:0006043 ! extracellular recording evidence relationship: IAO:0000136 GO:0001508 ! is about action potential relationship: OBI:0000312 OBI:0002189 ! is_specified_output_of local field potential recording created_by: rctauber creation_date: 2017-02-21T07:26:28Z [Term] id: ECO:0006048 name: field potential recording evidence used in manual assertion def: "A type of field potential recording evidence that is used in a manual assertion." [ECO:RCT] synonym: "local field potential recording evidence" RELATED [] is_a: ECO:0006044 {is_inferred="true"} ! extracellular recording evidence used in manual assertion is_a: ECO:0006047 ! field potential recording evidence intersection_of: ECO:0006047 ! field potential recording evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-02-21T07:26:28Z [Term] id: ECO:0006049 name: genetic transformation evidence used in manual assertion def: "A type of genetic transformation evidence that is used in a manual assertion" [ECO:RCT] is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion is_a: ECO:0005027 ! genetic transformation evidence intersection_of: ECO:0005027 ! genetic transformation evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 02-21-2017T18:98:58Z [Term] id: ECO:0006050 name: anti-sense experiment evidence used in manual assertion def: "A type of anti-sense experiment evidence that is used in a manual assertion." [ECO:RCT] synonym: "IMP: anti-sense experiments" BROAD [] is_a: ECO:0000018 ! anti-sense experiment evidence is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion intersection_of: ECO:0000018 ! anti-sense experiment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 02-21-2017T18:98:58Z [Term] id: ECO:0006051 name: morpholino experiment evidence used in manual assertion def: "A type of morpholino experiment evidence that is used in a manual assertion." [ECO:RCT] synonym: "anti-sense evidence" BROAD [] is_a: ECO:0000292 ! morpholino experiment evidence is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion intersection_of: ECO:0000292 ! morpholino experiment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 02-21-2017T18:98:58Z [Term] id: ECO:0006052 name: RNAi evidence used in manual assertion def: "A type of RNAi evidence that is used in a manual assertion." [ECO:RCT] synonym: "IMP: RNAi experiment" BROAD [] is_a: ECO:0000019 ! RNAi evidence is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion intersection_of: ECO:0000019 ! RNAi evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 02-21-2017T18:98:58Z [Term] id: ECO:0006053 name: pharmacological assay evidence def: "A type of experimental phenotypic evidence that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist." [GOC:DOS] is_a: ECO:0000059 ! experimental phenotypic evidence relationship: IAO:0000136 GO:0042221 ! is about response to chemical relationship: OBI:0000312 OBI:0000966 ! is_specified_output_of in live organism assay created_by: dosumis creation_date: 2017-03-07T08:51:02Z [Term] id: ECO:0006054 name: pharmacological assay evidence used in manual assertion def: "A type of experimental phenotypic evidence used in a manual assertion that arises from assaying the response of a cell, tissue, organ or organism following exposure to a receptor agonist or antagonist." [GOC:DOS] is_a: ECO:0006053 ! pharmacological assay evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0006053 ! pharmacological assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-03-07T08:51:02Z [Term] id: ECO:0006055 name: high throughput evidence def: "A type of evidence where data generation is automated with equipment to allow for assaying samples or molecules in parallel." [ECO:MCC] comment: Some relevant articles include: PMID: 23340846, doi:10.1038/nmeth0607-523 synonym: "high throughput cell biology evidence" NARROW [] synonym: "high throughput screening evidence" NARROW [] synonym: "high-throughput evidence" EXACT [] synonym: "HT evidence" EXACT [] is_a: ECO:0000000 ! evidence created_by: mchibucos creation_date: 2017-03-28T14:48:39Z [Term] id: ECO:0006056 name: high throughput evidence used in manual assertion def: "A type of evidence that is used in a manual assertion where data generation is automated with equipment to allow for assaying large numbers of samples or molecules in parallel." [ECO:RCT] synonym: "high throughput cell biology evidence" RELATED [] synonym: "high throughput screening evidence" RELATED [] synonym: "high-throughput evidence" BROAD [] synonym: "HT evidence" BROAD [] synonym: "HTP" EXACT [GOECO:HTP] synonym: "inferred from high throughput experiment" EXACT [GOECO:HTP] xref: GOECO:HTP "inferred from high throughput experiment" is_a: ECO:0000352 {is_inferred="true"} ! evidence used in manual assertion is_a: ECO:0006055 ! high throughput evidence intersection_of: ECO:0006055 ! high throughput evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-03-28T14:48:39Z [Term] id: ECO:0006057 name: high throughput evidence used in automatic assertion def: "A type of evidence that is used in an automatic assertion where data generation is automated with equipment to allow for assaying samples or molecules in parallel." [ECO:RCT] synonym: "high throughput cell biology evidence" RELATED [] synonym: "high throughput screening evidence" RELATED [] synonym: "high-throughput evidence" BROAD [] synonym: "HT evidence" BROAD [] is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion is_a: ECO:0006055 ! high throughput evidence intersection_of: ECO:0006055 ! high throughput evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2017-03-28T14:48:39Z [Term] id: ECO:0006058 name: high throughput cell biology evidence def: "A type of high throughput evidence where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel." [ECO:MCC] comment: HT methodologies may incorporate techniques from optics, chemistry, biology or image analysis (https://en.wikipedia.org/wiki/High_throughput_biology) synonym: "omics experiment" RELATED [] is_a: ECO:0006055 ! high throughput evidence created_by: mchibucos creation_date: 2017-03-28T14:48:39Z [Term] id: ECO:0006059 name: high throughput cell biology evidence used in manual assertion def: "A type of high throughput evidence used in a manual assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel." [ECO:RCT] synonym: "omics experiment" RELATED [] is_a: ECO:0006056 {is_inferred="true"} ! high throughput evidence used in manual assertion is_a: ECO:0006058 ! high throughput cell biology evidence intersection_of: ECO:0006058 ! high throughput cell biology evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-03-28T14:48:39Z [Term] id: ECO:0006060 name: high throughput cell biology evidence used in automatic assertion def: "A type of high throughput evidence used in an automatic assertion where a classical cell biology technique is automated with equipment to allow for assaying biomolecules in parallel." [ECO:RCT] synonym: "omics experiment" RELATED [] is_a: ECO:0006057 {is_inferred="true"} ! high throughput evidence used in automatic assertion is_a: ECO:0006058 ! high throughput cell biology evidence intersection_of: ECO:0006058 ! high throughput cell biology evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2017-03-28T14:48:39Z [Term] id: ECO:0006061 name: immunofluorescence wide-field microscopy evidence used in manual assertion def: "A type of wide-field fluorescence microscopy evidence used in a manual assertion where fluorescently tagged antibodies are imaged that are used to bind to their antigens." [ECO:SN, url:http\://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057135] synonym: "wide-field epifluorescence microscopy evidence" BROAD [] is_a: ECO:0005599 ! immunofluorescence wide-field microscopy evidence is_a: ECO:0005804 {is_inferred="true"} ! immunofluorescence evidence used in manual assertion is_a: ECO:0006062 {is_inferred="true"} ! wide-field fluorescence microscopy evidence used in manual assertion intersection_of: ECO:0005599 ! immunofluorescence wide-field microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-05-15T08:57:07Z [Term] id: ECO:0006062 name: wide-field fluorescence microscopy evidence used in manual assertion def: "A type of wide-field microscopy evidence that is used in a manual assertion where pure white and ultraviolet light are produced by a mercury lamp, passed through an optical filter (excitation filter), and directed to a sample via a dichroic mirror, followed by detection of the fluorescent light by a camera after it passes through an emission filter." [ECO:SN, url:http\://www.bristol.ac.uk/synaptic/research/techniques/widefield.html] is_a: ECO:0005590 {is_inferred="true"} ! wide-field microscopy evidence used in manual assertion is_a: ECO:0005598 ! wide-field fluorescence microscopy evidence intersection_of: ECO:0005598 ! wide-field fluorescence microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-05-15T09:01:19Z [Term] id: ECO:0006063 name: over expression analysis evidence used in manual assertion def: "A type of experimental phenotypic evidence that is used in a manual assertion where a gene and/or gene product is investigated in a transgenic organism that has been engineered to overexpress that gene product." [PMID:22419077] synonym: "IMP: analysis of overexpression/ectopic expression phenotype" RELATED [] is_a: ECO:0000120 ! over expression analysis evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0000120 ! over expression analysis evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-05-15T09:03:49Z [Term] id: ECO:0006064 name: cell-free assay evidence used in manual assertion def: "A type of cell-free assay evidence that is used in a manual assertion." [PMID:18453125] synonym: "in vitro assay evidence" BROAD [] is_a: ECO:0000183 ! cell-free assay evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000183 ! cell-free assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-05-15T09:08:17Z [Term] id: ECO:0006065 name: in vitro cell based assay evidence used in manual assertion comment: Use children of ECO:0001565 (cell-based assay evidence) in place of this term. is_obsolete: true created_by: rctauber creation_date: 2017-05-15T09:11:13Z [Term] id: ECO:0006066 name: fluorescence recovery after photobleaching evidence def: "A type of fluorescence evidence where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse." [PMID:26314367] comment: FRAP is a fluorescence microscopy-based technique. {xref="PMID:26314367"} synonym: "FRAP evidence" EXACT [] is_a: ECO:0001115 ! fluorescence evidence relationship: IAO:0000136 GO:0033036 ! is about macromolecule localization relationship: OBI:0000312 CHMO:0000087 ! is_specified_output_of fluorescence microscopy property_value: IAO:0000234 "dosumis" xsd:string created_by: rctauber creation_date: 2017-05-16T10:55:40Z [Term] id: ECO:0006067 name: fluorescence recovery after photobleaching evidence used in manual assertion def: "A type of fluorescence evidence that is used in a manual assertion where quantitative information on the diffusion properties of a sample is produced from the measurement of diffusion of fluorescent probes over time into an area that has been photobleached by a high-intensity laser pulse." [] synonym: "FRAP evidence" BROAD [] is_a: ECO:0001249 {is_inferred="true"} ! fluorescence evidence used in manual assertion is_a: ECO:0006066 ! fluorescence recovery after photobleaching evidence intersection_of: ECO:0006066 ! fluorescence recovery after photobleaching evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-05-16T10:55:40Z [Term] id: ECO:0006068 name: RNA-seq evidence used in manual assertion def: "A type of high throughput nucleotide sequencing assay evidence used in a manual assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules." [ECO:MCC] synonym: "RNA sequencing|differential gene expression evidence from RNA-seq experiment" RELATED [] synonym: "whole transcriptome shotgun sequencing" BROAD [] synonym: "WTSS evidence" BROAD [] is_a: ECO:0000291 {is_inferred="true"} ! transcript expression evidence used in manual assertion is_a: ECO:0000295 ! RNA-seq evidence intersection_of: ECO:0000295 ! RNA-seq evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-06-28T10:37:02Z [Term] id: ECO:0006069 name: RNA-seq evidence used in automatic assertion def: "A type of high throughput nucleotide sequencing assay evidence used in an automatic assertion based on high-throughput (HT) sequencing of fragmented cDNA molecules." [ECO:MCC] synonym: "RNA sequencing|differential gene expression evidence from RNA-seq experiment" RELATED [] synonym: "whole transcriptome shotgun sequencing" BROAD [] synonym: "WTSS evidence" BROAD [] is_a: ECO:0000295 ! RNA-seq evidence is_a: ECO:0007303 {is_inferred="true"} ! transcript expression evidence used in automatic assertion intersection_of: ECO:0000295 ! RNA-seq evidence intersection_of: used_in ECO:0000203 ! automatic assertion relationship: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2017-06-28T10:37:02Z [Term] id: ECO:0006070 name: immuno-labelling electron microscopy evidence def: "A type of electron microscopy evidence resulting from the use of antibodies to identify the localization of antigens in cells and tissues." [PMID:25151300] synonym: "immunolabelling electron microscopy evidence" EXACT [] is_a: ECO:0005033 ! electron microscopy evidence relationship: IAO:0000136 GO:0033036 ! is about macromolecule localization property_value: IAO:0000234 "dosumis" xsd:string created_by: rctauber creation_date: 2017-07-05T09:59:10Z [Term] id: ECO:0006071 name: immuno-labelling electron microscopy evidence used in manual assertion def: "A type of electron microscopy evidence used in a manual assertion resulting from the use of antibodies to identify the localization of antigens in cells and tissues." [PMID:25151300] synonym: "immunolabelling electron microscopy evidence" BROAD [] is_a: ECO:0006003 {is_inferred="true"} ! electron microscopy evidence used in manual assertion is_a: ECO:0006070 ! immuno-labelling electron microscopy evidence intersection_of: ECO:0006070 ! immuno-labelling electron microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000119 PMID:25151300 xsd:string property_value: IAO:0000234 "dosumis" xsd:string created_by: rctauber creation_date: 2017-07-05T09:59:10Z [Term] id: ECO:0006072 name: immunofluorescence super resolution microscopy evidence def: "A type of super-resolution microscopy evidence resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue." [PMID:19245833] is_a: ECO:0005578 ! super-resolution microscopy evidence property_value: IAO:0000234 "dosumis" xsd:string created_by: rctauber creation_date: 2017-07-05T09:59:10Z [Term] id: ECO:0006073 name: immunofluorescence super resolution microscopy evidence used in manual assertion def: "A type of super-resolution microscopy evidence used in a manual assertion resulting from the use of fluorescently-tagged antibodies to identify the localization of antigens in cells and tissue." [PMID:19245833] is_a: ECO:0006004 {is_inferred="true"} ! super-resolution microscopy evidence used in manual assertion is_a: ECO:0006072 ! immunofluorescence super resolution microscopy evidence intersection_of: ECO:0006072 ! immunofluorescence super resolution microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "dosumis" xsd:string created_by: rctauber creation_date: 2017-07-05T09:59:10Z [Term] id: ECO:0006074 name: co-purification evidence used in manual assertion def: "A type of physical interaction evidence that is used in manual assertion where a cellular component subunit is isolated as part of purification of its larger complex." [TAIR:TED] synonym: "IPI: co-purification" BROAD [] is_a: ECO:0000022 ! co-purification evidence is_a: ECO:0000353 {is_inferred="true"} ! physical interaction evidence used in manual assertion intersection_of: ECO:0000022 ! co-purification evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:19 [Term] id: ECO:0006075 name: affinity evidence used in manual assertion def: "A type of physical interaction evidence that is used in manual assertion that depends on the strength of the interaction between two entities." [ECO:MCC] synonym: "ligand binding evidence" RELATED [] is_a: ECO:0000023 ! affinity evidence is_a: ECO:0000353 {is_inferred="true"} ! physical interaction evidence used in manual assertion intersection_of: ECO:0000023 ! affinity evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:20 [Term] id: ECO:0006076 name: protein binding evidence used in manual assertion def: "A type of affinity evidence that is used in manual assertion resulting from the binding of a molecule to a protein or protein complex." [GO:0005515] is_a: ECO:0000024 ! protein binding evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0006075 {is_inferred="true"} ! affinity evidence used in manual assertion intersection_of: ECO:0000024 ! protein binding evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:21 [Term] id: ECO:0006077 name: hybrid interaction evidence used in manual assertion def: "A type of affinity evidence that is used in manual assertion where proteins of interest (bait and prey) are covalently linked to incomplete fragments of a third protein (reporter) and expressed in vivo, at which time interaction between bait and prey proteins brings reporter fragments in close enough proximity to allow them to reform and become a functional reporter protein." [ECO:MCC] is_a: ECO:0000025 ! hybrid interaction evidence is_a: ECO:0006075 {is_inferred="true"} ! affinity evidence used in manual assertion intersection_of: ECO:0000025 ! hybrid interaction evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:22 [Term] id: ECO:0006078 name: immunological assay evidence used in manual assertion def: "A type of affinity evidence that is used in manual assertion resulting from quantitation of the analyte which depends on the reaction of an antigen (analyte) and an antibody." [ERO:0001362] is_a: ECO:0000040 ! immunological assay evidence is_a: ECO:0006075 {is_inferred="true"} ! affinity evidence used in manual assertion intersection_of: ECO:0000040 ! immunological assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:23 [Term] id: ECO:0006079 name: yeast one-hybrid evidence used in manual assertion def: "A type of hybrid interaction evidence that is used in manual assertion that is based on a protein-DNA complementation assay where a single promoter acts as bait and is screened against a library of prey transcription factors." [ECO:MCC] synonym: "IPI: yeast one-hybrid assay" BROAD [] is_a: ECO:0000066 ! yeast one-hybrid evidence is_a: ECO:0006077 {is_inferred="true"} ! hybrid interaction evidence used in manual assertion intersection_of: ECO:0000066 ! yeast one-hybrid evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:24 [Term] id: ECO:0006080 name: split-ubiquitin assay evidence used in manual assertion def: "A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interaction between a bait and prey protein by in vivo reconstitution of split-ubiquitin (when bait and prey interact) and release of a reporter protein." [PMID:15064465] synonym: "IPI: split-ubiquitin assay" BROAD [] is_a: ECO:0000074 ! split-ubiquitin assay evidence is_a: ECO:0000353 {is_inferred="true"} ! physical interaction evidence used in manual assertion intersection_of: ECO:0000074 ! split-ubiquitin assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:25 [Term] id: ECO:0006081 name: far-Western blotting evidence used in manual assertion def: "A type of physical interaction evidence that is used in a manual assertion that is based on detection of protein-protein interactions by separation of target proteins by SDS-PAGE which are blotted to a membrane, followed by denaturation and renaturation, probing with purified bait proteins, and detection of the target-bait complexes." [PMID:18079728] synonym: "IPI: far-Western analysis" BROAD [] is_a: ECO:0000076 ! far-Western blotting evidence is_a: ECO:0000353 {is_inferred="true"} ! physical interaction evidence used in manual assertion intersection_of: ECO:0000076 ! far-Western blotting evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:26 [Term] id: ECO:0006082 name: affinity chromatography evidence used in manual assertion def: "A type of affinity evidence that is used in a manual assertion that results from separation of biochemical mixtures by selective binding of a compound to an immobilized compound on a polymeric matrix, subsequent removal of unattached components, and then displacement of the bond compound." [ECO:MCC] synonym: "IDA: affinity chromatography" BROAD [] is_a: ECO:0000079 ! affinity chromatography evidence is_a: ECO:0006075 {is_inferred="true"} ! affinity evidence used in manual assertion intersection_of: ECO:0000079 ! affinity chromatography evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:27 [Term] id: ECO:0006083 name: nucleic acid binding evidence used in manual assertion def: "A type of affinity evidence that is used in a manual assertion resulting from the binding of a molecule to a nucleic acid." [GO:0003676] is_a: ECO:0000136 ! nucleic acid binding evidence is_a: ECO:0006075 {is_inferred="true"} ! affinity evidence used in manual assertion intersection_of: ECO:0000136 ! nucleic acid binding evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:28 [Term] id: ECO:0006084 name: ribohomopolymer binding assay evidence used in manual assertion def: "A type of nucleic acid binding evidence that is used in a manual assertion resulting from an enzyme displaying binding activity to specific ribohomopolymer." [PMC:102612] synonym: "IDA: ribohomopolymer binding assay" BROAD [] is_a: ECO:0000138 ! ribohomopolymer binding assay evidence is_a: ECO:0006083 {is_inferred="true"} ! nucleic acid binding evidence used in manual assertion intersection_of: ECO:0000138 ! ribohomopolymer binding assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:29 [Term] id: ECO:0006085 name: protein:ion binding evidence used in manual assertion def: "A type of protein binding evidence that is used in a manual assertion resulting from a metal ion binding to a protein at a specific binding site." [PMID:2377604] is_a: ECO:0000142 ! protein:ion binding evidence is_a: ECO:0006076 {is_inferred="true"} ! protein binding evidence used in manual assertion intersection_of: ECO:0000142 ! protein:ion binding evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:30 [Term] id: ECO:0006086 name: Southwestern blot evidence used in manual assertion def: "A type of nucleic acid binding evidence that is used in a manual assertion in which DNA-protein binding is detected using labeled DNA as probes, hybridized to electrophoretically separated proteins." [ECO:RCT] synonym: "IDA: Southwestern analysis" BROAD [] is_a: ECO:0000144 ! Southwestern blot evidence is_a: ECO:0006083 {is_inferred="true"} ! nucleic acid binding evidence used in manual assertion intersection_of: ECO:0000144 ! Southwestern blot evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:31 [Term] id: ECO:0006087 name: Northwestern blot evidence used in manual assertion def: "A type of nucleic acid binding evidence that is used in a manual assertion in which RNA-protein binding is detected using labeled RNA as probes, hybridized to electrophoretically separated proteins." [ECO:RCT] synonym: "IDA: Northwestern analysis" BROAD [] is_a: ECO:0000146 ! Northwestern blot evidence is_a: ECO:0006083 {is_inferred="true"} ! nucleic acid binding evidence used in manual assertion intersection_of: ECO:0000146 ! Northwestern blot evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:32 [Term] id: ECO:0006088 name: systematic evolution of ligands by exponential amplification evidence used in manual assertion def: "A type of evidence that is used in a manual assertion arising from a physical interaction analysis where a combinatorial chemistry technique is used to identify oligonucleotides that bind to a target ligand." [ECO:MCC] synonym: "in vitro evolution evidence" RELATED [] synonym: "in vitro selection evidence" BROAD [] synonym: "SELEX evidence" BROAD [] is_a: ECO:0000293 ! systematic evolution of ligands by exponential amplification evidence is_a: ECO:0000353 {is_inferred="true"} ! physical interaction evidence used in manual assertion intersection_of: ECO:0000293 ! systematic evolution of ligands by exponential amplification evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:33 [Term] id: ECO:0006089 name: bacterial one-hybrid evidence used in manual assertion def: "A type of hybrid interaction evidence that is used in a manual assertion that uses bacterial transformation with two plasmids to assess in vivo binding of a DNA-binding domain (bait) and DNA target site (prey)." [ECO:MCC] synonym: "B1H evidence" BROAD [] is_a: ECO:0000294 ! bacterial one-hybrid evidence is_a: ECO:0006077 {is_inferred="true"} ! hybrid interaction evidence used in manual assertion intersection_of: ECO:0000294 ! bacterial one-hybrid evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:34 [Term] id: ECO:0006090 name: protein-binding microarray evidence used in manual assertion def: "A type of oligonucleotide microarray evidence that is used in a manual assertion that detects binding of a tagged protein to an array of oligonucleotide probes representing potential binding sites." [PMID:22146299] synonym: "PBM evidence" BROAD [] is_a: ECO:0001601 ! protein-binding microarray evidence is_a: ECO:0006076 {is_inferred="true"} ! protein binding evidence used in manual assertion is_a: ECO:0006083 {is_inferred="true"} ! nucleic acid binding evidence used in manual assertion intersection_of: ECO:0001601 ! protein-binding microarray evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:35 [Term] id: ECO:0006091 name: functional complementation evidence used in manual assertion def: "A type of genetic interaction evidence that is used in a manual assertion where a wild-type copy of the gene in question is inserted into a mutant cell to see if it restores the wild-type phenotype in the mutant background." [PMID:27403640] synonym: "IGI: functional complementation" BROAD [] is_a: ECO:0000012 ! functional complementation evidence is_a: ECO:0000316 {is_inferred="true"} ! genetic interaction evidence used in manual assertion intersection_of: ECO:0000012 ! functional complementation evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:36 [Term] id: ECO:0006092 name: transgenic rescue experiment evidence used in manual assertion def: "A type of functional complementation evidence that is used in a manual assertion that is used in manual assertion resulting from the introduction of a transgene to prevent, or \"rescue\" an organism from a condition." [url:http\://www.nature.com/gt/journal/v11/n15/full/3302282a.html] is_a: ECO:0000013 ! transgenic rescue experiment evidence is_a: ECO:0006091 {is_inferred="true"} ! functional complementation evidence used in manual assertion intersection_of: ECO:0000013 ! transgenic rescue experiment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:37 [Term] id: ECO:0006093 name: transient rescue experiment evidence used in manual assertion def: "A type of transient rescue experiment evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000038 ! transient rescue experiment evidence is_a: ECO:0006091 {is_inferred="true"} ! functional complementation evidence used in manual assertion intersection_of: ECO:0000038 ! transient rescue experiment evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:38 [Term] id: ECO:0006094 name: suppressor/enhancer interaction evidence used in manual assertion def: "A type of genetic interaction evidence that is used in a manual assertion resulting from a second mutation that either suppresses or enhances the phenotype expressed from an original mutation." [url:http\://www.wormbook.org/chapters/www\:geneticsuppression/geneticsuppression.html] synonym: "IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)" BROAD [] is_a: ECO:0000052 ! suppressor/enhancer interaction evidence is_a: ECO:0000316 {is_inferred="true"} ! genetic interaction evidence used in manual assertion intersection_of: ECO:0000052 ! suppressor/enhancer interaction evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:39 [Term] id: ECO:0006095 name: double mutant phenotype evidence used in manual assertion def: "A type of genetic interaction evidence that is used in a manual assertion that is based on the phenotypic outcome of two mutations in unrelated genetic loci." [ECO:RCT] synonym: "IGI: double mutant analysis" BROAD [] is_a: ECO:0000054 ! double mutant phenotype evidence is_a: ECO:0000316 {is_inferred="true"} ! genetic interaction evidence used in manual assertion intersection_of: ECO:0000054 ! double mutant phenotype evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:40 [Term] id: ECO:0006096 name: epistatic interaction evidence used in manual assertion def: "A type of genetic interaction evidence that is used in a manual assertion that is based on the suppression of one allelic effect by an allele at another genetic locus." [PMID:18852697] synonym: "IGI: epistatic interactions" BROAD [] is_a: ECO:0000056 ! epistatic interaction evidence is_a: ECO:0000316 {is_inferred="true"} ! genetic interaction evidence used in manual assertion intersection_of: ECO:0000056 ! epistatic interaction evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:41 [Term] id: ECO:0006097 name: functional complementation in heterologous system evidence used in manual assertion def: "A type of functional complementation evidence that is used in a manual assertion that is based on the insertion of a wild-type copy of a gene into a heterologous organism, with the mutation occurring in a homologous gene." [TAIR:TED] synonym: "IGI: functional complementation in heterologous system" BROAD [] is_a: ECO:0000064 ! functional complementation in heterologous system evidence is_a: ECO:0006091 {is_inferred="true"} ! functional complementation evidence used in manual assertion intersection_of: ECO:0000064 ! functional complementation in heterologous system evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-09-14T09:19:42 [Term] id: ECO:0006098 name: temperature-sensitive mutant phenotype evidence def: "A type of mutant phenotype evidence based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures." [GOC:PG, PMID:19596904] synonym: "Ts mutation evidence" EXACT [] is_a: ECO:0000015 ! mutant phenotype evidence property_value: IAO:0000234 "pgaudet" xsd:string created_by: rctauber creation_date: 2017-09-18T07:58:28 [Term] id: ECO:0006099 name: temperature-sensitive mutant phenotype evidence used in manual assertion def: "A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation that allows normal function of the organism at low temperatures, but altered function at higher temperatures." [GOC:PG, PMID:19596904] synonym: "Ts mutation evidence" BROAD [] is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion is_a: ECO:0006098 ! temperature-sensitive mutant phenotype evidence intersection_of: ECO:0006098 ! temperature-sensitive mutant phenotype evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "pgaudet" xsd:string created_by: rctauber creation_date: 2017-09-18T07:58:28 [Term] id: ECO:0006100 name: recessive mutant phenotype evidence def: "A type of mutant phenotype evidence based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself." [GOC:PG, NBK:21578] is_a: ECO:0000015 ! mutant phenotype evidence property_value: IAO:0000234 "pgaudet" xsd:string created_by: rctauber creation_date: 2017-09-18T07:58:28 [Term] id: ECO:0006101 name: recessive mutant phenotype evidence used in manual assertion def: "A type of mutant phenotype evidence that is used in a manual assertion based on the analysis of a mutation which, in diploid organisms, must be present in both alleles for a phenotype to manifest itself." [GOC:PG, NBK:21578] is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion is_a: ECO:0006100 ! recessive mutant phenotype evidence intersection_of: ECO:0006100 ! recessive mutant phenotype evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "pgaudet" xsd:string created_by: rctauber creation_date: 2017-09-18T07:58:28 [Term] id: ECO:0007000 name: high throughput mutant phenotype evidence def: "A type of high throughput evidence derived from high throughput analysis of differences in alleles of a corresponding gene." [GO:IMP] is_a: ECO:0000015 ! mutant phenotype evidence is_a: ECO:0006055 ! high throughput evidence property_value: IAO:0000234 "GOC" xsd:string created_by: rctauber creation_date: 2017-10–05T07:39:47Z [Term] id: ECO:0007001 name: high throughput mutant phenotype evidence used in manual assertion def: "A type of high throughput evidence that is used in a manual assertion derived from high throughput analysis of differences in alleles of a corresponding gene." [GO:IMP] comment: When using the HMP evidence code, the guidelines for IMP should be adhered to (http://geneontology.org/page/imp-inferred-mutant-phenotype) synonym: "HMP" EXACT [GOECO:HMP] synonym: "inferred from high throughput mutant phenotype" EXACT [GOECO:HMP] xref: GOECO:HMP "inferred from high throughput mutant phenotype" is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion is_a: ECO:0006056 {is_inferred="true"} ! high throughput evidence used in manual assertion is_a: ECO:0007000 ! high throughput mutant phenotype evidence intersection_of: ECO:0007000 ! high throughput mutant phenotype evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "GOC" xsd:string created_by: rctauber creation_date: 2017-10–05T07:39:47Z [Term] id: ECO:0007002 name: high throughput genetic interaction evidence def: "A type of high throughput evidence derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products." [PMID:11822023] is_a: ECO:0000011 ! genetic interaction evidence is_a: ECO:0006055 ! high throughput evidence property_value: IAO:0000234 "GOC" xsd:string created_by: rctauber creation_date: 2017-10–05T07:39:47Z [Term] id: ECO:0007003 name: high throughput genetic interaction evidence used in manual assertion def: "A type of high throughput evidence that is used in a manual assertion derived from the high throughput analysis of the effect that a given gene has on another gene or genes, and products." [PMID:11822023] comment: When using the HGI evidence code, the guidelines for IGI should be adhered to (http://geneontology.org/page/igi-inferred-genetic-interaction) synonym: "HGI" EXACT [GOECO:HGI] synonym: "inferred from high throughput genetic interaction" EXACT [GOECO:HGI] xref: GOECO:HGI "inferred from high throughput genetic interaction" is_a: ECO:0000316 {is_inferred="true"} ! genetic interaction evidence used in manual assertion is_a: ECO:0006056 {is_inferred="true"} ! high throughput evidence used in manual assertion is_a: ECO:0007002 ! high throughput genetic interaction evidence intersection_of: ECO:0007002 ! high throughput genetic interaction evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "GOC" xsd:string created_by: rctauber creation_date: 2017-10–05T07:39:47Z [Term] id: ECO:0007004 name: high throughput direct assay evidence def: "A type of high throughput evidence derived from the high throughput direct measurement of some aspect of a biological feature." [ECO:MCC] is_a: ECO:0000002 ! direct assay evidence is_a: ECO:0006055 ! high throughput evidence property_value: IAO:0000234 "GOC" xsd:string created_by: rctauber creation_date: 2017-10–05T07:39:47Z [Term] id: ECO:0007005 name: high throughput direct assay evidence used in manual assertion def: "A type of high throughput evidence that is used in a manual assertion derived from the high throughput direct measurement of some aspect of a biological feature." [ECO:MCC] comment: When using the HDA evidence code, the guidelines for IDA should be adhered to (http://geneontology.org/page/ida-inferred-direct-assay) synonym: "HDA" EXACT [GOECO:HDA] synonym: "inferred from high throughput direct assay" EXACT [GOECO:HDA] xref: GOECO:HDA "inferred from high throughput direct assay" is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0006056 {is_inferred="true"} ! high throughput evidence used in manual assertion is_a: ECO:0007004 ! high throughput direct assay evidence intersection_of: ECO:0007004 ! high throughput direct assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "GOC" xsd:string created_by: rctauber creation_date: 2017-10–05T07:39:47Z [Term] id: ECO:0007006 name: high throughput expression pattern evidence def: "A type of high throughput evidence derived from the high throughput characterization of gene expression." [GO:IEP] is_a: ECO:0000008 ! expression pattern evidence is_a: ECO:0006055 ! high throughput evidence property_value: IAO:0000234 "GOC" xsd:string created_by: rctauber creation_date: 2017-10–05T07:39:47Z [Term] id: ECO:0007007 name: high throughput expression pattern evidence used in manual assertion def: "A type of high throughput evidence that is used in a manual assertion derived from the high throughput characterization of gene expression." [GO:IEP] comment: When using the HEP evidence code, the guidelines for EXP should be adhered to (http://geneontology.org/page/iep-inferred-expression-pattern) synonym: "HEP" EXACT [GOECO:HEP] synonym: "inferred from high throughput expression pattern" EXACT [GOECO:HEP] xref: GOECO:HEP "inferred from high throughput expression pattern" is_a: ECO:0000270 {is_inferred="true"} ! expression evidence used in manual assertion is_a: ECO:0006056 {is_inferred="true"} ! high throughput evidence used in manual assertion is_a: ECO:0007006 ! high throughput expression pattern evidence intersection_of: ECO:0007006 ! high throughput expression pattern evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "GOC" xsd:string created_by: rctauber creation_date: 2017-10–05T07:39:47Z [Term] id: ECO:0007008 name: radioligand binding assay evidence def: "A type of protein binding evidence in which radioactive ligands are used to measure receptor-ligand interactions, such as in determining selectivity for a particular ligand." [PMID:27471749] synonym: "competitive binding assay evidence" NARROW [] synonym: "radioactive ligand binding assay evidence" EXACT [] synonym: "radiometric ligand-binding assay evidence" EXACT [] is_a: ECO:0000024 ! protein binding evidence property_value: IAO:0000234 "fjungo" xsd:string created_by: rctauber creation_date: 2017-12-15T10:46:19Z [Term] id: ECO:0007009 name: radioligand binding assay evidence used in manual assertion def: "A type of radioligand binding assay evidence that is used in a manual assertion." [ECO:RCT] synonym: "competitive binding assay evidence" RELATED [] synonym: "radioactive ligand binding assay evidence" BROAD [] is_a: ECO:0006076 {is_inferred="true"} ! protein binding evidence used in manual assertion is_a: ECO:0007008 ! radioligand binding assay evidence intersection_of: ECO:0007008 ! radioligand binding assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2017-12-15T10:48:44Z [Term] id: ECO:0007010 name: author inference def: "A type of inferential evidence resulting from a conclusion drawn by the author of the publication." [ECO:RCT] is_a: ECO:0000361 ! inferential evidence created_by: rctauber creation_date: 2018-02-08T09:11:07Z [Term] id: ECO:0007011 name: combinatorial evidence from author knowledge and experimental evidence def: "A type of combinatorial evidence in which the author draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments." [ECO:RCT] is_a: ECO:0000006 {is_inferred="true"} ! experimental evidence is_a: ECO:0000212 ! combinatorial evidence is_a: ECO:0007010 {is_inferred="true"} ! author inference intersection_of: ECO:0000006 ! experimental evidence intersection_of: ECO:0007010 ! author inference property_value: IAO:0000234 "sbello" xsd:string created_by: rctauber creation_date: 2018-02-15T11:17:11Z [Term] id: ECO:0007012 name: combinatorial evidence from curator knowledge and experimental evidence def: "A type of combinatorial evidence in which the curator draws a conclusion based on a combination of prior scientific background knowledge and evidence from one or more experiments." [ECO:RCT] is_a: ECO:0000006 {is_inferred="true"} ! experimental evidence is_a: ECO:0000205 {is_inferred="true"} ! curator inference is_a: ECO:0000212 ! combinatorial evidence intersection_of: ECO:0000006 ! experimental evidence intersection_of: ECO:0000205 ! curator inference property_value: IAO:0000234 "ZFIN" xsd:string created_by: rctauber creation_date: 2018-02-15T11:17:11Z [Term] id: ECO:0007013 name: combinatorial evidence from author knowledge and experimental evidence used in manual assertion def: "A type of combinatorial evidence from author knowledge and experimental evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000244 {is_inferred="true"} ! combinatorial evidence used in manual assertion is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0007011 ! combinatorial evidence from author knowledge and experimental evidence intersection_of: ECO:0007011 ! combinatorial evidence from author knowledge and experimental evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-02-15T11:22:10Z [Term] id: ECO:0007014 name: combinatorial evidence from curator knowledge and experimental evidence used in manual assertion def: "A type of combinatorial evidence from curator knowledge and experimental evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000244 {is_inferred="true"} ! combinatorial evidence used in manual assertion is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0000305 {is_inferred="true"} ! curator inference used in manual assertion is_a: ECO:0007012 ! combinatorial evidence from curator knowledge and experimental evidence intersection_of: ECO:0007012 ! combinatorial evidence from curator knowledge and experimental evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-02-15T11:22:10Z [Term] id: ECO:0007015 name: voltammetry evidence def: "A type of substance quantification evidence where an electrical gradient potential is applied to analyze an analyte of interest, resulting in a measurement amount of electrical current across the potential range applied." [ECO:JBM, PMID:28127962] is_a: ECO:0000335 ! substance quantification evidence property_value: IAO:0000234 "SynGO" xsd:string created_by: rctauber creation_date: 2018-02-28T12:11:00Z [Term] id: ECO:0007016 name: voltammetry evidence used in manual assertion def: "A type of voltammetry evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0007015 ! voltammetry evidence intersection_of: ECO:0007015 ! voltammetry evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-02-28T12:12:34Z [Term] id: ECO:0007017 name: photoconversion evidence def: "A type of fluorescence evidence where a molecule tagged with a fluorescent protein is exposed to ultraviolet or blue light to shift the spectral emission properties for visualization." [ECO:RCT, PMID:28574633] is_a: ECO:0001115 ! fluorescence evidence property_value: IAO:0000234 "SynGO" xsd:string created_by: rctauber creation_date: 2018-03-02T09:01:00Z [Term] id: ECO:0007018 name: photoconversion evidence used in manual assertion def: "A type of photoconversion evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001249 {is_inferred="true"} ! fluorescence evidence used in manual assertion is_a: ECO:0007017 ! photoconversion evidence intersection_of: ECO:0007017 ! photoconversion evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-03-02T09:05:04Z [Term] id: ECO:0007019 name: agglutination test evidence def: "A type of immunological assay evidence that involves observation of visible clumping of antibody and antigen into a complex." [URL:https\://www.ncbi.nlm.nih.gov/pmc/articles/PMC380037/] synonym: "agglutination assay evidence" EXACT [] is_a: ECO:0000040 ! immunological assay evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007020 name: agglutination test evidence used in manual assertion def: "A type of agglutination test evidence that is used in a manual assertion." [ECO:RCT] synonym: "agglutination assay evidence" BROAD [] is_a: ECO:0006078 {is_inferred="true"} ! immunological assay evidence used in manual assertion is_a: ECO:0007019 ! agglutination test evidence intersection_of: ECO:0007019 ! agglutination test evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007021 name: slide agglutination test evidence def: "A type of agglutination test evidence that involves observaiton of visible clumping of antibody and antigen into a complex on a slide." [URL:https\://www.ncbi.nlm.nih.gov/pmc/articles/PMC380037/] is_a: ECO:0007019 ! agglutination test evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007022 name: slide agglutination test evidence used in manual assertion def: "A type of slide agglutination test evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0007020 {is_inferred="true"} ! agglutination test evidence used in manual assertion is_a: ECO:0007021 ! slide agglutination test evidence intersection_of: ECO:0007021 ! slide agglutination test evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007023 name: direct Coombs test evidence def: "A type of agglutination test evidence that results in detection of nonagglutinating antibodies or complement proteins on red blood cells in vivo." [URL:https\://courses.lumenlearning.com/microbiology/chapter/agglutination-assays/] synonym: "direct antihuman globulin test (DAT)" EXACT [] is_a: ECO:0007019 ! agglutination test evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007024 name: direct Coombs test evidence used in manual assertion def: "A type of direct Coombs test evidence that is used in a manual assertion." [ECO:RCT] synonym: "direct antihuman globulin test (DAT)" BROAD [] is_a: ECO:0007020 {is_inferred="true"} ! agglutination test evidence used in manual assertion is_a: ECO:0007023 ! direct Coombs test evidence intersection_of: ECO:0007023 ! direct Coombs test evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007025 name: indirect Coombs test evidence def: "A type of agglutination test evidence that results in screening of antibodies against red blood cell antigens (other than the A and B antigens) that are unbound in a patient's serum in vitro." [URL:https\://courses.lumenlearning.com/microbiology/chapter/agglutination-assays/] synonym: "indirect antiglobulin test (IAT)" EXACT [] is_a: ECO:0007019 ! agglutination test evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007026 name: indirect Coombs test evidence used in manual assertion def: "A type of indirect Coombs test evidence that is used in a manual assertion." [ECO:RCT] synonym: "indirect antiglobulin test (IAT)" BROAD [] is_a: ECO:0007020 {is_inferred="true"} ! agglutination test evidence used in manual assertion is_a: ECO:0007025 ! indirect Coombs test evidence intersection_of: ECO:0007025 ! indirect Coombs test evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007027 name: direct hemagglutination assay evidence def: "A type of agglutination test evidence where some bacteria and viruses cross-link red blood cells and clump together." [URL:https\://courses.lumenlearning.com/microbiology/chapter/agglutination-assays/] is_a: ECO:0007019 ! agglutination test evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007028 name: direct hemagglutination assay evidence used in manual assertion def: "A type of direct hemagglutination assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0007020 {is_inferred="true"} ! agglutination test evidence used in manual assertion is_a: ECO:0007027 ! direct hemagglutination assay evidence intersection_of: ECO:0007027 ! direct hemagglutination assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007029 name: viral hemagglutination inhibition assay evidence def: "A type of agglutination test evidence where antiviral antibodies in a patient's serum or in a lab-produced antiserum neutralize the virus and block it from agglutinating the red blood cells." [URL:https\://courses.lumenlearning.com/microbiology/chapter/agglutination-assays/] is_a: ECO:0007019 ! agglutination test evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007030 name: viral hemagglutination inhibition assay evidence used in manual assertion def: "A type of viral hemagglutination inhibition assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0007020 {is_inferred="true"} ! agglutination test evidence used in manual assertion is_a: ECO:0007029 ! viral hemagglutination inhibition assay evidence intersection_of: ECO:0007029 ! viral hemagglutination inhibition assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007031 name: compement fixation assay evidence def: "A type of immunological assay evidence that results in the detection of presence of specific antibodies in the patient's serum based on the use of complement, a biologically labile serum factor." [URL:http\://laboratoryinfo.com/complement-fixation-test/] is_a: ECO:0000040 ! immunological assay evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007032 name: compement fixation assay evidence used in manual assertion def: "A type of compement fixation assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0006078 {is_inferred="true"} ! immunological assay evidence used in manual assertion is_a: ECO:0007031 ! compement fixation assay evidence intersection_of: ECO:0007031 ! compement fixation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007033 name: neutralization test assay evidence def: "A type of immunogical assay evidence that results in detection of specific neutralizing antibodies in a sample." [PMID:24899440, url:http\://www.creative-biolabs.com/drug-discovery/therapeutics/neutralization-assay.htm?gclid=Cj0KEQjwqvvLBRDIt-D7q7iqiOcBEiQAxi68ERRz00a0x9sWSKSLDu7d5-kMi4AdiLNdUq1mXzePdywaArli8P8HAQ)] is_a: ECO:0000040 ! immunological assay evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007034 name: neutralization test assay evidence used in manual assertion def: "A type of neutralization test assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0006078 {is_inferred="true"} ! immunological assay evidence used in manual assertion is_a: ECO:0007033 ! neutralization test assay evidence intersection_of: ECO:0007033 ! neutralization test assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007035 name: copper transport assay evidence def: "A type of transport assay evidence where the rate of copper transport is estimated." [URL:https\://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689948/] is_a: ECO:0000134 ! transport assay evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007036 name: copper transport assay evidence used in manual assertion def: "A type of copper transport assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0007035 ! copper transport assay evidence intersection_of: ECO:0007035 ! copper transport assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007037 name: 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence def: "A type of staining evidence that involves the use of the redox dye 5-cyano-2,3-ditolyl tetrazolium chloride to evaluate the respiratory activity of cells." [PMID:1622256] synonym: "CTC staining" EXACT [] is_a: ECO:0005019 ! staining evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007038 name: 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence used in manual assertion def: "A type of 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence that is used in a manual assertion." [ECO:RCT] synonym: "CTC staining" BROAD [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0007037 ! 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence intersection_of: ECO:0007037 ! 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007039 name: plaque assay evidence def: "A type of cell growth assay evidence resulting in direct quantification of infectious virons and antiviral substances through the counting of discrete plaques (infectious units and cellular dead zones) in cell culture." [PMID:25407402] is_a: ECO:0001563 ! cell growth assay evidence relationship: IAO:0000136 GO:0009607 ! is about response to biotic stimulus relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007040 name: plaque assay evidence used in manual assertion def: "A type of plaque assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0007039 ! plaque assay evidence intersection_of: ECO:0007039 ! plaque assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007041 name: epifluorescence microscopy evidence def: "A type of microscopy evidence where the light source is mounted above the specimen and the excitation light passes through the microscope objective lens on its way toward the specimen." [URL:http\://www.rsc.org/publishing/journals/prospect/ontology.asp?id=CMO\:0001096|URL\:https\://www.ncbi.nlm.nih.gov/pmc/articles/PMC4713126/] is_a: ECO:0001098 ! microscopy evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007042 name: epifluorescence microscopy evidence used in manual assertion def: "A type of epifluorescence microscopy evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001232 {is_inferred="true"} ! microscopy evidence used in manual assertion is_a: ECO:0007041 ! epifluorescence microscopy evidence intersection_of: ECO:0007041 ! epifluorescence microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007043 name: transmission electron microscopy evidence def: "A type of electron microscopy evidence where a beam of electrons are transmitted through an ultra thin specimen forming an image which is magnified and focused onto an imaging device, such as a fluorescent screen, on a layer of photographic film, or to be detected by a sensor such as a CCD camera." [ERO:0000329|URL\:https\://www.ncbi.nlm.nih.gov/pmc/articles/PMC3907272/] synonym: "conventional transmission electron microscopy(CTEM)" EXACT [] synonym: "TEM" EXACT [] is_a: ECO:0005033 ! electron microscopy evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007044 name: transmission electron microscopy evidence used in manual assertion def: "A type of transmission electron microscopy evidence that is used in a manual assertion." [ECO:RCT] synonym: "conventional transmission electron microscopy(CTEM)" BROAD [] synonym: "TEM" BROAD [] is_a: ECO:0006003 {is_inferred="true"} ! electron microscopy evidence used in manual assertion is_a: ECO:0007043 ! transmission electron microscopy evidence intersection_of: ECO:0007043 ! transmission electron microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007045 name: scanning electron microscopy evidence def: "A type of electron microscopy evidence where a focused beam of high-energy electrons is used to generate a variety of signals at the surface of solid specimens." [URL:https\://serc.carleton.edu/research_education/geochemsheets/techniques/SEM.html] is_a: ECO:0005033 ! electron microscopy evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007046 name: scanning electron microscopy evidence used in manual assertion def: "A type of scanning electron microscopy evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0006003 {is_inferred="true"} ! electron microscopy evidence used in manual assertion is_a: ECO:0007045 ! scanning electron microscopy evidence intersection_of: ECO:0007045 ! scanning electron microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007047 name: time-lapsed microscopy evidence def: "A type of microscopy evidence where a serial images are taken at regular time points to capture the dynamics of what is being observed." [URL:https\://www.nature.com/subjects/time-lapse-imaging] is_a: ECO:0001098 ! microscopy evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007048 name: time-lapsed microscopy evidence used in manual assertion def: "A type of time-lapsed microscopy evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001232 {is_inferred="true"} ! microscopy evidence used in manual assertion is_a: ECO:0007047 ! time-lapsed microscopy evidence intersection_of: ECO:0007047 ! time-lapsed microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007049 name: phase contrast microscopy evidence def: "A type of microscopy evidence where a transparent specimen is illuminated with visible light and small phase shifts in the light passing through the specimen are used to produce an image." [CHMO:0000110] is_a: ECO:0001098 ! microscopy evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007050 name: phase contrast microscopy evidence used in manual assertion def: "A type of phase contrast microscopy evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001232 {is_inferred="true"} ! microscopy evidence used in manual assertion is_a: ECO:0007049 ! phase contrast microscopy evidence intersection_of: ECO:0007049 ! phase contrast microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007051 name: transmitted light brightfied mircoscopy evidence def: "A type of microscopy evidence where a sample is illuminated with transmitted white light from below and observed from above." [BAO:0000457] is_a: ECO:0001098 ! microscopy evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007052 name: transmitted light brightfied mircoscopy evidence used in manual assertion def: "A type of transmitted light brightfied mircoscopy evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001232 {is_inferred="true"} ! microscopy evidence used in manual assertion is_a: ECO:0007051 ! transmitted light brightfied mircoscopy evidence intersection_of: ECO:0007051 ! transmitted light brightfied mircoscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007053 name: koehler illumination microscopy evidence def: "A type of microscopy evidence that results in a bright image without glare and minimum heating of the specimen by employing both field and an aperture iris diaphragm for illumination." [URL:http\://www.gonda.ucla.edu/bri_core/kohler.htm] is_a: ECO:0001098 ! microscopy evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007054 name: koehler illumination microscopy evidence used in manual assertion def: "A type of koehler illumination microscopy evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001232 {is_inferred="true"} ! microscopy evidence used in manual assertion is_a: ECO:0007053 ! koehler illumination microscopy evidence intersection_of: ECO:0007053 ! koehler illumination microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007055 name: differential interference contrast microscopy evidence def: "A type of microscopy evidence that results in visualization of living cells and transparent specimens by taking advantage of differences in the light refraction of different parts of the specimen." [URL:http\://www.microscopemaster.com/differential-interference-contrast.html] synonym: "DIC microscopy" EXACT [] synonym: "NIC microscopy" EXACT [] synonym: "Nomarski interference contrast microscopy" EXACT [] synonym: "Nomarski microscopy" EXACT [] is_a: ECO:0001098 ! microscopy evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007056 name: differential interference contrast microscopy evidence used in manual assertion def: "A type of differential interference contrast microscopy evidence that is used in a manual assertion." [ECO:RCT] synonym: "DIC microscopy" BROAD [] synonym: "NIC microscopy" BROAD [] synonym: "Nomarski interference contrast microscopy" BROAD [] synonym: "Nomarski microscopy" BROAD [] is_a: ECO:0001232 {is_inferred="true"} ! microscopy evidence used in manual assertion is_a: ECO:0007055 ! differential interference contrast microscopy evidence intersection_of: ECO:0007055 ! differential interference contrast microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007057 name: extended field laser confocal microscopy evidence def: "A type of confocal microscopy evidence that results in creation of a continuous confocal multi-colour mosaic from thousands of individually captured images." [PMID:18627634] synonym: "EFLCM" EXACT [] is_a: ECO:0005587 ! confocal microscopy evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007058 name: extended field laser confocal microscopy evidence used in manual assertion def: "A type of extended field laser confocal microscopy evidence that is used in a manual assertion." [ECO:RCT] synonym: "EFLCM" BROAD [] is_a: ECO:0005589 {is_inferred="true"} ! confocal microscopy evidence used in manual assertion is_a: ECO:0007057 ! extended field laser confocal microscopy evidence intersection_of: ECO:0007057 ! extended field laser confocal microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007059 name: confocal laser scanning microscopy evidence def: "A type of confocal microscopy evidence that results in an image that is built up pixel-by-pixel by collecting the emitted photons from the fluorophores in the sample by passing a laser beam through a light source aperture which is then focused by an objective lens into a small area on the surface of the sample.\n" [URL:http\://bitesizebio.com/19958/what-is-confocal-laser-scanning-microscopy/] synonym: "CLSM" EXACT [] synonym: "confocal laser scanning fluorescence microscopy" EXACT [] synonym: "confocal-laser scanning microscopy" EXACT [] synonym: "fluorescence confocal scanning laser microscopy" EXACT [] synonym: "LSCM" EXACT [] synonym: "scanning confocal fluorescence microscopy" EXACT [] is_a: ECO:0005587 ! confocal microscopy evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007060 name: confocal laser scanning microscopy evidence used in manual assertion def: "A type of confocal laser scanning microscopy evidence that is used in a manual assertion." [ECO:RCT] synonym: "CLSM" BROAD [] synonym: "confocal laser scanning fluorescence microscopy" BROAD [] synonym: "confocal-laser scanning microscopy" BROAD [] synonym: "fluorescence confocal scanning laser microscopy" BROAD [] synonym: "LSCM" BROAD [] synonym: "scanning confocal fluorescence microscopy" BROAD [] is_a: ECO:0005589 {is_inferred="true"} ! confocal microscopy evidence used in manual assertion is_a: ECO:0007059 ! confocal laser scanning microscopy evidence intersection_of: ECO:0007059 ! confocal laser scanning microscopy evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007061 name: light scattering assay evidence def: "A type of direct assay evidence derived from determining the properties of particles in a solution such as size, shape, structure, molecular weight, diffusion and interaction strength by illuminating the sample with a laser beam and the scattered intensity is probed at a certain angle by a detector." [PMID:9013660, url:http\://www.lsinstruments.ch/technology/dynamic_light_scattering_dls/, url:http\://www.soft-matter.uni-tuebingen.de/index.html?dls.html] is_a: ECO:0005031 ! structure determination evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007062 name: light scattering assay evidence used in manual assertion def: "A type of light scattering assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0007061 ! light scattering assay evidence intersection_of: ECO:0007061 ! light scattering assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007063 name: dynamic light scattering assay evidence def: "A type of light scattering assay evidence derived by analyzing the fluctuations in the internsity of the scattered light by the particles in motion." [PMID:9013660, url:http\://www.soft-matter.uni-tuebingen.de/index.html?dls.html] synonym: "Photon Correlation Spectroscopy" EXACT [] synonym: "Quasi-Elastic Light Scattering" EXACT [] is_a: ECO:0007061 ! light scattering assay evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007064 name: dynamic light scattering assay evidence used in manual assertion def: "A type of dynamic light scattering assay evidence that is used in a manual assertion." [ECO:RCT] synonym: "Photon Correlation Spectroscopy" BROAD [] synonym: "Quasi-Elastic Light Scattering" BROAD [] is_a: ECO:0007062 {is_inferred="true"} ! light scattering assay evidence used in manual assertion is_a: ECO:0007063 ! dynamic light scattering assay evidence intersection_of: ECO:0007063 ! dynamic light scattering assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007065 name: static light scattering assay evidence def: "A type of light scattering assay evidence derived by measuring the average intensity of scattered light by the particles at multiple angles." [PMID:9013660] synonym: "Rayleigh scattering" EXACT [] is_a: ECO:0007061 ! light scattering assay evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007066 name: static light scattering assay evidence used in manual assertion def: "A type of static light scattering assay evidence that is used in a manual assertion." [ECO:RCT] synonym: "Rayleigh scattering" BROAD [] is_a: ECO:0007062 {is_inferred="true"} ! light scattering assay evidence used in manual assertion is_a: ECO:0007065 ! static light scattering assay evidence intersection_of: ECO:0007065 ! static light scattering assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007067 name: colony papillation assay evidence def: "A type of mutant phenotype evidence derived from formation of papillae that protrude outwards from the main colony by mutant cells." [PMID:27447898] is_a: ECO:0000015 ! mutant phenotype evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007068 name: colony papillation assay evidence used in manual assertion def: "A type of colony papillation assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion is_a: ECO:0007067 ! colony papillation assay evidence intersection_of: ECO:0007067 ! colony papillation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007069 name: crystal violet staining evidence def: "A type of staining evidence that is derived from the use of gentian violet as a general biological stain and an acid-base indicator." [BAO:0002468] synonym: "gentian violet" EXACT [] synonym: "hexamethyl pararosaniline chloride" EXACT [] synonym: "methyl violet 10B" EXACT [] is_a: ECO:0005019 ! staining evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007070 name: crystal violet staining evidence used in manual assertion def: "A type of crystal violet staining evidence that is used in a manual assertion." [ECO:RCT] synonym: "gentian violet" BROAD [] synonym: "hexamethyl pararosaniline chloride" BROAD [] synonym: "methyl violet 10B" BROAD [] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0007069 ! crystal violet staining evidence intersection_of: ECO:0007069 ! crystal violet staining evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007071 name: flow cell biofilm assay evidence def: "A type of biofilm formation assay evidence derived from in vitro cultivation and evaluation of bacterial biofilms under hydrodynamic conditions of flow." [URL:https\://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438488/] is_a: ECO:0006020 ! biofilm formation assay evidence relationship: IAO:0000136 GO:0042710 ! is about biofilm formation property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007072 name: flow cell biofilm assay evidence used in manual assertion def: "A type of flow cell biofilm assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0006021 {is_inferred="true"} ! biofilm formation assay evidence used in manual assertion is_a: ECO:0007071 ! flow cell biofilm assay evidence intersection_of: ECO:0007071 ! flow cell biofilm assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007073 name: bacterial 2-hybrid assay evidence def: "A type of hybrid interaction evidence that involves the detection of protein-protein interaction by fusing the protein target (the \"bait\") to RNA polymerase and fusing protein or peptide library to be analyzed (the \"prey\") to DNA-binding domain." [URL:http\://www.pnas.org/content/97/13/7382.full.pdf] is_a: ECO:0000025 ! hybrid interaction evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007074 name: bacterial 2-hybrid assay evidence used in manual assertion def: "A type of bacterial 2-hybrid assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0006077 {is_inferred="true"} ! hybrid interaction evidence used in manual assertion is_a: ECO:0007073 ! bacterial 2-hybrid assay evidence intersection_of: ECO:0007073 ! bacterial 2-hybrid assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007075 name: phenomic profiling assay evidence def: "A type of experimental phenotypic evidence that results from the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors." [EDAM:topic\:3298] is_a: ECO:0000059 ! experimental phenotypic evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007076 name: phenomic profiling assay evidence used in manual assertion def: "A type of phenomic profiling assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0007075 ! phenomic profiling assay evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0007075 ! phenomic profiling assay evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007077 name: colony morphology evidence def: "A type of experimental phenotypic evidence that results from studying the physical characteristics of an assemblage of microorganisms growing on a solid surface such as the surface of an agar culture medium." [OMP:0000100] is_a: ECO:0000059 ! experimental phenotypic evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007078 name: colony morphology evidence used in manual assertion def: "A type of colony morphology evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0007077 ! colony morphology evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0007077 ! colony morphology evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007079 name: colony color evidence def: "A type of colony morphology evidence that results from studying the colony pigmentation." [URL:https\://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671912/] synonym: "colony pigmentation" EXACT [] is_a: ECO:0007077 ! colony morphology evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007080 name: colony color evidence used in manual assertion def: "A type of colony color evidence that is used in a manual assertion." [ECO:RCT] synonym: "colony pigmentation" BROAD [] is_a: ECO:0007078 {is_inferred="true"} ! colony morphology evidence used in manual assertion is_a: ECO:0007079 ! colony color evidence intersection_of: ECO:0007079 ! colony color evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007081 name: colony size evidence def: "A type of colony morphology evidence that results from studying the size of the colony." [URL:http\://www.nature.com/nrmicro/journal/v4/n4/full/nrmicro1384.html] is_a: ECO:0007077 ! colony morphology evidence property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007082 name: colony size evidence used in manual assertion def: "A type of colony size evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0007078 {is_inferred="true"} ! colony morphology evidence used in manual assertion is_a: ECO:0007081 ! colony size evidence intersection_of: ECO:0007081 ! colony size evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007083 name: zone of inhibition evidence def: "A type of cell growth assay evidence resulting from assessing the sensitivity or resistance of bacteria or fungi to an antimicrobial agent or chemical by measuring the size of the zone of inhibition that results when the test organism is grown on a solid surface in the presence of the antimicrobial agent or chemical." [URL:https\://www.ncbi.nlm.nih.gov/pmc/articles/PMC153338/] is_a: ECO:0001563 ! cell growth assay evidence relationship: IAO:0000136 GO:0042221 ! is about response to chemical relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007084 name: zone of inhibition evidence used in manual assertion def: "A type of zone of inhibition evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0007083 ! zone of inhibition evidence intersection_of: ECO:0007083 ! zone of inhibition evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007085 name: Etest evidence def: "A type of zone of inhibition evidence resulting from testing the antimicrobial susceptibility by using predefined, continuous, and exponential gradient of antibiotic concentrations immobilized along a rectangular plastic test strip." [URL:http\://www.joponline.org/doi/pdf/10.1902/jop.1992.63.7.576] synonym: "epsilometer test" EXACT [] is_a: ECO:0007083 ! zone of inhibition evidence relationship: IAO:0000136 GO:0046677 ! is about response to antibiotic relationship: OBI:0000312 OBI:0000978 ! is_specified_output_of in container assay property_value: IAO:0000234 "OMP" xsd:string created_by: snadendla creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007086 name: Etest evidence used in manual assertion def: "A type of Etest evidence that is used in a manual assertion." [ECO:RCT] synonym: "epsilometer test" BROAD [] is_a: ECO:0007084 {is_inferred="true"} ! zone of inhibition evidence used in manual assertion is_a: ECO:0007085 ! Etest evidence intersection_of: ECO:0007085 ! Etest evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion property_value: IAO:0000234 "OMP" xsd:string created_by: rctauber creation_date: 2018-03-14T12:44:11Z [Term] id: ECO:0007087 name: ribosome profiling evidence def: "A type of expression pattern evidence in which translation is measured by the positions of ribosomes active in a cell, identified through deep sequencing of ribosome-protected mRNA fragments." [PMID:27015305] synonym: "ribo-seq evidence" EXACT [] synonym: "ribosome footprinting evidence" EXACT [] is_a: ECO:0000008 ! expression pattern evidence property_value: IAO:0000234 GOC:VW xsd:string created_by: rctauber creation_date: 2018-03-28T10:27:09Z [Term] id: ECO:0007088 name: ribosome profiling evidence used in manual assertion def: "A type of ribosome profiling evidence that is used in a manual assertion." [ECO:RCT] synonym: "ribo-seq evidence" BROAD [] synonym: "ribosome footprinting evidence" BROAD [] is_a: ECO:0000270 {is_inferred="true"} ! expression evidence used in manual assertion is_a: ECO:0007087 ! ribosome profiling evidence intersection_of: ECO:0007087 ! ribosome profiling evidence intersection_of: used_in ECO:0000218 ! manual assertion relationship: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-03-28T10:33:26Z [Term] id: ECO:0007089 name: loss-of-function mutant phenotype evidence used in manual assertion def: "A type of loss-of-function mutant phenotype evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000016 {is_inferred="true"} ! loss-of-function mutant phenotype evidence is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion intersection_of: ECO:0000016 ! loss-of-function mutant phenotype evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007090 name: structural similarity evidence used in manual assertion def: "A type of structural similarity evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000027 {is_inferred="true"} ! structural similarity evidence is_a: ECO:0000252 {is_inferred="true"} ! similarity evidence used in manual assertion intersection_of: ECO:0000027 ! structural similarity evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007092 name: gain-of-function mutant phenotype evidence used in manual assertion def: "A type of gain-of-function mutant phenotype evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000042 {is_inferred="true"} ! gain-of-function mutant phenotype evidence is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion intersection_of: ECO:0000042 ! gain-of-function mutant phenotype evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007093 name: voucher specimen analysis evidence used in manual assertion def: "A type of voucher specimen analysis evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000050 {is_inferred="true"} ! voucher specimen analysis evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0000050 ! voucher specimen analysis evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007094 name: positional similarity evidence used in manual assertion def: "A type of positional similarity evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000060 {is_inferred="true"} ! positional similarity evidence is_a: ECO:0000252 {is_inferred="true"} ! similarity evidence used in manual assertion intersection_of: ECO:0000060 ! positional similarity evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007095 name: quantitative trait analysis evidence used in manual assertion def: "A type of quantitative trait analysis evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000061 {is_inferred="true"} ! quantitative trait analysis evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0000061 ! quantitative trait analysis evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007096 name: compositional similarity evidence used in manual assertion def: "A type of compositional similarity evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000063 {is_inferred="true"} ! compositional similarity evidence is_a: ECO:0000252 {is_inferred="true"} ! similarity evidence used in manual assertion intersection_of: ECO:0000063 ! compositional similarity evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007097 name: developmental similarity evidence used in manual assertion def: "A type of developmental similarity evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000067 {is_inferred="true"} ! developmental similarity evidence is_a: ECO:0000252 {is_inferred="true"} ! similarity evidence used in manual assertion intersection_of: ECO:0000067 ! developmental similarity evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007098 name: morphological similarity evidence used in manual assertion def: "A type of morphological similarity evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000071 {is_inferred="true"} ! morphological similarity evidence is_a: ECO:0000252 {is_inferred="true"} ! similarity evidence used in manual assertion intersection_of: ECO:0000071 ! morphological similarity evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007099 name: gene expression similarity evidence used in manual assertion def: "A type of gene expression similarity evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000075 {is_inferred="true"} ! gene expression similarity evidence is_a: ECO:0000252 {is_inferred="true"} ! similarity evidence used in manual assertion intersection_of: ECO:0000075 ! gene expression similarity evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007100 name: methylation-specific polymerase chain reaction evidence used in manual assertion def: "A type of methylation-specific polymerase chain reaction evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000077 {is_inferred="true"} ! methylation-specific polymerase chain reaction evidence is_a: ECO:0001198 {is_inferred="true"} ! in vitro methylation assay evidence used in manual assertion intersection_of: ECO:0000077 ! methylation-specific polymerase chain reaction evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007101 name: southern hybridization evidence used in manual assertion def: "A type of southern hybridization evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000078 {is_inferred="true"} ! southern hybridization evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000078 ! southern hybridization evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007102 name: intermethylated site amplification evidence used in manual assertion def: "A type of intermethylated site amplification evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000086 {is_inferred="true"} ! amplification of intermethylated sites evidence is_a: ECO:0001198 {is_inferred="true"} ! in vitro methylation assay evidence used in manual assertion intersection_of: ECO:0000086 ! amplification of intermethylated sites evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007103 name: epitope-tagged protein immunolocalization evidence used in manual assertion def: "A type of epitope-tagged protein immunolocalization evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000092 {is_inferred="true"} ! epitope-tagged protein immunolocalization evidence is_a: ECO:0006031 {is_inferred="true"} ! immunolocalization evidence used in manual assertion intersection_of: ECO:0000092 ! epitope-tagged protein immunolocalization evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007104 name: co-fractionation evidence used in manual assertion def: "A type of co-fractionation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000102 {is_inferred="true"} ! co-fractionation evidence is_a: ECO:0006005 {is_inferred="true"} ! fractionation evidence used in manual assertion intersection_of: ECO:0000102 ! co-fractionation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007106 name: green fluorescent protein fusion protein localization evidence used in manual assertion def: "A type of green fluorescent protein fusion protein localization evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000126 {is_inferred="true"} ! green fluorescent protein fusion protein localization evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000126 ! green fluorescent protein fusion protein localization evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007107 name: yellow fluorescent protein fusion protein localization evidence used in manual assertion def: "A type of yellow fluorescent protein fusion protein localization evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000128 {is_inferred="true"} ! yellow fluorescent protein fusion protein localization evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000128 ! yellow fluorescent protein fusion protein localization evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007108 name: beta-glucuronidase fusion protein localization evidence used in manual assertion def: "A type of beta-glucuronidase fusion protein localization evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000130 {is_inferred="true"} ! beta-glucuronidase fusion protein localization evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000130 ! beta-glucuronidase fusion protein localization evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007109 name: beta-galactosidase fusion protein localization evidence used in manual assertion def: "A type of beta-galactosidase fusion protein localization evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000132 {is_inferred="true"} ! beta-galactosidase fusion protein localization evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000132 ! beta-galactosidase fusion protein localization evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007110 name: thin layer chromatography evidence used in manual assertion def: "A type of thin layer chromatography evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000140 {is_inferred="true"} ! thin layer chromatography evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000140 ! thin layer chromatography evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007111 name: in vitro recombinant protein transcription reconstitution assay evidence used in manual assertion def: "A type of in vitro recombinant protein transcription reconstitution assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000152 {is_inferred="true"} ! in vitro recombinant protein transcription reconstitution assay evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000152 ! in vitro recombinant protein transcription reconstitution assay evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007112 name: protein separation followed by direct sequencing evidence used in manual assertion def: "A type of protein separation followed by direct sequencing evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000158 {is_inferred="true"} ! protein separation followed by direct sequencing evidence is_a: ECO:0006005 {is_inferred="true"} ! fractionation evidence used in manual assertion intersection_of: ECO:0000158 ! protein separation followed by direct sequencing evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007113 name: protein separation followed by fragment identification evidence used in manual assertion def: "A type of protein separation followed by fragment identification evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000160 {is_inferred="true"} ! protein separation followed by fragment identification evidence is_a: ECO:0006005 {is_inferred="true"} ! fractionation evidence used in manual assertion intersection_of: ECO:0000160 ! protein separation followed by fragment identification evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007114 name: heterologous system uptake evidence used in manual assertion def: "A type of heterologous system uptake evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000162 {is_inferred="true"} ! heterologous system uptake evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000162 ! heterologous system uptake evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007115 name: two-electrode voltage clamp recording evidence used in manual assertion def: "A type of two-electrode voltage clamp recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000166 {is_inferred="true"} ! two-electrode voltage clamp recording evidence is_a: ECO:0006006 {is_inferred="true"} ! electrophysiology assay evidence used in manual assertion intersection_of: ECO:0000166 ! two-electrode voltage clamp recording evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007116 name: biochemical trait analysis evidence used in manual assertion def: "A type of biochemical trait analysis evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000172 {is_inferred="true"} ! biochemical trait analysis evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0000172 ! biochemical trait analysis evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007117 name: mutant physiological response evidence used in manual assertion def: "A type of mutant physiological response evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000174 {is_inferred="true"} ! mutant physiological response evidence is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion intersection_of: ECO:0000174 ! mutant physiological response evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007118 name: mutant visible phenotype evidence used in manual assertion def: "A type of mutant visible phenotype evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000176 {is_inferred="true"} ! mutant visible phenotype evidence is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion intersection_of: ECO:0000176 ! mutant visible phenotype evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007119 name: in vivo assay evidence used in manual assertion def: "A type of in vivo assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000178 {is_inferred="true"} ! in vivo assay evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000178 ! in vivo assay evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007120 name: animal model system study evidence used in manual assertion def: "A type of animal model system study evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000179 {is_inferred="true"} ! animal model system study evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000179 ! animal model system study evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007121 name: clinical study evidence used in manual assertion def: "A type of clinical study evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000180 {is_inferred="true"} ! clinical study evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000180 ! clinical study evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007122 name: in vitro assay evidence used in manual assertion def: "A type of in vitro assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000181 {is_inferred="true"} ! in vitro assay evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000181 ! in vitro assay evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007123 name: enzyme inhibition evidence used in manual assertion def: "A type of enzyme inhibition evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000184 {is_inferred="true"} ! enzyme inhibition evidence is_a: ECO:0005801 {is_inferred="true"} ! enzyme assay evidence used in manual assertion intersection_of: ECO:0000184 ! enzyme inhibition evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007125 name: Illumina sequencing evidence used in manual assertion def: "A type of Illumina sequencing evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000222 {is_inferred="true"} ! Illumina sequencing evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000222 ! Illumina sequencing evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007126 name: 454 pyrosequencing evidence used in manual assertion def: "A type of 454 pyrosequencing evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000223 {is_inferred="true"} ! 454 pyrosequencing evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000223 ! 454 pyrosequencing evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007127 name: SOLiD sequencing evidence used in manual assertion def: "A type of SOLiD sequencing evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000224 {is_inferred="true"} ! SOLiD sequencing evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000224 ! SOLiD sequencing evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007128 name: chain termination sequencing evidence used in manual assertion def: "A type of chain termination sequencing evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000225 {is_inferred="true"} ! chain termination sequencing evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000225 ! chain termination sequencing evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007129 name: chromatin immunoprecipitation-qPCR evidence used in manual assertion def: "A type of chromatin immunoprecipitation-qPCR evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000228 {is_inferred="true"} ! chromatin immunoprecipitation-qPCR evidence is_a: ECO:0005644 {is_inferred="true"} ! immunoprecipitation evidence used in manual assertion intersection_of: ECO:0000228 ! chromatin immunoprecipitation-qPCR evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007130 name: 4C evidence used in manual assertion def: "A type of 4C evidence that is used in a manual assertion." [ECO:RCT] synonym: "circularized chromosome conformation capture evidence used in manual assertion" EXACT [] is_a: ECO:0000234 {is_inferred="true"} ! 4C evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000234 ! 4C evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007131 name: 5C evidence used in manual assertion def: "A type of 5C evidence that is used in a manual assertion." [ECO:RCT] synonym: "carbon-copy chromosome conformation capture evidence used in manual assertion" EXACT [] is_a: ECO:0000235 {is_inferred="true"} ! 5C evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000235 ! 5C evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007133 name: 3C-qPCR evidence used in manual assertion def: "A type of 3C-qPCR evidence that is used in a manual assertion." [ECO:RCT] synonym: "chromosome conformation capture-qPCR evidence used in manual assertion" EXACT [] is_a: ECO:0000237 {is_inferred="true"} ! 3C-qPCR evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000237 ! 3C-qPCR evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007134 name: Hi-C evidence used in manual assertion def: "A type of Hi-C evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000238 {is_inferred="true"} ! Hi-C evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000238 ! Hi-C evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007135 name: 3C-seq evidence used in manual assertion def: "A type of 3C-seq evidence that is used in a manual assertion." [ECO:RCT] synonym: "chromosome conformation capture sequencing evidence used in manual assertion" EXACT [] is_a: ECO:0000239 {is_inferred="true"} ! 3C-seq evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000239 ! 3C-seq evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007136 name: environmental perturbation evidence used in manual assertion def: "A type of environmental perturbation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000241 {is_inferred="true"} ! environmental perturbation evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0000241 ! environmental perturbation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007137 name: tissue ablation evidence used in manual assertion def: "A type of tissue ablation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000242 {is_inferred="true"} ! tissue ablation evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0000242 ! tissue ablation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007138 name: tissue grafting evidence used in manual assertion def: "A type of tissue grafting evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000243 {is_inferred="true"} ! tissue grafting evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0000243 ! tissue grafting evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007141 name: cytochalasin experiment evidence used in manual assertion def: "A type of cytochalasin experiment evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000299 {is_inferred="true"} ! cytochalasin experiment evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0000299 ! cytochalasin experiment evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007142 name: green fluorescent protein immunolocalization evidence used in manual assertion def: "A type of green fluorescent protein immunolocalization evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000300 {is_inferred="true"} ! green fluorescent protein immunolocalization evidence is_a: ECO:0006031 {is_inferred="true"} ! immunolocalization evidence used in manual assertion intersection_of: ECO:0000300 ! green fluorescent protein immunolocalization evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007143 name: beta-galactosidase protein immunolocalization evidence used in manual assertion def: "A type of beta-galactosidase protein immunolocalization evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000301 {is_inferred="true"} ! beta-galactosidase protein immunolocalization evidence is_a: ECO:0006031 {is_inferred="true"} ! immunolocalization evidence used in manual assertion intersection_of: ECO:0000301 ! beta-galactosidase protein immunolocalization evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007144 name: cap analysis of gene expression evidence used in manual assertion def: "A type of cap analysis of gene expression evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000291 {is_inferred="true"} ! transcript expression evidence used in manual assertion is_a: ECO:0000309 {is_inferred="true"} ! cap analysis of gene expression evidence intersection_of: ECO:0000309 ! cap analysis of gene expression evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007145 name: nano-cap analysis of gene expression evidence used in manual assertion def: "A type of nano-cap analysis of gene expression evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000291 {is_inferred="true"} ! transcript expression evidence used in manual assertion is_a: ECO:0000310 {is_inferred="true"} ! nano-cap analysis of gene expression evidence intersection_of: ECO:0000310 ! nano-cap analysis of gene expression evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007146 name: particle size and count assay evidence used in manual assertion def: "A type of particle size and count assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0000334 {is_inferred="true"} ! particle size and count assay evidence intersection_of: ECO:0000334 ! particle size and count assay evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007147 name: competitive growth assay evidence used in manual assertion def: "A type of competitive growth assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0000336 {is_inferred="true"} ! competitive growth assay evidence intersection_of: ECO:0000336 ! competitive growth assay evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007148 name: pulsed-field gel electrophoresis evidence used in manual assertion def: "A type of pulsed-field gel electrophoresis evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0000338 {is_inferred="true"} ! pulsed-field gel electrophoresis evidence intersection_of: ECO:0000338 ! pulsed-field gel electrophoresis evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007149 name: two-dimensional agarose gel electrophoresis evidence used in manual assertion def: "A type of two-dimensional agarose gel electrophoresis evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0000339 {is_inferred="true"} ! two-dimensional agarose gel electrophoresis evidence intersection_of: ECO:0000339 ! two-dimensional agarose gel electrophoresis evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007150 name: plasmid maintenance assay evidence used in manual assertion def: "A type of plasmid maintenance assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0000340 {is_inferred="true"} ! plasmid maintenance assay evidence intersection_of: ECO:0000340 ! plasmid maintenance assay evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007151 name: specific protein inhibition by antibody evidence used in manual assertion def: "A type of specific protein inhibition by antibody evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0000341 {is_inferred="true"} ! specific protein inhibition by antibody evidence intersection_of: ECO:0000341 ! specific protein inhibition by antibody evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007152 name: single exon transcript confirmation via alignment evidence used in manual assertion def: "A type of single exon transcript confirmation via alignment evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000247 {is_inferred="true"} ! sequence alignment evidence used in manual assertion is_a: ECO:0000345 {is_inferred="true"} ! single exon transcript confirmation via alignment evidence intersection_of: ECO:0000345 ! single exon transcript confirmation via alignment evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007153 name: phylogenetic distribution evidence used in manual assertion def: "A type of phylogenetic distribution evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000252 {is_inferred="true"} ! similarity evidence used in manual assertion is_a: ECO:0000355 {is_inferred="true"} ! phylogenetic distribution evidence intersection_of: ECO:0000355 ! phylogenetic distribution evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007154 name: differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) used in manual assertion def: "A type of differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000291 {is_inferred="true"} ! transcript expression evidence used in manual assertion is_a: ECO:0000358 {is_inferred="true"} ! differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) intersection_of: ECO:0000358 ! differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007155 name: differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) used in manual assertion def: "A type of differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000291 {is_inferred="true"} ! transcript expression evidence used in manual assertion is_a: ECO:0000359 {is_inferred="true"} ! differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) intersection_of: ECO:0000359 ! differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007156 name: biological target-disease association via drug used in manual assertion def: "A type of biological target-disease association via drug that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0000360 {is_inferred="true"} ! biological target-disease association via drug intersection_of: ECO:0000360 ! biological target-disease association via drug intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007157 name: cell staining evidence used in manual assertion def: "A type of cell staining evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001603 {is_inferred="true"} ! cell staining evidence intersection_of: ECO:0001603 ! cell staining evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007158 name: visual sequence inspection evidence used in manual assertion def: "A type of visual sequence inspection evidence that is used in a manual assertion." [ECO:RCT] is_obsolete: true created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007159 name: ATP bioluminescence assay evidence used in manual assertion def: "A type of ATP bioluminescence assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0005011 {is_inferred="true"} ! ATP bioluminescence assay evidence intersection_of: ECO:0005011 ! ATP bioluminescence assay evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007160 name: missense mutation evidence used in manual assertion def: "A type of missense mutation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001247 {is_inferred="true"} ! point mutation evidence used in manual assertion is_a: ECO:0005506 {is_inferred="true"} ! missense mutation evidence intersection_of: ECO:0005506 ! missense mutation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007161 name: nonsense mutation evidence used in manual assertion def: "A type of nonsense mutation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001247 {is_inferred="true"} ! point mutation evidence used in manual assertion is_a: ECO:0005507 {is_inferred="true"} ! nonsense mutation evidence intersection_of: ECO:0005507 ! nonsense mutation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007162 name: silent mutation evidence used in manual assertion def: "A type of silent mutation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001247 {is_inferred="true"} ! point mutation evidence used in manual assertion is_a: ECO:0005508 {is_inferred="true"} ! silent mutation evidence intersection_of: ECO:0005508 ! silent mutation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007163 name: insertion mutation evidence used in manual assertion def: "A type of insertion mutation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005509 {is_inferred="true"} ! insertion mutation evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0005509 ! insertion mutation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007164 name: duplication mutation evidence used in manual assertion def: "A type of duplication mutation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005511 {is_inferred="true"} ! duplication mutation evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0005511 ! duplication mutation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007165 name: frameshift mutation evidence used in manual assertion def: "A type of frameshift mutation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005512 {is_inferred="true"} ! frameshift mutation evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0005512 ! frameshift mutation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007166 name: repeat expansion mutation evidence used in manual assertion def: "A type of repeat expansion mutation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005513 {is_inferred="true"} ! repeat expansion mutation evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0005513 ! repeat expansion mutation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007167 name: splice site mutation evidence used in manual assertion def: "A type of splice site mutation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005514 {is_inferred="true"} ! splice site mutation evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0005514 ! splice site mutation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007168 name: translocation mutation evidence used in manual assertion def: "A type of translocation mutation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005515 {is_inferred="true"} ! translocation mutation evidence is_a: ECO:0007634 {is_inferred="true"} ! experimental phenotypic evidence used in manual assertion intersection_of: ECO:0005515 ! translocation mutation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007169 name: in-gel protein kinase assay evidence used in manual assertion def: "A type of in-gel protein kinase assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0005562 {is_inferred="true"} ! in-gel protein kinase assay evidence intersection_of: ECO:0005562 ! in-gel protein kinase assay evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007170 name: macroscopic current trace evidence used in manual assertion def: "A type of macroscopic current trace evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005563 {is_inferred="true"} ! macroscopic current trace evidence is_a: ECO:0006006 {is_inferred="true"} ! electrophysiology assay evidence used in manual assertion intersection_of: ECO:0005563 ! macroscopic current trace evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007171 name: current density evidence used in manual assertion def: "A type of current density evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005564 {is_inferred="true"} ! current density evidence is_a: ECO:0006006 {is_inferred="true"} ! electrophysiology assay evidence used in manual assertion intersection_of: ECO:0005564 ! current density evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007172 name: sustained current evidence used in manual assertion def: "A type of sustained current evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005566 {is_inferred="true"} ! sustained current evidence is_a: ECO:0006006 {is_inferred="true"} ! electrophysiology assay evidence used in manual assertion intersection_of: ECO:0005566 ! sustained current evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007173 name: use dependence of inactivation evidence used in manual assertion def: "A type of use dependence of inactivation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005570 {is_inferred="true"} ! use dependence of inactivation evidence is_a: ECO:0006006 {is_inferred="true"} ! electrophysiology assay evidence used in manual assertion intersection_of: ECO:0005570 ! use dependence of inactivation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007174 name: current clamp recording evidence used in manual assertion def: "A type of current clamp recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005571 {is_inferred="true"} ! current clamp recording evidence is_a: ECO:0006006 {is_inferred="true"} ! electrophysiology assay evidence used in manual assertion intersection_of: ECO:0005571 ! current clamp recording evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007175 name: whole-cell voltage clamp recording evidence used in manual assertion def: "A type of whole-cell voltage clamp recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005572 {is_inferred="true"} ! whole-cell voltage clamp recording evidence is_a: ECO:0006006 {is_inferred="true"} ! electrophysiology assay evidence used in manual assertion intersection_of: ECO:0005572 ! whole-cell voltage clamp recording evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007176 name: cell-attached single-channel recording evidence used in manual assertion def: "A type of cell-attached single-channel recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005573 {is_inferred="true"} ! cell-attached single-channel recording evidence is_a: ECO:0006013 {is_inferred="true"} ! patch-clamp recording evidence used in manual assertion intersection_of: ECO:0005573 ! cell-attached single-channel recording evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007177 name: cell-detached inside-out single-channel recording evidence used in manual assertion def: "A type of cell-detached inside-out single-channel recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005574 {is_inferred="true"} ! cell-detached inside-out single-channel recording evidence is_a: ECO:0006013 {is_inferred="true"} ! patch-clamp recording evidence used in manual assertion intersection_of: ECO:0005574 ! cell-detached inside-out single-channel recording evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007178 name: reconstituted bilayer single-channel patch recording evidence used in manual assertion def: "A type of reconstituted bilayer single-channel patch recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005575 {is_inferred="true"} ! reconstituted bilayer single-channel patch recording evidence is_a: ECO:0006013 {is_inferred="true"} ! patch-clamp recording evidence used in manual assertion intersection_of: ECO:0005575 ! reconstituted bilayer single-channel patch recording evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007179 name: electroencephalography recording evidence used in manual assertion def: "A type of electroencephalography recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005577 {is_inferred="true"} ! electroencephalography recording evidence is_a: ECO:0006006 {is_inferred="true"} ! electrophysiology assay evidence used in manual assertion intersection_of: ECO:0005577 ! electroencephalography recording evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007180 name: cell-detached outside-out single-channel recording evidence used in manual assertion def: "A type of cell-detached outside-out single-channel recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005582 {is_inferred="true"} ! cell-detached outside-out single-channel recording evidence is_a: ECO:0006013 {is_inferred="true"} ! patch-clamp recording evidence used in manual assertion intersection_of: ECO:0005582 ! cell-detached outside-out single-channel recording evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007181 name: cut-open oocyte voltage clamp recording evidence used in manual assertion def: "A type of cut-open oocyte voltage clamp recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005583 {is_inferred="true"} ! cut-open oocyte voltage clamp recording evidence is_a: ECO:0006006 {is_inferred="true"} ! electrophysiology assay evidence used in manual assertion intersection_of: ECO:0005583 ! cut-open oocyte voltage clamp recording evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007182 name: macropatch voltage clamp recording evidence used in manual assertion def: "A type of macropatch voltage clamp recording evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0005584 {is_inferred="true"} ! macropatch voltage clamp recording evidence is_a: ECO:0006006 {is_inferred="true"} ! electrophysiology assay evidence used in manual assertion intersection_of: ECO:0005584 ! macropatch voltage clamp recording evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007183 name: protein expression level evidence based on western blot used in manual assertion def: "A type of protein expression level evidence based on western blot that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000279 {is_inferred="true"} ! western blot evidence used in manual assertion is_a: ECO:0000280 {is_inferred="true"} ! protein expression level evidence used in manual assertion is_a: ECO:0005602 {is_inferred="true"} ! protein expression level evidence based on western blot intersection_of: ECO:0005602 ! protein expression level evidence based on western blot intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007184 name: protein mass spectrometry evidence used in manual assertion def: "A type of protein mass spectrometry evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0001230 {is_inferred="true"} ! mass spectrometry evidence used in manual assertion is_a: ECO:0005603 {is_inferred="true"} ! protein mass spectrometry evidence intersection_of: ECO:0005603 ! protein mass spectrometry evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007185 name: cross-streak test evidence used in manual assertion def: "A type of cross-streak test evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0005604 {is_inferred="true"} ! cross-streak test evidence intersection_of: ECO:0005604 ! cross-streak test evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007186 name: tethered cell assay evidence used in manual assertion def: "A type of tethered cell assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0005607 {is_inferred="true"} ! tethered cell assay evidence intersection_of: ECO:0005607 ! tethered cell assay evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007187 name: tumble frequency assay evidence used in manual assertion def: "A type of tumble frequency assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0005608 {is_inferred="true"} ! tumble frequency assay evidence intersection_of: ECO:0005608 ! tumble frequency assay evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007188 name: capillary assay evidence used in manual assertion def: "A type of capillary assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0005609 {is_inferred="true"} ! capillary assay evidence intersection_of: ECO:0005609 ! capillary assay evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007189 name: inference from experimental data evidence used in manual assertion def: "A type of inference from experimental data evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0005611 ! inference from experimental data evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007190 name: inference from phenotype manipulation evidence used in manual assertion def: "A type of inference from phenotype manipulation evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000315 {is_inferred="true"} ! mutant phenotype evidence used in manual assertion intersection_of: ECO:0005612 ! inference from phenotype manipulation evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007191 name: inference by association of genotype from phenotype used in manual assertion def: "A type of inference by association of genotype from phenotype that is used in a manual assertion." [ECO:RCT] is_a: ECO:0001237 {is_inferred="true"} ! natural variation mutant evidence used in manual assertion intersection_of: ECO:0005613 ! inference by association of genotype from phenotype intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007192 name: motility assay evidence used in manual assertion def: "A type of motility assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion is_a: ECO:0005803 {is_inferred="true"} ! motility assay evidence intersection_of: ECO:0005803 ! motility assay evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007193 name: loss-of-function mutant phenotype evidence used in automatic assertion def: "A type of loss-of-function mutant phenotype evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000016 {is_inferred="true"} ! loss-of-function mutant phenotype evidence is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0000016 ! loss-of-function mutant phenotype evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007194 name: structural similarity evidence used in automatic assertion def: "A type of structural similarity evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000027 {is_inferred="true"} ! structural similarity evidence is_a: ECO:0000251 {is_inferred="true"} ! similarity evidence used in automatic assertion intersection_of: ECO:0000027 ! structural similarity evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007196 name: gain-of-function mutant phenotype evidence used in automatic assertion def: "A type of gain-of-function mutant phenotype evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000042 {is_inferred="true"} ! gain-of-function mutant phenotype evidence is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0000042 ! gain-of-function mutant phenotype evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007197 name: voucher specimen analysis evidence used in automatic assertion def: "A type of voucher specimen analysis evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000050 {is_inferred="true"} ! voucher specimen analysis evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0000050 ! voucher specimen analysis evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007198 name: positional similarity evidence used in automatic assertion def: "A type of positional similarity evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000060 {is_inferred="true"} ! positional similarity evidence is_a: ECO:0000251 {is_inferred="true"} ! similarity evidence used in automatic assertion intersection_of: ECO:0000060 ! positional similarity evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007199 name: quantitative trait analysis evidence used in automatic assertion def: "A type of quantitative trait analysis evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000061 {is_inferred="true"} ! quantitative trait analysis evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0000061 ! quantitative trait analysis evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007200 name: compositional similarity evidence used in automatic assertion def: "A type of compositional similarity evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000063 {is_inferred="true"} ! compositional similarity evidence is_a: ECO:0000251 {is_inferred="true"} ! similarity evidence used in automatic assertion intersection_of: ECO:0000063 ! compositional similarity evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007201 name: developmental similarity evidence used in automatic assertion def: "A type of developmental similarity evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000067 {is_inferred="true"} ! developmental similarity evidence is_a: ECO:0000251 {is_inferred="true"} ! similarity evidence used in automatic assertion intersection_of: ECO:0000067 ! developmental similarity evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007202 name: morphological similarity evidence used in automatic assertion def: "A type of morphological similarity evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000071 {is_inferred="true"} ! morphological similarity evidence is_a: ECO:0000251 {is_inferred="true"} ! similarity evidence used in automatic assertion intersection_of: ECO:0000071 ! morphological similarity evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007203 name: gene expression similarity evidence used in automatic assertion def: "A type of gene expression similarity evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000075 {is_inferred="true"} ! gene expression similarity evidence is_a: ECO:0000251 {is_inferred="true"} ! similarity evidence used in automatic assertion intersection_of: ECO:0000075 ! gene expression similarity evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007204 name: methylation-specific polymerase chain reaction evidence used in automatic assertion def: "A type of methylation-specific polymerase chain reaction evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000077 {is_inferred="true"} ! methylation-specific polymerase chain reaction evidence is_a: ECO:0007401 {is_inferred="true"} ! in vitro methylation assay evidence used in automatic assertion intersection_of: ECO:0000077 ! methylation-specific polymerase chain reaction evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007205 name: southern hybridization evidence used in automatic assertion def: "A type of southern hybridization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000078 {is_inferred="true"} ! southern hybridization evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000078 ! southern hybridization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007206 name: intermethylated site amplification evidence used in automatic assertion def: "A type of intermethylated site amplification evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000086 {is_inferred="true"} ! amplification of intermethylated sites evidence is_a: ECO:0007401 {is_inferred="true"} ! in vitro methylation assay evidence used in automatic assertion intersection_of: ECO:0000086 ! amplification of intermethylated sites evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007207 name: epitope-tagged protein immunolocalization evidence used in automatic assertion def: "A type of epitope-tagged protein immunolocalization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000092 {is_inferred="true"} ! epitope-tagged protein immunolocalization evidence is_a: ECO:0007486 {is_inferred="true"} ! immunolocalization evidence used in automatic assertion intersection_of: ECO:0000092 ! epitope-tagged protein immunolocalization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007208 name: co-fractionation evidence used in automatic assertion def: "A type of co-fractionation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000102 {is_inferred="true"} ! co-fractionation evidence is_a: ECO:0007534 {is_inferred="true"} ! fractionation evidence used in automatic assertion intersection_of: ECO:0000102 ! co-fractionation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007210 name: green fluorescent protein fusion protein localization evidence used in automatic assertion def: "A type of green fluorescent protein fusion protein localization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000126 {is_inferred="true"} ! green fluorescent protein fusion protein localization evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000126 ! green fluorescent protein fusion protein localization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007211 name: yellow fluorescent protein fusion protein localization evidence used in automatic assertion def: "A type of yellow fluorescent protein fusion protein localization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000128 {is_inferred="true"} ! yellow fluorescent protein fusion protein localization evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000128 ! yellow fluorescent protein fusion protein localization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007212 name: beta-glucuronidase fusion protein localization evidence used in automatic assertion def: "A type of beta-glucuronidase fusion protein localization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000130 {is_inferred="true"} ! beta-glucuronidase fusion protein localization evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000130 ! beta-glucuronidase fusion protein localization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007213 name: beta-galactosidase fusion protein localization evidence used in automatic assertion def: "A type of beta-galactosidase fusion protein localization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000132 {is_inferred="true"} ! beta-galactosidase fusion protein localization evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000132 ! beta-galactosidase fusion protein localization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007214 name: thin layer chromatography evidence used in automatic assertion def: "A type of thin layer chromatography evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000140 {is_inferred="true"} ! thin layer chromatography evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000140 ! thin layer chromatography evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007215 name: in vitro recombinant protein transcription reconstitution assay evidence used in automatic assertion def: "A type of in vitro recombinant protein transcription reconstitution assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000152 {is_inferred="true"} ! in vitro recombinant protein transcription reconstitution assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000152 ! in vitro recombinant protein transcription reconstitution assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007216 name: protein separation followed by direct sequencing evidence used in automatic assertion def: "A type of protein separation followed by direct sequencing evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000158 {is_inferred="true"} ! protein separation followed by direct sequencing evidence is_a: ECO:0007534 {is_inferred="true"} ! fractionation evidence used in automatic assertion intersection_of: ECO:0000158 ! protein separation followed by direct sequencing evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007217 name: protein separation followed by fragment identification evidence used in automatic assertion def: "A type of protein separation followed by fragment identification evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000160 {is_inferred="true"} ! protein separation followed by fragment identification evidence is_a: ECO:0007534 {is_inferred="true"} ! fractionation evidence used in automatic assertion intersection_of: ECO:0000160 ! protein separation followed by fragment identification evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007218 name: heterologous system uptake evidence used in automatic assertion def: "A type of heterologous system uptake evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000162 {is_inferred="true"} ! heterologous system uptake evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000162 ! heterologous system uptake evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007219 name: two-electrode voltage clamp recording evidence used in automatic assertion def: "A type of two-electrode voltage clamp recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000166 {is_inferred="true"} ! two-electrode voltage clamp recording evidence is_a: ECO:0007535 {is_inferred="true"} ! electrophysiology assay evidence used in automatic assertion intersection_of: ECO:0000166 ! two-electrode voltage clamp recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007220 name: biochemical trait analysis evidence used in automatic assertion def: "A type of biochemical trait analysis evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000172 {is_inferred="true"} ! biochemical trait analysis evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0000172 ! biochemical trait analysis evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007221 name: mutant physiological response evidence used in automatic assertion def: "A type of mutant physiological response evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000174 {is_inferred="true"} ! mutant physiological response evidence is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0000174 ! mutant physiological response evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007222 name: mutant visible phenotype evidence used in automatic assertion def: "A type of mutant visible phenotype evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000176 {is_inferred="true"} ! mutant visible phenotype evidence is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0000176 ! mutant visible phenotype evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007223 name: in vivo assay evidence used in automatic assertion def: "A type of in vivo assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000178 {is_inferred="true"} ! in vivo assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000178 ! in vivo assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007224 name: animal model system study evidence used in automatic assertion def: "A type of animal model system study evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000179 {is_inferred="true"} ! animal model system study evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000179 ! animal model system study evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007225 name: clinical study evidence used in automatic assertion def: "A type of clinical study evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000180 {is_inferred="true"} ! clinical study evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000180 ! clinical study evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007226 name: in vitro assay evidence used in automatic assertion def: "A type of in vitro assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000181 {is_inferred="true"} ! in vitro assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000181 ! in vitro assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007227 name: enzyme inhibition evidence used in automatic assertion def: "A type of enzyme inhibition evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000184 {is_inferred="true"} ! enzyme inhibition evidence is_a: ECO:0007468 {is_inferred="true"} ! enzyme assay evidence used in automatic assertion intersection_of: ECO:0000184 ! enzyme inhibition evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007229 name: Illumina sequencing evidence used in automatic assertion def: "A type of Illumina sequencing evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000222 {is_inferred="true"} ! Illumina sequencing evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000222 ! Illumina sequencing evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007230 name: 454 pyrosequencing evidence used in automatic assertion def: "A type of 454 pyrosequencing evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000223 {is_inferred="true"} ! 454 pyrosequencing evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000223 ! 454 pyrosequencing evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007231 name: SOLiD sequencing evidence used in automatic assertion def: "A type of SOLiD sequencing evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000224 {is_inferred="true"} ! SOLiD sequencing evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000224 ! SOLiD sequencing evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007232 name: chain termination sequencing evidence used in automatic assertion def: "A type of chain termination sequencing evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000225 {is_inferred="true"} ! chain termination sequencing evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000225 ! chain termination sequencing evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007233 name: chromatin immunoprecipitation-qPCR evidence used in automatic assertion def: "A type of chromatin immunoprecipitation-qPCR evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000228 {is_inferred="true"} ! chromatin immunoprecipitation-qPCR evidence is_a: ECO:0007503 {is_inferred="true"} ! immunoprecipitation evidence used in automatic assertion intersection_of: ECO:0000228 ! chromatin immunoprecipitation-qPCR evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007234 name: 4C evidence used in automatic assertion def: "A type of 4C evidence that is used in an automatic assertion." [ECO:RCT] synonym: "circularized chromosome conformation capture evidence used in automatic assertion" EXACT [] is_a: ECO:0000234 {is_inferred="true"} ! 4C evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000234 ! 4C evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007235 name: 5C evidence used in automatic assertion def: "A type of 5C evidence that is used in an automatic assertion." [ECO:RCT] synonym: "carbon-copy chromosome conformation capture evidence used in automatic assertion" EXACT [] is_a: ECO:0000235 {is_inferred="true"} ! 5C evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000235 ! 5C evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007237 name: 3C-qPCR evidence used in automatic assertion def: "A type of 3C-qPCR evidence that is used in an automatic assertion." [ECO:RCT] synonym: "chromosome conformation capture-qPCR evidence used in automatic assertion" EXACT [] is_a: ECO:0000237 {is_inferred="true"} ! 3C-qPCR evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000237 ! 3C-qPCR evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007238 name: Hi-C evidence used in automatic assertion def: "A type of Hi-C evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000238 {is_inferred="true"} ! Hi-C evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000238 ! Hi-C evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007239 name: 3C-seq evidence used in automatic assertion def: "A type of 3C-seq evidence that is used in an automatic assertion." [ECO:RCT] synonym: "chromosome conformation capture sequencing evidence used in automatic assertion" EXACT [] is_a: ECO:0000239 {is_inferred="true"} ! 3C-seq evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000239 ! 3C-seq evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007240 name: environmental perturbation evidence used in automatic assertion def: "A type of environmental perturbation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000241 {is_inferred="true"} ! environmental perturbation evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0000241 ! environmental perturbation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007241 name: tissue ablation evidence used in automatic assertion def: "A type of tissue ablation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000242 {is_inferred="true"} ! tissue ablation evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0000242 ! tissue ablation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007242 name: tissue grafting evidence used in automatic assertion def: "A type of tissue grafting evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000243 {is_inferred="true"} ! tissue grafting evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0000243 ! tissue grafting evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007245 name: cytochalasin experiment evidence used in automatic assertion def: "A type of cytochalasin experiment evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000299 {is_inferred="true"} ! cytochalasin experiment evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0000299 ! cytochalasin experiment evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007246 name: green fluorescent protein immunolocalization evidence used in automatic assertion def: "A type of green fluorescent protein immunolocalization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000300 {is_inferred="true"} ! green fluorescent protein immunolocalization evidence is_a: ECO:0007486 {is_inferred="true"} ! immunolocalization evidence used in automatic assertion intersection_of: ECO:0000300 ! green fluorescent protein immunolocalization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007247 name: beta-galactosidase protein immunolocalization evidence used in automatic assertion def: "A type of beta-galactosidase protein immunolocalization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000301 {is_inferred="true"} ! beta-galactosidase protein immunolocalization evidence is_a: ECO:0007486 {is_inferred="true"} ! immunolocalization evidence used in automatic assertion intersection_of: ECO:0000301 ! beta-galactosidase protein immunolocalization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007248 name: cap analysis of gene expression evidence used in automatic assertion def: "A type of cap analysis of gene expression evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000309 {is_inferred="true"} ! cap analysis of gene expression evidence is_a: ECO:0007303 {is_inferred="true"} ! transcript expression evidence used in automatic assertion intersection_of: ECO:0000309 ! cap analysis of gene expression evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007249 name: nano-cap analysis of gene expression evidence used in automatic assertion def: "A type of nano-cap analysis of gene expression evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000310 {is_inferred="true"} ! nano-cap analysis of gene expression evidence is_a: ECO:0007303 {is_inferred="true"} ! transcript expression evidence used in automatic assertion intersection_of: ECO:0000310 ! nano-cap analysis of gene expression evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007250 name: particle size and count assay evidence used in automatic assertion def: "A type of particle size and count assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000334 {is_inferred="true"} ! particle size and count assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000334 ! particle size and count assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007251 name: competitive growth assay evidence used in automatic assertion def: "A type of competitive growth assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000336 {is_inferred="true"} ! competitive growth assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000336 ! competitive growth assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007252 name: pulsed-field gel electrophoresis evidence used in automatic assertion def: "A type of pulsed-field gel electrophoresis evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000338 {is_inferred="true"} ! pulsed-field gel electrophoresis evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000338 ! pulsed-field gel electrophoresis evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007253 name: two-dimensional agarose gel electrophoresis evidence used in automatic assertion def: "A type of two-dimensional agarose gel electrophoresis evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000339 {is_inferred="true"} ! two-dimensional agarose gel electrophoresis evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000339 ! two-dimensional agarose gel electrophoresis evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007254 name: plasmid maintenance assay evidence used in automatic assertion def: "A type of plasmid maintenance assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000340 {is_inferred="true"} ! plasmid maintenance assay evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000340 ! plasmid maintenance assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007255 name: specific protein inhibition by antibody evidence used in automatic assertion def: "A type of specific protein inhibition by antibody evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000341 {is_inferred="true"} ! specific protein inhibition by antibody evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000341 ! specific protein inhibition by antibody evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007256 name: single exon transcript confirmation via alignment evidence used in automatic assertion def: "A type of single exon transcript confirmation via alignment evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000248 {is_inferred="true"} ! sequence alignment evidence used in automatic assertion is_a: ECO:0000345 {is_inferred="true"} ! single exon transcript confirmation via alignment evidence intersection_of: ECO:0000345 ! single exon transcript confirmation via alignment evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007257 name: phylogenetic distribution evidence used in automatic assertion def: "A type of phylogenetic distribution evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000251 {is_inferred="true"} ! similarity evidence used in automatic assertion is_a: ECO:0000355 {is_inferred="true"} ! phylogenetic distribution evidence intersection_of: ECO:0000355 ! phylogenetic distribution evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007258 name: differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) used in automatic assertion def: "A type of differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000358 {is_inferred="true"} ! differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) is_a: ECO:0007303 {is_inferred="true"} ! transcript expression evidence used in automatic assertion intersection_of: ECO:0000358 ! differential geneset expression evidence from microarray experiment (GSEA, Fisher-exact) intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007259 name: differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) used in automatic assertion def: "A type of differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000359 {is_inferred="true"} ! differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) is_a: ECO:0007303 {is_inferred="true"} ! transcript expression evidence used in automatic assertion intersection_of: ECO:0000359 ! differential geneset expression evidence from RNA-seq experiment (GSEA, Fisher-exact) intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007260 name: biological target-disease association via drug used in automatic assertion def: "A type of biological target-disease association via drug that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000360 {is_inferred="true"} ! biological target-disease association via drug is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000360 ! biological target-disease association via drug intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007261 name: cell staining evidence used in automatic assertion def: "A type of cell staining evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001603 {is_inferred="true"} ! cell staining evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001603 ! cell staining evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007262 name: visual sequence inspection evidence used in automatic assertion def: "A type of visual sequence inspection evidence that is used in an automatic assertion." [ECO:RCT] is_obsolete: true created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007263 name: ATP bioluminescence assay evidence used in automatic assertion def: "A type of ATP bioluminescence assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005011 {is_inferred="true"} ! ATP bioluminescence assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0005011 ! ATP bioluminescence assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007264 name: missense mutation evidence used in automatic assertion def: "A type of missense mutation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005506 {is_inferred="true"} ! missense mutation evidence is_a: ECO:0007448 {is_inferred="true"} ! point mutation evidence used in automatic assertion intersection_of: ECO:0005506 ! missense mutation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007265 name: nonsense mutation evidence used in automatic assertion def: "A type of nonsense mutation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005507 {is_inferred="true"} ! nonsense mutation evidence is_a: ECO:0007448 {is_inferred="true"} ! point mutation evidence used in automatic assertion intersection_of: ECO:0005507 ! nonsense mutation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007266 name: silent mutation evidence used in automatic assertion def: "A type of silent mutation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005508 {is_inferred="true"} ! silent mutation evidence is_a: ECO:0007448 {is_inferred="true"} ! point mutation evidence used in automatic assertion intersection_of: ECO:0005508 ! silent mutation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007267 name: insertion mutation evidence used in automatic assertion def: "A type of insertion mutation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005509 {is_inferred="true"} ! insertion mutation evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0005509 ! insertion mutation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007268 name: duplication mutation evidence used in automatic assertion def: "A type of duplication mutation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005511 {is_inferred="true"} ! duplication mutation evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0005511 ! duplication mutation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007269 name: frameshift mutation evidence used in automatic assertion def: "A type of frameshift mutation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005512 {is_inferred="true"} ! frameshift mutation evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0005512 ! frameshift mutation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007270 name: repeat expansion mutation evidence used in automatic assertion def: "A type of repeat expansion mutation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005513 {is_inferred="true"} ! repeat expansion mutation evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0005513 ! repeat expansion mutation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007271 name: splice site mutation evidence used in automatic assertion def: "A type of splice site mutation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005514 {is_inferred="true"} ! splice site mutation evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0005514 ! splice site mutation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007272 name: translocation mutation evidence used in automatic assertion def: "A type of translocation mutation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005515 {is_inferred="true"} ! translocation mutation evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0005515 ! translocation mutation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007273 name: in-gel protein kinase assay evidence used in automatic assertion def: "A type of in-gel protein kinase assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005562 {is_inferred="true"} ! in-gel protein kinase assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0005562 ! in-gel protein kinase assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007274 name: macroscopic current trace evidence used in automatic assertion def: "A type of macroscopic current trace evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005563 {is_inferred="true"} ! macroscopic current trace evidence is_a: ECO:0007535 {is_inferred="true"} ! electrophysiology assay evidence used in automatic assertion intersection_of: ECO:0005563 ! macroscopic current trace evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007275 name: current density evidence used in automatic assertion def: "A type of current density evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005564 {is_inferred="true"} ! current density evidence is_a: ECO:0007535 {is_inferred="true"} ! electrophysiology assay evidence used in automatic assertion intersection_of: ECO:0005564 ! current density evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007276 name: sustained current evidence used in automatic assertion def: "A type of sustained current evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005566 {is_inferred="true"} ! sustained current evidence is_a: ECO:0007535 {is_inferred="true"} ! electrophysiology assay evidence used in automatic assertion intersection_of: ECO:0005566 ! sustained current evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007277 name: use dependence of inactivation evidence used in automatic assertion def: "A type of use dependence of inactivation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005570 {is_inferred="true"} ! use dependence of inactivation evidence is_a: ECO:0007535 {is_inferred="true"} ! electrophysiology assay evidence used in automatic assertion intersection_of: ECO:0005570 ! use dependence of inactivation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007278 name: current clamp recording evidence used in automatic assertion def: "A type of current clamp recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005571 {is_inferred="true"} ! current clamp recording evidence is_a: ECO:0007535 {is_inferred="true"} ! electrophysiology assay evidence used in automatic assertion intersection_of: ECO:0005571 ! current clamp recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007279 name: whole-cell voltage clamp recording evidence used in automatic assertion def: "A type of whole-cell voltage clamp recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005572 {is_inferred="true"} ! whole-cell voltage clamp recording evidence is_a: ECO:0007535 {is_inferred="true"} ! electrophysiology assay evidence used in automatic assertion intersection_of: ECO:0005572 ! whole-cell voltage clamp recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007280 name: cell-attached single-channel recording evidence used in automatic assertion def: "A type of cell-attached single-channel recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005573 {is_inferred="true"} ! cell-attached single-channel recording evidence is_a: ECO:0007537 {is_inferred="true"} ! patch-clamp recording evidence used in automatic assertion intersection_of: ECO:0005573 ! cell-attached single-channel recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007281 name: cell-detached inside-out single-channel recording evidence used in automatic assertion def: "A type of cell-detached inside-out single-channel recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005574 {is_inferred="true"} ! cell-detached inside-out single-channel recording evidence is_a: ECO:0007537 {is_inferred="true"} ! patch-clamp recording evidence used in automatic assertion intersection_of: ECO:0005574 ! cell-detached inside-out single-channel recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007282 name: reconstituted bilayer single-channel patch recording evidence used in automatic assertion def: "A type of reconstituted bilayer single-channel patch recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005575 {is_inferred="true"} ! reconstituted bilayer single-channel patch recording evidence is_a: ECO:0007537 {is_inferred="true"} ! patch-clamp recording evidence used in automatic assertion intersection_of: ECO:0005575 ! reconstituted bilayer single-channel patch recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007283 name: electroencephalography recording evidence used in automatic assertion def: "A type of electroencephalography recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005577 {is_inferred="true"} ! electroencephalography recording evidence is_a: ECO:0007535 {is_inferred="true"} ! electrophysiology assay evidence used in automatic assertion intersection_of: ECO:0005577 ! electroencephalography recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007284 name: cell-detached outside-out single-channel recording evidence used in automatic assertion def: "A type of cell-detached outside-out single-channel recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005582 {is_inferred="true"} ! cell-detached outside-out single-channel recording evidence is_a: ECO:0007537 {is_inferred="true"} ! patch-clamp recording evidence used in automatic assertion intersection_of: ECO:0005582 ! cell-detached outside-out single-channel recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007285 name: cut-open oocyte voltage clamp recording evidence used in automatic assertion def: "A type of cut-open oocyte voltage clamp recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005583 {is_inferred="true"} ! cut-open oocyte voltage clamp recording evidence is_a: ECO:0007535 {is_inferred="true"} ! electrophysiology assay evidence used in automatic assertion intersection_of: ECO:0005583 ! cut-open oocyte voltage clamp recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007286 name: macropatch voltage clamp recording evidence used in automatic assertion def: "A type of macropatch voltage clamp recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005584 {is_inferred="true"} ! macropatch voltage clamp recording evidence is_a: ECO:0007535 {is_inferred="true"} ! electrophysiology assay evidence used in automatic assertion intersection_of: ECO:0005584 ! macropatch voltage clamp recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007287 name: protein expression level evidence based on western blot used in automatic assertion def: "A type of protein expression level evidence based on western blot that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005602 {is_inferred="true"} ! protein expression level evidence based on western blot is_a: ECO:0007306 {is_inferred="true"} ! western blot evidence used in automatic assertion is_a: ECO:0007308 {is_inferred="true"} ! protein expression level evidence used in automatic assertion intersection_of: ECO:0005602 ! protein expression level evidence based on western blot intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007288 name: protein mass spectrometry evidence used in automatic assertion def: "A type of protein mass spectrometry evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005603 {is_inferred="true"} ! protein mass spectrometry evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion is_a: ECO:0007433 {is_inferred="true"} ! mass spectrometry evidence used in automatic assertion intersection_of: ECO:0005603 ! protein mass spectrometry evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007289 name: cross-streak test evidence used in automatic assertion def: "A type of cross-streak test evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005604 {is_inferred="true"} ! cross-streak test evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0005604 ! cross-streak test evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007290 name: tethered cell assay evidence used in automatic assertion def: "A type of tethered cell assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005607 {is_inferred="true"} ! tethered cell assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0005607 ! tethered cell assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007291 name: tumble frequency assay evidence used in automatic assertion def: "A type of tumble frequency assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005608 {is_inferred="true"} ! tumble frequency assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0005608 ! tumble frequency assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007292 name: capillary assay evidence used in automatic assertion def: "A type of capillary assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005609 {is_inferred="true"} ! capillary assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0005609 ! capillary assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007293 name: inference from experimental data evidence used in automatic assertion def: "A type of inference from experimental data evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005611 {is_inferred="true"} ! inference from experimental data evidence is_a: ECO:0007189 {is_inferred="true"} ! inference from experimental data evidence used in manual assertion is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0005611 ! inference from experimental data evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007294 name: inference from phenotype manipulation evidence used in automatic assertion def: "A type of inference from phenotype manipulation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005612 {is_inferred="true"} ! inference from phenotype manipulation evidence is_a: ECO:0007190 {is_inferred="true"} ! inference from phenotype manipulation evidence used in manual assertion is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0005612 ! inference from phenotype manipulation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007295 name: inference by association of genotype from phenotype used in automatic assertion def: "A type of inference by association of genotype from phenotype that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005613 {is_inferred="true"} ! inference by association of genotype from phenotype is_a: ECO:0007191 {is_inferred="true"} ! inference by association of genotype from phenotype used in manual assertion is_a: ECO:0007440 {is_inferred="true"} ! natural variation mutant evidence used in automatic assertion intersection_of: ECO:0005613 ! inference by association of genotype from phenotype intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007296 name: motility assay evidence used in automatic assertion def: "A type of motility assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005803 {is_inferred="true"} ! motility assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0005803 ! motility assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007297 name: experimental evidence used in automatic assertion def: "A type of experimental evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000006 {is_inferred="true"} ! experimental evidence is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion intersection_of: ECO:0000006 ! experimental evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007298 name: expression pattern evidence used in automatic assertion def: "A type of expression pattern evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000008 {is_inferred="true"} ! expression pattern evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000008 ! expression pattern evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007299 name: Affymetrix GeneChip evidence used in automatic assertion def: "A type of Affymetrix GeneChip evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000101 {is_inferred="true"} ! Affymetrix GeneChip evidence is_a: ECO:0007300 {is_inferred="true"} ! cRNA to DNA expression microarray evidence used in automatic assertion intersection_of: ECO:0000101 ! Affymetrix GeneChip evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007300 name: cRNA to DNA expression microarray evidence used in automatic assertion def: "A type of cRNA to DNA expression microarray evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000062 {is_inferred="true"} ! cRNA to DNA expression microarray evidence is_a: ECO:0007301 {is_inferred="true"} ! expression microarray evidence used in automatic assertion intersection_of: ECO:0000062 ! cRNA to DNA expression microarray evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007301 name: expression microarray evidence used in automatic assertion def: "A type of expression microarray evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000058 {is_inferred="true"} ! expression microarray evidence is_a: ECO:0007303 {is_inferred="true"} ! transcript expression evidence used in automatic assertion intersection_of: ECO:0000058 ! expression microarray evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007302 name: differential methylation hybridization evidence used in automatic assertion def: "A type of differential methylation hybridization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000069 {is_inferred="true"} ! differential methylation hybridization evidence is_a: ECO:0007401 {is_inferred="true"} ! in vitro methylation assay evidence used in automatic assertion intersection_of: ECO:0000069 ! differential methylation hybridization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007303 name: transcript expression evidence used in automatic assertion def: "A type of transcript expression evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000009 {is_inferred="true"} ! transcript expression evidence is_a: ECO:0007298 {is_inferred="true"} ! expression pattern evidence used in automatic assertion intersection_of: ECO:0000009 ! transcript expression evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007304 name: Nimblegen array evidence used in automatic assertion def: "A type of Nimblegen array evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000105 {is_inferred="true"} ! Nimblegen array evidence is_a: ECO:0005630 {is_inferred="true"} ! cDNA to DNA expression microarray evidence used in automatic assertion intersection_of: ECO:0000105 ! Nimblegen array evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007305 name: array-based sequence capture evidence used in automatic assertion def: "A type of array-based sequence capture evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000093 {is_inferred="true"} ! array-based sequence capture evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000093 ! array-based sequence capture evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007306 name: western blot evidence used in automatic assertion def: "A type of western blot evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000112 {is_inferred="true"} ! western blot evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000112 ! western blot evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007307 name: direct assay evidence used in automatic assertion def: "A type of direct assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000002 {is_inferred="true"} ! direct assay evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000002 ! direct assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007308 name: protein expression level evidence used in automatic assertion def: "A type of protein expression level evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000046 {is_inferred="true"} ! protein expression level evidence is_a: ECO:0007309 {is_inferred="true"} ! protein expression evidence used in automatic assertion intersection_of: ECO:0000046 ! protein expression level evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007309 name: protein expression evidence used in automatic assertion def: "A type of protein expression evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000010 {is_inferred="true"} ! protein expression evidence is_a: ECO:0007298 {is_inferred="true"} ! expression pattern evidence used in automatic assertion is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000010 ! protein expression evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007310 name: expression library screen evidence used in automatic assertion def: "A type of expression library screen evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000114 {is_inferred="true"} ! expression library screen evidence is_a: ECO:0007309 {is_inferred="true"} ! protein expression evidence used in automatic assertion intersection_of: ECO:0000114 ! expression library screen evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007311 name: heterologous protein expression evidence used in automatic assertion def: "A type of heterologous protein expression evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000154 {is_inferred="true"} ! heterologous protein expression evidence is_a: ECO:0007309 {is_inferred="true"} ! protein expression evidence used in automatic assertion intersection_of: ECO:0000154 ! heterologous protein expression evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007312 name: spatial pattern of protein expression evidence used in automatic assertion def: "A type of spatial pattern of protein expression evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000045 {is_inferred="true"} ! spatial pattern of protein expression evidence is_a: ECO:0007309 {is_inferred="true"} ! protein expression evidence used in automatic assertion intersection_of: ECO:0000045 ! spatial pattern of protein expression evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007313 name: DNA to cDNA expression microarray evidence used in automatic assertion def: "A type of DNA to cDNA expression microarray evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000104 {is_inferred="true"} ! DNA to cDNA expression microarray evidence is_a: ECO:0007301 {is_inferred="true"} ! expression microarray evidence used in automatic assertion intersection_of: ECO:0000104 ! DNA to cDNA expression microarray evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007314 name: differential hybridization evidence used in automatic assertion def: "A type of differential hybridization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000116 {is_inferred="true"} ! differential hybridization evidence is_a: ECO:0007303 {is_inferred="true"} ! transcript expression evidence used in automatic assertion intersection_of: ECO:0000116 ! differential hybridization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007315 name: RNA protection assay evidence used in automatic assertion def: "A type of RNA protection assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000110 {is_inferred="true"} ! RNA protection assay evidence is_a: ECO:0007316 {is_inferred="true"} ! nuclease protection assay evidence used in automatic assertion intersection_of: ECO:0000110 ! RNA protection assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007316 name: nuclease protection assay evidence used in automatic assertion def: "A type of nuclease protection assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001106 {is_inferred="true"} ! nuclease protection assay evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001106 ! nuclease protection assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007317 name: spatial pattern of transcript expression evidence used in automatic assertion def: "A type of spatial pattern of transcript expression evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000047 {is_inferred="true"} ! spatial pattern of transcript expression evidence is_a: ECO:0007303 {is_inferred="true"} ! transcript expression evidence used in automatic assertion intersection_of: ECO:0000047 ! spatial pattern of transcript expression evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007318 name: subtractive hybridization evidence used in automatic assertion def: "A type of subtractive hybridization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000118 {is_inferred="true"} ! subtractive hybridization evidence is_a: ECO:0007303 {is_inferred="true"} ! transcript expression evidence used in automatic assertion intersection_of: ECO:0000118 ! subtractive hybridization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007319 name: author statement used in automatic assertion def: "A type of author statement that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000204 {is_inferred="true"} ! author statement is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion intersection_of: ECO:0000204 ! author statement intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007320 name: author statement without traceable support used in automatic assertion def: "A type of author statement without traceable support that is used in an automatic assertion." [ECO:RCT] synonym: "non-traceable author statement used in automatic assertion" RELATED [] is_a: ECO:0000034 {is_inferred="true"} ! author statement without traceable support is_a: ECO:0007319 {is_inferred="true"} ! author statement used in automatic assertion intersection_of: ECO:0000034 ! author statement without traceable support intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007321 name: author statement supported by traceable reference used in automatic assertion def: "A type of author statement supported by traceable reference that is used in an automatic assertion." [ECO:RCT] synonym: "traceable author statement used in automatic assertion" RELATED [] is_a: ECO:0000033 {is_inferred="true"} ! author statement supported by traceable reference is_a: ECO:0007319 {is_inferred="true"} ! author statement used in automatic assertion intersection_of: ECO:0000033 ! author statement supported by traceable reference intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007322 name: curator inference used in automatic assertion def: "A type of curator inference that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000205 {is_inferred="true"} ! curator inference is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion intersection_of: ECO:0000205 ! curator inference intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007323 name: inference from background scientific knowledge used in automatic assertion def: "A type of inference from background scientific knowledge that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000001 {is_inferred="true"} ! inference from background scientific knowledge is_a: ECO:0007322 {is_inferred="true"} ! curator inference used in automatic assertion intersection_of: ECO:0000001 ! inference from background scientific knowledge intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007324 name: no biological data found used in automatic assertion def: "A type of no biological data found that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000035 {is_inferred="true"} ! no biological data found is_a: ECO:0007322 {is_inferred="true"} ! curator inference used in automatic assertion intersection_of: ECO:0000035 ! no biological data found intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007325 name: mutant phenotype evidence used in automatic assertion def: "A type of mutant phenotype evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000015 {is_inferred="true"} ! mutant phenotype evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0000015 ! mutant phenotype evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007326 name: genetic interaction evidence used in automatic assertion def: "A type of genetic interaction evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000011 {is_inferred="true"} ! genetic interaction evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0000011 ! genetic interaction evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007327 name: genomic context evidence used in automatic assertion def: "A type of genomic context evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000177 {is_inferred="true"} ! genomic context evidence is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion intersection_of: ECO:0000177 ! genomic context evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007328 name: biological aspect of ancestor evidence used in automatic assertion def: "A type of biological aspect of ancestor evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000251 {is_inferred="true"} ! similarity evidence used in automatic assertion is_a: ECO:0000308 {is_inferred="true"} ! biological aspect of ancestor evidence intersection_of: ECO:0000308 ! biological aspect of ancestor evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007329 name: biological aspect of descendant evidence used in automatic assertion def: "A type of biological aspect of descendant evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000214 {is_inferred="true"} ! biological aspect of descendant evidence is_a: ECO:0000251 {is_inferred="true"} ! similarity evidence used in automatic assertion intersection_of: ECO:0000214 ! biological aspect of descendant evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007330 name: phylogenetic determination of loss of key residues evidence used in automatic assertion def: "A type of phylogenetic determination of loss of key residues evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000216 {is_inferred="true"} ! phylogenetic determination of loss of key residues evidence is_a: ECO:0000251 {is_inferred="true"} ! similarity evidence used in automatic assertion intersection_of: ECO:0000216 ! phylogenetic determination of loss of key residues evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007331 name: rapid divergence from ancestral sequence evidence used in automatic assertion def: "A type of rapid divergence from ancestral sequence evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000215 {is_inferred="true"} ! rapid divergence from ancestral sequence evidence is_a: ECO:0000251 {is_inferred="true"} ! similarity evidence used in automatic assertion intersection_of: ECO:0000215 ! rapid divergence from ancestral sequence evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007332 name: physical interaction evidence used in automatic assertion def: "A type of physical interaction evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000021 {is_inferred="true"} ! physical interaction evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000021 ! physical interaction evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007333 name: gene neighbors evidence used in automatic assertion def: "A type of gene neighbors evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000084 {is_inferred="true"} ! gene neighbors evidence is_a: ECO:0007327 {is_inferred="true"} ! genomic context evidence used in automatic assertion intersection_of: ECO:0000084 ! gene neighbors evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007334 name: Edman degradation evidence used in automatic assertion def: "A type of Edman degradation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001044 {is_inferred="true"} ! Edman degradation evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001044 ! Edman degradation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007335 name: 3D cell culture evidence used in automatic assertion def: "A type of 3D cell culture evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001001 {is_inferred="true"} ! 3D cell culture evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001001 ! 3D cell culture evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007336 name: 51Cr release assay evidence used in automatic assertion def: "A type of 51Cr release assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001004 {is_inferred="true"} ! 51Cr release assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001004 ! 51Cr release assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007337 name: 7-aminoactinomycin staining evidence used in automatic assertion def: "A type of 7-aminoactinomycin staining evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001005 {is_inferred="true"} ! 7-aminoactinomycin staining evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001005 ! 7-aminoactinomycin staining evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007338 name: [3H]-thymidine incorporation assay evidence used in automatic assertion def: "A type of [3H]-thymidine incorporation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001003 {is_inferred="true"} ! [3H]-thymidine incorporation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001003 ! [3H]-thymidine incorporation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007339 name: [3H]arachidonic acid release assay evidence used in automatic assertion def: "A type of [3H]arachidonic acid release assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001002 {is_inferred="true"} ! [3H]arachidonic acid release assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001002 ! [3H]arachidonic acid release assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007340 name: adhesion assay evidence used in automatic assertion def: "A type of adhesion assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001006 {is_inferred="true"} ! adhesion assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001006 ! adhesion assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007341 name: adoptive cell transfer evidence used in automatic assertion def: "A type of adoptive cell transfer evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001007 {is_inferred="true"} ! adoptive cell transfer evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001007 ! adoptive cell transfer evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007342 name: alamarBlue assay evidence used in automatic assertion def: "A type of alamarBlue assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001008 {is_inferred="true"} ! alamarBlue assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001008 ! alamarBlue assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007343 name: allograft transplantation experiment evidence used in automatic assertion def: "A type of allograft transplantation experiment evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001009 {is_inferred="true"} ! allograft transplantation experiment evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001009 ! allograft transplantation experiment evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007344 name: anion-exchange chromatography evidence used in automatic assertion def: "A type of anion-exchange chromatography evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001010 {is_inferred="true"} ! anion-exchange chromatography evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001010 ! anion-exchange chromatography evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007345 name: annexin-V staining evidence used in automatic assertion def: "A type of annexin-V staining evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001011 {is_inferred="true"} ! annexin-V staining evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001011 ! annexin-V staining evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007346 name: behavioral assay evidence used in automatic assertion def: "A type of behavioral assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001012 {is_inferred="true"} ! behavioral assay evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001012 ! behavioral assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007347 name: blocking monoclonal antibody evidence used in automatic assertion def: "A type of blocking monoclonal antibody evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001013 {is_inferred="true"} ! blocking monoclonal antibody evidence is_a: ECO:0007348 {is_inferred="true"} ! immunological assay evidence used in automatic assertion intersection_of: ECO:0001013 ! blocking monoclonal antibody evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007348 name: immunological assay evidence used in automatic assertion def: "A type of immunological assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000040 {is_inferred="true"} ! immunological assay evidence is_a: ECO:0007384 {is_inferred="true"} ! affinity evidence used in automatic assertion intersection_of: ECO:0000040 ! immunological assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007349 name: blocking peptide evidence used in automatic assertion def: "A type of blocking peptide evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001014 {is_inferred="true"} ! blocking peptide evidence is_a: ECO:0007348 {is_inferred="true"} ! immunological assay evidence used in automatic assertion intersection_of: ECO:0001014 ! blocking peptide evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007350 name: blocking polyclonal antibody evidence used in automatic assertion def: "A type of blocking polyclonal antibody evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001015 {is_inferred="true"} ! blocking polyclonal antibody evidence is_a: ECO:0007348 {is_inferred="true"} ! immunological assay evidence used in automatic assertion intersection_of: ECO:0001015 ! blocking polyclonal antibody evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007351 name: blood test evidence used in automatic assertion def: "A type of blood test evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001016 {is_inferred="true"} ! blood test evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001016 ! blood test evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007352 name: Boyden chamber assay evidence used in automatic assertion def: "A type of Boyden chamber assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001017 {is_inferred="true"} ! Boyden chamber assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001017 ! Boyden chamber assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007353 name: bromodeoxyuridine incorporation assay evidence used in automatic assertion def: "A type of bromodeoxyuridine incorporation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001018 {is_inferred="true"} ! bromodeoxyuridine incorporation assay evidence is_a: ECO:0007354 {is_inferred="true"} ! nucleotide analog incorporation assay evidence used in automatic assertion intersection_of: ECO:0001018 ! bromodeoxyuridine incorporation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007354 name: nucleotide analog incorporation assay evidence used in automatic assertion def: "A type of nucleotide analog incorporation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001107 {is_inferred="true"} ! nucleotide analog incorporation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001107 ! nucleotide analog incorporation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007355 name: caspase assay evidence used in automatic assertion def: "A type of caspase assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001019 {is_inferred="true"} ! caspase assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001019 ! caspase assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007356 name: cell counting evidence used in automatic assertion def: "A type of cell counting evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001020 {is_inferred="true"} ! cell counting evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001020 ! cell counting evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007357 name: cell permeability assay evidence used in automatic assertion def: "A type of cell permeability assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001021 {is_inferred="true"} ! cell permeability assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001021 ! cell permeability assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007358 name: carboxyfluorescein diacetate succinimidyl ester staining evidence used in automatic assertion def: "A type of carboxyfluorescein diacetate succinimidyl ester staining evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001022 {is_inferred="true"} ! carboxyfluorescein diacetate succinimidyl ester staining evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001022 ! carboxyfluorescein diacetate succinimidyl ester staining evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007359 name: chemiluminescence-linked immunoassay evidence used in automatic assertion def: "A type of chemiluminescence-linked immunoassay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001023 {is_inferred="true"} ! chemiluminescence-linked immunoassay evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001023 ! chemiluminescence-linked immunoassay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007360 name: chimeric protein evidence used in automatic assertion def: "A type of chimeric protein evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001024 {is_inferred="true"} ! chimeric protein evidence is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0001024 ! chimeric protein evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007361 name: co-electrophoresis evidence used in automatic assertion def: "A type of co-electrophoresis evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001025 {is_inferred="true"} ! co-electrophoresis evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001025 ! co-electrophoresis evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007362 name: co-localization evidence used in automatic assertion def: "A type of co-localization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001026 {is_inferred="true"} ! co-localization evidence is_a: ECO:0007363 {is_inferred="true"} ! imaging assay evidence used in automatic assertion intersection_of: ECO:0001026 ! co-localization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007363 name: imaging assay evidence used in automatic assertion def: "A type of imaging assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000324 {is_inferred="true"} ! imaging assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000324 ! imaging assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007364 name: co-sedimentation assay evidence used in automatic assertion def: "A type of co-sedimentation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001028 {is_inferred="true"} ! co-sedimentation assay evidence is_a: ECO:0007332 {is_inferred="true"} ! physical interaction evidence used in automatic assertion intersection_of: ECO:0001028 ! co-sedimentation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007365 name: colony counting evidence used in automatic assertion def: "A type of colony counting evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001027 {is_inferred="true"} ! colony counting evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001027 ! colony counting evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007366 name: comet assay evidence used in automatic assertion def: "A type of comet assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001029 {is_inferred="true"} ! comet assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001029 ! comet assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007367 name: conditional knockin evidence used in automatic assertion def: "A type of conditional knockin evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001031 {is_inferred="true"} ! conditional knockin evidence is_a: ECO:0007368 {is_inferred="true"} ! knockin evidence used in automatic assertion intersection_of: ECO:0001031 ! conditional knockin evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007368 name: knockin evidence used in automatic assertion def: "A type of knockin evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001090 {is_inferred="true"} ! knockin evidence is_a: ECO:0007427 {is_inferred="true"} ! genetic transformation evidence used in automatic assertion intersection_of: ECO:0001090 ! knockin evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007369 name: conditional knockout evidence used in automatic assertion def: "A type of conditional knockout evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001030 {is_inferred="true"} ! conditional knockout evidence is_a: ECO:0007370 {is_inferred="true"} ! knockout evidence used in automatic assertion intersection_of: ECO:0001030 ! conditional knockout evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007370 name: knockout evidence used in automatic assertion def: "A type of knockout evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001091 {is_inferred="true"} ! knockout evidence is_a: ECO:0007427 {is_inferred="true"} ! genetic transformation evidence used in automatic assertion intersection_of: ECO:0001091 ! knockout evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007371 name: constitutively active mutant evidence used in automatic assertion def: "A type of constitutively active mutant evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001032 {is_inferred="true"} ! constitutively active mutant evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001032 ! constitutively active mutant evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007372 name: cross-linking evidence used in automatic assertion def: "A type of cross-linking evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001033 {is_inferred="true"} ! cross-linking evidence is_a: ECO:0007373 {is_inferred="true"} ! protein binding evidence used in automatic assertion intersection_of: ECO:0001033 ! cross-linking evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007373 name: protein binding evidence used in automatic assertion def: "A type of protein binding evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000024 {is_inferred="true"} ! protein binding evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion is_a: ECO:0007384 {is_inferred="true"} ! affinity evidence used in automatic assertion intersection_of: ECO:0000024 ! protein binding evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007374 name: crystallography evidence used in automatic assertion def: "A type of crystallography evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001034 {is_inferred="true"} ! crystallography evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001034 ! crystallography evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007375 name: cytochemistry evidence used in automatic assertion def: "A type of cytochemistry evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001035 {is_inferred="true"} ! cytochemistry evidence is_a: ECO:0007376 {is_inferred="true"} ! histochemistry evidence used in automatic assertion intersection_of: ECO:0001035 ! cytochemistry evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007376 name: histochemistry evidence used in automatic assertion def: "A type of histochemistry evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001050 {is_inferred="true"} ! histochemistry evidence is_a: ECO:0007389 {is_inferred="true"} ! histology evidence used in automatic assertion intersection_of: ECO:0001050 ! histochemistry evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007377 name: cytochrome C release assay evidence used in automatic assertion def: "A type of cytochrome C release assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001036 {is_inferred="true"} ! cytochrome C release assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001036 ! cytochrome C release assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007378 name: 4',6-diamidino-2-phenylindole staining evidence used in automatic assertion def: "A type of 4',6-diamidino-2-phenylindole staining evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001037 {is_inferred="true"} ! 4',6-diamidino-2-phenylindole staining evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001037 ! 4',6-diamidino-2-phenylindole staining evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007379 name: deletion mutation evidence used in automatic assertion def: "A type of deletion mutation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001038 {is_inferred="true"} ! deletion mutation evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001038 ! deletion mutation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007380 name: DNA laddering assay evidence used in automatic assertion def: "A type of DNA laddering assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001039 {is_inferred="true"} ! DNA laddering assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001039 ! DNA laddering assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007381 name: RNA dot blot assay evidence used in automatic assertion def: "A type of RNA dot blot assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001040 {is_inferred="true"} ! RNA dot blot assay evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001040 ! RNA dot blot assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007382 name: dominant-negative mutant evidence used in automatic assertion def: "A type of dominant-negative mutant evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001042 {is_inferred="true"} ! dominant-negative mutant evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001042 ! dominant-negative mutant evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007383 name: eTag assay evidence used in automatic assertion def: "A type of eTag assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001045 {is_inferred="true"} ! eTag assay evidence is_a: ECO:0007384 {is_inferred="true"} ! affinity evidence used in automatic assertion intersection_of: ECO:0001045 ! eTag assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007384 name: affinity evidence used in automatic assertion def: "A type of affinity evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000023 {is_inferred="true"} ! affinity evidence is_a: ECO:0007332 {is_inferred="true"} ! physical interaction evidence used in automatic assertion intersection_of: ECO:0000023 ! affinity evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007385 name: filter binding assay evidence used in automatic assertion def: "A type of filter binding assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001046 {is_inferred="true"} ! filter binding assay evidence is_a: ECO:0007332 {is_inferred="true"} ! physical interaction evidence used in automatic assertion intersection_of: ECO:0001046 ! filter binding assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007386 name: fluorescence in situ hybridization evidence used in automatic assertion def: "A type of fluorescence in situ hybridization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001047 {is_inferred="true"} ! fluorescence in situ hybridization evidence is_a: ECO:0007298 {is_inferred="true"} ! expression pattern evidence used in automatic assertion is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001047 ! fluorescence in situ hybridization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007387 name: fluorescence resonance energy transfer evidence used in automatic assertion def: "A type of fluorescence resonance energy transfer evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001048 {is_inferred="true"} ! fluorescence resonance energy transfer evidence is_a: ECO:0007332 {is_inferred="true"} ! physical interaction evidence used in automatic assertion intersection_of: ECO:0001048 ! fluorescence resonance energy transfer evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007388 name: gel-filtration evidence used in automatic assertion def: "A type of gel-filtration evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001049 {is_inferred="true"} ! gel-filtration evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001049 ! gel-filtration evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007389 name: histology evidence used in automatic assertion def: "A type of histology evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001051 {is_inferred="true"} ! histology evidence is_a: ECO:0007363 {is_inferred="true"} ! imaging assay evidence used in automatic assertion intersection_of: ECO:0001051 ! histology evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007390 name: immunocytochemistry evidence used in automatic assertion def: "A type of immunocytochemistry evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001053 {is_inferred="true"} ! immunocytochemistry evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001053 ! immunocytochemistry evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007391 name: immunodepletion evidence used in automatic assertion def: "A type of immunodepletion evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001054 {is_inferred="true"} ! immunodepletion evidence is_a: ECO:0007348 {is_inferred="true"} ! immunological assay evidence used in automatic assertion intersection_of: ECO:0001054 ! immunodepletion evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007392 name: immunohistochemistry evidence used in automatic assertion def: "A type of immunohistochemistry evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001055 {is_inferred="true"} ! immunohistochemistry evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001055 ! immunohistochemistry evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007393 name: in vitro acetylation assay evidence used in automatic assertion def: "A type of in vitro acetylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001057 {is_inferred="true"} ! in vitro acetylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001057 ! in vitro acetylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007394 name: in vitro cleavage assay evidence used in automatic assertion def: "A type of in vitro cleavage assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001058 {is_inferred="true"} ! in vitro cleavage assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001058 ! in vitro cleavage assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007395 name: in vitro deacetylation assay evidence used in automatic assertion def: "A type of in vitro deacetylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001060 {is_inferred="true"} ! in vitro deacetylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001060 ! in vitro deacetylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007396 name: in vitro defarnesylation assay evidence used in automatic assertion def: "A type of in vitro defarnesylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001061 {is_inferred="true"} ! in vitro defarnesylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001061 ! in vitro defarnesylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007397 name: in vitro demethylation assay evidence used in automatic assertion def: "A type of in vitro demethylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001062 {is_inferred="true"} ! in vitro demethylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001062 ! in vitro demethylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007398 name: in vitro desumoylation assay evidence used in automatic assertion def: "A type of in vitro desumoylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001063 {is_inferred="true"} ! in vitro desumoylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001063 ! in vitro desumoylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007399 name: in vitro deubiquitination assay evidence used in automatic assertion def: "A type of in vitro deubiquitination assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001059 {is_inferred="true"} ! in vitro deubiquitination assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001059 ! in vitro deubiquitination assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007400 name: in vitro farnesylation assay evidence used in automatic assertion def: "A type of in vitro farnesylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001064 {is_inferred="true"} ! in vitro farnesylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001064 ! in vitro farnesylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007401 name: in vitro methylation assay evidence used in automatic assertion def: "A type of in vitro methylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001065 {is_inferred="true"} ! in vitro methylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001065 ! in vitro methylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007402 name: in vitro palmitoylation assay evidence used in automatic assertion def: "A type of in vitro palmitoylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001066 {is_inferred="true"} ! in vitro palmitoylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001066 ! in vitro palmitoylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007403 name: in vitro phosphatase assay evidence used in automatic assertion def: "A type of in vitro phosphatase assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001067 {is_inferred="true"} ! in vitro phosphatase assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001067 ! in vitro phosphatase assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007404 name: in vitro polyADP-ribosylation assay evidence used in automatic assertion def: "A type of in vitro polyADP-ribosylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001069 {is_inferred="true"} ! in vitro polyADP-ribosylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001069 ! in vitro polyADP-ribosylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007405 name: in vitro protein kinase assay evidence used in automatic assertion def: "A type of in vitro protein kinase assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001068 {is_inferred="true"} ! in vitro protein kinase assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001068 ! in vitro protein kinase assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007406 name: in vitro sumoylation assay evidence used in automatic assertion def: "A type of in vitro sumoylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001070 {is_inferred="true"} ! in vitro sumoylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001070 ! in vitro sumoylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007407 name: in vitro transcription assay evidence used in automatic assertion def: "A type of in vitro transcription assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001071 {is_inferred="true"} ! in vitro transcription assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001071 ! in vitro transcription assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007408 name: in vitro translation assay evidence used in automatic assertion def: "A type of in vitro translation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001072 {is_inferred="true"} ! in vitro translation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001072 ! in vitro translation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007409 name: in vitro ubiquitination assay evidence used in automatic assertion def: "A type of in vitro ubiquitination assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001073 {is_inferred="true"} ! in vitro ubiquitination assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001073 ! in vitro ubiquitination assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007410 name: in vivo acetylation assay evidence used in automatic assertion def: "A type of in vivo acetylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001074 {is_inferred="true"} ! in vivo acetylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001074 ! in vivo acetylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007411 name: in vivo cleavage assay evidence used in automatic assertion def: "A type of in vivo cleavage assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001075 {is_inferred="true"} ! in vivo cleavage assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001075 ! in vivo cleavage assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007412 name: in vivo deacetylation assay evidence used in automatic assertion def: "A type of in vivo deacetylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001076 {is_inferred="true"} ! in vivo deacetylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001076 ! in vivo deacetylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007413 name: in vivo defarnesylation assay evidence used in automatic assertion def: "A type of in vivo defarnesylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001077 {is_inferred="true"} ! in vivo defarnesylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001077 ! in vivo defarnesylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007414 name: in vivo demethylation assay evidence used in automatic assertion def: "A type of in vivo demethylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001078 {is_inferred="true"} ! in vivo demethylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001078 ! in vivo demethylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007415 name: in vivo desumoylation assay evidence used in automatic assertion def: "A type of in vivo desumoylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001080 {is_inferred="true"} ! in vivo desumoylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001080 ! in vivo desumoylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007416 name: in vivo deubiquitination assay evidence used in automatic assertion def: "A type of in vivo deubiquitination assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001079 {is_inferred="true"} ! in vivo deubiquitination assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001079 ! in vivo deubiquitination assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007417 name: in vivo farnesylation assay evidence used in automatic assertion def: "A type of in vivo farnesylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001081 {is_inferred="true"} ! in vivo farnesylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001081 ! in vivo farnesylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007418 name: in vivo methylation assay evidence used in automatic assertion def: "A type of in vivo methylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001082 {is_inferred="true"} ! in vivo methylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001082 ! in vivo methylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007419 name: in vivo palmitoylation assay evidence used in automatic assertion def: "A type of in vivo palmitoylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001083 {is_inferred="true"} ! in vivo palmitoylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001083 ! in vivo palmitoylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007420 name: in vivo phosphatase assay evidence used in automatic assertion def: "A type of in vivo phosphatase assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001084 {is_inferred="true"} ! in vivo phosphatase assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001084 ! in vivo phosphatase assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007421 name: in vivo protein kinase assay evidence used in automatic assertion def: "A type of in vivo protein kinase assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001085 {is_inferred="true"} ! in vivo protein kinase assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001085 ! in vivo protein kinase assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007422 name: in vivo sumoylation assay evidence used in automatic assertion def: "A type of in vivo sumoylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001086 {is_inferred="true"} ! in vivo sumoylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001086 ! in vivo sumoylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007423 name: in vivo transcription assay evidence used in automatic assertion def: "A type of in vivo transcription assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001087 {is_inferred="true"} ! in vivo transcription assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001087 ! in vivo transcription assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007424 name: in vivo translation assay evidence used in automatic assertion def: "A type of in vivo translation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001088 {is_inferred="true"} ! in vivo translation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001088 ! in vivo translation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007425 name: in vivo ubiquitination assay evidence used in automatic assertion def: "A type of in vivo ubiquitination assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001089 {is_inferred="true"} ! in vivo ubiquitination assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001089 ! in vivo ubiquitination assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007426 name: induced mutation evidence used in automatic assertion def: "A type of induced mutation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001056 {is_inferred="true"} ! induced mutation evidence is_a: ECO:0007427 {is_inferred="true"} ! genetic transformation evidence used in automatic assertion intersection_of: ECO:0001056 ! induced mutation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007427 name: genetic transformation evidence used in automatic assertion def: "A type of genetic transformation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005027 {is_inferred="true"} ! genetic transformation evidence is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0005027 ! genetic transformation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007428 name: lipid binding assay evidence used in automatic assertion def: "A type of lipid binding assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001092 {is_inferred="true"} ! lipid binding assay evidence is_a: ECO:0007332 {is_inferred="true"} ! physical interaction evidence used in automatic assertion intersection_of: ECO:0001092 ! lipid binding assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007429 name: luminescence-based mammalian interactome mapping assay evidence used in automatic assertion def: "A type of luminescence-based mammalian interactome mapping assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001093 {is_inferred="true"} ! luminescence-based mammalian interactome mapping assay evidence is_a: ECO:0007332 {is_inferred="true"} ! physical interaction evidence used in automatic assertion intersection_of: ECO:0001093 ! luminescence-based mammalian interactome mapping assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007430 name: macroscopy evidence used in automatic assertion def: "A type of macroscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001094 {is_inferred="true"} ! macroscopy evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001094 ! macroscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007431 name: mammalian 2-hybrid assay evidence used in automatic assertion def: "A type of mammalian 2-hybrid assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001095 {is_inferred="true"} ! mammalian 2-hybrid assay evidence is_a: ECO:0007432 {is_inferred="true"} ! hybrid interaction evidence used in automatic assertion intersection_of: ECO:0001095 ! mammalian 2-hybrid assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007432 name: hybrid interaction evidence used in automatic assertion def: "A type of hybrid interaction evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000025 {is_inferred="true"} ! hybrid interaction evidence is_a: ECO:0007384 {is_inferred="true"} ! affinity evidence used in automatic assertion intersection_of: ECO:0000025 ! hybrid interaction evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007433 name: mass spectrometry evidence used in automatic assertion def: "A type of mass spectrometry evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001096 {is_inferred="true"} ! mass spectrometry evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001096 ! mass spectrometry evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007434 name: medical imaging evidence used in automatic assertion def: "A type of medical imaging evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001097 {is_inferred="true"} ! medical imaging evidence is_a: ECO:0007363 {is_inferred="true"} ! imaging assay evidence used in automatic assertion intersection_of: ECO:0001097 ! medical imaging evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007435 name: microscopy evidence used in automatic assertion def: "A type of microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001098 {is_inferred="true"} ! microscopy evidence is_a: ECO:0007363 {is_inferred="true"} ! imaging assay evidence used in automatic assertion intersection_of: ECO:0001098 ! microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007436 name: motility wound healing assay evidence used in automatic assertion def: "A type of motility wound healing assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001099 {is_inferred="true"} ! motility wound healing assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001099 ! motility wound healing assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007437 name: MTS assay evidence used in automatic assertion def: "A type of MTS assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001100 {is_inferred="true"} ! MTS assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001100 ! MTS assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007438 name: MTT assay evidence used in automatic assertion def: "A type of MTT assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001101 {is_inferred="true"} ! MTT assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001101 ! MTT assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007439 name: multiplex bead-based immunoassay evidence used in automatic assertion def: "A type of multiplex bead-based immunoassay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001102 {is_inferred="true"} ! multiplex bead-based immunoassay evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001102 ! multiplex bead-based immunoassay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007440 name: natural variation mutant evidence used in automatic assertion def: "A type of natural variation mutant evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001103 {is_inferred="true"} ! natural variation mutant evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001103 ! natural variation mutant evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007441 name: nuclear magnetic resonance spectroscopy evidence used in automatic assertion def: "A type of nuclear magnetic resonance spectroscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001105 {is_inferred="true"} ! nuclear magnetic resonance spectroscopy evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001105 ! nuclear magnetic resonance spectroscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007442 name: nuclear fragmentation evidence used in automatic assertion def: "A type of nuclear fragmentation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001104 {is_inferred="true"} ! nuclear fragmentation evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001104 ! nuclear fragmentation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007443 name: phage display evidence used in automatic assertion def: "A type of phage display evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001108 {is_inferred="true"} ! phage display evidence is_a: ECO:0007373 {is_inferred="true"} ! protein binding evidence used in automatic assertion intersection_of: ECO:0001108 ! phage display evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007444 name: phosphoamino acid analysis evidence used in automatic assertion def: "A type of phosphoamino acid analysis evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001109 {is_inferred="true"} ! phosphoamino acid analysis evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001109 ! phosphoamino acid analysis evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007445 name: peptide affinity enrichment evidence used in automatic assertion def: "A type of peptide affinity enrichment evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001110 {is_inferred="true"} ! peptide affinity enrichment evidence is_a: ECO:0007384 {is_inferred="true"} ! affinity evidence used in automatic assertion intersection_of: ECO:0001110 ! peptide affinity enrichment evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007446 name: peptide array evidence used in automatic assertion def: "A type of peptide array evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001112 {is_inferred="true"} ! peptide array evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001112 ! peptide array evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007447 name: physical examination evidence used in automatic assertion def: "A type of physical examination evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001111 {is_inferred="true"} ! physical examination evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001111 ! physical examination evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007448 name: point mutation evidence used in automatic assertion def: "A type of point mutation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001113 {is_inferred="true"} ! point mutation evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001113 ! point mutation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007449 name: propidium iodide staining evidence used in automatic assertion def: "A type of propidium iodide staining evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001114 {is_inferred="true"} ! propidium iodide staining evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001114 ! propidium iodide staining evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007450 name: fluorescence evidence used in automatic assertion def: "A type of fluorescence evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001115 {is_inferred="true"} ! fluorescence evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001115 ! fluorescence evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007451 name: protein dot blot assay evidence used in automatic assertion def: "A type of protein dot blot assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001116 {is_inferred="true"} ! protein dot blot assay evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001116 ! protein dot blot assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007452 name: protein microarray evidence used in automatic assertion def: "A type of protein microarray evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001117 {is_inferred="true"} ! protein microarray evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001117 ! protein microarray evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007453 name: protein sequencing assay evidence used in automatic assertion def: "A type of protein sequencing assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001118 {is_inferred="true"} ! protein sequencing assay evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001118 ! protein sequencing assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007454 name: quantitative mass spectrometry evidence used in automatic assertion def: "A type of quantitative mass spectrometry evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001119 {is_inferred="true"} ! quantitative mass spectrometry evidence is_a: ECO:0007433 {is_inferred="true"} ! mass spectrometry evidence used in automatic assertion intersection_of: ECO:0001119 ! quantitative mass spectrometry evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007455 name: radioisotope assay evidence used in automatic assertion def: "A type of radioisotope assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001120 {is_inferred="true"} ! radioisotope assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001120 ! radioisotope assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007456 name: radioimmunoassay evidence used in automatic assertion def: "A type of radioimmunoassay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001121 {is_inferred="true"} ! radioimmunoassay evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001121 ! radioimmunoassay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007457 name: restriction fragment detection evidence used in automatic assertion def: "A type of restriction fragment detection evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001124 {is_inferred="true"} ! restriction fragment detection evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001124 ! restriction fragment detection evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007458 name: spectrophotometry evidence used in automatic assertion def: "A type of spectrophotometry evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001126 {is_inferred="true"} ! spectrophotometry evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001126 ! spectrophotometry evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007459 name: syngeneic transplantation experiment evidence used in automatic assertion def: "A type of syngeneic transplantation experiment evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001128 {is_inferred="true"} ! syngeneic transplantation experiment evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001128 ! syngeneic transplantation experiment evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007460 name: xenotransplantation experiment evidence used in automatic assertion def: "A type of xenotransplantation experiment evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001137 {is_inferred="true"} ! xenotransplantation experiment evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001137 ! xenotransplantation experiment evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007461 name: WST-1 assay evidence used in automatic assertion def: "A type of WST-1 assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001136 {is_inferred="true"} ! WST-1 assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001136 ! WST-1 assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007462 name: urine test evidence used in automatic assertion def: "A type of urine test evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001134 {is_inferred="true"} ! urine test evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001134 ! urine test evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007463 name: terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence used in automatic assertion def: "A type of terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001133 {is_inferred="true"} ! terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001133 ! terminal deoxynucleotidyl transferase dUTP nick end labeling assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007464 name: tryptic phosphopeptide mapping assay evidence used in automatic assertion def: "A type of tryptic phosphopeptide mapping assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001132 {is_inferred="true"} ! tryptic phosphopeptide mapping assay evidence is_a: ECO:0007433 {is_inferred="true"} ! mass spectrometry evidence used in automatic assertion intersection_of: ECO:0001132 ! tryptic phosphopeptide mapping assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007465 name: transgenic organism evidence used in automatic assertion def: "A type of transgenic organism evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001131 {is_inferred="true"} ! transgenic organism evidence is_a: ECO:0007427 {is_inferred="true"} ! genetic transformation evidence used in automatic assertion intersection_of: ECO:0001131 ! transgenic organism evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007466 name: tissue microarray evidence used in automatic assertion def: "A type of tissue microarray evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001130 {is_inferred="true"} ! tissue microarray evidence is_a: ECO:0007375 {is_inferred="true"} ! cytochemistry evidence used in automatic assertion intersection_of: ECO:0001130 ! tissue microarray evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007467 name: TACE activity assay evidence used in automatic assertion def: "A type of TACE activity assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001129 {is_inferred="true"} ! TACE activity assay evidence is_a: ECO:0007468 {is_inferred="true"} ! enzyme assay evidence used in automatic assertion intersection_of: ECO:0001129 ! TACE activity assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007468 name: enzyme assay evidence used in automatic assertion def: "A type of enzyme assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000005 {is_inferred="true"} ! enzyme assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000005 ! enzyme assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007469 name: surface plasmon resonance evidence used in automatic assertion def: "A type of surface plasmon resonance evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001127 {is_inferred="true"} ! surface plasmon resonance evidence is_a: ECO:0007332 {is_inferred="true"} ! physical interaction evidence used in automatic assertion intersection_of: ECO:0001127 ! surface plasmon resonance evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007470 name: restriction landmark genomic scanning evidence used in automatic assertion def: "A type of restriction landmark genomic scanning evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000089 {is_inferred="true"} ! restriction landmark genomic scanning evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000089 ! restriction landmark genomic scanning evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007471 name: resonant mirror biosensor evidence used in automatic assertion def: "A type of resonant mirror biosensor evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001123 {is_inferred="true"} ! resonant mirror biosensor evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0001123 ! resonant mirror biosensor evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007472 name: high-performance liquid chromatography evidence used in automatic assertion def: "A type of high-performance liquid chromatography evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001052 {is_inferred="true"} ! high-performance liquid chromatography evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001052 ! high-performance liquid chromatography evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007473 name: ectopic expression evidence used in automatic assertion def: "A type of ectopic expression evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000017 {is_inferred="true"} ! ectopic expression evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0000017 ! ectopic expression evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007474 name: electrophoretic mobility shift assay evidence used in automatic assertion def: "A type of electrophoretic mobility shift assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000096 {is_inferred="true"} ! electrophoretic mobility shift assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000096 ! electrophoretic mobility shift assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007475 name: reverse transcription polymerase chain reaction evidence used in automatic assertion alt_id: ECO:000108 def: "A type of reverse transcription polymerase chain reaction evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000109 {is_inferred="true"} ! reverse transcription polymerase chain reaction evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000109 ! reverse transcription polymerase chain reaction evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007476 name: in vivo polyADP-ribosylation assay evidence used in automatic assertion def: "A type of in vivo polyADP-ribosylation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005500 {is_inferred="true"} ! in vivo polyADP-ribosylation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0005500 ! in vivo polyADP-ribosylation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007477 name: DNA dot blot assay evidence used in automatic assertion def: "A type of DNA dot blot assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005522 {is_inferred="true"} ! DNA dot blot assay evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0005522 ! DNA dot blot assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007478 name: random mutagenesis evidence used in automatic assertion def: "A type of random mutagenesis evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005529 {is_inferred="true"} ! random mutagenesis evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0005529 ! random mutagenesis evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007479 name: biological system reconstruction evidence by experimental evidence from single species used in automatic assertion def: "A type of biological system reconstruction evidence by experimental evidence from single species that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion is_a: ECO:0005553 {is_inferred="true"} ! biological system reconstruction evidence by experimental evidence from single species intersection_of: ECO:0005553 ! biological system reconstruction evidence by experimental evidence from single species intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007480 name: biological system reconstruction evidence by experimental evidence from mixed species used in automatic assertion def: "A type of biological system reconstruction evidence by experimental evidence from mixed species that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion is_a: ECO:0005552 {is_inferred="true"} ! biological system reconstruction evidence by experimental evidence from mixed species intersection_of: ECO:0005552 ! biological system reconstruction evidence by experimental evidence from mixed species intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007481 name: biological system reconstruction evidence based on orthology evidence used in automatic assertion def: "A type of biological system reconstruction evidence based on orthology evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005545 {is_inferred="true"} ! biological system reconstruction evidence based on orthology evidence is_a: ECO:0007482 {is_inferred="true"} ! biological system reconstruction evidence based on homology evidence used in automatic assertion intersection_of: ECO:0005545 ! biological system reconstruction evidence based on orthology evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007482 name: biological system reconstruction evidence based on homology evidence used in automatic assertion def: "A type of biological system reconstruction evidence based on homology evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion is_a: ECO:0005549 {is_inferred="true"} ! biological system reconstruction evidence based on homology evidence intersection_of: ECO:0005549 ! biological system reconstruction evidence based on homology evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007483 name: biological system reconstruction evidence based on paralogy evidence used in automatic assertion def: "A type of biological system reconstruction evidence based on paralogy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005550 {is_inferred="true"} ! biological system reconstruction evidence based on paralogy evidence is_a: ECO:0007482 {is_inferred="true"} ! biological system reconstruction evidence based on homology evidence used in automatic assertion intersection_of: ECO:0005550 ! biological system reconstruction evidence based on paralogy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007484 name: biological system reconstruction evidence based on inference from background scientific knowledge used in automatic assertion def: "A type of biological system reconstruction evidence based on inference from background scientific knowledge that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion is_a: ECO:0005548 {is_inferred="true"} ! biological system reconstruction evidence based on inference from background scientific knowledge intersection_of: ECO:0005548 ! biological system reconstruction evidence based on inference from background scientific knowledge intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007485 name: immunogold labelling evidence used in automatic assertion def: "A type of immunogold labelling evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000090 {is_inferred="true"} ! immunogold labelling evidence is_a: ECO:0007486 {is_inferred="true"} ! immunolocalization evidence used in automatic assertion intersection_of: ECO:0000090 ! immunogold labelling evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007486 name: immunolocalization evidence used in automatic assertion def: "A type of immunolocalization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000087 {is_inferred="true"} ! immunolocalization evidence is_a: ECO:0007435 {is_inferred="true"} ! microscopy evidence used in automatic assertion intersection_of: ECO:0000087 ! immunolocalization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007487 name: flow cytometry evidence used in automatic assertion def: "A type of flow cytometry evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000268 {is_inferred="true"} ! flow cytometry evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000268 ! flow cytometry evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007488 name: enzyme-linked immunoabsorbent assay evidence used in automatic assertion def: "A type of enzyme-linked immunoabsorbent assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000267 {is_inferred="true"} ! enzyme-linked immunoabsorbent assay evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000267 ! enzyme-linked immunoabsorbent assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007489 name: high throughput mass spectrometry evidence used in automatic assertion def: "A type of high throughput mass spectrometry evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005585 {is_inferred="true"} ! high throughput mass spectrometry evidence is_a: ECO:0007433 {is_inferred="true"} ! mass spectrometry evidence used in automatic assertion intersection_of: ECO:0005585 ! high throughput mass spectrometry evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007490 name: confocal microscopy evidence used in automatic assertion def: "A type of confocal microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005587 {is_inferred="true"} ! confocal microscopy evidence is_a: ECO:0007435 {is_inferred="true"} ! microscopy evidence used in automatic assertion intersection_of: ECO:0005587 ! confocal microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007491 name: wide-field microscopy evidence used in automatic assertion def: "A type of wide-field microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005588 {is_inferred="true"} ! wide-field microscopy evidence is_a: ECO:0007435 {is_inferred="true"} ! microscopy evidence used in automatic assertion intersection_of: ECO:0005588 ! wide-field microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007492 name: immunogold labelling electron microscopy assay evidence used in automatic assertion def: "A type of immunogold labelling electron microscopy assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005591 {is_inferred="true"} ! immunogold labelling electron microscopy assay evidence is_a: ECO:0007485 {is_inferred="true"} ! immunogold labelling evidence used in automatic assertion is_a: ECO:0007493 {is_inferred="true"} ! electron microscopy evidence used in automatic assertion intersection_of: ECO:0005591 ! immunogold labelling electron microscopy assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007493 name: electron microscopy evidence used in automatic assertion def: "A type of electron microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005033 {is_inferred="true"} ! electron microscopy evidence is_a: ECO:0007435 {is_inferred="true"} ! microscopy evidence used in automatic assertion intersection_of: ECO:0005033 ! electron microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007494 name: immunoperoxidase immunolocalization evidence used in automatic assertion def: "A type of immunoperoxidase immunolocalization evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005594 {is_inferred="true"} ! immunoperoxidase immunolocalization evidence is_a: ECO:0007486 {is_inferred="true"} ! immunolocalization evidence used in automatic assertion intersection_of: ECO:0005594 ! immunoperoxidase immunolocalization evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007495 name: immunoperoxidase immunolocalization electron microscopy evidence used in automatic assertion def: "A type of immunoperoxidase immunolocalization electron microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005596 {is_inferred="true"} ! immunoperoxidase immunolocalization electron microscopy evidence is_a: ECO:0007493 {is_inferred="true"} ! electron microscopy evidence used in automatic assertion is_a: ECO:0007494 {is_inferred="true"} ! immunoperoxidase immunolocalization evidence used in automatic assertion intersection_of: ECO:0005596 ! immunoperoxidase immunolocalization electron microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007496 name: immunofluorescence confocal microscopy evidence used in automatic assertion def: "A type of immunofluorescence confocal microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005600 {is_inferred="true"} ! immunofluorescence confocal microscopy evidence is_a: ECO:0007490 {is_inferred="true"} ! confocal microscopy evidence used in automatic assertion is_a: ECO:0007497 {is_inferred="true"} ! immunofluorescence evidence used in automatic assertion intersection_of: ECO:0005600 ! immunofluorescence confocal microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007497 name: immunofluorescence evidence used in automatic assertion def: "A type of immunofluorescence evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000007 {is_inferred="true"} ! immunofluorescence evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000007 ! immunofluorescence evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007498 name: two-dimensional polyacrylamide gel electrophoresis evidence used in automatic assertion def: "A type of two-dimensional polyacrylamide gel electrophoresis evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005503 {is_inferred="true"} ! two-dimensional polyacrylamide gel electrophoresis evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0005503 ! two-dimensional polyacrylamide gel electrophoresis evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007499 name: alkaline phosphatase reporter gene assay evidence used in automatic assertion def: "A type of alkaline phosphatase reporter gene assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001801 {is_inferred="true"} ! alkaline phosphatase reporter gene assay evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001801 ! alkaline phosphatase reporter gene assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007500 name: beta-galactosidase reporter gene assay evidence used in automatic assertion def: "A type of beta-galactosidase reporter gene assay evidence that is used in an automatic assertion." [ECO:RCT] synonym: "LacZ transcript localization evidence used in automatic assertion" EXACT [] is_a: ECO:0001802 {is_inferred="true"} ! beta-galactosidase reporter gene assay evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001802 ! beta-galactosidase reporter gene assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007501 name: chloramphenicol acetyltransferase reporter gene assay evidence used in automatic assertion def: "A type of chloramphenicol acetyltransferase reporter gene assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001803 {is_inferred="true"} ! chloramphenicol acetyltransferase reporter gene assay evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001803 ! chloramphenicol acetyltransferase reporter gene assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007502 name: chromatin immunoprecipitation-PCR evidence used in automatic assertion def: "A type of chromatin immunoprecipitation-PCR evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000227 {is_inferred="true"} ! chromatin immunoprecipitation-PCR evidence is_a: ECO:0007503 {is_inferred="true"} ! immunoprecipitation evidence used in automatic assertion intersection_of: ECO:0000227 ! chromatin immunoprecipitation-PCR evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007503 name: immunoprecipitation evidence used in automatic assertion def: "A type of immunoprecipitation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000085 {is_inferred="true"} ! immunoprecipitation evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000085 ! immunoprecipitation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007504 name: copper-phenanthroline footprinting evidence used in automatic assertion def: "A type of copper-phenanthroline footprinting evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001815 {is_inferred="true"} ! copper-phenanthroline footprinting evidence is_a: ECO:0007505 {is_inferred="true"} ! nucleic acid binding evidence used in automatic assertion intersection_of: ECO:0001815 ! copper-phenanthroline footprinting evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007505 name: nucleic acid binding evidence used in automatic assertion def: "A type of nucleic acid binding evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000136 {is_inferred="true"} ! nucleic acid binding evidence is_a: ECO:0007384 {is_inferred="true"} ! affinity evidence used in automatic assertion intersection_of: ECO:0000136 ! nucleic acid binding evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007506 name: DNA affinity chromatography evidence used in automatic assertion def: "A type of DNA affinity chromatography evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001809 {is_inferred="true"} ! DNA affinity chromatography evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001809 ! DNA affinity chromatography evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007507 name: DNAse footprinting evidence used in automatic assertion def: "A type of DNAse footprinting evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001810 {is_inferred="true"} ! DNAse footprinting evidence is_a: ECO:0007505 {is_inferred="true"} ! nucleic acid binding evidence used in automatic assertion intersection_of: ECO:0001810 ! DNAse footprinting evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007508 name: fluorescence anisotropy evidence used in automatic assertion def: "A type of fluorescence anisotropy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001811 {is_inferred="true"} ! fluorescence anisotropy evidence is_a: ECO:0007450 {is_inferred="true"} ! fluorescence evidence used in automatic assertion intersection_of: ECO:0001811 ! fluorescence anisotropy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007509 name: ferric uptake regulator titration assay evidence used in automatic assertion def: "A type of ferric uptake regulator titration assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001829 {is_inferred="true"} ! ferric uptake regulator titration assay evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001829 ! ferric uptake regulator titration assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007510 name: systematic evolution of ligands by exponential amplification evidence used in automatic assertion def: "A type of systematic evolution of ligands by exponential amplification evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000293 {is_inferred="true"} ! systematic evolution of ligands by exponential amplification evidence is_a: ECO:0007332 {is_inferred="true"} ! physical interaction evidence used in automatic assertion intersection_of: ECO:0000293 ! systematic evolution of ligands by exponential amplification evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007511 name: glutathione S-transferase pull-down assay evidence used in automatic assertion def: "A type of glutathione S-transferase pull-down assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001817 {is_inferred="true"} ! glutathione S-transferase pull-down assay evidence is_a: ECO:0007373 {is_inferred="true"} ! protein binding evidence used in automatic assertion intersection_of: ECO:0001817 ! glutathione S-transferase pull-down assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007512 name: beta-glucuronidase reporter gene assay evidence used in automatic assertion def: "A type of beta-glucuronidase reporter gene assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001804 {is_inferred="true"} ! beta-glucuronidase reporter gene assay evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001804 ! beta-glucuronidase reporter gene assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007513 name: heteronuclear single quantum coherence spectroscopy evidence used in automatic assertion def: "A type of heteronuclear single quantum coherence spectroscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001813 {is_inferred="true"} ! heteronuclear single quantum coherence spectroscopy evidence is_a: ECO:0007441 {is_inferred="true"} ! nuclear magnetic resonance spectroscopy evidence used in automatic assertion intersection_of: ECO:0001813 ! heteronuclear single quantum coherence spectroscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007514 name: hydroxyl-radical footprinting evidence used in automatic assertion def: "A type of hydroxyl-radical footprinting evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001818 {is_inferred="true"} ! hydroxyl-radical footprinting evidence is_a: ECO:0007505 {is_inferred="true"} ! nucleic acid binding evidence used in automatic assertion intersection_of: ECO:0001818 ! hydroxyl-radical footprinting evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007515 name: isothermal titration calorimetry evidence used in automatic assertion def: "A type of isothermal titration calorimetry evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001825 {is_inferred="true"} ! isothermal titration calorimetry evidence is_a: ECO:0007384 {is_inferred="true"} ! affinity evidence used in automatic assertion intersection_of: ECO:0001825 ! isothermal titration calorimetry evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007516 name: luciferase reporter gene assay evidence used in automatic assertion def: "A type of luciferase reporter gene assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001805 {is_inferred="true"} ! luciferase reporter gene assay evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0001805 ! luciferase reporter gene assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007517 name: methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence used in automatic assertion def: "A type of methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001814 {is_inferred="true"} ! methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence is_a: ECO:0007505 {is_inferred="true"} ! nucleic acid binding evidence used in automatic assertion intersection_of: ECO:0001814 ! methidiumpropyl-ethylenediaminetetraacetic acid iron (II) footprinting evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007518 name: northern blot evidence used in automatic assertion def: "A type of northern blot evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000106 {is_inferred="true"} ! northern blot evidence is_a: ECO:0007303 {is_inferred="true"} ! transcript expression evidence used in automatic assertion intersection_of: ECO:0000106 ! northern blot evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007519 name: methylation interference footprinting evidence used in automatic assertion def: "A type of methylation interference footprinting evidence that is used in an automatic assertion." [ECO:RCT] synonym: "premethylation interference footprinting evidence used in automatic assertion" EXACT [] is_a: ECO:0001827 {is_inferred="true"} ! methylation interference footprinting evidence is_a: ECO:0007505 {is_inferred="true"} ! nucleic acid binding evidence used in automatic assertion intersection_of: ECO:0001827 ! methylation interference footprinting evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007520 name: primer extension assay evidence used in automatic assertion def: "A type of primer extension assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001819 {is_inferred="true"} ! primer extension assay evidence is_a: ECO:0007303 {is_inferred="true"} ! transcript expression evidence used in automatic assertion intersection_of: ECO:0001819 ! primer extension assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007521 name: quantitative polymerase chain reaction evidence used in automatic assertion def: "A type of quantitative polymerase chain reaction evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000231 {is_inferred="true"} ! quantitative polymerase chain reaction evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000231 ! quantitative polymerase chain reaction evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007522 name: rapid amplification of cDNA ends polymerase chain reaction evidence used in automatic assertion def: "A type of rapid amplification of cDNA ends polymerase chain reaction evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001820 {is_inferred="true"} ! rapid amplification of cDNA ends polymerase chain reaction evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0001820 ! rapid amplification of cDNA ends polymerase chain reaction evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007523 name: S1 nuclease protection assay evidence used in automatic assertion def: "A type of S1 nuclease protection assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005521 {is_inferred="true"} ! S1 nuclease protection assay evidence is_a: ECO:0007316 {is_inferred="true"} ! nuclease protection assay evidence used in automatic assertion intersection_of: ECO:0005521 ! S1 nuclease protection assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007524 name: site-directed mutagenesis evidence used in automatic assertion def: "A type of site-directed mutagenesis evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005528 {is_inferred="true"} ! site-directed mutagenesis evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0005528 ! site-directed mutagenesis evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007525 name: survival rate analysis evidence used in automatic assertion def: "A type of survival rate analysis evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001822 {is_inferred="true"} ! survival rate analysis evidence is_a: ECO:0007370 {is_inferred="true"} ! knockout evidence used in automatic assertion intersection_of: ECO:0001822 ! survival rate analysis evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007526 name: ultraviolet light footprinting evidence used in automatic assertion def: "A type of ultraviolet light footprinting evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001826 {is_inferred="true"} ! ultraviolet light footprinting evidence is_a: ECO:0007505 {is_inferred="true"} ! nucleic acid binding evidence used in automatic assertion intersection_of: ECO:0001826 ! ultraviolet light footprinting evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007527 name: xylE reporter gene assay evidence used in automatic assertion def: "A type of xylE reporter gene assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005537 {is_inferred="true"} ! xylE reporter gene assay evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0005537 ! xylE reporter gene assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007528 name: ad-hoc qualitative phenotype observation evidence used in automatic assertion def: "A type of ad-hoc qualitative phenotype observation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005673 {is_inferred="true"} ! ad-hoc qualitative phenotype observation evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0005673 ! ad-hoc qualitative phenotype observation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007529 name: ad-hoc quantitative phenotype observation evidence used in automatic assertion def: "A type of ad-hoc quantitative phenotype observation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005675 {is_inferred="true"} ! ad-hoc quantitative phenotype observation evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0005675 ! ad-hoc quantitative phenotype observation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007530 name: cell transfection experiment evidence used in automatic assertion def: "A type of cell transfection experiment evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005606 {is_inferred="true"} ! cell transfection experiment evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0005606 ! cell transfection experiment evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007531 name: yeast 2-hybrid evidence used in automatic assertion def: "A type of yeast 2-hybrid evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000068 {is_inferred="true"} ! yeast 2-hybrid evidence is_a: ECO:0007432 {is_inferred="true"} ! hybrid interaction evidence used in automatic assertion intersection_of: ECO:0000068 ! yeast 2-hybrid evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007532 name: Cya fusion reporter assay evidence used in automatic assertion def: "A type of Cya fusion reporter assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006001 {is_inferred="true"} ! Cya fusion reporter assay evidence is_a: ECO:0007473 {is_inferred="true"} ! ectopic expression evidence used in automatic assertion intersection_of: ECO:0006001 ! Cya fusion reporter assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007533 name: super-resolution microscopy evidence used in automatic assertion def: "A type of super-resolution microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005578 {is_inferred="true"} ! super-resolution microscopy evidence is_a: ECO:0007435 {is_inferred="true"} ! microscopy evidence used in automatic assertion intersection_of: ECO:0005578 ! super-resolution microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007534 name: fractionation evidence used in automatic assertion def: "A type of fractionation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000100 {is_inferred="true"} ! fractionation evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000100 ! fractionation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007535 name: electrophysiology assay evidence used in automatic assertion def: "A type of electrophysiology assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000164 {is_inferred="true"} ! electrophysiology assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000164 ! electrophysiology assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007536 name: mRNA interactome capture evidence used in automatic assertion def: "A type of mRNA interactome capture evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006010 {is_inferred="true"} ! mRNA interactome capture evidence is_a: ECO:0007505 {is_inferred="true"} ! nucleic acid binding evidence used in automatic assertion intersection_of: ECO:0006010 ! mRNA interactome capture evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007537 name: patch-clamp recording evidence used in automatic assertion def: "A type of patch-clamp recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006012 {is_inferred="true"} ! patch-clamp recording evidence is_a: ECO:0007535 {is_inferred="true"} ! electrophysiology assay evidence used in automatic assertion intersection_of: ECO:0006012 ! patch-clamp recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007538 name: whole-cell patch-clamp recording evidence used in automatic assertion def: "A type of whole-cell patch-clamp recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006014 {is_inferred="true"} ! whole-cell patch-clamp recording evidence is_a: ECO:0007537 {is_inferred="true"} ! patch-clamp recording evidence used in automatic assertion intersection_of: ECO:0006014 ! whole-cell patch-clamp recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007539 name: author statement from published clinical study used in automatic assertion def: "A type of author statement from published clinical study that is used in an automatic assertion." [ECO:RCT] synonym: "traceable author statement from published clinical study used in automatic assertion" RELATED [] is_a: ECO:0006016 {is_inferred="true"} ! author statement from published clinical study is_a: ECO:0007319 {is_inferred="true"} ! author statement used in automatic assertion intersection_of: ECO:0006016 ! author statement from published clinical study intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007540 name: inference based on individual clinical experience used in automatic assertion def: "A type of inference based on individual clinical experience that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006018 {is_inferred="true"} ! inference based on individual clinical experience is_a: ECO:0007322 {is_inferred="true"} ! curator inference used in automatic assertion intersection_of: ECO:0006018 ! inference based on individual clinical experience intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007541 name: biofilm formation assay evidence used in automatic assertion def: "A type of biofilm formation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006020 {is_inferred="true"} ! biofilm formation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0006020 ! biofilm formation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007542 name: microtiter plate biofilm assay evidence used in automatic assertion def: "A type of microtiter plate biofilm assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006022 {is_inferred="true"} ! microtiter plate biofilm assay evidence is_a: ECO:0007541 {is_inferred="true"} ! biofilm formation assay evidence used in automatic assertion intersection_of: ECO:0006022 ! microtiter plate biofilm assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007543 name: air-liquid interface assay evidence used in automatic assertion def: "A type of air-liquid interface assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006024 {is_inferred="true"} ! air-liquid interface assay evidence is_a: ECO:0007541 {is_inferred="true"} ! biofilm formation assay evidence used in automatic assertion intersection_of: ECO:0006024 ! air-liquid interface assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007544 name: colony biofilm assay evidence used in automatic assertion def: "A type of colony biofilm assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006026 {is_inferred="true"} ! colony biofilm assay evidence is_a: ECO:0007541 {is_inferred="true"} ! biofilm formation assay evidence used in automatic assertion intersection_of: ECO:0006026 ! colony biofilm assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007545 name: Kadouri drip-fed biofilm assay evidence used in automatic assertion def: "A type of Kadouri drip-fed biofilm assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006028 {is_inferred="true"} ! Kadouri drip-fed biofilm assay evidence is_a: ECO:0007541 {is_inferred="true"} ! biofilm formation assay evidence used in automatic assertion intersection_of: ECO:0006028 ! Kadouri drip-fed biofilm assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007546 name: co-immunoprecipitation evidence used in automatic assertion def: "A type of co-immunoprecipitation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000070 {is_inferred="true"} ! co-immunoprecipitation evidence is_a: ECO:0007332 {is_inferred="true"} ! physical interaction evidence used in automatic assertion is_a: ECO:0007503 {is_inferred="true"} ! immunoprecipitation evidence used in automatic assertion intersection_of: ECO:0000070 ! co-immunoprecipitation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007547 name: optogenetic evidence used in automatic assertion def: "A type of optogenetic evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006032 {is_inferred="true"} ! optogenetic evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0006032 ! optogenetic evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007548 name: fluorescent sensor evidence used in automatic assertion def: "A type of fluorescent sensor evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006034 {is_inferred="true"} ! fluorescent sensor evidence is_a: ECO:0007450 {is_inferred="true"} ! fluorescence evidence used in automatic assertion intersection_of: ECO:0006034 ! fluorescent sensor evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007549 name: genetically encoded fluorescent sensor evidence used in automatic assertion def: "A type of genetically encoded fluorescent sensor evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006036 {is_inferred="true"} ! genetically encoded fluorescent sensor evidence is_a: ECO:0007548 {is_inferred="true"} ! fluorescent sensor evidence used in automatic assertion intersection_of: ECO:0006036 ! genetically encoded fluorescent sensor evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007550 name: genetically encoded fluorescent electrophysiology assay evidence used in automatic assertion def: "A type of genetically encoded fluorescent electrophysiology assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006038 {is_inferred="true"} ! genetically encoded fluorescent electrophysiology assay evidence is_a: ECO:0007535 {is_inferred="true"} ! electrophysiology assay evidence used in automatic assertion is_a: ECO:0007548 {is_inferred="true"} ! fluorescent sensor evidence used in automatic assertion intersection_of: ECO:0006038 ! genetically encoded fluorescent electrophysiology assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007551 name: genetically encoded fluorescent ion concentration sensor assay evidence used in automatic assertion def: "A type of genetically encoded fluorescent ion concentration sensor assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006040 {is_inferred="true"} ! genetically encoded fluorescent ion concentration sensor assay evidence is_a: ECO:0007550 {is_inferred="true"} ! genetically encoded fluorescent electrophysiology assay evidence used in automatic assertion intersection_of: ECO:0006040 ! genetically encoded fluorescent ion concentration sensor assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007552 name: cell fractionation evidence used in automatic assertion def: "A type of cell fractionation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000004 {is_inferred="true"} ! cell fractionation evidence is_a: ECO:0007534 {is_inferred="true"} ! fractionation evidence used in automatic assertion intersection_of: ECO:0000004 ! cell fractionation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007553 name: extracellular recording evidence used in automatic assertion def: "A type of extracellular recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006043 {is_inferred="true"} ! extracellular recording evidence is_a: ECO:0007535 {is_inferred="true"} ! electrophysiology assay evidence used in automatic assertion intersection_of: ECO:0006043 ! extracellular recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007554 name: single-unit extracellular recording evidence used in automatic assertion def: "A type of single-unit extracellular recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006045 {is_inferred="true"} ! single-unit extracellular recording evidence is_a: ECO:0007553 {is_inferred="true"} ! extracellular recording evidence used in automatic assertion intersection_of: ECO:0006045 ! single-unit extracellular recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007555 name: field potential recording evidence used in automatic assertion def: "A type of field potential recording evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006047 {is_inferred="true"} ! field potential recording evidence is_a: ECO:0007553 {is_inferred="true"} ! extracellular recording evidence used in automatic assertion intersection_of: ECO:0006047 ! field potential recording evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007556 name: anti-sense experiment evidence used in automatic assertion def: "A type of anti-sense experiment evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000018 {is_inferred="true"} ! anti-sense experiment evidence is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0000018 ! anti-sense experiment evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007557 name: morpholino experiment evidence used in automatic assertion def: "A type of morpholino experiment evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000292 {is_inferred="true"} ! morpholino experiment evidence is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0000292 ! morpholino experiment evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007558 name: RNAi evidence used in automatic assertion def: "A type of RNAi evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000019 {is_inferred="true"} ! RNAi evidence is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0000019 ! RNAi evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007559 name: pharmacological assay evidence used in automatic assertion def: "A type of pharmacological assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006053 {is_inferred="true"} ! pharmacological assay evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0006053 ! pharmacological assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007560 name: immunofluorescence wide-field microscopy evidence used in automatic assertion def: "A type of immunofluorescence wide-field microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005599 {is_inferred="true"} ! immunofluorescence wide-field microscopy evidence is_a: ECO:0007497 {is_inferred="true"} ! immunofluorescence evidence used in automatic assertion is_a: ECO:0007561 {is_inferred="true"} ! wide-field fluorescence microscopy evidence used in automatic assertion intersection_of: ECO:0005599 ! immunofluorescence wide-field microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007561 name: wide-field fluorescence microscopy evidence used in automatic assertion def: "A type of wide-field fluorescence microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0005598 {is_inferred="true"} ! wide-field fluorescence microscopy evidence is_a: ECO:0007491 {is_inferred="true"} ! wide-field microscopy evidence used in automatic assertion intersection_of: ECO:0005598 ! wide-field fluorescence microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007562 name: over expression analysis evidence used in automatic assertion def: "A type of over expression analysis evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000120 {is_inferred="true"} ! over expression analysis evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0000120 ! over expression analysis evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007563 name: cell-free assay evidence used in automatic assertion def: "A type of cell-free assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000183 {is_inferred="true"} ! cell-free assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000183 ! cell-free assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007564 name: fluorescence recovery after photobleaching evidence used in automatic assertion def: "A type of fluorescence recovery after photobleaching evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006066 {is_inferred="true"} ! fluorescence recovery after photobleaching evidence is_a: ECO:0007450 {is_inferred="true"} ! fluorescence evidence used in automatic assertion intersection_of: ECO:0006066 ! fluorescence recovery after photobleaching evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007565 name: immuno-labelling electron microscopy evidence used in automatic assertion def: "A type of immuno-labelling electron microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006070 {is_inferred="true"} ! immuno-labelling electron microscopy evidence is_a: ECO:0007493 {is_inferred="true"} ! electron microscopy evidence used in automatic assertion intersection_of: ECO:0006070 ! immuno-labelling electron microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007566 name: immunofluorescence super resolution microscopy evidence used in automatic assertion def: "A type of immunofluorescence super resolution microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006072 {is_inferred="true"} ! immunofluorescence super resolution microscopy evidence is_a: ECO:0007533 {is_inferred="true"} ! super-resolution microscopy evidence used in automatic assertion intersection_of: ECO:0006072 ! immunofluorescence super resolution microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007567 name: co-purification evidence used in automatic assertion def: "A type of co-purification evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000022 {is_inferred="true"} ! co-purification evidence is_a: ECO:0007332 {is_inferred="true"} ! physical interaction evidence used in automatic assertion intersection_of: ECO:0000022 ! co-purification evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007568 name: yeast one-hybrid evidence used in automatic assertion def: "A type of yeast one-hybrid evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000066 {is_inferred="true"} ! yeast one-hybrid evidence is_a: ECO:0007432 {is_inferred="true"} ! hybrid interaction evidence used in automatic assertion intersection_of: ECO:0000066 ! yeast one-hybrid evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007569 name: split-ubiquitin assay evidence used in automatic assertion def: "A type of split-ubiquitin assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000074 {is_inferred="true"} ! split-ubiquitin assay evidence is_a: ECO:0007332 {is_inferred="true"} ! physical interaction evidence used in automatic assertion intersection_of: ECO:0000074 ! split-ubiquitin assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007570 name: far-Western blotting evidence used in automatic assertion def: "A type of far-Western blotting evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000076 {is_inferred="true"} ! far-Western blotting evidence is_a: ECO:0007332 {is_inferred="true"} ! physical interaction evidence used in automatic assertion intersection_of: ECO:0000076 ! far-Western blotting evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007571 name: affinity chromatography evidence used in automatic assertion def: "A type of affinity chromatography evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000079 {is_inferred="true"} ! affinity chromatography evidence is_a: ECO:0007384 {is_inferred="true"} ! affinity evidence used in automatic assertion intersection_of: ECO:0000079 ! affinity chromatography evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007572 name: ribohomopolymer binding assay evidence used in automatic assertion def: "A type of ribohomopolymer binding assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000138 {is_inferred="true"} ! ribohomopolymer binding assay evidence is_a: ECO:0007505 {is_inferred="true"} ! nucleic acid binding evidence used in automatic assertion intersection_of: ECO:0000138 ! ribohomopolymer binding assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007573 name: protein:ion binding evidence used in automatic assertion def: "A type of protein:ion binding evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000142 {is_inferred="true"} ! protein:ion binding evidence is_a: ECO:0007373 {is_inferred="true"} ! protein binding evidence used in automatic assertion intersection_of: ECO:0000142 ! protein:ion binding evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007574 name: Southwestern blot evidence used in automatic assertion def: "A type of Southwestern blot evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000144 {is_inferred="true"} ! Southwestern blot evidence is_a: ECO:0007505 {is_inferred="true"} ! nucleic acid binding evidence used in automatic assertion intersection_of: ECO:0000144 ! Southwestern blot evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007575 name: Northwestern blot evidence used in automatic assertion def: "A type of Northwestern blot evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000146 {is_inferred="true"} ! Northwestern blot evidence is_a: ECO:0007505 {is_inferred="true"} ! nucleic acid binding evidence used in automatic assertion intersection_of: ECO:0000146 ! Northwestern blot evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007576 name: bacterial one-hybrid evidence used in automatic assertion def: "A type of bacterial one-hybrid evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000294 {is_inferred="true"} ! bacterial one-hybrid evidence is_a: ECO:0007432 {is_inferred="true"} ! hybrid interaction evidence used in automatic assertion intersection_of: ECO:0000294 ! bacterial one-hybrid evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007577 name: protein-binding microarray evidence used in automatic assertion def: "A type of protein-binding microarray evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0001601 {is_inferred="true"} ! protein-binding microarray evidence is_a: ECO:0007373 {is_inferred="true"} ! protein binding evidence used in automatic assertion is_a: ECO:0007505 {is_inferred="true"} ! nucleic acid binding evidence used in automatic assertion intersection_of: ECO:0001601 ! protein-binding microarray evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007578 name: functional complementation evidence used in automatic assertion def: "A type of functional complementation evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000012 {is_inferred="true"} ! functional complementation evidence is_a: ECO:0007326 {is_inferred="true"} ! genetic interaction evidence used in automatic assertion intersection_of: ECO:0000012 ! functional complementation evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007579 name: transgenic rescue experiment evidence used in automatic assertion def: "A type of transgenic rescue experiment evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000013 {is_inferred="true"} ! transgenic rescue experiment evidence is_a: ECO:0007578 {is_inferred="true"} ! functional complementation evidence used in automatic assertion intersection_of: ECO:0000013 ! transgenic rescue experiment evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007580 name: transient rescue experiment evidence used in automatic assertion def: "A type of transient rescue experiment evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000038 {is_inferred="true"} ! transient rescue experiment evidence is_a: ECO:0007578 {is_inferred="true"} ! functional complementation evidence used in automatic assertion intersection_of: ECO:0000038 ! transient rescue experiment evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007581 name: suppressor/enhancer interaction evidence used in automatic assertion def: "A type of suppressor/enhancer interaction evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000052 {is_inferred="true"} ! suppressor/enhancer interaction evidence is_a: ECO:0007326 {is_inferred="true"} ! genetic interaction evidence used in automatic assertion intersection_of: ECO:0000052 ! suppressor/enhancer interaction evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007582 name: double mutant phenotype evidence used in automatic assertion def: "A type of double mutant phenotype evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000054 {is_inferred="true"} ! double mutant phenotype evidence is_a: ECO:0007326 {is_inferred="true"} ! genetic interaction evidence used in automatic assertion intersection_of: ECO:0000054 ! double mutant phenotype evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007583 name: epistatic interaction evidence used in automatic assertion def: "A type of epistatic interaction evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000056 {is_inferred="true"} ! epistatic interaction evidence is_a: ECO:0007326 {is_inferred="true"} ! genetic interaction evidence used in automatic assertion intersection_of: ECO:0000056 ! epistatic interaction evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007584 name: functional complementation in heterologous system evidence used in automatic assertion def: "A type of functional complementation in heterologous system evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000064 {is_inferred="true"} ! functional complementation in heterologous system evidence is_a: ECO:0007578 {is_inferred="true"} ! functional complementation evidence used in automatic assertion intersection_of: ECO:0000064 ! functional complementation in heterologous system evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007585 name: temperature-sensitive mutant phenotype evidence used in automatic assertion def: "A type of temperature-sensitive mutant phenotype evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006098 {is_inferred="true"} ! temperature-sensitive mutant phenotype evidence is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0006098 ! temperature-sensitive mutant phenotype evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007586 name: recessive mutant phenotype evidence used in automatic assertion def: "A type of recessive mutant phenotype evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006100 {is_inferred="true"} ! recessive mutant phenotype evidence is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0006100 ! recessive mutant phenotype evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007587 name: high throughput mutant phenotype evidence used in automatic assertion def: "A type of high throughput mutant phenotype evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006057 {is_inferred="true"} ! high throughput evidence used in automatic assertion is_a: ECO:0007000 {is_inferred="true"} ! high throughput mutant phenotype evidence is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0007000 ! high throughput mutant phenotype evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007588 name: high throughput genetic interaction evidence used in automatic assertion def: "A type of high throughput genetic interaction evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006057 {is_inferred="true"} ! high throughput evidence used in automatic assertion is_a: ECO:0007002 {is_inferred="true"} ! high throughput genetic interaction evidence is_a: ECO:0007326 {is_inferred="true"} ! genetic interaction evidence used in automatic assertion intersection_of: ECO:0007002 ! high throughput genetic interaction evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007589 name: high throughput direct assay evidence used in automatic assertion def: "A type of high throughput direct assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006057 {is_inferred="true"} ! high throughput evidence used in automatic assertion is_a: ECO:0007004 {is_inferred="true"} ! high throughput direct assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0007004 ! high throughput direct assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007590 name: high throughput expression pattern evidence used in automatic assertion def: "A type of high throughput expression pattern evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0006057 {is_inferred="true"} ! high throughput evidence used in automatic assertion is_a: ECO:0007006 {is_inferred="true"} ! high throughput expression pattern evidence is_a: ECO:0007298 {is_inferred="true"} ! expression pattern evidence used in automatic assertion intersection_of: ECO:0007006 ! high throughput expression pattern evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007591 name: radioligand binding assay evidence used in automatic assertion def: "A type of radioligand binding assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007008 {is_inferred="true"} ! radioligand binding assay evidence is_a: ECO:0007373 {is_inferred="true"} ! protein binding evidence used in automatic assertion intersection_of: ECO:0007008 ! radioligand binding assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007592 name: combinatorial evidence from author knowledge and experimental evidence used in automatic assertion def: "A type of combinatorial evidence from author knowledge and experimental evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000213 {is_inferred="true"} ! combinatorial evidence used in automatic assertion is_a: ECO:0007011 {is_inferred="true"} ! combinatorial evidence from author knowledge and experimental evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0007011 ! combinatorial evidence from author knowledge and experimental evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007593 name: combinatorial evidence from curator knowledge and experimental evidence used in automatic assertion def: "A type of combinatorial evidence from curator knowledge and experimental evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000213 {is_inferred="true"} ! combinatorial evidence used in automatic assertion is_a: ECO:0007012 {is_inferred="true"} ! combinatorial evidence from curator knowledge and experimental evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion is_a: ECO:0007322 {is_inferred="true"} ! curator inference used in automatic assertion intersection_of: ECO:0007012 ! combinatorial evidence from curator knowledge and experimental evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007594 name: voltammetry evidence used in automatic assertion def: "A type of voltammetry evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007015 {is_inferred="true"} ! voltammetry evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0007015 ! voltammetry evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007595 name: photoconversion evidence used in automatic assertion def: "A type of photoconversion evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007017 {is_inferred="true"} ! photoconversion evidence is_a: ECO:0007450 {is_inferred="true"} ! fluorescence evidence used in automatic assertion intersection_of: ECO:0007017 ! photoconversion evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007596 name: agglutination test evidence used in automatic assertion def: "A type of agglutination test evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007019 {is_inferred="true"} ! agglutination test evidence is_a: ECO:0007348 {is_inferred="true"} ! immunological assay evidence used in automatic assertion intersection_of: ECO:0007019 ! agglutination test evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007597 name: slide agglutination test evidence used in automatic assertion def: "A type of slide agglutination test evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007021 {is_inferred="true"} ! slide agglutination test evidence is_a: ECO:0007596 {is_inferred="true"} ! agglutination test evidence used in automatic assertion intersection_of: ECO:0007021 ! slide agglutination test evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007598 name: direct Coombs test evidence used in automatic assertion def: "A type of direct Coombs test evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007023 {is_inferred="true"} ! direct Coombs test evidence is_a: ECO:0007596 {is_inferred="true"} ! agglutination test evidence used in automatic assertion intersection_of: ECO:0007023 ! direct Coombs test evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007599 name: indirect Coombs test evidence used in automatic assertion def: "A type of indirect Coombs test evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007025 {is_inferred="true"} ! indirect Coombs test evidence is_a: ECO:0007596 {is_inferred="true"} ! agglutination test evidence used in automatic assertion intersection_of: ECO:0007025 ! indirect Coombs test evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007600 name: direct hemagglutination assay evidence used in automatic assertion def: "A type of direct hemagglutination assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007027 {is_inferred="true"} ! direct hemagglutination assay evidence is_a: ECO:0007596 {is_inferred="true"} ! agglutination test evidence used in automatic assertion intersection_of: ECO:0007027 ! direct hemagglutination assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007601 name: viral hemagglutination inhibition assay evidence used in automatic assertion def: "A type of viral hemagglutination inhibition assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007029 {is_inferred="true"} ! viral hemagglutination inhibition assay evidence is_a: ECO:0007596 {is_inferred="true"} ! agglutination test evidence used in automatic assertion intersection_of: ECO:0007029 ! viral hemagglutination inhibition assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007602 name: compement fixation assay evidence used in automatic assertion def: "A type of compement fixation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007031 {is_inferred="true"} ! compement fixation assay evidence is_a: ECO:0007348 {is_inferred="true"} ! immunological assay evidence used in automatic assertion intersection_of: ECO:0007031 ! compement fixation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007603 name: neutralization test assay evidence used in automatic assertion def: "A type of neutralization test assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007033 {is_inferred="true"} ! neutralization test assay evidence is_a: ECO:0007348 {is_inferred="true"} ! immunological assay evidence used in automatic assertion intersection_of: ECO:0007033 ! neutralization test assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007604 name: copper transport assay evidence used in automatic assertion def: "A type of copper transport assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007035 {is_inferred="true"} ! copper transport assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0007035 ! copper transport assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007605 name: 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence used in automatic assertion def: "A type of 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007037 {is_inferred="true"} ! 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0007037 ! 5-cyano-2,3-ditolyl tetrazolium chloride staining evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007606 name: plaque assay evidence used in automatic assertion def: "A type of plaque assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007039 {is_inferred="true"} ! plaque assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0007039 ! plaque assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007607 name: epifluorescence microscopy evidence used in automatic assertion def: "A type of epifluorescence microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007041 {is_inferred="true"} ! epifluorescence microscopy evidence is_a: ECO:0007435 {is_inferred="true"} ! microscopy evidence used in automatic assertion intersection_of: ECO:0007041 ! epifluorescence microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007608 name: transmission electron microscopy evidence used in automatic assertion def: "A type of transmission electron microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007043 {is_inferred="true"} ! transmission electron microscopy evidence is_a: ECO:0007493 {is_inferred="true"} ! electron microscopy evidence used in automatic assertion intersection_of: ECO:0007043 ! transmission electron microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007609 name: scanning electron microscopy evidence used in automatic assertion def: "A type of scanning electron microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007045 {is_inferred="true"} ! scanning electron microscopy evidence is_a: ECO:0007493 {is_inferred="true"} ! electron microscopy evidence used in automatic assertion intersection_of: ECO:0007045 ! scanning electron microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007610 name: time-lapsed microscopy evidence used in automatic assertion def: "A type of time-lapsed microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007047 {is_inferred="true"} ! time-lapsed microscopy evidence is_a: ECO:0007435 {is_inferred="true"} ! microscopy evidence used in automatic assertion intersection_of: ECO:0007047 ! time-lapsed microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007611 name: phase contrast microscopy evidence used in automatic assertion def: "A type of phase contrast microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007049 {is_inferred="true"} ! phase contrast microscopy evidence is_a: ECO:0007435 {is_inferred="true"} ! microscopy evidence used in automatic assertion intersection_of: ECO:0007049 ! phase contrast microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007612 name: transmitted light brightfied mircoscopy evidence used in automatic assertion def: "A type of transmitted light brightfied mircoscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007051 {is_inferred="true"} ! transmitted light brightfied mircoscopy evidence is_a: ECO:0007435 {is_inferred="true"} ! microscopy evidence used in automatic assertion intersection_of: ECO:0007051 ! transmitted light brightfied mircoscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007613 name: koehler illumination microscopy evidence used in automatic assertion def: "A type of koehler illumination microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007053 {is_inferred="true"} ! koehler illumination microscopy evidence is_a: ECO:0007435 {is_inferred="true"} ! microscopy evidence used in automatic assertion intersection_of: ECO:0007053 ! koehler illumination microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007614 name: differential interference contrast microscopy evidence used in automatic assertion def: "A type of differential interference contrast microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007055 {is_inferred="true"} ! differential interference contrast microscopy evidence is_a: ECO:0007435 {is_inferred="true"} ! microscopy evidence used in automatic assertion intersection_of: ECO:0007055 ! differential interference contrast microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007615 name: extended field laser confocal microscopy evidence used in automatic assertion def: "A type of extended field laser confocal microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007057 {is_inferred="true"} ! extended field laser confocal microscopy evidence is_a: ECO:0007490 {is_inferred="true"} ! confocal microscopy evidence used in automatic assertion intersection_of: ECO:0007057 ! extended field laser confocal microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007616 name: confocal laser scanning microscopy evidence used in automatic assertion def: "A type of confocal laser scanning microscopy evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007059 {is_inferred="true"} ! confocal laser scanning microscopy evidence is_a: ECO:0007490 {is_inferred="true"} ! confocal microscopy evidence used in automatic assertion intersection_of: ECO:0007059 ! confocal laser scanning microscopy evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007617 name: light scattering assay evidence used in automatic assertion def: "A type of light scattering assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007061 {is_inferred="true"} ! light scattering assay evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0007061 ! light scattering assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007618 name: dynamic light scattering assay evidence used in automatic assertion def: "A type of dynamic light scattering assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007063 {is_inferred="true"} ! dynamic light scattering assay evidence is_a: ECO:0007617 {is_inferred="true"} ! light scattering assay evidence used in automatic assertion intersection_of: ECO:0007063 ! dynamic light scattering assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007619 name: static light scattering assay evidence used in automatic assertion def: "A type of static light scattering assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007065 {is_inferred="true"} ! static light scattering assay evidence is_a: ECO:0007617 {is_inferred="true"} ! light scattering assay evidence used in automatic assertion intersection_of: ECO:0007065 ! static light scattering assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007620 name: colony papillation assay evidence used in automatic assertion def: "A type of colony papillation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007067 {is_inferred="true"} ! colony papillation assay evidence is_a: ECO:0007325 {is_inferred="true"} ! mutant phenotype evidence used in automatic assertion intersection_of: ECO:0007067 ! colony papillation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007621 name: crystal violet staining evidence used in automatic assertion def: "A type of crystal violet staining evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007069 {is_inferred="true"} ! crystal violet staining evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0007069 ! crystal violet staining evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007622 name: flow cell biofilm assay evidence used in automatic assertion def: "A type of flow cell biofilm assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007071 {is_inferred="true"} ! flow cell biofilm assay evidence is_a: ECO:0007541 {is_inferred="true"} ! biofilm formation assay evidence used in automatic assertion intersection_of: ECO:0007071 ! flow cell biofilm assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007623 name: bacterial 2-hybrid assay evidence used in automatic assertion def: "A type of bacterial 2-hybrid assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007073 {is_inferred="true"} ! bacterial 2-hybrid assay evidence is_a: ECO:0007432 {is_inferred="true"} ! hybrid interaction evidence used in automatic assertion intersection_of: ECO:0007073 ! bacterial 2-hybrid assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007624 name: phenomic profiling assay evidence used in automatic assertion def: "A type of phenomic profiling assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007075 {is_inferred="true"} ! phenomic profiling assay evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0007075 ! phenomic profiling assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007625 name: colony morphology evidence used in automatic assertion def: "A type of colony morphology evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007077 {is_inferred="true"} ! colony morphology evidence is_a: ECO:0007635 {is_inferred="true"} ! experimental phenotypic evidence used in automatic assertion intersection_of: ECO:0007077 ! colony morphology evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007626 name: colony color evidence used in automatic assertion def: "A type of colony color evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007079 {is_inferred="true"} ! colony color evidence is_a: ECO:0007625 {is_inferred="true"} ! colony morphology evidence used in automatic assertion intersection_of: ECO:0007079 ! colony color evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007627 name: colony size evidence used in automatic assertion def: "A type of colony size evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007081 {is_inferred="true"} ! colony size evidence is_a: ECO:0007625 {is_inferred="true"} ! colony morphology evidence used in automatic assertion intersection_of: ECO:0007081 ! colony size evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007628 name: zone of inhibition evidence used in automatic assertion def: "A type of zone of inhibition evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007083 {is_inferred="true"} ! zone of inhibition evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0007083 ! zone of inhibition evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007629 name: Etest evidence used in automatic assertion def: "A type of Etest evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007085 {is_inferred="true"} ! Etest evidence is_a: ECO:0007628 {is_inferred="true"} ! zone of inhibition evidence used in automatic assertion intersection_of: ECO:0007085 ! Etest evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007630 name: ribosome profiling evidence used in automatic assertion def: "A type of ribosome profiling evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0007087 {is_inferred="true"} ! ribosome profiling evidence is_a: ECO:0007298 {is_inferred="true"} ! expression pattern evidence used in automatic assertion intersection_of: ECO:0007087 ! ribosome profiling evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007631 name: evidence based on computational logical inference used in manual assertion def: "A type of evidence based on computational logical inference that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000352 {is_inferred="true"} ! evidence used in manual assertion is_a: ECO:0000362 {is_inferred="true"} ! evidence based on computational logical inference intersection_of: ECO:0000362 ! evidence based on computational logical inference intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-14T09:47:55Z [Term] id: ECO:0007632 name: transcriptional activation assay evidence used in manual assertion def: "A type of transcriptional activation assay evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000170 {is_inferred="true"} ! transcriptional activation assay evidence is_a: ECO:0000314 {is_inferred="true"} ! direct assay evidence used in manual assertion intersection_of: ECO:0000170 ! transcriptional activation assay evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-05-18T08:34:35Z [Term] id: ECO:0007633 name: transcriptional activation assay evidence used in automatic assertion def: "A type of transcriptional activation assay evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000170 {is_inferred="true"} ! transcriptional activation assay evidence is_a: ECO:0007307 {is_inferred="true"} ! direct assay evidence used in automatic assertion intersection_of: ECO:0000170 ! transcriptional activation assay evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-05-18T08:34:35Z [Term] id: ECO:0007634 name: experimental phenotypic evidence used in manual assertion def: "A type of experimental phenotypic evidence that is used in a manual assertion." [ECO:RCT] is_a: ECO:0000059 {is_inferred="true"} ! experimental phenotypic evidence is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion intersection_of: ECO:0000059 ! experimental phenotypic evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: rctauber creation_date: 2018-06-20T02:12:00Z [Term] id: ECO:0007635 name: experimental phenotypic evidence used in automatic assertion def: "A type of experimental phenotypic evidence that is used in an automatic assertion." [ECO:RCT] is_a: ECO:0000059 {is_inferred="true"} ! experimental phenotypic evidence is_a: ECO:0007297 {is_inferred="true"} ! experimental evidence used in automatic assertion intersection_of: ECO:0000059 ! experimental phenotypic evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: rctauber creation_date: 2018-06-20T02:12:00Z [Term] id: GO:0000737 name: DNA catabolic process, endonucleolytic namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of DNA, involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of deoxyribonucleotides." [GOC:elh, GOC:mah] synonym: "DNA breakdown, endonucleolytic" EXACT [] synonym: "DNA degradation, endonucleolytic" EXACT [] synonym: "endonucleolytic degradation of DNA" EXACT [] synonym: "endonucleolytic DNA catabolism" EXACT [] is_a: GO:0006308 ! DNA catabolic process is_a: GO:0090305 ! nucleic acid phosphodiester bond hydrolysis relationship: has_part GO:0004520 ! endodeoxyribonuclease activity [Term] id: GO:0001047 name: core promoter binding namespace: molecular_function def: "Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:txnOH] is_a: GO:0044212 ! transcription regulatory region DNA binding is_a: OBI:0001588 ! binding property_value: IAO:0000111 "core promoter binding" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl created_by: kchris creation_date: 2010-08-27T03:00:52Z [Term] id: GO:0001067 name: regulatory region nucleic acid binding namespace: molecular_function def: "Interacting selectively and non-covalently with a nucleic acid region that regulates a nucleic acid-based process. Such processes include transcription, DNA replication, and DNA repair." [GOC:txnOH] is_a: GO:0003676 ! nucleic acid binding created_by: kchris creation_date: 2010-10-21T04:08:56Z [Term] id: GO:0001508 name: action potential namespace: biological_process 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." [GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] comment: Action potentials typically propagate across excitable membranes. This class covers both action potentials that propagate and those that fail to do so. is_a: GO:0042391 ! regulation of membrane potential property_value: IAO:0000111 "action potential" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0001558 name: regulation of cell growth namespace: biological_process def: "Any process that modulates the frequency, rate, extent or direction of cell growth." [GOC:go_curators] xref: Reactome:REACT_6201 "DTOR is positively regulated by DRheb-GTP, Drosophila melanogaster" is_a: GO:0040008 ! regulation of growth is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0016049 ! cell growth relationship: regulates GO:0016049 ! cell growth [Term] id: GO:0001677 name: formation of translation initiation ternary complex namespace: biological_process def: "Formation of a complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2 (either eIF2 in eukaryotes, or IF2 in prokaryotes). In prokaryotes, fMet-tRNA (initiator) is used rather than Met-tRNA (initiator)." [GOC:hjd] synonym: "translation initiation ternary complex assembly" EXACT [] is_a: GO:0022618 ! ribonucleoprotein complex assembly relationship: part_of GO:0006413 ! translational initiation [Term] id: GO:0001816 name: cytokine production namespace: biological_process 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." [GOC:add, ISBN:0781735149] comment: Note that this term is intended for use when a gene product is seen to cause apparent increases in intracellular or extracellular cytokine levels, without specific regard as to whether the increase is due to increased biosynthesis, increased secretion of preexisting cytokine molecules, or increased conversion from precursor molecules. subset: goslim_pir synonym: "interferon production" NARROW [GOC:add, GOC:mah] synonym: "interleukin production" NARROW [GOC:add, GOC:mah, http://wiki.geneontology.org/index.php/Why_isn%27t_interleukin_in_GO%3F] is_a: GO:0032501 ! multicellular organismal process [Term] id: GO:0001817 name: regulation of cytokine production namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of production of a cytokine." [GOC:add, ISBN:0781735149] is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0001816 ! cytokine production relationship: regulates GO:0001816 ! cytokine production [Term] id: GO:0001818 name: negative regulation of cytokine production namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of production of a cytokine." [GOC:add, ISBN:0781735149] synonym: "down regulation of cytokine production" EXACT [] synonym: "down-regulation of cytokine production" EXACT [] synonym: "downregulation of cytokine production" EXACT [] synonym: "inhibition of cytokine production" NARROW [] is_a: GO:0001817 ! regulation of cytokine production is_a: GO:0051241 ! negative regulation of multicellular organismal process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0001816 ! cytokine production relationship: negatively_regulates GO:0001816 ! cytokine production [Term] id: GO:0001819 name: positive regulation of cytokine production namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of production of a cytokine." [GOC:add, ISBN:0781735149] synonym: "activation of cytokine production" NARROW [] synonym: "stimulation of cytokine production" NARROW [] synonym: "up regulation of cytokine production" EXACT [] synonym: "up-regulation of cytokine production" EXACT [] synonym: "upregulation of cytokine production" EXACT [] is_a: GO:0001817 ! regulation of cytokine production is_a: GO:0051240 ! positive regulation of multicellular organismal process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0001816 ! cytokine production relationship: positively_regulates GO:0001816 ! cytokine production [Term] id: GO:0001906 name: cell killing namespace: biological_process 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." [GOC:add] subset: goslim_pir synonym: "necrosis" RELATED [] is_a: GO:0008150 ! biological_process property_value: IAO:0000111 "cell killing" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0002790 name: peptide secretion namespace: biological_process def: "The controlled release of a peptide from a cell or a tissue." [GOC:add] is_a: GO:0015833 ! peptide transport is_a: GO:0046903 ! secretion [Term] id: GO:0002791 name: regulation of peptide secretion namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of peptide secretion." [GOC:add] is_a: GO:0051046 ! regulation of secretion is_a: GO:0090087 ! regulation of peptide transport intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0002790 ! peptide secretion relationship: regulates GO:0002790 ! peptide secretion [Term] id: GO:0002792 name: negative regulation of peptide secretion namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of peptide secretion." [GOC:add] synonym: "down regulation of peptide secretion" EXACT [] synonym: "down-regulation of peptide secretion" EXACT [] synonym: "downregulation of peptide secretion" EXACT [] synonym: "inhibition of peptide secretion" NARROW [] is_a: GO:0002791 ! regulation of peptide secretion is_a: GO:0051048 ! negative regulation of secretion intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0002790 ! peptide secretion relationship: negatively_regulates GO:0002790 ! peptide secretion [Term] id: GO:0002793 name: positive regulation of peptide secretion namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of peptide secretion." [GOC:add] synonym: "activation of peptide secretion" NARROW [] synonym: "stimulation of peptide secretion" NARROW [] synonym: "up regulation of peptide secretion" EXACT [] synonym: "up-regulation of peptide secretion" EXACT [] synonym: "upregulation of peptide secretion" EXACT [] is_a: GO:0002791 ! regulation of peptide secretion is_a: GO:0051047 ! positive regulation of secretion intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0002790 ! peptide secretion relationship: positively_regulates GO:0002790 ! peptide secretion [Term] id: GO:0002831 name: regulation of response to biotic stimulus namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of a response to biotic stimulus." [GOC:add] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0009607 ! response to biotic stimulus relationship: regulates GO:0009607 ! response to biotic stimulus [Term] id: GO:0002832 name: negative regulation of response to biotic stimulus namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of a response to biotic stimulus." [GOC:add] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate synonym: "down regulation of response to biotic stimulus" EXACT [] synonym: "down-regulation of response to biotic stimulus" EXACT [] synonym: "downregulation of response to biotic stimulus" EXACT [] synonym: "inhibition of response to biotic stimulus" NARROW [] is_a: GO:0002831 ! regulation of response to biotic stimulus is_a: GO:0048585 ! negative regulation of response to stimulus intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0009607 ! response to biotic stimulus relationship: negatively_regulates GO:0009607 ! response to biotic stimulus [Term] id: GO:0002833 name: positive regulation of response to biotic stimulus namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of a response to biotic stimulus." [GOC:add] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate synonym: "activation of response to biotic stimulus" NARROW [] synonym: "stimulation of response to biotic stimulus" NARROW [] synonym: "up regulation of response to biotic stimulus" EXACT [] synonym: "up-regulation of response to biotic stimulus" EXACT [] synonym: "upregulation of response to biotic stimulus" EXACT [] is_a: GO:0002831 ! regulation of response to biotic stimulus is_a: GO:0048584 ! positive regulation of response to stimulus intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0009607 ! response to biotic stimulus relationship: positively_regulates GO:0009607 ! response to biotic stimulus [Term] id: GO:0003674 name: GO:molecular_function name: molecular_function namespace: molecular_function alt_id: GO:0005554 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." [GOC:pdt] comment: Note that, in addition to forming the root of the molecular function ontology, this term is recommended for use for the annotation of gene products whose molecular function is unknown. When this term is used for annotation, it indicates that no information was available about the molecular function of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. Despite its name, this is not a type of 'function' in the sense typically defined by upper ontologies such as Basic Formal Ontology (BFO). It is instead a BFO:process carried out by a single gene product or complex. subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "molecular function" EXACT [] is_a: BFO:0000015 ! process property_value: IAO:0000111 "molecular_function" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0003676 name: nucleic acid binding namespace: molecular_function def: "Interacting selectively and non-covalently with any nucleic acid." [GOC:jl] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant is_a: GO:0097159 ! organic cyclic compound binding is_a: GO:1901363 ! heterocyclic compound binding [Term] id: GO:0003677 name: DNA binding namespace: molecular_function alt_id: GO:0043566 def: "Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid)." [GOC:dph, GOC:jl, GOC:tb, GOC:vw] subset: goslim_agr subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_generic subset: goslim_mouse subset: goslim_plant subset: goslim_yeast synonym: "microtubule/chromatin interaction" RELATED [] synonym: "plasmid binding" NARROW [] synonym: "structure specific DNA binding" RELATED [] synonym: "structure-specific DNA binding" RELATED [] is_a: GO:0003676 ! nucleic acid binding [Term] id: GO:0003823 name: antigen binding namespace: molecular_function def: "Interacting selectively and non-covalently with 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." [GOC:jl, ISBN:0198506732, ISBN:0721662544] subset: goslim_chembl subset: goslim_pir synonym: "antibody" RELATED [] synonym: "B cell receptor activity" RELATED [] synonym: "immunoglobulin" RELATED [] synonym: "opsonin activity" RELATED [] is_a: GO:0005488 ! binding [Term] id: GO:0003824 name: catalytic activity namespace: molecular_function 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." [GOC:vw, ISBN:0198506732] subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant synonym: "enzyme activity" EXACT [GOC:dph, GOC:tb] xref: Wikipedia:Enzyme is_a: GO:0003674 ! GO:molecular_function property_value: IAO:0000111 "catalytic activity" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [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 property_value: IAO:0000111 "RNA-directed DNA polymerase activity" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0004518 name: nuclease activity namespace: molecular_function def: "Catalysis of the hydrolysis of ester linkages within nucleic acids." [ISBN:0198547684] comment: Note that 'tRNA nucleotidyltransferase activity ; GO:0009022', also known as 'ribonuclease PH', and 'DNA-(apurinic or apyrimidinic site) lyase activity ; GO:0003906' do not have parentage in the 'nuclease activity' branch of the ontology because both GO and the Enzyme Commission define nuclease activity as a type of hydrolysis. subset: goslim_chembl subset: goslim_generic subset: goslim_plant subset: goslim_yeast xref: EC:3.1 is_a: GO:0016788 ! hydrolase activity, acting on ester bonds relationship: part_of GO:0090305 ! nucleic acid phosphodiester bond hydrolysis [Term] id: GO:0004519 name: endonuclease activity namespace: molecular_function def: "Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks." [GOC:mah, ISBN:0198547684] xref: Reactome:REACT_100654 "3'- incision of DNA by XPG in GG-NER, Arabidopsis thaliana" xref: Reactome:REACT_101397 "3'- incision of DNA by XPG in GG-NER, Danio rerio" xref: Reactome:REACT_103600 "3'- incision of DNA by XPG in GG-NER, Gallus gallus" xref: Reactome:REACT_106502 "3'- incision of DNA by XPG in GG-NER, Rattus norvegicus" xref: Reactome:REACT_108614 "3'- incision of DNA by XPG in GG-NER, Taeniopygia guttata" xref: Reactome:REACT_110731 "3'- incision of DNA by XPG in GG-NER, Xenopus tropicalis" xref: Reactome:REACT_112366 "Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Danio rerio" xref: Reactome:REACT_1124 "3'- incision of DNA by XPG in GG-NER, Homo sapiens" xref: Reactome:REACT_112509 "Cleavage of mRNA at the 3'-end, Arabidopsis thaliana" xref: Reactome:REACT_112615 "Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Rattus norvegicus" xref: Reactome:REACT_112782 "Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Xenopus tropicalis" xref: Reactome:REACT_113127 "Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Taeniopygia guttata" xref: Reactome:REACT_113480 "Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Gallus gallus" xref: Reactome:REACT_113819 "Cleavage of mRNA at the 3'-end, Drosophila melanogaster" xref: Reactome:REACT_114931 "Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Canis familiaris" xref: Reactome:REACT_115221 "Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Mus musculus" xref: Reactome:REACT_115226 "Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Bos taurus" xref: Reactome:REACT_115382 "Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Sus scrofa" xref: Reactome:REACT_115937 "Displacement of DNA glycosylase and endonucleolytic cleavage by DNA-lyase, Gallus gallus" xref: Reactome:REACT_116011 "Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Gallus gallus" xref: Reactome:REACT_1914 "Cleavage of mRNA at the 3'-end, Homo sapiens" xref: Reactome:REACT_34610 "Cleavage of mRNA at the 3'-end, Bos taurus" xref: Reactome:REACT_6746 "Removal of 3'-phosphate moiety from DSB ends, Homo sapiens" xref: Reactome:REACT_6774 "Removal of 3'-phosphoglycolate (PG) moiety from DSB ends, Homo sapiens" xref: Reactome:REACT_77706 "Cleavage of mRNA at the 3'-end, Taeniopygia guttata" xref: Reactome:REACT_78624 "3'- incision of DNA by XPG in GG-NER, Canis familiaris" xref: Reactome:REACT_79198 "Cleavage of mRNA at the 3'-end, Canis familiaris" xref: Reactome:REACT_80387 "3'- incision of DNA by XPG in GG-NER, Caenorhabditis elegans" xref: Reactome:REACT_80628 "3'- incision of DNA by XPG in GG-NER, Saccharomyces cerevisiae" xref: Reactome:REACT_80681 "3'- incision of DNA by XPG in GG-NER, Bos taurus" xref: Reactome:REACT_80797 "Cleavage of mRNA at the 3'-end, Mus musculus" xref: Reactome:REACT_81714 "3'- incision of DNA by XPG in GG-NER, Oryza sativa" xref: Reactome:REACT_87541 "Cleavage of mRNA at the 3'-end, Xenopus tropicalis" xref: Reactome:REACT_89800 "3'- incision of DNA by XPG in GG-NER, Schizosaccharomyces pombe" xref: Reactome:REACT_90034 "3'- incision of DNA by XPG in GG-NER, Mus musculus" xref: Reactome:REACT_90935 "3'- incision of DNA by XPG in GG-NER, Sus scrofa" xref: Reactome:REACT_92894 "3'- incision of DNA by XPG in GG-NER, Drosophila melanogaster" is_a: GO:0004518 ! nuclease activity [Term] id: GO:0004520 name: endodeoxyribonuclease activity namespace: molecular_function def: "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC:mah, ISBN:0198547684] synonym: "DNA nicking activity" RELATED [GOC:mah] synonym: "endonuclease G activity" RELATED [] xref: Reactome:REACT_101184 "5'-incision of DNA by ERCC1-XPF in GG-NER, Danio rerio" xref: Reactome:REACT_101250 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Caenorhabditis elegans" xref: Reactome:REACT_101987 "APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Dictyostelium discoideum" xref: Reactome:REACT_103441 "APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Rattus norvegicus" xref: Reactome:REACT_103771 "3' incision of the lesioned strand of DNA in TC-NER, Xenopus tropicalis" xref: Reactome:REACT_104010 "APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Danio rerio" xref: Reactome:REACT_104673 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Schizosaccharomyces pombe" xref: Reactome:REACT_104703 "APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Taeniopygia guttata" xref: Reactome:REACT_104968 "APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Sus scrofa" xref: Reactome:REACT_106756 "3' incision of the lesioned strand of DNA in TC-NER, Drosophila melanogaster" xref: Reactome:REACT_109040 "3' incision of the lesioned strand of DNA in TC-NER, Canis familiaris" xref: Reactome:REACT_109537 "APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Xenopus tropicalis" xref: Reactome:REACT_109692 "3' incision of the lesioned strand of DNA in TC-NER, Sus scrofa" xref: Reactome:REACT_110386 "3' incision of the lesioned strand of DNA in TC-NER, Danio rerio" xref: Reactome:REACT_112122 "5'-incision of DNA by ERCC1-XPF in GG-NER, Xenopus tropicalis" xref: Reactome:REACT_112152 "3' incision of the lesioned strand of DNA in TC-NER, Taeniopygia guttata" xref: Reactome:REACT_115154 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Gallus gallus" xref: Reactome:REACT_115463 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Taeniopygia guttata" xref: Reactome:REACT_115479 "3' incision of the lesioned strand of DNA in TC-NER, Gallus gallus" xref: Reactome:REACT_1274 "3' incision of the lesioned strand of DNA in TC-NER, Homo sapiens" xref: Reactome:REACT_1311 "5'-incision of DNA by ERCC1-XPF in GG-NER, Homo sapiens" xref: Reactome:REACT_1964 "APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Homo sapiens" xref: Reactome:REACT_27164 "Removal of SPO11 and Resection of 5' Ends of DNA (yeast), Saccharomyces cerevisiae" xref: Reactome:REACT_27209 "Removal of SPO11 and Resection of 5' Ends of DNA, Homo sapiens" xref: Reactome:REACT_28610 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Bos taurus" xref: Reactome:REACT_28960 "3' incision of the lesioned strand of DNA in TC-NER, Rattus norvegicus" xref: Reactome:REACT_30718 "3' incision of the lesioned strand of DNA in TC-NER, Dictyostelium discoideum" xref: Reactome:REACT_31162 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Arabidopsis thaliana" xref: Reactome:REACT_31548 "APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Caenorhabditis elegans" xref: Reactome:REACT_31660 "3' incision of the lesioned strand of DNA in TC-NER, Schizosaccharomyces pombe" xref: Reactome:REACT_31823 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Oryza sativa" xref: Reactome:REACT_32833 "3' incision of the lesioned strand of DNA in TC-NER, Saccharomyces cerevisiae" xref: Reactome:REACT_33043 "3' incision of the lesioned strand of DNA in TC-NER, Bos taurus" xref: Reactome:REACT_78421 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Sus scrofa" xref: Reactome:REACT_79265 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Dictyostelium discoideum" xref: Reactome:REACT_80173 "APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Mus musculus" xref: Reactome:REACT_80298 "3' incision of the lesioned strand of DNA in TC-NER, Caenorhabditis elegans" xref: Reactome:REACT_80967 "3' incision of the lesioned strand of DNA in TC-NER, Oryza sativa" xref: Reactome:REACT_811 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Homo sapiens" xref: Reactome:REACT_81197 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Mus musculus" xref: Reactome:REACT_82925 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Canis familiaris" xref: Reactome:REACT_83838 "5'-incision of DNA by ERCC1-XPF in GG-NER, Rattus norvegicus" xref: Reactome:REACT_85019 "APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Drosophila melanogaster" xref: Reactome:REACT_88339 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Rattus norvegicus" xref: Reactome:REACT_90087 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Danio rerio" xref: Reactome:REACT_92741 "3' incision of the lesioned strand of DNA in TC-NER, Arabidopsis thaliana" xref: Reactome:REACT_94592 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Drosophila melanogaster" xref: Reactome:REACT_94820 "APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Canis familiaris" xref: Reactome:REACT_95903 "5'-incision of DNA by ERCC1-XPF in GG-NER, Mus musculus" xref: Reactome:REACT_97114 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Xenopus tropicalis" xref: Reactome:REACT_98405 "5' incision leading to excision of DNA fragment with lesion in TC-NER, Saccharomyces cerevisiae" xref: Reactome:REACT_98417 "APE1 mediated endonucleolytic cleavage at the 5' side of the base-free deoxyribose residue, Bos taurus" xref: Reactome:REACT_99783 "3' incision of the lesioned strand of DNA in TC-NER, Mus musculus" is_a: GO:0004519 ! endonuclease activity is_a: GO:0004536 ! deoxyribonuclease activity [Term] id: GO:0004536 name: deoxyribonuclease activity namespace: molecular_function alt_id: GO:0004537 def: "Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid." [GOC:mah, ISBN:0198547684] synonym: "caspase-activated deoxyribonuclease activity" NARROW [] xref: Reactome:REACT_100642 "Cleavage of DNA by DFF40, Xenopus tropicalis" xref: Reactome:REACT_101208 "Cleavage of DNA by DFF40, Bos taurus" xref: Reactome:REACT_110575 "Cleavage of DNA by DFF40, Sus scrofa" xref: Reactome:REACT_13702 "Cleavage of DNA by DFF40, Homo sapiens" xref: Reactome:REACT_29722 "Cleavage of DNA by DFF40, Danio rerio" xref: Reactome:REACT_31853 "Cleavage of DNA by DFF40, Taeniopygia guttata" xref: Reactome:REACT_90424 "Cleavage of DNA by DFF40, Gallus gallus" xref: Reactome:REACT_95359 "Cleavage of DNA by DFF40, Rattus norvegicus" xref: Reactome:REACT_98682 "Cleavage of DNA by DFF40, Canis familiaris" is_a: GO:0004518 ! nuclease activity is_a: GO:0140097 ! catalytic activity, acting on DNA relationship: part_of GO:0006259 ! DNA metabolic process [Term] id: GO:0005215 name: transporter activity namespace: molecular_function alt_id: GO:0005478 def: "Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells." [GOC:ai, GOC:dgf] comment: Some transporters, such as certain members of the SLC family, are referred to as 'carriers'; however GO uses carrier with a different meaning: a carrier binds to and transports the substance (see GO:0140104 molecular carrier activity), whereas a transporter forms some pore that allows the passing of molecules. subset: goslim_agr subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant synonym: "carrier" RELATED [] xref: Reactome:REACT_6315 "Virion-associated M2 protein mediated ion infusion, Homo sapiens" is_a: GO:0003674 ! GO:molecular_function [Term] id: GO:0005216 name: ion channel activity namespace: molecular_function 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)." [GOC:cy, GOC:mtg_transport, GOC:pr, ISBN:0815340729] is_a: GO:0009987 ! cellular process is_a: GO:0015075 ! ion transmembrane transporter activity is_a: GO:0015318 ! inorganic molecular entity transmembrane transporter activity is_a: GO:0022838 ! substrate-specific channel activity property_value: IAO:0000111 "ion channel activity" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005488 name: binding namespace: molecular_function def: "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732] comment: Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. subset: gocheck_do_not_manually_annotate subset: goslim_pir subset: goslim_plant synonym: "ligand" NARROW [] xref: Wikipedia:Binding_(molecular) is_a: GO:0003674 ! GO:molecular_function [Term] id: GO:0005575 name: cellular_component namespace: cellular_component alt_id: GO:0008372 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)." [GOC:pdt, NIF_Subcellular:sao-1337158144] comment: Note that, in addition to forming the root of the cellular component ontology, this term is recommended for use for the annotation of gene products whose cellular component is unknown. When this term is used for annotation, it indicates that no information was available about the cellular component of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_yeast synonym: "cell or subcellular entity" EXACT [] synonym: "cellular component" EXACT [] synonym: "subcellular entity" RELATED [NIF_Subcellular:nlx_subcell_100315] xref: NIF_Subcellular:sao-1337158144 xref: NIF_Subcellular:sao1337158144 is_a: BFO:0000040 ! material entity property_value: IAO:0000111 "cellular_component" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0005622 name: intracellular namespace: cellular_component def: "The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [ISBN:0198506732] subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_plant synonym: "internal to cell" EXACT [] synonym: "nucleocytoplasm" RELATED [GOC:mah] synonym: "protoplasm" EXACT [] synonym: "protoplast" RELATED [GOC:mah] xref: Wikipedia:Intracellular is_a: GO:0044464 ! cell part [Term] id: GO:0005623 name: cell namespace: cellular_component def: "The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:go_curators] subset: goslim_chembl subset: goslim_generic subset: goslim_plant xref: NIF_Subcellular:sao1813327414 xref: Wikipedia:Cell_(biology) is_a: GO:0005575 ! cellular_component property_value: IAO:0000589 "cell and encapsulating structures" xsd:string [Term] id: GO:0006139 name: nucleobase-containing compound metabolic process namespace: biological_process alt_id: GO:0055134 def: "Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:ai] subset: goslim_pir subset: goslim_plant synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "cellular nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] synonym: "nucleobase, nucleoside and nucleotide metabolic process" RELATED [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] is_a: GO:0006725 ! cellular aromatic compound metabolic process is_a: GO:0034641 ! cellular nitrogen compound metabolic process is_a: GO:0044238 ! primary metabolic process is_a: GO:0046483 ! heterocycle metabolic process is_a: GO:1901360 ! organic cyclic compound metabolic process [Term] id: GO:0006259 name: DNA metabolic process namespace: biological_process alt_id: GO:0055132 def: "Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides." [ISBN:0198506732] subset: goslim_agr subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant synonym: "cellular DNA metabolism" EXACT [] synonym: "DNA metabolism" EXACT [] is_a: GO:0044260 ! cellular macromolecule metabolic process is_a: GO:0090304 ! nucleic acid metabolic process [Term] id: GO:0006260 name: DNA replication namespace: biological_process alt_id: GO:0055133 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." [GOC:mah] comment: DNA biosynthesis is only part of this process. See also the biological process terms 'DNA-dependent DNA replication ; GO:0006261' and 'RNA-dependent DNA replication ; GO:0006278'. subset: goslim_pir subset: goslim_pombe subset: goslim_yeast xref: Reactome:REACT_100559 "Activation of ATR in response to replication stress, Mus musculus" xref: Reactome:REACT_101280 "Activation of claspin, Xenopus tropicalis" xref: Reactome:REACT_101497 "Activation of claspin, Bos taurus" xref: Reactome:REACT_102679 "Activation of ATR in response to replication stress, Gallus gallus" xref: Reactome:REACT_103614 "Stalling of DNA replication fork and RPA binding, Taeniopygia guttata" xref: Reactome:REACT_104547 "Recruitment and activation of Chk1, Gallus gallus" xref: Reactome:REACT_105292 "Activation of ATR in response to replication stress, Xenopus tropicalis" xref: Reactome:REACT_105467 "Loading of claspin onto DNA during replication origin firing, Danio rerio" xref: Reactome:REACT_105835 "Stalling of DNA replication fork and RPA binding, Gallus gallus" xref: Reactome:REACT_106018 "Recruitment of Rad17-RFC complex to DNA, Gallus gallus" xref: Reactome:REACT_106104 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Bos taurus" xref: Reactome:REACT_106382 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Drosophila melanogaster" xref: Reactome:REACT_106434 "Activation of claspin, Canis familiaris" xref: Reactome:REACT_106732 "Recruitment and activation of Chk1, Canis familiaris" xref: Reactome:REACT_107075 "Activation of ATR in response to replication stress, Danio rerio" xref: Reactome:REACT_107423 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Caenorhabditis elegans" xref: Reactome:REACT_108461 "Recruitment and activation of Chk1, Bos taurus" xref: Reactome:REACT_108634 "Loading of claspin onto DNA during replication origin firing, Mus musculus" xref: Reactome:REACT_108739 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Xenopus tropicalis" xref: Reactome:REACT_108768 "Activation of ATR in response to replication stress, Bos taurus" xref: Reactome:REACT_108929 "Activation of ATR in response to replication stress, Drosophila melanogaster" xref: Reactome:REACT_109137 "Stalling of DNA replication fork and RPA binding, Rattus norvegicus" xref: Reactome:REACT_112472 "Activation of ATR in response to replication stress, Saccharomyces cerevisiae" xref: Reactome:REACT_113703 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Gallus gallus" xref: Reactome:REACT_29423 "Activation of ATR in response to replication stress, Schizosaccharomyces pombe" xref: Reactome:REACT_29444 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Taeniopygia guttata" xref: Reactome:REACT_29691 "Activation of ATR in response to replication stress, Rattus norvegicus" xref: Reactome:REACT_29764 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Taeniopygia guttata" xref: Reactome:REACT_30149 "Activation of claspin, Rattus norvegicus" xref: Reactome:REACT_31024 "Recruitment of Rad17-RFC complex to DNA, Xenopus tropicalis" xref: Reactome:REACT_31919 "Loading of claspin onto DNA during replication origin firing, Rattus norvegicus" xref: Reactome:REACT_32546 "Recruitment of Rad17-RFC complex to DNA, Mus musculus" xref: Reactome:REACT_32932 "Recruitment and activation of Chk1, Taeniopygia guttata" xref: Reactome:REACT_33572 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Dictyostelium discoideum" xref: Reactome:REACT_33874 "Recruitment and activation of Chk1, Xenopus tropicalis" xref: Reactome:REACT_50018 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Rattus norvegicus" xref: Reactome:REACT_53588 "Loading of claspin onto DNA during replication origin firing, Canis familiaris" xref: Reactome:REACT_6729 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Homo sapiens" xref: Reactome:REACT_6738 "Loading of claspin onto DNA during replication origin firing, Homo sapiens" xref: Reactome:REACT_6750 "Activation of claspin, Homo sapiens" xref: Reactome:REACT_6769 "Activation of ATR in response to replication stress, Homo sapiens" xref: Reactome:REACT_6798 "Recruitment of Rad17-RFC complex to DNA, Homo sapiens" xref: Reactome:REACT_6869 "Recruitment and activation of Chk1, Homo sapiens" xref: Reactome:REACT_6936 "Stalling of DNA replication fork and RPA binding, Homo sapiens" xref: Reactome:REACT_6939 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Homo sapiens" xref: Reactome:REACT_77532 "Stalling of DNA replication fork and RPA binding, Canis familiaris" xref: Reactome:REACT_79188 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Canis familiaris" xref: Reactome:REACT_79450 "Activation of ATR in response to replication stress, Dictyostelium discoideum" xref: Reactome:REACT_80432 "Loading of claspin onto DNA during replication origin firing, Taeniopygia guttata" xref: Reactome:REACT_80571 "Activation of claspin, Mus musculus" xref: Reactome:REACT_80896 "Recruitment and activation of Chk1, Sus scrofa" xref: Reactome:REACT_80988 "Loading of claspin onto DNA during replication origin firing, Bos taurus" xref: Reactome:REACT_81803 "Recruitment of Rad17-RFC complex to DNA, Canis familiaris" xref: Reactome:REACT_83095 "Recruitment of Rad17-RFC complex to DNA, Danio rerio" xref: Reactome:REACT_84829 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Danio rerio" xref: Reactome:REACT_85561 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Rattus norvegicus" xref: Reactome:REACT_86410 "Stalling of DNA replication fork and RPA binding, Mus musculus" xref: Reactome:REACT_86739 "Recruitment and activation of Chk1, Rattus norvegicus" xref: Reactome:REACT_87233 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Canis familiaris" xref: Reactome:REACT_87449 "Recruitment of Rad17-RFC complex to DNA, Rattus norvegicus" xref: Reactome:REACT_87590 "Recruitment of Rad17-RFC complex to DNA, Bos taurus" xref: Reactome:REACT_88085 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Gallus gallus" xref: Reactome:REACT_88384 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Schizosaccharomyces pombe" xref: Reactome:REACT_88529 "Activation of claspin, Gallus gallus" xref: Reactome:REACT_89355 "Activation of claspin, Danio rerio" xref: Reactome:REACT_89439 "Activation of ATR in response to replication stress, Sus scrofa" xref: Reactome:REACT_89725 "Loading of claspin onto DNA during replication origin firing, Drosophila melanogaster" xref: Reactome:REACT_90512 "Stalling of DNA replication fork and RPA binding, Bos taurus" xref: Reactome:REACT_90809 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Danio rerio" xref: Reactome:REACT_90838 "Recruitment of Rad17-RFC complex to DNA, Taeniopygia guttata" xref: Reactome:REACT_91184 "Recruitment and activation of Chk1, Danio rerio" xref: Reactome:REACT_91302 "Activation of ATR in response to replication stress, Canis familiaris" xref: Reactome:REACT_92527 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Mus musculus" xref: Reactome:REACT_92644 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Xenopus tropicalis" xref: Reactome:REACT_92706 "Stalling of DNA replication fork and RPA binding, Danio rerio" xref: Reactome:REACT_94983 "Stalling of DNA replication fork and RPA binding, Xenopus tropicalis" xref: Reactome:REACT_95253 "Activation of ATR in response to replication stress, Taeniopygia guttata" xref: Reactome:REACT_95329 "Activation of claspin, Taeniopygia guttata" xref: Reactome:REACT_96115 "Binding of ATR-ATRIP to the RPA-ssDNA complex, Mus musculus" xref: Reactome:REACT_96804 "Recruitment and activation of Chk1, Mus musculus" xref: Reactome:REACT_96998 "Recruitment of the Rad9-Hus1-Rad1 complex to DNA, Bos taurus" xref: Reactome:REACT_97204 "Loading of claspin onto DNA during replication origin firing, Gallus gallus" xref: Reactome:REACT_97726 "Activation of ATR in response to replication stress, Caenorhabditis elegans" xref: Reactome:REACT_99948 "Loading of claspin onto DNA during replication origin firing, Xenopus tropicalis" xref: Wikipedia:DNA_replication is_a: GO:0006259 ! DNA metabolic process is_a: GO:0034645 ! cellular macromolecule biosynthetic process relationship: has_part GO:0071897 ! DNA biosynthetic process [Term] id: GO:0006275 name: regulation of DNA replication namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA replication." [GOC:go_curators] is_a: GO:0051052 ! regulation of DNA metabolic process is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006260 ! DNA replication relationship: regulates GO:0006260 ! DNA replication [Term] id: GO:0006276 name: plasmid maintenance namespace: biological_process def: "The maintenance of the integrity of extrachromosomal plasmid DNA; includes processes that ensure plasmids are retained in the daughter cells after cell division." [GOC:ai] subset: goslim_pir is_a: GO:0009987 ! cellular process [Term] id: GO:0006304 name: DNA modification namespace: biological_process def: "The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties." [GOC:jl, GOC:ma] subset: goslim_pir is_a: GO:0006259 ! DNA metabolic process is_a: GO:0043412 ! macromolecule modification [Term] id: GO:0006305 name: DNA alkylation namespace: biological_process def: "The addition of alkyl groups to many positions on all four bases of DNA. Alkylating agents can also modify the bases of incoming nucleotides in the course of DNA synthesis." [ISBN:0716735970] is_a: GO:0006304 ! DNA modification [Term] id: GO:0006306 name: DNA methylation namespace: biological_process def: "The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine." [GOC:ems, ISBN:0198506732] xref: Wikipedia:DNA_methylation is_a: GO:0006305 ! DNA alkylation is_a: GO:0043414 ! macromolecule methylation is_a: GO:0044728 ! DNA methylation or demethylation [Term] id: GO:0006308 name: DNA catabolic process namespace: biological_process def: "The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC:go_curators, ISBN:0198506732] synonym: "DNA breakdown" EXACT [] synonym: "DNA catabolism" EXACT [] synonym: "DNA degradation" EXACT [] is_a: GO:0006259 ! DNA metabolic process is_a: GO:0034655 ! nucleobase-containing compound catabolic process is_a: GO:0044265 ! cellular macromolecule catabolic process relationship: has_part GO:0004536 ! deoxyribonuclease activity [Term] id: GO:0006309 name: apoptotic DNA fragmentation namespace: biological_process alt_id: GO:0008178 def: "The cleavage of DNA during apoptosis, which usually occurs in two stages: cleavage into fragments of about 50 kbp followed by cleavage between nucleosomes to yield 200 bp fragments." [GOC:dph, GOC:mah, GOC:mtg_apoptosis, GOC:tb, ISBN:0721639976, PMID:15723341, PMID:23379520] comment: DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases. In human, these include DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G) (reviewed in PMID:15723341). Caution is needed when apoptotic DNA laddering assays show presence of fragmented DNA. A positive assay may simply reflect the end point of a whole apoptotic process. Unless clear experimental evidence is available to show that a gene product is directly involved in fragmenting DNA, please do not annotate to GO:0006309 'apoptotic DNA fragmentation' and consider annotating instead to a more upstream process such as, e.g., GO:0042981 'regulation of apoptotic process', GO:0006915 'apoptotic process', GO:0097190 'apoptotic signaling pathway'. Also, note that gene products involved in compartmentalization of apoptotic nucleases and in activation or repression of their enzymatic activity should be annotated to the regulation term GO:1902510 'regulation of apoptotic DNA fragmentation' or to one of its children (see PMID:15723341). synonym: "chromatinolysis" BROAD [GOC:mtg_apoptosis] synonym: "DNA catabolic process during apoptosis" EXACT [] synonym: "DNA catabolism during apoptosis" EXACT [] synonym: "DNA fragmentation" BROAD [] synonym: "DNA fragmentation involved in apoptotic nuclear change" EXACT [GOC:cjm, GOC:dph, GOC:tb] synonym: "endonucleolytic DNA catabolic process involved in apoptosis" EXACT [] xref: Reactome:REACT_102783 "Apoptosis induced DNA fragmentation, Bos taurus" xref: Reactome:REACT_105342 "Apoptosis induced DNA fragmentation, Sus scrofa" xref: Reactome:REACT_110358 "Apoptosis induced DNA fragmentation, Xenopus tropicalis" xref: Reactome:REACT_113418 "Apoptosis induced DNA fragmentation, Plasmodium falciparum" xref: Reactome:REACT_1213 "Apoptosis induced DNA fragmentation, Homo sapiens" xref: Reactome:REACT_28808 "Apoptosis induced DNA fragmentation, Rattus norvegicus" xref: Reactome:REACT_33113 "Apoptosis induced DNA fragmentation, Mus musculus" xref: Reactome:REACT_92967 "Apoptosis induced DNA fragmentation, Drosophila melanogaster" xref: Reactome:REACT_94135 "Apoptosis induced DNA fragmentation, Taeniopygia guttata" xref: Reactome:REACT_98713 "Apoptosis induced DNA fragmentation, Canis familiaris" xref: Reactome:REACT_99275 "Apoptosis induced DNA fragmentation, Gallus gallus" xref: Reactome:REACT_99925 "Apoptosis induced DNA fragmentation, Danio rerio" is_a: GO:0000737 ! DNA catabolic process, endonucleolytic intersection_of: GO:0000737 ! DNA catabolic process, endonucleolytic intersection_of: part_of GO:0030262 ! apoptotic nuclear changes relationship: part_of GO:0030262 ! apoptotic nuclear changes [Term] id: GO:0006338 name: chromatin remodeling def: "Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation." [] is_a: GO:0009987 ! cellular process property_value: IAO:0000111 "chromatin remodeling" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006351 name: transcription, DNA-templated namespace: biological_process alt_id: GO:0006350 alt_id: GO:0061018 alt_id: GO:0061022 def: "The cellular synthesis of RNA on a template of DNA." [GOC:jl, GOC:txnOH] subset: goslim_aspergillus subset: goslim_metagenomics subset: goslim_pir subset: goslim_pombe synonym: "cellular transcription" BROAD [] synonym: "cellular transcription, DNA-dependent" EXACT [] synonym: "DNA-dependent transcription" EXACT [] synonym: "transcription" BROAD [] synonym: "transcription regulator activity" RELATED [] synonym: "transcription, DNA-dependent" EXACT [GOC:txnOH] xref: Wikipedia:Transcription_(genetics) is_a: GO:0034645 ! cellular macromolecule biosynthetic process is_a: GO:0097659 ! nucleic acid-templated transcription relationship: part_of GO:0010467 ! gene expression [Term] id: GO:0006355 name: regulation of transcription, DNA-templated namespace: biological_process alt_id: GO:0032583 alt_id: GO:0045449 alt_id: GO:0061019 def: "Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH] subset: goslim_pombe synonym: "regulation of cellular transcription, DNA-dependent" EXACT [] synonym: "regulation of gene-specific transcription" RELATED [] synonym: "regulation of transcription, DNA-dependent" EXACT [GOC:txnOH] synonym: "transcriptional control" BROAD [] is_a: GO:0010468 ! regulation of gene expression is_a: GO:1903506 ! regulation of nucleic acid-templated transcription is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006351 ! transcription, DNA-templated relationship: regulates GO:0006351 ! transcription, DNA-templated [Term] id: GO:0006412 name: translation namespace: biological_process alt_id: GO:0006416 alt_id: GO:0006453 alt_id: GO:0043037 def: "The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome." [GOC:go_curators] subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant synonym: "protein anabolism" EXACT [] synonym: "protein biosynthesis" EXACT [] synonym: "protein biosynthetic process" EXACT [GOC:curators] synonym: "protein formation" EXACT [] synonym: "protein synthesis" EXACT [] synonym: "protein translation" EXACT [] xref: Reactome:REACT_100338 "Translation, Sus scrofa" xref: Reactome:REACT_100851 "Translation, Saccharomyces cerevisiae" xref: Reactome:REACT_101045 "Translation, Dictyostelium discoideum" xref: Reactome:REACT_101324 "Translation, Canis familiaris" xref: Reactome:REACT_1014 "Translation, Homo sapiens" xref: Reactome:REACT_103420 "Translation, Plasmodium falciparum" xref: Reactome:REACT_105544 "Translation, Arabidopsis thaliana" xref: Reactome:REACT_29980 "Translation, Bos taurus" xref: Reactome:REACT_33559 "Translation, Rattus norvegicus" xref: Reactome:REACT_77710 "Translation, Drosophila melanogaster" xref: Reactome:REACT_79784 "Translation, Danio rerio" xref: Reactome:REACT_81734 "Translation, Schizosaccharomyces pombe" xref: Reactome:REACT_81833 "Translation, Caenorhabditis elegans" xref: Reactome:REACT_82171 "Translation, Xenopus tropicalis" xref: Reactome:REACT_83429 "Translation, Taeniopygia guttata" xref: Reactome:REACT_83530 "Translation, Gallus gallus" xref: Reactome:REACT_86996 "Translation, Oryza sativa" xref: Reactome:REACT_95535 "Translation, Mus musculus" xref: Reactome:REACT_96394 "Translation, Escherichia coli" xref: Wikipedia:Translation_(genetics) is_a: GO:0034645 ! cellular macromolecule biosynthetic process is_a: GO:0043043 ! peptide biosynthetic process is_a: GO:0044267 ! cellular protein metabolic process relationship: has_part GO:0006413 ! translational initiation relationship: has_part GO:0006414 ! translational elongation relationship: has_part GO:0006415 ! translational termination relationship: part_of GO:0010467 ! gene expression [Term] id: GO:0006413 name: translational initiation namespace: biological_process alt_id: GO:0006440 alt_id: GO:0006454 def: "The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA." [ISBN:019879276X] subset: goslim_yeast synonym: "biopolymerisation" BROAD [] synonym: "biopolymerization" BROAD [] synonym: "protein synthesis initiation" BROAD [] synonym: "translation initiation" EXACT [] xref: Reactome:REACT_101789 "Eukaryotic Translation Initiation, Gallus gallus" xref: Reactome:REACT_104290 "Eukaryotic Translation Initiation, Xenopus tropicalis" xref: Reactome:REACT_2159 "Eukaryotic Translation Initiation, Homo sapiens" xref: Reactome:REACT_29447 "Eukaryotic Translation Initiation, Dictyostelium discoideum" xref: Reactome:REACT_30389 "Eukaryotic Translation Initiation, Oryza sativa" xref: Reactome:REACT_33969 "Eukaryotic Translation Initiation, Caenorhabditis elegans" xref: Reactome:REACT_34354 "Eukaryotic Translation Initiation, Taeniopygia guttata" xref: Reactome:REACT_77252 "Eukaryotic Translation Initiation, Drosophila melanogaster" xref: Reactome:REACT_79705 "Eukaryotic Translation Initiation, Rattus norvegicus" xref: Reactome:REACT_85780 "Eukaryotic Translation Initiation, Bos taurus" xref: Reactome:REACT_88031 "Eukaryotic Translation Initiation, Schizosaccharomyces pombe" xref: Reactome:REACT_91066 "Eukaryotic Translation Initiation, Arabidopsis thaliana" xref: Reactome:REACT_95293 "Eukaryotic Translation Initiation, Plasmodium falciparum" xref: Reactome:REACT_95552 "Eukaryotic Translation Initiation, Mus musculus" xref: Reactome:REACT_95685 "Eukaryotic Translation Initiation, Canis familiaris" xref: Reactome:REACT_97707 "Eukaryotic Translation Initiation, Sus scrofa" xref: Reactome:REACT_98138 "Eukaryotic Translation Initiation, Saccharomyces cerevisiae" xref: Reactome:REACT_99004 "Eukaryotic Translation Initiation, Danio rerio" is_a: GO:0044237 ! cellular metabolic process relationship: has_part GO:0001677 ! formation of translation initiation ternary complex relationship: part_of GO:0006412 ! translation [Term] id: GO:0006414 name: translational elongation namespace: biological_process alt_id: GO:0006442 alt_id: GO:0006455 def: "The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis." [GOC:ems] subset: goslim_yeast synonym: "protein synthesis elongation" BROAD [] synonym: "translation elongation" EXACT [] xref: Reactome:REACT_100207 "Eukaryotic Translation Elongation, Dictyostelium discoideum" xref: Reactome:REACT_100561 "Eukaryotic Translation Elongation, Canis familiaris" xref: Reactome:REACT_101290 "Eukaryotic Translation Elongation, Gallus gallus" xref: Reactome:REACT_101737 "Eukaryotic Translation Elongation, Escherichia coli" xref: Reactome:REACT_102082 "Eukaryotic Translation Elongation, Mus musculus" xref: Reactome:REACT_103580 "Eukaryotic Translation Elongation, Danio rerio" xref: Reactome:REACT_108124 "Eukaryotic Translation Elongation, Xenopus tropicalis" xref: Reactome:REACT_108677 "Eukaryotic Translation Elongation, Taeniopygia guttata" xref: Reactome:REACT_108858 "Eukaryotic Translation Elongation, Caenorhabditis elegans" xref: Reactome:REACT_1477 "Eukaryotic Translation Elongation, Homo sapiens" xref: Reactome:REACT_30678 "Eukaryotic Translation Elongation, Arabidopsis thaliana" xref: Reactome:REACT_31079 "Eukaryotic Translation Elongation, Sus scrofa" xref: Reactome:REACT_80015 "Eukaryotic Translation Elongation, Bos taurus" xref: Reactome:REACT_80831 "Eukaryotic Translation Elongation, Rattus norvegicus" xref: Reactome:REACT_81624 "Eukaryotic Translation Elongation, Drosophila melanogaster" xref: Reactome:REACT_82124 "Eukaryotic Translation Elongation, Saccharomyces cerevisiae" xref: Reactome:REACT_88049 "Eukaryotic Translation Elongation, Schizosaccharomyces pombe" xref: Reactome:REACT_93503 "Eukaryotic Translation Elongation, Oryza sativa" xref: Reactome:REACT_96070 "Eukaryotic Translation Elongation, Plasmodium falciparum" is_a: GO:0034645 ! cellular macromolecule biosynthetic process relationship: part_of GO:0006412 ! translation [Term] id: GO:0006415 name: translational termination namespace: biological_process alt_id: GO:0006443 alt_id: GO:0006456 def: "The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code)." [GOC:hjd, ISBN:019879276X] synonym: "protein synthesis termination" BROAD [] synonym: "translation termination" EXACT [] synonym: "translational complex disassembly" EXACT [] xref: Reactome:REACT_100227 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Taeniopygia guttata" xref: Reactome:REACT_100585 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Dictyostelium discoideum" xref: Reactome:REACT_100730 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Danio rerio" xref: Reactome:REACT_1034 "Eukaryotic Translation Termination, Saccharomyces cerevisiae" xref: Reactome:REACT_103749 "Eukaryotic Translation Termination, Oryza sativa" xref: Reactome:REACT_104420 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Caenorhabditis elegans" xref: Reactome:REACT_104616 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Taeniopygia guttata" xref: Reactome:REACT_106326 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Plasmodium falciparum" xref: Reactome:REACT_107138 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Schizosaccharomyces pombe" xref: Reactome:REACT_107171 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Danio rerio" xref: Reactome:REACT_107771 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Oryza sativa" xref: Reactome:REACT_107964 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Schizosaccharomyces pombe" xref: Reactome:REACT_109127 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Caenorhabditis elegans" xref: Reactome:REACT_109494 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Plasmodium falciparum" xref: Reactome:REACT_110009 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Mus musculus" xref: Reactome:REACT_112381 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Gallus gallus" xref: Reactome:REACT_112559 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Rattus norvegicus" xref: Reactome:REACT_112632 "Eukaryotic Translation Termination, Rattus norvegicus" xref: Reactome:REACT_113540 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Gallus gallus" xref: Reactome:REACT_114287 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Gallus gallus" xref: Reactome:REACT_114807 "Eukaryotic Translation Termination, Gallus gallus" xref: Reactome:REACT_1152 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Saccharomyces cerevisiae" xref: Reactome:REACT_115292 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Rattus norvegicus" xref: Reactome:REACT_1654 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Homo sapiens" xref: Reactome:REACT_1986 "Eukaryotic Translation Termination, Homo sapiens" xref: Reactome:REACT_227 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Homo sapiens" xref: Reactome:REACT_28115 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Canis familiaris" xref: Reactome:REACT_28238 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Xenopus tropicalis" xref: Reactome:REACT_28773 "Eukaryotic Translation Termination, Danio rerio" xref: Reactome:REACT_29257 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Drosophila melanogaster" xref: Reactome:REACT_31194 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Canis familiaris" xref: Reactome:REACT_31222 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Oryza sativa" xref: Reactome:REACT_32804 "Eukaryotic Translation Termination, Drosophila melanogaster" xref: Reactome:REACT_33545 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Dictyostelium discoideum" xref: Reactome:REACT_34123 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Mus musculus" xref: Reactome:REACT_34462 "Eukaryotic Translation Termination, Saccharomyces cerevisiae" xref: Reactome:REACT_389 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Homo sapiens" xref: Reactome:REACT_393 "GTP bound eRF3:eRF1 complex binds the peptidyl-tRNA:mRNA:Ribosome complex, Saccharomyces cerevisiae" xref: Reactome:REACT_716 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Saccharomyces cerevisiae" xref: Reactome:REACT_78279 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Arabidopsis thaliana" xref: Reactome:REACT_78389 "Eukaryotic Translation Termination, Schizosaccharomyces pombe" xref: Reactome:REACT_78823 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Dictyostelium discoideum" xref: Reactome:REACT_80339 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Xenopus tropicalis" xref: Reactome:REACT_81067 "Eukaryotic Translation Termination, Canis familiaris" xref: Reactome:REACT_81196 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Arabidopsis thaliana" xref: Reactome:REACT_81882 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Caenorhabditis elegans" xref: Reactome:REACT_83324 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Xenopus tropicalis" xref: Reactome:REACT_83432 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Drosophila melanogaster" xref: Reactome:REACT_84537 "Eukaryotic Translation Termination, Plasmodium falciparum" xref: Reactome:REACT_84840 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Plasmodium falciparum" xref: Reactome:REACT_84975 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Arabidopsis thaliana" xref: Reactome:REACT_86647 "Eukaryotic Translation Termination, Xenopus tropicalis" xref: Reactome:REACT_86888 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Taeniopygia guttata" xref: Reactome:REACT_87882 "Eukaryotic Translation Termination, Dictyostelium discoideum" xref: Reactome:REACT_88395 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Canis familiaris" xref: Reactome:REACT_88662 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Danio rerio" xref: Reactome:REACT_91109 "GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex, Oryza sativa" xref: Reactome:REACT_92456 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Schizosaccharomyces pombe" xref: Reactome:REACT_92895 "Eukaryotic Translation Termination, Taeniopygia guttata" xref: Reactome:REACT_93205 "Eukaryotic Translation Termination, Caenorhabditis elegans" xref: Reactome:REACT_93556 "Eukaryotic Translation Termination, Mus musculus" xref: Reactome:REACT_94459 "GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex, Drosophila melanogaster" xref: Reactome:REACT_94463 "Eukaryotic Translation Termination, Arabidopsis thaliana" xref: Reactome:REACT_97483 "Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex, Mus musculus" is_a: GO:0043624 ! cellular protein complex disassembly relationship: part_of GO:0006412 ! translation [Term] id: GO:0006417 name: regulation of translation namespace: biological_process alt_id: GO:0006445 def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA." [GOC:isa_complete] subset: goslim_yeast synonym: "regulation of protein anabolism" EXACT [] synonym: "regulation of protein biosynthesis" EXACT [] synonym: "regulation of protein formation" EXACT [] synonym: "regulation of protein synthesis" EXACT [] is_a: GO:0010608 ! posttranscriptional regulation of gene expression is_a: GO:0032268 ! regulation of cellular protein metabolic process is_a: GO:0034248 ! regulation of cellular amide metabolic process is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006412 ! translation relationship: regulates GO:0006412 ! translation [Term] id: GO:0006446 name: regulation of translational initiation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of translational initiation." [GOC:go_curators] is_a: GO:0006417 ! regulation of translation intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006413 ! translational initiation relationship: regulates GO:0006413 ! translational initiation [Term] id: GO:0006448 name: regulation of translational elongation namespace: biological_process def: "Any process that modulates the frequency, rate, extent or accuracy of translational elongation." [GOC:go_curators] is_a: GO:0006417 ! regulation of translation intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006414 ! translational elongation relationship: regulates GO:0006414 ! translational elongation [Term] id: GO:0006449 name: regulation of translational termination namespace: biological_process def: "Any process that modulates the frequency, rate or extent of translational termination." [GOC:go_curators] is_a: GO:0006417 ! regulation of translation is_a: GO:0043244 ! regulation of protein complex disassembly intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006415 ! translational termination relationship: regulates GO:0006415 ! translational termination [Term] id: GO:0006518 name: peptide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another." [CHEBI:16670, GOC:go_curators] subset: goslim_pir synonym: "peptide metabolism" EXACT [] is_a: GO:0043603 ! cellular amide metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process [Term] id: GO:0006725 name: cellular aromatic compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells." [GOC:ai, ISBN:0198506732] subset: goslim_pir synonym: "aromatic compound metabolism" EXACT [] synonym: "aromatic hydrocarbon metabolic process" NARROW [] synonym: "aromatic hydrocarbon metabolism" NARROW [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0006807 name: nitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen." [CHEBI:51143, GOC:go_curators, GOC:jl, ISBN:0198506732] subset: goslim_metagenomics subset: goslim_pir synonym: "nitrogen compound metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0006810 name: transport namespace: biological_process alt_id: GO:0015457 alt_id: GO:0015460 alt_id: GO:0044765 def: "The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein." [GOC:dos, GOC:dph, GOC:jl, GOC:mah] comment: Note that this term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term, for e.g. to transmembrane transport, to microtubule-based transport or to vesicle-mediated transport. subset: gocheck_do_not_annotate subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant synonym: "single-organism transport" RELATED [] synonym: "small molecule transport" NARROW [] synonym: "solute:solute exchange" NARROW [] is_a: GO:0051234 ! establishment of localization created_by: janelomax creation_date: 2012-12-13T16:25:32Z [Term] id: GO:0006811 name: ion transport namespace: biological_process def: "The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir subset: goslim_yeast xref: Reactome:REACT_102356 "Transport of inorganic cations/anions and amino acids/oligopeptides, Xenopus tropicalis" xref: Reactome:REACT_102895 "Transport of inorganic cations/anions and amino acids/oligopeptides, Staphylococcus aureus N315" xref: Reactome:REACT_106972 "Transport of inorganic cations/anions and amino acids/oligopeptides, Sus scrofa" xref: Reactome:REACT_109067 "Transport of inorganic cations/anions and amino acids/oligopeptides, Saccharomyces cerevisiae" xref: Reactome:REACT_110862 "Transport of inorganic cations/anions and amino acids/oligopeptides, Arabidopsis thaliana" xref: Reactome:REACT_19397 "Transport of inorganic cations/anions and amino acids/oligopeptides, Homo sapiens" xref: Reactome:REACT_29110 "Transport of inorganic cations/anions and amino acids/oligopeptides, Oryza sativa" xref: Reactome:REACT_31978 "Transport of inorganic cations/anions and amino acids/oligopeptides, Mus musculus" xref: Reactome:REACT_33992 "Transport of inorganic cations/anions and amino acids/oligopeptides, Danio rerio" xref: Reactome:REACT_34201 "Transport of inorganic cations/anions and amino acids/oligopeptides, Gallus gallus" xref: Reactome:REACT_79109 "Transport of inorganic cations/anions and amino acids/oligopeptides, Caenorhabditis elegans" xref: Reactome:REACT_82618 "Transport of inorganic cations/anions and amino acids/oligopeptides, Escherichia coli" xref: Reactome:REACT_87822 "Transport of inorganic cations/anions and amino acids/oligopeptides, Bos taurus" xref: Reactome:REACT_91472 "Transport of inorganic cations/anions and amino acids/oligopeptides, Dictyostelium discoideum" xref: Reactome:REACT_91958 "Transport of inorganic cations/anions and amino acids/oligopeptides, Drosophila melanogaster" xref: Reactome:REACT_92903 "Transport of inorganic cations/anions and amino acids/oligopeptides, Mycobacterium tuberculosis" xref: Reactome:REACT_93485 "Transport of inorganic cations/anions and amino acids/oligopeptides, Canis familiaris" xref: Reactome:REACT_94357 "Transport of inorganic cations/anions and amino acids/oligopeptides, Rattus norvegicus" xref: Reactome:REACT_96078 "Transport of inorganic cations/anions and amino acids/oligopeptides, Plasmodium falciparum" xref: Reactome:REACT_96919 "Transport of inorganic cations/anions and amino acids/oligopeptides, Taeniopygia guttata" xref: Reactome:REACT_98077 "Transport of inorganic cations/anions and amino acids/oligopeptides, Schizosaccharomyces pombe" is_a: GO:0006810 ! transport [Term] id: GO:0006820 name: anion transport namespace: biological_process alt_id: GO:0006822 def: "The directed movement of anions, atoms or small molecules with a net negative charge, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] is_a: GO:0006811 ! ion transport [Term] id: GO:0006869 name: lipid transport namespace: biological_process def: "The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent." [ISBN:0198506732] subset: goslim_pir subset: goslim_yeast is_a: GO:0071702 ! organic substance transport relationship: part_of GO:0010876 ! lipid localization [Term] id: GO:0006915 name: apoptotic process namespace: biological_process alt_id: GO:0006917 alt_id: GO:0008632 def: "A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." [GOC:cjm, GOC:dhl, GOC:ecd, GOC:go_curators, GOC:mtg_apoptosis, GOC:tb, ISBN:0198506732, PMID:18846107, PMID:21494263] subset: goslim_pombe synonym: "activation of apoptosis" NARROW [] synonym: "apoptosis" NARROW [] synonym: "apoptosis activator activity" RELATED [] synonym: "apoptosis signaling" NARROW [] synonym: "apoptotic cell death" EXACT [GOC:sl] synonym: "apoptotic program" NARROW [GOC:add] synonym: "apoptotic programmed cell death" EXACT [] synonym: "caspase-dependent programmed cell death" RELATED [] synonym: "cell suicide" BROAD [] synonym: "cellular suicide" BROAD [] synonym: "commitment to apoptosis" RELATED [] synonym: "induction of apoptosis" RELATED [] synonym: "induction of apoptosis by p53" RELATED [] synonym: "programmed cell death by apoptosis" EXACT [] synonym: "signaling (initiator) caspase activity" RELATED [] synonym: "type I programmed cell death" NARROW [] xref: Reactome:REACT_100045 "Apoptosis, Drosophila melanogaster" xref: Reactome:REACT_100962 "Apoptosis, Mus musculus" xref: Reactome:REACT_101249 "NRIF signals cell death from the nucleus, Danio rerio" xref: Reactome:REACT_104187 "NRAGE signals death through JNK, Taeniopygia guttata" xref: Reactome:REACT_105149 "NADE modulates death signalling, Rattus norvegicus" xref: Reactome:REACT_106405 "NRAGE signals death through JNK, Xenopus tropicalis" xref: Reactome:REACT_106672 "NADE modulates death signalling, Sus scrofa" xref: Reactome:REACT_107264 "NRIF signals cell death from the nucleus, Xenopus tropicalis" xref: Reactome:REACT_108651 "NRAGE signals death through JNK, Mus musculus" xref: Reactome:REACT_109165 "NRAGE signals death through JNK, Arabidopsis thaliana" xref: Reactome:REACT_110081 "NRAGE signals death through JNK, Schizosaccharomyces pombe" xref: Reactome:REACT_111964 "NRAGE signals death through JNK, Dictyostelium discoideum" xref: Reactome:REACT_13526 "NADE modulates death signalling, Homo sapiens" xref: Reactome:REACT_13638 "NRAGE signals death through JNK, Homo sapiens" xref: Reactome:REACT_13643 "NRIF signals cell death from the nucleus, Homo sapiens" xref: Reactome:REACT_28087 "Apoptosis, Saccharomyces cerevisiae" xref: Reactome:REACT_28795 "Apoptosis, Oryza sativa" xref: Reactome:REACT_28816 "Apoptosis, Danio rerio" xref: Reactome:REACT_30266 "Apoptosis, Arabidopsis thaliana" xref: Reactome:REACT_30361 "Apoptosis, Canis familiaris" xref: Reactome:REACT_30371 "NRAGE signals death through JNK, Saccharomyces cerevisiae" xref: Reactome:REACT_30548 "NRAGE signals death through JNK, Caenorhabditis elegans" xref: Reactome:REACT_30763 "NRAGE signals death through JNK, Oryza sativa" xref: Reactome:REACT_31349 "NRAGE signals death through JNK, Canis familiaris" xref: Reactome:REACT_34139 "NRAGE signals death through JNK, Gallus gallus" xref: Reactome:REACT_578 "Apoptosis, Homo sapiens" xref: Reactome:REACT_77132 "NRAGE signals death through JNK, Drosophila melanogaster" xref: Reactome:REACT_77313 "NADE modulates death signalling, Bos taurus" xref: Reactome:REACT_77415 "NRIF signals cell death from the nucleus, Canis familiaris" xref: Reactome:REACT_78287 "Apoptosis, Gallus gallus" xref: Reactome:REACT_78802 "NADE modulates death signalling, Canis familiaris" xref: Reactome:REACT_79809 "Apoptosis, Schizosaccharomyces pombe" xref: Reactome:REACT_82724 "Apoptosis, Taeniopygia guttata" xref: Reactome:REACT_83328 "Apoptosis, Sus scrofa" xref: Reactome:REACT_85877 "NRAGE signals death through JNK, Rattus norvegicus" xref: Reactome:REACT_86749 "Apoptosis, Rattus norvegicus" xref: Reactome:REACT_86873 "NRIF signals cell death from the nucleus, Gallus gallus" xref: Reactome:REACT_87570 "NRIF signals cell death from the nucleus, Rattus norvegicus" xref: Reactome:REACT_88740 "NRIF signals cell death from the nucleus, Sus scrofa" xref: Reactome:REACT_88784 "NRIF signals cell death from the nucleus, Mus musculus" xref: Reactome:REACT_89196 "Apoptosis, Dictyostelium discoideum" xref: Reactome:REACT_90267 "NRIF signals cell death from the nucleus, Taeniopygia guttata" xref: Reactome:REACT_91011 "Apoptosis, Caenorhabditis elegans" xref: Reactome:REACT_91243 "NADE modulates death signalling, Mus musculus" xref: Reactome:REACT_93937 "Apoptosis, Bos taurus" xref: Reactome:REACT_94099 "NRAGE signals death through JNK, Danio rerio" xref: Reactome:REACT_95069 "Apoptosis, Xenopus tropicalis" xref: Reactome:REACT_95675 "Apoptosis, Plasmodium falciparum" xref: Reactome:REACT_97627 "NRIF signals cell death from the nucleus, Bos taurus" xref: Reactome:REACT_99784 "NRAGE signals death through JNK, Bos taurus" xref: Reactome:REACT_99799 "NRAGE signals death through JNK, Sus scrofa" xref: Wikipedia:Apoptosis is_a: GO:0012501 ! programmed cell death relationship: has_part GO:0097190 ! apoptotic signaling pathway relationship: has_part GO:0097194 ! execution phase of apoptosis [Term] id: GO:0006921 name: cellular component disassembly involved in execution phase of apoptosis namespace: biological_process def: "The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis." [GOC:dph, GOC:mah, GOC:mtg_apoptosis, GOC:tb] synonym: "cellular component disassembly involved in apoptosis" NARROW [] synonym: "cellular component disassembly involved in apoptotic process" BROAD [] synonym: "disassembly of cell structures" BROAD [] xref: Reactome:REACT_100800 "Apoptotic execution phase, Danio rerio" xref: Reactome:REACT_108463 "Apoptotic execution phase, Taeniopygia guttata" xref: Reactome:REACT_29660 "Apoptotic execution phase, Oryza sativa" xref: Reactome:REACT_77151 "Apoptotic execution phase, Sus scrofa" xref: Reactome:REACT_78666 "Apoptotic execution phase, Saccharomyces cerevisiae" xref: Reactome:REACT_79472 "Apoptotic execution phase, Schizosaccharomyces pombe" xref: Reactome:REACT_79859 "Apoptotic execution phase, Rattus norvegicus" xref: Reactome:REACT_80493 "Apoptotic execution phase, Dictyostelium discoideum" xref: Reactome:REACT_81021 "Apoptotic execution phase, Drosophila melanogaster" xref: Reactome:REACT_81052 "Apoptotic execution phase, Canis familiaris" xref: Reactome:REACT_84120 "Apoptotic execution phase, Xenopus tropicalis" xref: Reactome:REACT_89424 "Apoptotic execution phase, Arabidopsis thaliana" xref: Reactome:REACT_90988 "Apoptotic execution phase, Plasmodium falciparum" xref: Reactome:REACT_92689 "Apoptotic execution phase, Caenorhabditis elegans" xref: Reactome:REACT_93576 "Apoptotic execution phase, Gallus gallus" xref: Reactome:REACT_94230 "Apoptotic execution phase, Bos taurus" xref: Reactome:REACT_97703 "Apoptotic execution phase, Mus musculus" xref: Reactome:REACT_995 "Apoptotic execution phase, Homo sapiens" is_a: GO:0022411 ! cellular component disassembly intersection_of: GO:0022411 ! cellular component disassembly intersection_of: part_of GO:0097194 ! execution phase of apoptosis relationship: part_of GO:0097194 ! execution phase of apoptosis [Term] id: GO:0006928 name: movement of cell or subcellular component namespace: biological_process def: "The directed, self-propelled movement of a cell or subcellular component without the involvement of an external agent such as a transporter or a pore." [GOC:dgh, GOC:dph, GOC:jl, GOC:mlg] comment: Note that in GO cellular components include whole cells (cell is_a cellular component). subset: goantislim_grouping subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cell movement" RELATED [] synonym: "cellular component motion" EXACT [GOC:dph, GOC:jl] synonym: "cellular component movement" EXACT [] is_a: GO:0009987 ! cellular process [Term] id: GO:0006935 name: chemotaxis namespace: biological_process def: "The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." [ISBN:0198506732] synonym: "taxis in response to chemical stimulus" EXACT [] xref: Wikipedia:Chemotaxis is_a: GO:0042330 ! taxis relationship: part_of GO:0042221 ! response to chemical [Term] id: GO:0006950 name: response to stress namespace: biological_process 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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_plant synonym: "response to abiotic stress" RELATED [] synonym: "response to biotic stress" RELATED [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0006974 name: cellular response to DNA damage stimulus namespace: biological_process alt_id: GO:0034984 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." [GOC:go_curators] subset: goslim_yeast synonym: "cellular DNA damage response" EXACT [] synonym: "DNA damage response" EXACT [] synonym: "response to DNA damage stimulus" BROAD [] synonym: "response to genotoxic stress" EXACT [] is_a: GO:0033554 ! cellular response to stress property_value: IAO:0000111 "cellular response to DNA damage stimulus" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0006996 name: organelle organization namespace: biological_process alt_id: GO:1902589 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an organelle within a cell. An organelle is an organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:mah] subset: goslim_aspergillus subset: goslim_candida subset: goslim_pir synonym: "organelle organisation" EXACT [GOC:curators] synonym: "organelle organization and biogenesis" RELATED [GOC:dph, GOC:jl, GOC:mah] synonym: "single organism organelle organization" EXACT [GOC:TermGenie] synonym: "single-organism organelle organization" RELATED [] is_a: GO:0016043 ! cellular component organization created_by: jl creation_date: 2013-12-19T15:25:51Z [Term] id: GO:0006997 name: nucleus organization namespace: biological_process alt_id: GO:0048287 def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleus." [GOC:dph, GOC:ems, GOC:jl, GOC:mah] subset: goslim_aspergillus subset: goslim_candida subset: goslim_pir subset: goslim_yeast synonym: "nuclear morphology" RELATED [] synonym: "nuclear organisation" EXACT [GOC:curators] synonym: "nuclear organization" EXACT [GOC:curators] synonym: "nuclear organization and biogenesis" RELATED [GOC:mah] synonym: "nucleus organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006996 ! organelle organization [Term] id: GO:0007000 name: nucleolus organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nucleolus." [GOC:dph, GOC:jid, GOC:jl, GOC:mah] synonym: "nucleolus organisation" EXACT [GOC:curators] synonym: "nucleolus organization and biogenesis" RELATED [GOC:mah] is_a: GO:0006997 ! nucleus organization [Term] id: GO:0007154 name: cell communication namespace: biological_process def: "Any process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:mah] subset: goslim_pir subset: goslim_plant xref: Wikipedia:Cell_signaling is_a: GO:0009987 ! cellular process [Term] id: GO:0007165 name: signal transduction namespace: biological_process alt_id: GO:0023033 def: "The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell." [GOC:go_curators, GOC:mtg_signaling_feb11] comment: Note that signal transduction is defined broadly to include a ligand interacting with a receptor, downstream signaling steps and a response being triggered. A change in form of the signal in every step is not necessary. Note that in many cases the end of this process is regulation of the initiation of transcription. Note that specific transcription factors may be annotated to this term, but core/general transcription machinery such as RNA polymerase should not. subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_plant synonym: "signaling cascade" NARROW [] synonym: "signaling pathway" RELATED [] synonym: "signalling cascade" NARROW [] synonym: "signalling pathway" RELATED [GOC:mah] xref: Reactome:REACT_100624 "EGFR interacts with phospholipase C-gamma, Gallus gallus" xref: Reactome:REACT_102354 "EGFR interacts with phospholipase C-gamma, Canis familiaris" xref: Reactome:REACT_112130 "EGFR interacts with phospholipase C-gamma, Oryza sativa" xref: Reactome:REACT_112549 "EGFR interacts with phospholipase C-gamma, Arabidopsis thaliana" xref: Reactome:REACT_113151 "EGFR interacts with phospholipase C-gamma, Mycobacterium tuberculosis" xref: Reactome:REACT_113601 "EGFR interacts with phospholipase C-gamma, Drosophila melanogaster" xref: Reactome:REACT_113964 "EGFR interacts with phospholipase C-gamma, Bos taurus" xref: Reactome:REACT_114657 "EGFR interacts with phospholipase C-gamma, Dictyostelium discoideum" xref: Reactome:REACT_114690 "EGFR interacts with phospholipase C-gamma, Saccharomyces cerevisiae" xref: Reactome:REACT_114820 "EGFR interacts with phospholipase C-gamma, Sus scrofa" xref: Reactome:REACT_114910 "EGFR interacts with phospholipase C-gamma, Caenorhabditis elegans" xref: Reactome:REACT_115037 "EGFR interacts with phospholipase C-gamma, Plasmodium falciparum" xref: Reactome:REACT_115147 "EGFR interacts with phospholipase C-gamma, Schizosaccharomyces pombe" xref: Reactome:REACT_12478 "EGFR interacts with phospholipase C-gamma, Homo sapiens" xref: Reactome:REACT_31232 "EGFR interacts with phospholipase C-gamma, Rattus norvegicus" xref: Reactome:REACT_78535 "EGFR interacts with phospholipase C-gamma, Xenopus tropicalis" xref: Reactome:REACT_89740 "EGFR interacts with phospholipase C-gamma, Taeniopygia guttata" xref: Reactome:REACT_93680 "EGFR interacts with phospholipase C-gamma, Danio rerio" xref: Reactome:REACT_98872 "EGFR interacts with phospholipase C-gamma, Mus musculus" xref: Wikipedia:Signal_transduction is_a: GO:0009987 ! cellular process is_a: GO:0050794 ! regulation of cellular process relationship: part_of GO:0007154 ! cell communication relationship: part_of GO:0023052 ! signaling relationship: part_of GO:0051716 ! cellular response to stimulus [Term] id: GO:0007568 name: aging namespace: biological_process alt_id: GO:0016280 def: "A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700)." [GOC:PO_curators] subset: goslim_chembl subset: goslim_generic synonym: "ageing" EXACT [] xref: Wikipedia:Aging is_a: GO:0032502 ! developmental process [Term] id: GO:0007569 name: cell aging namespace: biological_process def: "An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469)." [GOC:PO_curators] synonym: "cell ageing" EXACT [] is_a: GO:0007568 ! aging is_a: GO:0048869 ! cellular developmental process [Term] id: GO:0007576 name: nucleolar fragmentation namespace: biological_process alt_id: GO:0046616 def: "The cell aging process that results in the nucleolus breaking down into fragments." [GOC:mah, PMID:9271578] synonym: "nucleolar size increase" RELATED [] is_a: GO:0007000 ! nucleolus organization relationship: part_of GO:0007569 ! cell aging [Term] id: GO:0008104 name: protein localization namespace: biological_process alt_id: GO:0008105 def: "Any process in which a protein is transported to, or maintained in, a specific location." [GOC:ai] synonym: "asymmetric protein localisation" RELATED [GOC:mah] synonym: "asymmetric protein localization" RELATED [] synonym: "establishment and maintenance of asymmetric protein localization" RELATED [] synonym: "establishment and maintenance of protein localization" RELATED [] synonym: "protein localisation" EXACT [GOC:mah] is_a: GO:0033036 ! macromolecule localization [Term] id: GO:0008150 name: biological_process namespace: biological_process alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 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." [GOC:pdt] comment: Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code "no data" (ND), is used to indicate this. subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant subset: goslim_pombe subset: goslim_yeast synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process is_a: BFO:0000015 ! process disjoint_from: OBI:0000011 ! planned process property_value: IAO:0000111 "biological_process" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl created_by: janelomax creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process alt_id: GO:0044236 alt_id: GO:0044710 def: "The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation." [GOC:go_curators, ISBN:0198547684] comment: Note that metabolic processes do not include single functions or processes such as protein-protein interactions, protein-nucleic acids, nor receptor-ligand interactions. subset: gocheck_do_not_manually_annotate subset: goslim_chembl subset: goslim_metagenomics subset: goslim_pir subset: goslim_plant synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] synonym: "metabolism resulting in cell growth" NARROW [] synonym: "multicellular organism metabolic process" NARROW [] synonym: "single-organism metabolic process" RELATED [] xref: Wikipedia:Metabolism is_a: GO:0008150 ! biological_process created_by: janelomax creation_date: 2012-10-17T15:46:40Z [Term] id: GO:0008156 name: negative regulation of DNA replication namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication." [GOC:go_curators] synonym: "DNA replication inhibitor" RELATED [] synonym: "down regulation of DNA replication" EXACT [] synonym: "down-regulation of DNA replication" EXACT [] synonym: "downregulation of DNA replication" EXACT [] synonym: "inhibition of DNA replication" NARROW [] is_a: GO:0006275 ! regulation of DNA replication is_a: GO:0051053 ! negative regulation of DNA metabolic process is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006260 ! DNA replication relationship: negatively_regulates GO:0006260 ! DNA replication [Term] id: GO:0008219 name: cell death namespace: biological_process def: "Any biological process that results in permanent cessation of all vital functions of a cell. A cell should be considered dead when any one of the following molecular or morphological criteria is met: (1) the cell has lost the integrity of its plasma membrane; (2) the cell, including its nucleus, has undergone complete fragmentation into discrete bodies (frequently referred to as apoptotic bodies). The cell corpse (or its fragments) may be engulfed by an adjacent cell in vivo, but engulfment of whole cells should not be considered a strict criteria to define cell death as, under some circumstances, live engulfed cells can be released from phagosomes (see PMID:18045538)." [GOC:mah, GOC:mtg_apoptosis, PMID:25236395] comment: This term should not be used for direct annotation. The only exception should be when experimental data (e.g., staining with trypan blue or propidium iodide) show that cell death has occurred, but fail to provide details on death modality (accidental versus programmed). When information is provided on the cell death mechanism, annotations should be made to the appropriate descendant of 'cell death' (such as, but not limited to, GO:0097300 'programmed necrotic cell death' or GO:0006915 'apoptotic process'). Also, if experimental data suggest that a gene product influences cell death indirectly, rather than being involved in the death process directly, consider annotating to a 'regulation' term. subset: goslim_agr subset: goslim_chembl subset: goslim_generic subset: goslim_mouse subset: goslim_plant synonym: "accidental cell death" RELATED [] synonym: "necrosis" RELATED [] is_a: GO:0009987 ! cellular process [Term] id: GO:0008283 name: cell proliferation namespace: biological_process def: "The multiplication or reproduction of cells, resulting in the expansion of a cell population." [GOC:mah, GOC:mb] comment: This term was moved out from being a child of 'cellular process' because it is a cell population-level process, and cellular processes are restricted to those processes that involve individual cells. Also note that this term is intended to be used for the proliferation of cells within a multicellular organism, not for the expansion of a population of single-celled organisms. subset: goslim_agr subset: goslim_chembl subset: goslim_generic subset: goslim_mouse subset: goslim_pir is_a: GO:0008150 ! biological_process property_value: IAO:0000111 "cell proliferation" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0008284 name: positive regulation of cell proliferation namespace: biological_process def: "Any process that activates or increases the rate or extent of cell proliferation." [GOC:go_curators] synonym: "activation of cell proliferation" NARROW [] synonym: "stimulation of cell proliferation" NARROW [] synonym: "up regulation of cell proliferation" EXACT [] synonym: "up-regulation of cell proliferation" EXACT [] synonym: "upregulation of cell proliferation" EXACT [] is_a: GO:0042127 ! regulation of cell proliferation is_a: GO:0048522 ! positive regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0008283 ! cell proliferation relationship: positively_regulates GO:0008283 ! cell proliferation [Term] id: GO:0008285 name: negative regulation of cell proliferation namespace: biological_process def: "Any process that stops, prevents or reduces the rate or extent of cell proliferation." [GOC:go_curators] synonym: "down regulation of cell proliferation" EXACT [] synonym: "down-regulation of cell proliferation" EXACT [] synonym: "downregulation of cell proliferation" EXACT [] synonym: "inhibition of cell proliferation" NARROW [] is_a: GO:0042127 ! regulation of cell proliferation is_a: GO:0048523 ! negative regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0008283 ! cell proliferation relationship: negatively_regulates GO:0008283 ! cell proliferation [Term] id: GO:0009056 name: catabolic process namespace: biological_process alt_id: GO:0044243 alt_id: GO:0044712 def: "The chemical reactions and pathways resulting in the breakdown of substances, including the breakdown of carbon compounds with the liberation of energy for use by the cell or organism." [ISBN:0198547684] subset: goslim_agr subset: goslim_chembl subset: goslim_generic subset: goslim_plant synonym: "breakdown" EXACT [] synonym: "catabolism" EXACT [] synonym: "degradation" EXACT [] synonym: "multicellular organismal catabolic process" NARROW [] synonym: "single-organism catabolic process" RELATED [] xref: Wikipedia:Catabolism is_a: GO:0008152 ! metabolic process created_by: janelomax creation_date: 2012-10-17T15:52:35Z [Term] id: GO:0009057 name: macromolecule catabolic process namespace: biological_process alt_id: GO:0043285 alt_id: GO:0044266 def: "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any 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." [CHEBI:33694, GOC:mah] subset: goslim_pir synonym: "biopolymer catabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "macromolecule breakdown" EXACT [] synonym: "macromolecule catabolism" EXACT [] synonym: "macromolecule degradation" EXACT [] synonym: "multicellular organismal macromolecule catabolic process" NARROW [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:1901575 ! organic substance catabolic process [Term] id: GO:0009058 name: biosynthetic process namespace: biological_process alt_id: GO:0044274 alt_id: GO:0044711 def: "The chemical reactions and pathways resulting in the formation of substances; typically the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones." [GOC:curators, ISBN:0198547684] subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_plant synonym: "anabolism" EXACT [] synonym: "biosynthesis" EXACT [] synonym: "formation" BROAD [] synonym: "multicellular organismal biosynthetic process" NARROW [] synonym: "single-organism biosynthetic process" RELATED [] synonym: "synthesis" EXACT [] xref: Wikipedia:Anabolism is_a: GO:0008152 ! metabolic process created_by: janelomax creation_date: 2012-10-17T15:52:18Z [Term] id: GO:0009059 name: macromolecule biosynthetic process namespace: biological_process alt_id: GO:0043284 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any 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." [CHEBI:33694, GOC:mah] subset: goslim_pir synonym: "biopolymer biosynthetic process" EXACT [GOC:mtg_chebi_dec09] synonym: "macromolecule anabolism" EXACT [] synonym: "macromolecule biosynthesis" EXACT [] synonym: "macromolecule formation" EXACT [] synonym: "macromolecule synthesis" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:1901576 ! organic substance biosynthetic process [Term] id: GO:0009300 name: antisense RNA transcription namespace: biological_process def: "The synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA." [GOC:jl] is_a: GO:0006351 ! transcription, DNA-templated is_a: GO:0042868 ! antisense RNA metabolic process [Term] id: GO:0009306 name: protein secretion namespace: biological_process alt_id: GO:0045166 alt_id: GO:0045731 def: "The controlled release of proteins from a cell." [GOC:ai] synonym: "glycoprotein secretion" NARROW [] synonym: "protein secretion during cell fate commitment" NARROW [] synonym: "protein secretion resulting in cell fate commitment" NARROW [] is_a: GO:0002790 ! peptide secretion is_a: GO:0015031 ! protein transport is_a: GO:0032940 ! secretion by cell [Term] id: GO:0009605 name: response to external stimulus namespace: biological_process 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 an external stimulus." [GOC:hb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate subset: goslim_plant synonym: "response to environmental stimulus" EXACT [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0009607 name: response to biotic stimulus namespace: biological_process 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 biotic stimulus, a stimulus caused or produced by a living organism." [GOC:hb] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate subset: goslim_metagenomics subset: goslim_plant synonym: "response to biotic stress" NARROW [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0009611 name: response to wounding namespace: biological_process alt_id: GO:0002245 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 indicating damage to the organism." [GOC:go_curators] synonym: "physiological response to wounding" EXACT [] is_a: GO:0006950 ! response to stress [Term] id: GO:0009636 name: response to toxic substance namespace: biological_process 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 toxic stimulus." [GOC:lr] subset: goslim_chembl synonym: "detoxification response" NARROW [] synonym: "toxin resistance" RELATED [] synonym: "toxin susceptibility/resistance" RELATED [] is_a: GO:0042221 ! response to chemical [Term] id: GO:0009653 name: anatomical structure morphogenesis namespace: biological_process def: "The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form." [GOC:go_curators, ISBN:0521436125] subset: goslim_plant synonym: "anatomical structure organization" EXACT [] synonym: "embryogenesis and morphogenesis" BROAD [] synonym: "morphogenesis" EXACT [] xref: Wikipedia:Morphogenesis is_a: GO:0032502 ! developmental process relationship: part_of GO:0048856 ! anatomical structure development [Term] id: GO:0009719 name: response to endogenous stimulus namespace: biological_process 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 arising within the organism." [GOC:sm] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate subset: goslim_plant is_a: GO:0050896 ! response to stimulus [Term] id: GO:0009889 name: regulation of biosynthetic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances." [GOC:go_curators] synonym: "regulation of anabolism" EXACT [] synonym: "regulation of biosynthesis" EXACT [] synonym: "regulation of formation" EXACT [] synonym: "regulation of synthesis" EXACT [] is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0009058 ! biosynthetic process relationship: regulates GO:0009058 ! biosynthetic process [Term] id: GO:0009890 name: negative regulation of biosynthetic process namespace: biological_process def: "Any process that stops, prevents, or reduces the rate of the chemical reactions and pathways resulting in the formation of substances." [GOC:go_curators] synonym: "down regulation of biosynthetic process" EXACT [] synonym: "down-regulation of biosynthetic process" EXACT [] synonym: "downregulation of biosynthetic process" EXACT [] synonym: "inhibition of biosynthetic process" NARROW [] synonym: "negative regulation of anabolism" EXACT [] synonym: "negative regulation of biosynthesis" EXACT [] synonym: "negative regulation of formation" EXACT [] synonym: "negative regulation of synthesis" EXACT [] is_a: GO:0009889 ! regulation of biosynthetic process is_a: GO:0009892 ! negative regulation of metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0009058 ! biosynthetic process relationship: negatively_regulates GO:0009058 ! biosynthetic process [Term] id: GO:0009891 name: positive regulation of biosynthetic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances." [GOC:go_curators] synonym: "activation of biosynthetic process" NARROW [] synonym: "positive regulation of anabolism" EXACT [] synonym: "positive regulation of biosynthesis" EXACT [] synonym: "positive regulation of formation" EXACT [] synonym: "positive regulation of synthesis" EXACT [] synonym: "stimulation of biosynthetic process" NARROW [] synonym: "up regulation of biosynthetic process" EXACT [] synonym: "up-regulation of biosynthetic process" EXACT [] synonym: "upregulation of biosynthetic process" EXACT [] is_a: GO:0009889 ! regulation of biosynthetic process is_a: GO:0009893 ! positive regulation of metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0009058 ! biosynthetic process relationship: positively_regulates GO:0009058 ! biosynthetic process [Term] id: GO:0009892 name: negative regulation of metabolic process namespace: biological_process alt_id: GO:0044252 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] synonym: "down regulation of metabolic process" EXACT [] synonym: "down-regulation of metabolic process" EXACT [] synonym: "downregulation of metabolic process" EXACT [] synonym: "inhibition of metabolic process" NARROW [] synonym: "inhibition of organismal metabolic process" NARROW [] synonym: "negative regulation of metabolism" EXACT [] synonym: "negative regulation of multicellular organismal metabolic process" NARROW [] synonym: "negative regulation of organismal metabolism" EXACT [] is_a: GO:0019222 ! regulation of metabolic process is_a: GO:0048519 ! negative regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0008152 ! metabolic process relationship: negatively_regulates GO:0008152 ! metabolic process [Term] id: GO:0009893 name: positive regulation of metabolic process namespace: biological_process alt_id: GO:0044253 def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] synonym: "activation of metabolic process" NARROW [] synonym: "positive regulation of metabolism" EXACT [] synonym: "positive regulation of multicellular organismal metabolic process" NARROW [] synonym: "positive regulation of organismal metabolism" NARROW [] synonym: "stimulation of metabolic process" NARROW [] synonym: "stimulation of organismal metabolic process" NARROW [] synonym: "up regulation of metabolic process" EXACT [] synonym: "up-regulation of metabolic process" EXACT [] synonym: "up-regulation of organismal metabolic process" NARROW [] synonym: "upregulation of metabolic process" EXACT [] is_a: GO:0019222 ! regulation of metabolic process is_a: GO:0048518 ! positive regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0008152 ! metabolic process relationship: positively_regulates GO:0008152 ! metabolic process [Term] id: GO:0009894 name: regulation of catabolic process namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators] synonym: "regulation of breakdown" EXACT [] synonym: "regulation of catabolism" EXACT [] synonym: "regulation of degradation" EXACT [] is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0009056 ! catabolic process relationship: regulates GO:0009056 ! catabolic process [Term] id: GO:0009895 name: negative regulation of catabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators] synonym: "down regulation of catabolic process" EXACT [] synonym: "down-regulation of catabolic process" EXACT [] synonym: "downregulation of catabolic process" EXACT [] synonym: "inhibition of catabolic process" NARROW [] synonym: "negative regulation of breakdown" EXACT [] synonym: "negative regulation of catabolism" EXACT [] synonym: "negative regulation of degradation" EXACT [] is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:0009894 ! regulation of catabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0009056 ! catabolic process relationship: negatively_regulates GO:0009056 ! catabolic process [Term] id: GO:0009896 name: positive regulation of catabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances." [GOC:go_curators] synonym: "activation of catabolic process" NARROW [] synonym: "positive regulation of breakdown" EXACT [] synonym: "positive regulation of catabolism" EXACT [] synonym: "positive regulation of degradation" EXACT [] synonym: "stimulation of catabolic process" NARROW [] synonym: "up regulation of catabolic process" EXACT [] synonym: "up-regulation of catabolic process" EXACT [] synonym: "upregulation of catabolic process" EXACT [] is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0009894 ! regulation of catabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0009056 ! catabolic process relationship: positively_regulates GO:0009056 ! catabolic process [Term] id: GO:0009966 name: regulation of signal transduction namespace: biological_process alt_id: GO:0035466 def: "Any process that modulates the frequency, rate or extent of signal transduction." [GOC:sm] synonym: "regulation of signaling pathway" RELATED [] synonym: "regulation of signalling pathway" RELATED [GOC:mah] is_a: GO:0010646 ! regulation of cell communication is_a: GO:0023051 ! regulation of signaling is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0007165 ! signal transduction relationship: regulates GO:0007165 ! signal transduction [Term] id: GO:0009967 name: positive regulation of signal transduction namespace: biological_process alt_id: GO:0035468 def: "Any process that activates or increases the frequency, rate or extent of signal transduction." [GOC:sm] synonym: "activation of signal transduction" NARROW [] synonym: "positive regulation of signaling pathway" RELATED [] synonym: "positive regulation of signalling pathway" RELATED [GOC:mah] synonym: "stimulation of signal transduction" NARROW [] synonym: "up regulation of signal transduction" EXACT [] synonym: "up-regulation of signal transduction" EXACT [] synonym: "upregulation of signal transduction" EXACT [] xref: Reactome:REACT_6227 "Activated DTOR also phosphorylates D4EBP, Drosophila melanogaster" is_a: GO:0009966 ! regulation of signal transduction is_a: GO:0010647 ! positive regulation of cell communication is_a: GO:0023056 ! positive regulation of signaling is_a: GO:0048584 ! positive regulation of response to stimulus intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0007165 ! signal transduction relationship: positively_regulates GO:0007165 ! signal transduction [Term] id: GO:0009968 name: negative regulation of signal transduction namespace: biological_process alt_id: GO:0035467 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction." [GOC:sm] synonym: "down regulation of signal transduction" EXACT [] synonym: "down-regulation of signal transduction" EXACT [] synonym: "downregulation of signal transduction" EXACT [] synonym: "inhibition of signal transduction" NARROW [] synonym: "negative regulation of signaling pathway" RELATED [] synonym: "negative regulation of signalling pathway" RELATED [GOC:mah] xref: Reactome:REACT_6334 "DTSC1 AND DTSC2 form a complex, Drosophila melanogaster" is_a: GO:0009966 ! regulation of signal transduction is_a: GO:0010648 ! negative regulation of cell communication is_a: GO:0023057 ! negative regulation of signaling is_a: GO:0048585 ! negative regulation of response to stimulus intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0007165 ! signal transduction relationship: negatively_regulates GO:0007165 ! signal transduction [Term] id: GO:0009987 name: cellular process namespace: biological_process alt_id: GO:0008151 alt_id: GO:0044763 alt_id: GO:0050875 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." [GOC:go_curators, GOC:isa_complete] subset: goslim_plant synonym: "cell growth and/or maintenance" NARROW [] synonym: "cell physiology" EXACT [] synonym: "cellular physiological process" EXACT [] synonym: "single-organism cellular process" RELATED [] is_a: GO:0008150 ! biological_process property_value: IAO:0000111 "cellular process" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl created_by: janelomax creation_date: 2012-12-11T16:56:55Z [Term] id: GO:0010033 name: response to organic substance namespace: biological_process 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 an organic substance stimulus." [GOC:sm] is_a: GO:0042221 ! response to chemical [Term] id: GO:0010046 name: response to mycotoxin namespace: biological_process 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 mycotoxin stimulus. A mycotoxin is a toxic chemical substance produced by fungi." [GOC:sm] is_a: GO:0009636 ! response to toxic substance [Term] id: GO:0010243 name: response to organonitrogen compound namespace: biological_process 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 an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond." [CHEBI:35352, PMID:9869419] synonym: "response to organic nitrogen" EXACT [] is_a: GO:0010033 ! response to organic substance is_a: GO:1901698 ! response to nitrogen compound [Term] id: GO:0010467 name: gene expression namespace: biological_process def: "The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] xref: Reactome:REACT_100537 "Gene Expression, Xenopus tropicalis" xref: Reactome:REACT_101147 "Gene Expression, Danio rerio" xref: Reactome:REACT_101952 "Gene Expression, Sus scrofa" xref: Reactome:REACT_105649 "Gene Expression, Drosophila melanogaster" xref: Reactome:REACT_108313 "Gene Expression, Caenorhabditis elegans" xref: Reactome:REACT_29068 "Gene Expression, Escherichia coli" xref: Reactome:REACT_34240 "Gene Expression, Staphylococcus aureus N315" xref: Reactome:REACT_71 "Gene Expression, Homo sapiens" xref: Reactome:REACT_78136 "Gene Expression, Mus musculus" xref: Reactome:REACT_78959 "Gene Expression, Taeniopygia guttata" xref: Reactome:REACT_79662 "Gene Expression, Plasmodium falciparum" xref: Reactome:REACT_85241 "Gene Expression, Oryza sativa" xref: Reactome:REACT_85359 "Gene Expression, Gallus gallus" xref: Reactome:REACT_86357 "Gene Expression, Canis familiaris" xref: Reactome:REACT_89816 "Gene Expression, Mycobacterium tuberculosis" xref: Reactome:REACT_91657 "Gene Expression, Arabidopsis thaliana" xref: Reactome:REACT_91965 "Gene Expression, Rattus norvegicus" xref: Reactome:REACT_93586 "Gene Expression, Dictyostelium discoideum" xref: Reactome:REACT_93968 "Gene Expression, Bos taurus" xref: Reactome:REACT_94814 "Gene Expression, Schizosaccharomyces pombe" xref: Reactome:REACT_98256 "Gene Expression, Saccharomyces cerevisiae" xref: Wikipedia:Gene_expression is_a: GO:0043170 ! macromolecule metabolic process property_value: IAO:0000111 "gene expression" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0010468 name: regulation of gene expression namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] comment: This class covers any process that regulates the rate of production of a mature gene product, and so includes processes that regulate that rate by regulating the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that regulates the level, stability or availability of mRNA or circRNA for translation and thereby regulates the rate of production of the encoded protein via translation. synonym: "regulation of gene product expression" RELATED [GOC:curators] synonym: "regulation of protein expression" NARROW [GOC:curators] xref: Wikipedia:Regulation_of_gene_expression is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0010467 ! gene expression relationship: regulates GO:0010467 ! gene expression [Term] id: GO:0010556 name: regulation of macromolecule biosynthetic process namespace: biological_process def: "Any process that modulates the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any 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." [GOC:dph, GOC:tb] is_a: GO:0009889 ! regulation of biosynthetic process is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0009059 ! macromolecule biosynthetic process relationship: regulates GO:0009059 ! macromolecule biosynthetic process [Term] id: GO:0010557 name: positive regulation of macromolecule biosynthetic process namespace: biological_process def: "Any process that increases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any 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." [GOC:dph, GOC:tb] is_a: GO:0009891 ! positive regulation of biosynthetic process is_a: GO:0010556 ! regulation of macromolecule biosynthetic process is_a: GO:0010604 ! positive regulation of macromolecule metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0009059 ! macromolecule biosynthetic process relationship: positively_regulates GO:0009059 ! macromolecule biosynthetic process [Term] id: GO:0010558 name: negative regulation of macromolecule biosynthetic process namespace: biological_process def: "Any process that decreases the rate, frequency or extent of the chemical reactions and pathways resulting in the formation of a macromolecule, any 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." [GOC:dph, GOC:tb] is_a: GO:0009890 ! negative regulation of biosynthetic process is_a: GO:0010556 ! regulation of macromolecule biosynthetic process is_a: GO:0010605 ! negative regulation of macromolecule metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0009059 ! macromolecule biosynthetic process relationship: negatively_regulates GO:0009059 ! macromolecule biosynthetic process [Term] id: GO:0010604 name: positive regulation of macromolecule metabolic process namespace: biological_process def: "Any process that increases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any 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." [GOC:dph, GOC:tb] is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0043170 ! macromolecule metabolic process relationship: positively_regulates GO:0043170 ! macromolecule metabolic process [Term] id: GO:0010605 name: negative regulation of macromolecule metabolic process namespace: biological_process def: "Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any 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." [GOC:dph, GOC:tb] is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0043170 ! macromolecule metabolic process relationship: negatively_regulates GO:0043170 ! macromolecule metabolic process [Term] id: GO:0010608 name: posttranscriptional regulation of gene expression namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression after the production of an RNA transcript." [GOC:dph, GOC:tb] is_a: GO:0010468 ! regulation of gene expression [Term] id: GO:0010628 name: positive regulation of gene expression namespace: biological_process def: "Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] is_a: GO:0010468 ! regulation of gene expression is_a: GO:0010604 ! positive regulation of macromolecule metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0010467 ! gene expression relationship: positively_regulates GO:0010467 ! gene expression [Term] id: GO:0010629 name: negative regulation of gene expression namespace: biological_process def: "Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form." [GOC:dph, GOC:tb] comment: This term covers any process that negatively regulates the rate of production of a mature gene product, and so includes processes that negatively regulate that rate by reducing the level, stability or availability of intermediates in the process of gene expression. For example, it covers any process that reduces the level, stability or availability of mRNA or circRNA for translation and thereby reduces the rate of production of the encoded protein via translation. is_a: GO:0010468 ! regulation of gene expression is_a: GO:0010605 ! negative regulation of macromolecule metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0010467 ! gene expression relationship: negatively_regulates GO:0010467 ! gene expression [Term] id: GO:0010638 name: positive regulation of organelle organization namespace: biological_process def: "Any process that increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle." [GOC:dph, GOC:tb] synonym: "positive regulation of organelle organisation" EXACT [GOC:mah] synonym: "positive regulation of organelle organization and biogenesis" RELATED [GOC:mah] is_a: GO:0033043 ! regulation of organelle organization is_a: GO:0051130 ! positive regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006996 ! organelle organization relationship: positively_regulates GO:0006996 ! organelle organization [Term] id: GO:0010639 name: negative regulation of organelle organization namespace: biological_process def: "Any process that decreases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle." [GOC:dph, GOC:tb] synonym: "negative regulation of organelle organisation" EXACT [GOC:mah] synonym: "negative regulation of organelle organization and biogenesis" RELATED [GOC:mah] is_a: GO:0033043 ! regulation of organelle organization is_a: GO:0051129 ! negative regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006996 ! organelle organization relationship: negatively_regulates GO:0006996 ! organelle organization [Term] id: GO:0010646 name: regulation of cell communication namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:dph, GOC:tb] is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0007154 ! cell communication relationship: regulates GO:0007154 ! cell communication [Term] id: GO:0010647 name: positive regulation of cell communication namespace: biological_process def: "Any process that increases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:dph, GOC:tb] is_a: GO:0010646 ! regulation of cell communication is_a: GO:0048522 ! positive regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0007154 ! cell communication relationship: positively_regulates GO:0007154 ! cell communication [Term] id: GO:0010648 name: negative regulation of cell communication namespace: biological_process def: "Any process that decreases the frequency, rate or extent of cell communication. Cell communication is the process that mediates interactions between a cell and its surroundings. Encompasses interactions such as signaling or attachment between one cell and another cell, between a cell and an extracellular matrix, or between a cell and any other aspect of its environment." [GOC:dph, GOC:tb] is_a: GO:0010646 ! regulation of cell communication is_a: GO:0048523 ! negative regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0007154 ! cell communication relationship: negatively_regulates GO:0007154 ! cell communication [Term] id: GO:0010876 name: lipid localization namespace: biological_process def: "Any process in which a lipid is transported to, or maintained in, a specific location." [GOC:BHF, GOC:dph, GOC:tb] synonym: "lipid localisation" EXACT [GOC:mah] is_a: GO:0033036 ! macromolecule localization [Term] id: GO:0010927 name: cellular component assembly involved in morphogenesis namespace: biological_process def: "The cellular component assembly that is part of the initial shaping of the component during its developmental progression." [GOC:dph, GOC:tb] is_a: GO:0022607 ! cellular component assembly is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis intersection_of: GO:0022607 ! cellular component assembly intersection_of: part_of GO:0009653 ! anatomical structure morphogenesis relationship: part_of GO:0032989 ! cellular component morphogenesis [Term] id: GO:0010941 name: regulation of cell death namespace: biological_process def: "Any process that modulates the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:dph, GOC:tb] is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0008219 ! cell death relationship: regulates GO:0008219 ! cell death [Term] id: GO:0010942 name: positive regulation of cell death namespace: biological_process def: "Any process that increases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:dph, GOC:tb] is_a: GO:0010941 ! regulation of cell death is_a: GO:0048522 ! positive regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0008219 ! cell death relationship: positively_regulates GO:0008219 ! cell death [Term] id: GO:0012501 name: programmed cell death namespace: biological_process alt_id: GO:0016244 def: "A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell." [GOC:lr, GOC:mtg_apoptosis] comment: Note that this term should be used to annotate gene products in the organism undergoing the programmed cell death. To annotate genes in another organism whose products modulate programmed cell death in a host organism, consider the term 'modulation by symbiont of host programmed cell death ; GO:0052040'. Also, note that 'programmed cell death ; GO:0012501' should be used to refer to instances of caspase-independent cell death mechanisms, in the absence of further indications on the process taking place. At present, caspase-independent cell death is not yet represented in GO due to the lack of consensus and in-depth research on the topic. 'programmed cell death ; GO:0012501' may also be used to annotate gene products in taxa where apoptosis as defined in GO:0006915 does not occur, such as plants. You may also consider these specific children: GO:0097468 'programmed cell death in response to reactive oxygen species' (with descendants GO:0010421 'hydrogen peroxide-mediated programmed cell death' and GO:0010343 'singlet oxygen-mediated programmed cell death'), and GO:0009626 'plant-type hypersensitive response' and its children, which are descendants of GO:0034050 'host programmed cell death induced by symbiont'. synonym: "caspase-independent apoptosis" RELATED [] synonym: "caspase-independent cell death" NARROW [] synonym: "non-apoptotic programmed cell death" NARROW [] synonym: "nonapoptotic programmed cell death" NARROW [] synonym: "PCD" RELATED [] synonym: "RCD" RELATED [] synonym: "regulated cell death" BROAD [] xref: Wikipedia:Programmed_cell_death is_a: GO:0008219 ! cell death relationship: has_part GO:0007165 ! signal transduction [Term] id: GO:0014070 name: response to organic cyclic compound namespace: biological_process 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 an organic cyclic compound stimulus." [CHEBI:33832, GOC:ef] synonym: "response to organic cyclic substance" EXACT [GOC:mah] is_a: GO:0010033 ! response to organic substance [Term] id: GO:0015031 name: protein transport namespace: biological_process alt_id: GO:0015831 def: "The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir synonym: "enzyme transport" NARROW [] is_a: GO:0015833 ! peptide transport is_a: GO:0045184 ! establishment of protein localization [Term] id: GO:0015075 name: ion transmembrane transporter activity namespace: molecular_function def: "Enables the transfer of an ion from one side of a membrane to the other." [GOC:dgf, GOC:mtg_transport, ISBN:0815340729] synonym: "ion transporter activity" EXACT [] is_a: GO:0022857 ! transmembrane transporter activity relationship: part_of GO:0034220 ! ion transmembrane transport [Term] id: GO:0015267 name: channel activity namespace: molecular_function alt_id: GO:0015249 alt_id: GO:0015268 def: "Enables the energy-independent facilitated diffusion, mediated by passage of a solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules." [GOC:mtg_transport, ISBN:0815340729, TC:1.-.-.-.-] synonym: "alpha-type channel activity" RELATED [] synonym: "channel-forming toxin activity" RELATED [] synonym: "channel/pore class transporter activity" EXACT [] synonym: "nonselective channel activity" EXACT [] synonym: "pore activity" BROAD [] synonym: "pore class transporter activity" RELATED [] xref: TC:1 is_a: GO:0022803 ! passive transmembrane transporter activity [Term] id: GO:0015318 name: inorganic molecular entity transmembrane transporter activity namespace: molecular_function def: "Enables the transfer of an inorganic molecular entity from the outside of a cell to the inside of the cell across a membrane. An inorganic molecular entity is a molecular entity that contains no carbon." [GOC:mtg_transport, ISBN:0815340729] comment: Renamed term see https://github.com/geneontology/go-ontology/issues/14372 subset: gocheck_do_not_annotate synonym: "inorganic solute uptake transmembrane transporter activity" EXACT [] synonym: "inorganic uptake permease activity" EXACT [] is_a: GO:0022857 ! transmembrane transporter activity [Term] id: GO:0015711 name: organic anion transport namespace: biological_process def: "The directed movement of organic anions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic anions are atoms or small molecules with a negative charge which contain carbon in covalent linkage." [GOC:ai, GOC:krc] is_a: GO:0006820 ! anion transport is_a: GO:0071702 ! organic substance transport [Term] id: GO:0015718 name: monocarboxylic acid transport namespace: biological_process def: "The directed movement of monocarboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:krc] is_a: GO:0046942 ! carboxylic acid transport [Term] id: GO:0015833 name: peptide transport namespace: biological_process def: "The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_pir is_a: GO:0042886 ! amide transport is_a: GO:0071702 ! organic substance transport [Term] id: GO:0015849 name: organic acid transport namespace: biological_process def: "The directed movement of organic acids, any acidic compound containing carbon in covalent linkage, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [ISBN:0198506732] subset: goslim_pir is_a: GO:0071702 ! organic substance transport [Term] id: GO:0015908 name: fatty acid transport namespace: biological_process def: "The directed movement of fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Fatty acids are aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis." [GOC:ai] is_a: GO:0006869 ! lipid transport is_a: GO:0015718 ! monocarboxylic acid transport [Term] id: GO:0015909 name: long-chain fatty acid transport namespace: biological_process def: "The directed movement of long-chain fatty acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A long-chain fatty acid is a fatty acid with a chain length between C13 and C22." [CHEBI:15904, GOC:ai] xref: Reactome:REACT_23892 "Transport of fatty acids, Homo sapiens" is_a: GO:0015908 ! fatty acid transport [Term] id: GO:0016043 name: cellular component organization namespace: biological_process alt_id: GO:0044235 alt_id: GO:0071842 def: "A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:ai, GOC:jl, GOC:mah] subset: goslim_agr subset: goslim_mouse subset: goslim_pir subset: goslim_plant synonym: "cell organisation" EXACT [] synonym: "cell organization and biogenesis" RELATED [GOC:mah] synonym: "cellular component organisation at cellular level" EXACT [GOC:mah] synonym: "cellular component organisation in other organism" EXACT [GOC:mah] synonym: "cellular component organization at cellular level" EXACT [] synonym: "cellular component organization in other organism" EXACT [] is_a: GO:0009987 ! cellular process is_a: GO:0071840 ! cellular component organization or biogenesis [Term] id: GO:0016049 name: cell growth namespace: biological_process alt_id: GO:0048591 def: "The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present." [GOC:ai] subset: gocheck_do_not_annotate subset: goslim_pir subset: goslim_plant synonym: "cell expansion" RELATED [] synonym: "cellular growth" EXACT [] synonym: "growth of cell" EXACT [] synonym: "metabolic process resulting in cell growth" RELATED [] synonym: "metabolism resulting in cell growth" RELATED [] synonym: "non-developmental cell growth" RELATED [GOC:mah] synonym: "non-developmental growth of a unicellular organism" RELATED [GOC:mah] is_a: GO:0009987 ! cellular process is_a: GO:0040007 ! growth [Term] id: GO:0016070 name: RNA metabolic process namespace: biological_process def: "The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage." [ISBN:0198506732] subset: goslim_agr subset: goslim_aspergillus subset: goslim_candida subset: goslim_metagenomics subset: goslim_pir synonym: "RNA metabolism" EXACT [] xref: Reactome:REACT_107259 "Metabolism of RNA, Sus scrofa" xref: Reactome:REACT_107652 "Metabolism of RNA, Schizosaccharomyces pombe" xref: Reactome:REACT_110289 "Metabolism of RNA, Danio rerio" xref: Reactome:REACT_21257 "Metabolism of RNA, Homo sapiens" xref: Reactome:REACT_30579 "Metabolism of RNA, Xenopus tropicalis" xref: Reactome:REACT_31367 "Metabolism of RNA, Dictyostelium discoideum" xref: Reactome:REACT_33720 "Metabolism of RNA, Plasmodium falciparum" xref: Reactome:REACT_80071 "Metabolism of RNA, Caenorhabditis elegans" xref: Reactome:REACT_83630 "Metabolism of RNA, Taeniopygia guttata" xref: Reactome:REACT_84169 "Metabolism of RNA, Canis familiaris" xref: Reactome:REACT_85788 "Metabolism of RNA, Oryza sativa" xref: Reactome:REACT_88316 "Metabolism of RNA, Mus musculus" xref: Reactome:REACT_89992 "Metabolism of RNA, Saccharomyces cerevisiae" xref: Reactome:REACT_91556 "Metabolism of RNA, Bos taurus" xref: Reactome:REACT_92152 "Metabolism of RNA, Drosophila melanogaster" xref: Reactome:REACT_94876 "Metabolism of RNA, Arabidopsis thaliana" xref: Reactome:REACT_99403 "Metabolism of RNA, Rattus norvegicus" xref: Reactome:REACT_99885 "Metabolism of RNA, Gallus gallus" is_a: GO:0090304 ! nucleic acid metabolic process [Term] id: GO:0016246 name: RNA interference namespace: biological_process def: "The process in which double-stranded RNAs silence cognate genes. Involves posttranscriptional gene inactivation ('silencing') both of transgenes or dsRNA introduced into a germline, and of the host gene(s) homologous to the transgenes or dsRNA. This silencing is triggered by the introduction of transgenes or double-stranded RNA (dsRNA), and can occur through a specific decrease in the level of mRNA, or by negative regulation of translation, of both host genes and transgenes." [GOC:ems, PMID:11201747, PMID:11713190, PMID:18771919] comment: Note that this term refers specifically to posttranscriptional mechanisms by which small interfering RNAs down-regulate gene expression. Also consider annotating to other descendants of 'gene silencing by RNA ; GO:0031047'. synonym: "posttranscriptional gene silencing by siRNA" EXACT [GOC:mah] synonym: "RNAi" EXACT [] xref: Wikipedia:RNA_interference is_a: GO:0035194 ! posttranscriptional gene silencing by RNA [Term] id: GO:0016441 name: posttranscriptional gene silencing namespace: biological_process def: "The inactivation of gene expression by a posttranscriptional mechanism." [GOC:mah, PMID:15020054] synonym: "cosuppression" RELATED [] synonym: "post-transcriptional gene silencing" EXACT [GOC:vw] synonym: "PTGS" EXACT [] synonym: "quelling" EXACT [] xref: Wikipedia:Post_transcriptional_gene_silencing is_a: GO:0010608 ! posttranscriptional regulation of gene expression is_a: GO:0016458 ! gene silencing is_a: GO:0040029 ! regulation of gene expression, epigenetic [Term] id: GO:0016458 name: gene silencing namespace: biological_process def: "Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression." [GOC:dos, GOC:dph, GOC:jid, GOC:tb] comment: This is a rather broad grouping term. While it was originally defined for long-term, heritable, epigenetic effects, short term effects on expression mediated by RNA are also frequently referred to as gene silencing, and are grouped under this class. subset: goslim_pir synonym: "long-term maintenance of gene inactivation" NARROW [] xref: Wikipedia:Gene_silencing is_a: GO:0009987 ! cellular process is_a: GO:0010629 ! negative regulation of gene expression [Term] id: GO:0016477 name: cell migration namespace: biological_process def: "The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms." [GOC:cjm, GOC:dph, GOC:ems, GOC:pf, http://en.wikipedia.org/wiki/Cell_migration] xref: Wikipedia:Cell_migration is_a: GO:0048870 ! cell motility [Term] id: GO:0016787 name: hydrolase activity namespace: molecular_function def: "Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [ISBN:0198506732] subset: goslim_agr subset: goslim_aspergillus subset: goslim_candida subset: goslim_chembl subset: goslim_metagenomics subset: goslim_mouse subset: goslim_pir subset: goslim_plant subset: goslim_yeast xref: EC:3 xref: Reactome:REACT_110436 "Hydrolysis of phosphatidylcholine, Bos taurus" xref: Reactome:REACT_111159 "Partial proteolysis of antigen in phagolysosomes, Homo sapiens" xref: Reactome:REACT_15331 "Hydrolysis of phosphatidylcholine, Homo sapiens" xref: Reactome:REACT_83734 "Hydrolysis of phosphatidylcholine, Danio rerio" xref: Reactome:REACT_84047 "Hydrolysis of phosphatidylcholine, Xenopus tropicalis" xref: Reactome:REACT_87959 "Hydrolysis of phosphatidylcholine, Gallus gallus" xref: Reactome:REACT_88159 "Hydrolysis of phosphatidylcholine, Canis familiaris" xref: Reactome:REACT_90118 "Hydrolysis of phosphatidylcholine, Mus musculus" xref: Reactome:REACT_91045 "Hydrolysis of phosphatidylcholine, Taeniopygia guttata" xref: Reactome:REACT_98572 "Hydrolysis of phosphatidylcholine, Rattus norvegicus" is_a: GO:0003824 ! catalytic activity [Term] id: GO:0016788 name: hydrolase activity, acting on ester bonds namespace: molecular_function def: "Catalysis of the hydrolysis of any ester bond." [GOC:jl] subset: goslim_chembl synonym: "esterase activity" EXACT [] xref: EC:3.1 xref: Reactome:REACT_106563 "Deacylation of Acyl Ghrelin, Mus musculus" xref: Reactome:REACT_109748 "Deacylation of Acyl Ghrelin, Bos taurus" xref: Reactome:REACT_112177 "uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Xenopus tropicalis" xref: Reactome:REACT_19294 "Deacylation of Acyl Ghrelin, Homo sapiens" xref: Reactome:REACT_1978 "uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Homo sapiens" xref: Reactome:REACT_45174 "uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Mus musculus" xref: Reactome:REACT_77112 "uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Danio rerio" xref: Reactome:REACT_81282 "Deacylation of Acyl Ghrelin, Rattus norvegicus" xref: Reactome:REACT_83347 "Deacylation of Acyl Ghrelin, Gallus gallus" xref: Reactome:REACT_88228 "Deacylation of Acyl Ghrelin, Canis familiaris" xref: Reactome:REACT_88314 "uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Sus scrofa" xref: Reactome:REACT_89615 "uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Rattus norvegicus" xref: Reactome:REACT_92446 "uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Canis familiaris" xref: Reactome:REACT_94475 "uPAR-acyl-GPI + H2O -> uPAR + long-chain fatty acid, Bos taurus" is_a: GO:0016787 ! hydrolase activity [Term] id: GO:0017148 name: negative regulation of translation namespace: biological_process alt_id: GO:0016478 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA." [GOC:isa_complete] synonym: "down regulation of protein biosynthetic process" EXACT [] synonym: "down-regulation of protein biosynthetic process" EXACT [] synonym: "downregulation of protein biosynthetic process" EXACT [] synonym: "inhibition of protein biosynthetic process" NARROW [] synonym: "negative regulation of protein anabolism" EXACT [] synonym: "negative regulation of protein biosynthesis" EXACT [] synonym: "negative regulation of protein biosynthetic process" EXACT [] synonym: "negative regulation of protein formation" EXACT [] synonym: "negative regulation of protein synthesis" EXACT [] synonym: "protein biosynthesis inhibitor activity" RELATED [] synonym: "protein biosynthetic process inhibitor activity" RELATED [] is_a: GO:0006417 ! regulation of translation is_a: GO:0010629 ! negative regulation of gene expression is_a: GO:0032269 ! negative regulation of cellular protein metabolic process is_a: GO:0034249 ! negative regulation of cellular amide metabolic process is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006412 ! translation relationship: negatively_regulates GO:0006412 ! translation [Term] id: GO:0018130 name: heterocycle biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [ISBN:0198547684] synonym: "heterocycle anabolism" EXACT [] synonym: "heterocycle biosynthesis" EXACT [] synonym: "heterocycle formation" EXACT [] synonym: "heterocycle synthesis" EXACT [] is_a: GO:0044249 ! cellular biosynthetic process is_a: GO:0046483 ! heterocycle metabolic process [Term] id: GO:0019219 name: regulation of nucleobase-containing compound metabolic process namespace: biological_process def: "Any cellular process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] synonym: "regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] synonym: "regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0051171 ! regulation of nitrogen compound metabolic process is_a: GO:0080090 ! regulation of primary metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006139 ! nucleobase-containing compound metabolic process relationship: regulates GO:0006139 ! nucleobase-containing compound metabolic process [Term] id: GO:0019222 name: regulation of metabolic process namespace: biological_process alt_id: GO:0044246 def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism." [GOC:go_curators] subset: goslim_metagenomics synonym: "regulation of metabolism" EXACT [] synonym: "regulation of multicellular organismal metabolic process" NARROW [] synonym: "regulation of organismal metabolic process" NARROW [GOC:tb] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0008152 ! metabolic process relationship: regulates GO:0008152 ! metabolic process [Term] id: GO:0019438 name: aromatic compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of aromatic compounds, any substance containing an aromatic carbon ring." [GOC:ai] synonym: "aromatic compound anabolism" EXACT [] synonym: "aromatic compound biosynthesis" EXACT [] synonym: "aromatic compound formation" EXACT [] synonym: "aromatic compound synthesis" EXACT [] synonym: "aromatic hydrocarbon biosynthesis" NARROW [] synonym: "aromatic hydrocarbon biosynthetic process" NARROW [] is_a: GO:0006725 ! cellular aromatic compound metabolic process is_a: GO:0044249 ! cellular biosynthetic process [Term] id: GO:0019439 name: aromatic compound catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring." [GOC:ai] synonym: "aromatic compound breakdown" EXACT [] synonym: "aromatic compound catabolism" EXACT [] synonym: "aromatic compound degradation" EXACT [] synonym: "aromatic hydrocarbon catabolic process" NARROW [] synonym: "aromatic hydrocarbon catabolism" NARROW [] is_a: GO:0006725 ! cellular aromatic compound metabolic process is_a: GO:0044248 ! cellular catabolic process [Term] id: GO:0019538 name: protein metabolic process namespace: biological_process alt_id: GO:0006411 alt_id: GO:0044268 def: "The chemical reactions and pathways involving a protein. Includes protein modification." [GOC:ma] subset: goslim_agr subset: goslim_mouse subset: goslim_pir subset: goslim_plant synonym: "multicellular organismal protein metabolic process" NARROW [] synonym: "protein metabolic process and modification" EXACT [] synonym: "protein metabolism" EXACT [] synonym: "protein metabolism and modification" EXACT [] xref: Wikipedia:Protein_metabolism is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044238 ! primary metabolic process is_a: GO:1901564 ! organonitrogen compound metabolic process [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:0043234 ! protein complex property_value: IAO:0000111 "immunoglobulin complex" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [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 property_value: IAO:0000111 "B cell receptor complex" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0022411 name: cellular component disassembly namespace: biological_process alt_id: GO:0071845 def: "A cellular process that results in the breakdown of a cellular component." [GOC:isa_complete] subset: goslim_pir synonym: "cell structure disassembly" EXACT [] synonym: "cellular component disassembly at cellular level" EXACT [] is_a: GO:0016043 ! cellular component organization [Term] id: GO:0022603 name: regulation of anatomical structure morphogenesis namespace: biological_process def: "Any process that modulates the frequency, rate or extent of anatomical structure morphogenesis." [GOC:mah] synonym: "regulation of morphogenesis" EXACT [] is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0009653 ! anatomical structure morphogenesis relationship: regulates GO:0009653 ! anatomical structure morphogenesis [Term] id: GO:0022607 name: cellular component assembly namespace: biological_process alt_id: GO:0071844 def: "The aggregation, arrangement and bonding together of a cellular component." [GOC:isa_complete] subset: goslim_chembl subset: goslim_generic subset: goslim_pir synonym: "cell structure assembly" EXACT [] synonym: "cellular component assembly at cellular level" EXACT [] is_a: GO:0016043 ! cellular component organization relationship: part_of GO:0044085 ! cellular component biogenesis [Term] id: GO:0022613 name: ribonucleoprotein complex biogenesis namespace: biological_process def: "A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a complex containing RNA and proteins. Includes the biosynthesis of the constituent RNA and protein molecules, and those macromolecular modifications that are involved in synthesis or assembly of the ribonucleoprotein complex." [GOC:isa_complete, GOC:mah] synonym: "ribonucleoprotein complex biogenesis and assembly" EXACT [GOC:mah] synonym: "RNA-protein complex biogenesis" EXACT [GOC:mah] is_a: GO:0044085 ! cellular component biogenesis [Term] id: GO:0022618 name: ribonucleoprotein complex assembly namespace: biological_process def: "The aggregation, arrangement and bonding together of proteins and RNA molecules to form a ribonucleoprotein complex." [GOC:jl] subset: goslim_chembl subset: goslim_generic synonym: "protein-RNA complex assembly" EXACT [] synonym: "RNA-protein complex assembly" EXACT [] synonym: "RNP complex assembly" EXACT [] is_a: GO:0034622 ! cellular protein-containing complex assembly is_a: GO:0071826 ! ribonucleoprotein complex subunit organization relationship: part_of GO:0022613 ! ribonucleoprotein complex biogenesis [Term] id: GO:0022803 name: passive transmembrane transporter activity namespace: molecular_function alt_id: GO:0022814 def: "Enables the transfer of a single solute from one side of a membrane to the other by a mechanism involving conformational change, either by facilitated diffusion or in a membrane potential dependent process if the solute is charged." [GOC:mtg_transport, ISBN:0815340729] synonym: "facilitated diffusion" RELATED [] synonym: "porters" BROAD [] synonym: "uniporter activity z" NARROW [] xref: Reactome:REACT_118066 "Passive I- efflux mediated by SMCT1, Staphylococcus aureus N315" xref: Reactome:REACT_118091 "Passive I- efflux mediated by SMCT1, Xenopus tropicalis" xref: Reactome:REACT_118204 "Passive I- efflux mediated by SMCT1, Mus musculus" xref: Reactome:REACT_118231 "Passive I- efflux mediated by SMCT1, Bos taurus" xref: Reactome:REACT_118327 "Passive I- efflux mediated by SMCT1, Taeniopygia guttata" xref: Reactome:REACT_118347 "Passive I- efflux mediated by SMCT1, Rattus norvegicus" xref: Reactome:REACT_118350 "Passive I- efflux mediated by SMCT1, Canis familiaris" xref: Reactome:REACT_118478 "Passive I- efflux mediated by SMCT1, Sus scrofa" xref: Reactome:REACT_118490 "Passive I- efflux mediated by SMCT1, Gallus gallus" xref: Reactome:REACT_118544 "Passive I- efflux mediated by SMCT1, Danio rerio" xref: Reactome:REACT_19251 "Passive I- efflux mediated by SMCT1, Homo sapiens" xref: Wikipedia:Facilitated_diffusion is_a: GO:0022857 ! transmembrane transporter activity [Term] id: GO:0022838 name: substrate-specific channel activity namespace: molecular_function def: "Enables the energy-independent facilitated diffusion, mediated by passage of a specific solute through a transmembrane aqueous pore or channel. Stereospecificity is not exhibited but this transport may be specific for a particular molecular species or class of molecules." [GOC:mtg_transport] is_a: GO:0015267 ! channel activity [Term] id: GO:0022857 name: transmembrane transporter activity namespace: molecular_function alt_id: GO:0005386 alt_id: GO:0015563 alt_id: GO:0015646 alt_id: GO:0022891 alt_id: GO:0022892 def: "Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other." [GOC:jid, GOC:mtg_transport, ISBN:0815340729] subset: goslim_chembl subset: goslim_generic subset: goslim_yeast synonym: "substrate-specific transmembrane transporter activity" RELATED [] synonym: "substrate-specific transporter activity" NARROW [] synonym: "uptake permease activity" RELATED [] synonym: "uptake transmembrane transporter activity" RELATED [] xref: Reactome:REACT_100033 "GLUT9 transports glucose, fructose and urate, Gallus gallus" xref: Reactome:REACT_106735 "GLUT9 transports glucose, fructose and urate, Xenopus tropicalis" xref: Reactome:REACT_111088 "Egress of internalized antigen to the cytosol via sec61, Homo sapiens" xref: Reactome:REACT_111933 "GLUT9 transports glucose, fructose and urate, Plasmodium falciparum" xref: Reactome:REACT_113047 "GLUT9 transports glucose, fructose and urate, Dictyostelium discoideum" xref: Reactome:REACT_113116 "GLUT9 transports glucose, fructose and urate, Mycobacterium tuberculosis" xref: Reactome:REACT_113829 "GLUT9 transports glucose, fructose and urate, Arabidopsis thaliana" xref: Reactome:REACT_114161 "GLUT9 transports glucose, fructose and urate, Oryza sativa" xref: Reactome:REACT_19288 "GLUT9 transports glucose, fructose and urate, Homo sapiens" xref: Reactome:REACT_77235 "GLUT9 transports glucose, fructose and urate, Canis familiaris" xref: Reactome:REACT_81225 "GLUT9 transports glucose, fructose and urate, Bos taurus" xref: Reactome:REACT_88503 "GLUT9 transports glucose, fructose and urate, Taeniopygia guttata" xref: Reactome:REACT_91849 "GLUT9 transports glucose, fructose and urate, Mus musculus" xref: Reactome:REACT_94185 "GLUT9 transports glucose, fructose and urate, Rattus norvegicus" is_a: GO:0005215 ! transporter activity relationship: part_of GO:0055085 ! transmembrane transport [Term] id: GO:0022898 name: regulation of transmembrane transporter activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transmembrane transporter activity." [GOC:dph, GOC:mtg_cardio, GOC:mtg_transport] is_a: GO:0032409 ! regulation of transporter activity is_a: GO:0034762 ! regulation of transmembrane transport intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0022857 ! transmembrane transporter activity relationship: regulates GO:0022857 ! transmembrane transporter activity [Term] id: GO:0023019 name: signal transduction involved in regulation of gene expression namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another." [GOC:mtg_signal] synonym: "regulation of gene expression as a consequence of signal transmission" RELATED [GOC:bf] is_a: GO:0007165 ! signal transduction intersection_of: GO:0007165 ! signal transduction intersection_of: part_of GO:0010468 ! regulation of gene expression relationship: part_of GO:0010468 ! regulation of gene expression creation_date: 2010-02-16T09:30:50Z [Term] id: GO:0023051 name: regulation of signaling namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a signaling process." [GOC:mtg_signal] synonym: "regulation of signaling process" RELATED [GOC:bf] synonym: "regulation of signalling process" RELATED [GOC:mah] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0023052 ! signaling relationship: regulates GO:0023052 ! signaling creation_date: 2010-02-16T09:30:50Z [Term] id: GO:0023052 name: signaling namespace: biological_process alt_id: GO:0023046 alt_id: GO:0044700 def: "The entirety of a process in which information is transmitted within a biological system. This process begins with an active signal and ends when a cellular response has been triggered." [GOC:mtg_signal, GOC:mtg_signaling_feb11, GOC:signaling] comment: Note that a signal is any variable property or parameter that serves to convey information, and may be a physical entity such as a gene product or small molecule, a photon, or a change in state such as movement or voltage change. subset: goslim_agr subset: goslim_mouse subset: goslim_pombe subset: goslim_yeast synonym: "biological signaling" EXACT [] synonym: "signaling process" EXACT [] synonym: "signalling" EXACT [] synonym: "signalling process" RELATED [GOC:mah] synonym: "single organism signaling" RELATED [] is_a: GO:0008150 ! biological_process created_by: janelomax creation_date: 2010-02-16T09:30:50Z [Term] id: GO:0023056 name: positive regulation of signaling namespace: biological_process def: "Any process that activates, maintains or increases the frequency, rate or extent of a signaling process." [GOC:mtg_signal] synonym: "positive regulation of signaling process" RELATED [GOC:bf] synonym: "positive regulation of signalling process" EXACT [GOC:mah] is_a: GO:0023051 ! regulation of signaling is_a: GO:0048518 ! positive regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0023052 ! signaling relationship: positively_regulates GO:0023052 ! signaling creation_date: 2010-02-16T09:30:50Z [Term] id: GO:0023057 name: negative regulation of signaling namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a signaling process." [GOC:mtg_signal] synonym: "negative regulation of signaling process" RELATED [GOC:bf] synonym: "negative regulation of signalling process" RELATED [GOC:mah] is_a: GO:0023051 ! regulation of signaling is_a: GO:0048519 ! negative regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0023052 ! signaling relationship: negatively_regulates GO:0023052 ! signaling creation_date: 2010-02-16T09:30:50Z [Term] id: GO:0030030 name: cell projection organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] synonym: "cell projection organisation" EXACT [GOC:curators] synonym: "cell projection organization and biogenesis" RELATED [GOC:mah] synonym: "cell surface structure organization and biogenesis" RELATED [GOC:mah] is_a: GO:0016043 ! cellular component organization [Term] id: GO:0030031 name: cell projection assembly namespace: biological_process def: "Formation of a prolongation or process extending from a cell, e.g. a flagellum or axon." [GOC:jl, GOC:mah, http://www.cogsci.princeton.edu/~wn/] synonym: "cell projection biogenesis" RELATED [GOC:mah] synonym: "formation of a cell surface projection" EXACT [] is_a: GO:0022607 ! cellular component assembly is_a: GO:0030030 ! cell projection organization [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 property_value: IAO:0000111 "actin filament polymerization" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [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 property_value: IAO:0000111 "hemopoiesis" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0030262 name: apoptotic nuclear changes namespace: biological_process def: "Alterations undergone by nuclei at the molecular and morphological level as part of the execution phase of apoptosis." [GOC:mah, GOC:mtg_apoptosis] synonym: "apoptotic nuclear change" NARROW [] is_a: GO:0006921 ! cellular component disassembly involved in execution phase of apoptosis [Term] id: GO:0030307 name: positive regulation of cell growth namespace: biological_process def: "Any process that activates or increases the frequency, rate, extent or direction of cell growth." [GOC:go_curators] synonym: "activation of cell growth" NARROW [] synonym: "stimulation of cell growth" NARROW [] synonym: "up regulation of cell growth" EXACT [] synonym: "up-regulation of cell growth" EXACT [] synonym: "upregulation of cell growth" EXACT [] is_a: GO:0001558 ! regulation of cell growth is_a: GO:0045927 ! positive regulation of growth is_a: GO:0048522 ! positive regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0016049 ! cell growth relationship: positively_regulates GO:0016049 ! cell growth [Term] id: GO:0030308 name: negative regulation of cell growth namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate, extent or direction of cell growth." [GOC:go_curators] synonym: "down regulation of cell growth" EXACT [] synonym: "down-regulation of cell growth" EXACT [] synonym: "downregulation of cell growth" EXACT [] synonym: "inhibition of cell growth" NARROW [] xref: Reactome:REACT_6328 "DRheb is inhibited by the TSC1/2 complex, Drosophila melanogaster" is_a: GO:0001558 ! regulation of cell growth is_a: GO:0045926 ! negative regulation of growth is_a: GO:0048523 ! negative regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0016049 ! cell growth relationship: negatively_regulates GO:0016049 ! cell growth [Term] id: GO:0030334 name: regulation of cell migration namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cell migration." [GOC:go_curators] is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0016477 ! cell migration relationship: regulates GO:0016477 ! cell migration [Term] id: GO:0030335 name: positive regulation of cell migration namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cell migration." [GOC:go_curators] synonym: "activation of cell migration" NARROW [] synonym: "stimulation of cell migration" NARROW [] synonym: "up regulation of cell migration" EXACT [] synonym: "up-regulation of cell migration" EXACT [] synonym: "upregulation of cell migration" EXACT [] is_a: GO:0030334 ! regulation of cell migration is_a: GO:2000147 ! positive regulation of cell motility intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0016477 ! cell migration relationship: positively_regulates GO:0016477 ! cell migration [Term] id: GO:0030336 name: negative regulation of cell migration namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell migration." [GOC:go_curators] synonym: "down regulation of cell migration" EXACT [] synonym: "down-regulation of cell migration" EXACT [] synonym: "downregulation of cell migration" EXACT [] synonym: "inhibition of cell migration" NARROW [] is_a: GO:0030334 ! regulation of cell migration is_a: GO:2000146 ! negative regulation of cell motility intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0016477 ! cell migration relationship: negatively_regulates GO:0016477 ! cell migration [Term] id: GO:0031047 name: gene silencing by RNA namespace: biological_process def: "Any process in which RNA molecules inactivate expression of target genes." [GOC:dph, GOC:mah, GOC:tb, PMID:15020054] synonym: "RNA-mediated gene silencing" EXACT [GOC:dph, GOC:tb] is_a: GO:0016458 ! gene silencing [Term] id: GO:0031323 name: regulation of cellular metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] synonym: "regulation of cellular metabolism" EXACT [] is_a: GO:0019222 ! regulation of metabolic process is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0044237 ! cellular metabolic process relationship: regulates GO:0044237 ! cellular metabolic process [Term] id: GO:0031324 name: negative regulation of cellular metabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] synonym: "down regulation of cellular metabolic process" EXACT [] synonym: "down-regulation of cellular metabolic process" EXACT [] synonym: "downregulation of cellular metabolic process" EXACT [] synonym: "inhibition of cellular metabolic process" NARROW [] synonym: "negative regulation of cellular metabolism" EXACT [] is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0048523 ! negative regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0044237 ! cellular metabolic process relationship: negatively_regulates GO:0044237 ! cellular metabolic process [Term] id: GO:0031325 name: positive regulation of cellular metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances." [GOC:mah] synonym: "activation of cellular metabolic process" NARROW [] synonym: "positive regulation of cellular metabolism" EXACT [] synonym: "stimulation of cellular metabolic process" NARROW [] synonym: "up regulation of cellular metabolic process" EXACT [] synonym: "up-regulation of cellular metabolic process" EXACT [] synonym: "upregulation of cellular metabolic process" EXACT [] xref: Reactome:REACT_101225 "ChREBP activates metabolic gene expression, Mus musculus" xref: Reactome:REACT_102187 "ChREBP activates metabolic gene expression, Escherichia coli" xref: Reactome:REACT_102331 "ChREBP activates metabolic gene expression, Caenorhabditis elegans" xref: Reactome:REACT_105293 "ChREBP activates metabolic gene expression, Plasmodium falciparum" xref: Reactome:REACT_108571 "ChREBP activates metabolic gene expression, Drosophila melanogaster" xref: Reactome:REACT_109170 "ChREBP activates metabolic gene expression, Xenopus tropicalis" xref: Reactome:REACT_2122 "ChREBP activates metabolic gene expression, Homo sapiens" xref: Reactome:REACT_28360 "ChREBP activates metabolic gene expression, Arabidopsis thaliana" xref: Reactome:REACT_31270 "ChREBP activates metabolic gene expression, Mycobacterium tuberculosis" xref: Reactome:REACT_79603 "ChREBP activates metabolic gene expression, Canis familiaris" xref: Reactome:REACT_80902 "ChREBP activates metabolic gene expression, Saccharomyces cerevisiae" xref: Reactome:REACT_83058 "ChREBP activates metabolic gene expression, Taeniopygia guttata" xref: Reactome:REACT_84314 "ChREBP activates metabolic gene expression, Oryza sativa" xref: Reactome:REACT_86633 "ChREBP activates metabolic gene expression, Dictyostelium discoideum" xref: Reactome:REACT_87840 "ChREBP activates metabolic gene expression, Danio rerio" xref: Reactome:REACT_88060 "ChREBP activates metabolic gene expression, Rattus norvegicus" xref: Reactome:REACT_91293 "ChREBP activates metabolic gene expression, Staphylococcus aureus N315" xref: Reactome:REACT_91429 "ChREBP activates metabolic gene expression, Gallus gallus" xref: Reactome:REACT_91906 "ChREBP activates metabolic gene expression, Schizosaccharomyces pombe" xref: Reactome:REACT_92487 "ChREBP activates metabolic gene expression, Bos taurus" xref: Reactome:REACT_99393 "ChREBP activates metabolic gene expression, Sus scrofa" is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0048522 ! positive regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0044237 ! cellular metabolic process relationship: positively_regulates GO:0044237 ! cellular metabolic process [Term] id: GO:0031326 name: regulation of cellular biosynthetic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:mah] synonym: "regulation of cellular anabolism" EXACT [] synonym: "regulation of cellular biosynthesis" EXACT [] synonym: "regulation of cellular formation" EXACT [] synonym: "regulation of cellular synthesis" EXACT [] is_a: GO:0009889 ! regulation of biosynthetic process is_a: GO:0031323 ! regulation of cellular metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0044249 ! cellular biosynthetic process relationship: regulates GO:0044249 ! cellular biosynthetic process [Term] id: GO:0031327 name: negative regulation of cellular biosynthetic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:mah] synonym: "down regulation of cellular biosynthetic process" EXACT [] synonym: "down-regulation of cellular biosynthetic process" EXACT [] synonym: "downregulation of cellular biosynthetic process" EXACT [] synonym: "inhibition of cellular biosynthetic process" NARROW [] synonym: "negative regulation of cellular anabolism" EXACT [] synonym: "negative regulation of cellular biosynthesis" EXACT [] synonym: "negative regulation of cellular formation" EXACT [] synonym: "negative regulation of cellular synthesis" EXACT [] is_a: GO:0009890 ! negative regulation of biosynthetic process is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0031326 ! regulation of cellular biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0044249 ! cellular biosynthetic process relationship: negatively_regulates GO:0044249 ! cellular biosynthetic process [Term] id: GO:0031328 name: positive regulation of cellular biosynthetic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:mah] synonym: "activation of cellular biosynthetic process" NARROW [] synonym: "positive regulation of cellular anabolism" EXACT [] synonym: "positive regulation of cellular biosynthesis" EXACT [] synonym: "positive regulation of cellular formation" EXACT [] synonym: "positive regulation of cellular synthesis" EXACT [] synonym: "stimulation of cellular biosynthetic process" NARROW [] synonym: "up regulation of cellular biosynthetic process" EXACT [] synonym: "up-regulation of cellular biosynthetic process" EXACT [] synonym: "upregulation of cellular biosynthetic process" EXACT [] is_a: GO:0009891 ! positive regulation of biosynthetic process is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0031326 ! regulation of cellular biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0044249 ! cellular biosynthetic process relationship: positively_regulates GO:0044249 ! cellular biosynthetic process [Term] id: GO:0031329 name: regulation of cellular catabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] synonym: "regulation of cellular breakdown" EXACT [] synonym: "regulation of cellular catabolism" EXACT [] synonym: "regulation of cellular degradation" EXACT [] is_a: GO:0009894 ! regulation of catabolic process is_a: GO:0031323 ! regulation of cellular metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0044248 ! cellular catabolic process relationship: regulates GO:0044248 ! cellular catabolic process [Term] id: GO:0031330 name: negative regulation of cellular catabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] synonym: "down regulation of cellular catabolic process" EXACT [] synonym: "down-regulation of cellular catabolic process" EXACT [] synonym: "downregulation of cellular catabolic process" EXACT [] synonym: "inhibition of cellular catabolic process" NARROW [] synonym: "negative regulation of cellular breakdown" EXACT [] synonym: "negative regulation of cellular catabolism" EXACT [] synonym: "negative regulation of cellular degradation" EXACT [] is_a: GO:0009895 ! negative regulation of catabolic process is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0031329 ! regulation of cellular catabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0044248 ! cellular catabolic process relationship: negatively_regulates GO:0044248 ! cellular catabolic process [Term] id: GO:0031331 name: positive regulation of cellular catabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:mah] synonym: "activation of cellular catabolic process" NARROW [] synonym: "positive regulation of cellular breakdown" EXACT [] synonym: "positive regulation of cellular catabolism" EXACT [] synonym: "positive regulation of cellular degradation" EXACT [] synonym: "stimulation of cellular catabolic process" NARROW [] synonym: "up regulation of cellular catabolic process" EXACT [] synonym: "up-regulation of cellular catabolic process" EXACT [] synonym: "upregulation of cellular catabolic process" EXACT [] is_a: GO:0009896 ! positive regulation of catabolic process is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0031329 ! regulation of cellular catabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0044248 ! cellular catabolic process relationship: positively_regulates GO:0044248 ! cellular catabolic process [Term] id: GO:0031333 name: negative regulation of protein complex assembly namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly." [GOC:mah] synonym: "down regulation of protein complex assembly" EXACT [] synonym: "down-regulation of protein complex assembly" EXACT [] synonym: "downregulation of protein complex assembly" EXACT [] synonym: "inhibition of protein complex assembly" NARROW [] is_a: GO:0043254 ! regulation of protein complex assembly is_a: GO:0051129 ! negative regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0065003 ! protein-containing complex assembly relationship: negatively_regulates GO:0065003 ! protein-containing complex assembly [Term] id: GO:0031334 name: positive regulation of protein complex assembly namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of protein complex assembly." [GOC:mah] synonym: "activation of protein complex assembly" NARROW [] synonym: "stimulation of protein complex assembly" NARROW [] synonym: "up regulation of protein complex assembly" EXACT [] synonym: "up-regulation of protein complex assembly" EXACT [] synonym: "upregulation of protein complex assembly" EXACT [] is_a: GO:0043254 ! regulation of protein complex assembly is_a: GO:0044089 ! positive regulation of cellular component biogenesis is_a: GO:0051130 ! positive regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0065003 ! protein-containing complex assembly relationship: positively_regulates GO:0065003 ! protein-containing complex assembly [Term] id: GO:0031341 name: regulation of cell killing namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cell killing, the process in which a cell brings about the death of another cell, either in the same or a different organism." [GOC:mah] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0001906 ! cell killing relationship: regulates GO:0001906 ! cell killing [Term] id: GO:0031342 name: negative regulation of cell killing namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell killing." [GOC:mah] synonym: "down regulation of cell killing" EXACT [] synonym: "down-regulation of cell killing" EXACT [] synonym: "downregulation of cell killing" EXACT [] synonym: "inhibition of cell killing" NARROW [] is_a: GO:0031341 ! regulation of cell killing is_a: GO:0048519 ! negative regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0001906 ! cell killing relationship: negatively_regulates GO:0001906 ! cell killing [Term] id: GO:0031343 name: positive regulation of cell killing namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cell killing." [GOC:mah] synonym: "activation of cell killing" NARROW [] synonym: "stimulation of cell killing" NARROW [] synonym: "up regulation of cell killing" EXACT [] synonym: "up-regulation of cell killing" EXACT [] synonym: "upregulation of cell killing" EXACT [] is_a: GO:0031341 ! regulation of cell killing is_a: GO:0048518 ! positive regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0001906 ! cell killing relationship: positively_regulates GO:0001906 ! cell killing [Term] id: GO:0031344 name: regulation of cell projection organization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections." [GOC:mah] synonym: "regulation of cell projection organisation" EXACT [GOC:curators] synonym: "regulation of cell projection organization and biogenesis" RELATED [GOC:mah] is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0030030 ! cell projection organization relationship: regulates GO:0030030 ! cell projection organization [Term] id: GO:0031345 name: negative regulation of cell projection organization namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell projections." [GOC:mah] synonym: "down regulation of cell projection organization" EXACT [GOC:mah] synonym: "down-regulation of cell projection organization" EXACT [] synonym: "downregulation of cell projection organization" EXACT [] synonym: "inhibition of cell projection organization" NARROW [] synonym: "negative regulation of cell projection organisation" EXACT [GOC:curators] synonym: "negative regulation of cell projection organization and biogenesis" RELATED [GOC:mah] is_a: GO:0031344 ! regulation of cell projection organization is_a: GO:0051129 ! negative regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0030030 ! cell projection organization relationship: negatively_regulates GO:0030030 ! cell projection organization [Term] id: GO:0031346 name: positive regulation of cell projection organization namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the process involved in the formation, arrangement of constituent parts, or disassembly of cell projections." [GOC:mah] synonym: "activation of cell projection organization" NARROW [] synonym: "positive regulation of cell projection organisation" EXACT [GOC:curators] synonym: "positive regulation of cell projection organization and biogenesis" RELATED [GOC:mah] synonym: "stimulation of cell projection organization" NARROW [] synonym: "up regulation of cell projection organization" EXACT [] synonym: "up-regulation of cell projection organization" EXACT [] synonym: "upregulation of cell projection organization" EXACT [] is_a: GO:0031344 ! regulation of cell projection organization is_a: GO:0051130 ! positive regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0030030 ! cell projection organization relationship: positively_regulates GO:0030030 ! cell projection organization [Term] id: GO:0032060 name: bleb assembly namespace: biological_process def: "The assembly of a bleb, a cell extension caused by localized decoupling of the cytoskeleton from the plasma membrane and characterized by rapid formation, rounded shape, and scarcity of organelles within the protrusion. Plasma membrane blebbing occurs during apoptosis and other cellular processes, including cell locomotion, cell division, and as a result of physical or chemical stresses." [GOC:mah, GOC:mtg_apoptosis, http://en.wikipedia.org/wiki/Bleb_(cell_biology), PMID:12083798, PMID:16624291] synonym: "blebbing" BROAD [GOC:pr] synonym: "cell blebbing" EXACT [] synonym: "membrane blebbing" BROAD [GOC:pr] synonym: "plasma membrane bleb assembly" EXACT [GOC:pr] synonym: "plasma membrane blebbing" EXACT [GOC:pr] is_a: GO:0120031 ! plasma membrane bounded cell projection assembly [Term] id: GO:0032069 name: regulation of nuclease activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids." [GOC:mah] synonym: "nuclease regulator activity" RELATED [] is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process is_a: GO:0051336 ! regulation of hydrolase activity is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0004518 ! nuclease activity relationship: regulates GO:0004518 ! nuclease activity [Term] id: GO:0032070 name: regulation of deoxyribonuclease activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid." [GOC:mah] synonym: "deoxyribonuclease regulator" RELATED [] synonym: "DNase regulator" RELATED [] is_a: GO:0032069 ! regulation of nuclease activity is_a: GO:0051052 ! regulation of DNA metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0004536 ! deoxyribonuclease activity relationship: regulates GO:0004536 ! deoxyribonuclease activity [Term] id: GO:0032071 name: regulation of endodeoxyribonuclease activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC:mah] synonym: "endodeoxyribonuclease regulator" RELATED [] is_a: GO:0032070 ! regulation of deoxyribonuclease activity intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0004520 ! endodeoxyribonuclease activity relationship: regulates GO:0004520 ! endodeoxyribonuclease activity [Term] id: GO:0032074 name: negative regulation of nuclease activity namespace: biological_process def: "Any process that stops or reduces the rate of nuclease activity, the hydrolysis of ester linkages within nucleic acids." [GOC:mah] synonym: "down regulation of nuclease activity" EXACT [] synonym: "down-regulation of nuclease activity" EXACT [] synonym: "downregulation of nuclease activity" EXACT [] synonym: "inhibition of nuclease activity" NARROW [] synonym: "nuclease inhibitor" RELATED [] is_a: GO:0010605 ! negative regulation of macromolecule metabolic process is_a: GO:0032069 ! regulation of nuclease activity is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process is_a: GO:0051346 ! negative regulation of hydrolase activity intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0004518 ! nuclease activity relationship: negatively_regulates GO:0004518 ! nuclease activity [Term] id: GO:0032075 name: positive regulation of nuclease activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids." [GOC:mah] synonym: "activation of nuclease activity" NARROW [] synonym: "nuclease activator" RELATED [] synonym: "stimulation of nuclease activity" NARROW [] synonym: "up regulation of nuclease activity" EXACT [] synonym: "up-regulation of nuclease activity" EXACT [] synonym: "upregulation of nuclease activity" EXACT [] is_a: GO:0010604 ! positive regulation of macromolecule metabolic process is_a: GO:0032069 ! regulation of nuclease activity is_a: GO:0045935 ! positive regulation of nucleobase-containing compound metabolic process is_a: GO:0051345 ! positive regulation of hydrolase activity intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0004518 ! nuclease activity relationship: positively_regulates GO:0004518 ! nuclease activity [Term] id: GO:0032076 name: negative regulation of deoxyribonuclease activity namespace: biological_process def: "Any process that stops or reduces the rate of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid." [GOC:mah] synonym: "deoxyribonuclease inhibitor" RELATED [] synonym: "DNase inhibitor" RELATED [] synonym: "down regulation of deoxyribonuclease activity" EXACT [] synonym: "down-regulation of deoxyribonuclease activity" EXACT [] synonym: "downregulation of deoxyribonuclease activity" EXACT [] synonym: "inhibition of deoxyribonuclease activity" NARROW [] is_a: GO:0032070 ! regulation of deoxyribonuclease activity is_a: GO:0032074 ! negative regulation of nuclease activity is_a: GO:0051053 ! negative regulation of DNA metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0004536 ! deoxyribonuclease activity relationship: negatively_regulates GO:0004536 ! deoxyribonuclease activity [Term] id: GO:0032077 name: positive regulation of deoxyribonuclease activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid." [GOC:mah] synonym: "activation of deoxyribonuclease activity" NARROW [] synonym: "deoxyribonuclease activator" RELATED [] synonym: "DNase activator" RELATED [] synonym: "stimulation of deoxyribonuclease activity" NARROW [] synonym: "up regulation of deoxyribonuclease activity" EXACT [] synonym: "up-regulation of deoxyribonuclease activity" EXACT [] synonym: "upregulation of deoxyribonuclease activity" EXACT [] is_a: GO:0032070 ! regulation of deoxyribonuclease activity is_a: GO:0032075 ! positive regulation of nuclease activity is_a: GO:0051054 ! positive regulation of DNA metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0004536 ! deoxyribonuclease activity relationship: positively_regulates GO:0004536 ! deoxyribonuclease activity [Term] id: GO:0032078 name: negative regulation of endodeoxyribonuclease activity namespace: biological_process def: "Any process that stops or reduces the rate of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC:mah] synonym: "down regulation of endodeoxyribonuclease activity" EXACT [] synonym: "down-regulation of endodeoxyribonuclease activity" EXACT [] synonym: "downregulation of endodeoxyribonuclease activity" EXACT [] synonym: "endodeoxyribonuclease inhibitor" RELATED [] synonym: "inhibition of endodeoxyribonuclease activity" NARROW [] is_a: GO:0032071 ! regulation of endodeoxyribonuclease activity is_a: GO:0032076 ! negative regulation of deoxyribonuclease activity intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0004520 ! endodeoxyribonuclease activity relationship: negatively_regulates GO:0004520 ! endodeoxyribonuclease activity [Term] id: GO:0032079 name: positive regulation of endodeoxyribonuclease activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks." [GOC:mah] synonym: "activation of endodeoxyribonuclease activity" NARROW [] synonym: "endodeoxyribonuclease activator" RELATED [] synonym: "stimulation of endodeoxyribonuclease activity" NARROW [] synonym: "up regulation of endodeoxyribonuclease activity" EXACT [] synonym: "up-regulation of endodeoxyribonuclease activity" EXACT [] synonym: "upregulation of endodeoxyribonuclease activity" EXACT [] is_a: GO:0032071 ! regulation of endodeoxyribonuclease activity is_a: GO:0032077 ! positive regulation of deoxyribonuclease activity intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0004520 ! endodeoxyribonuclease activity relationship: positively_regulates GO:0004520 ! endodeoxyribonuclease activity [Term] id: GO:0032101 name: regulation of response to external stimulus namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a response to an external stimulus." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0009605 ! response to external stimulus relationship: regulates GO:0009605 ! response to external stimulus [Term] id: GO:0032102 name: negative regulation of response to external stimulus namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a response to an external stimulus." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate synonym: "down regulation of response to external stimulus" EXACT [] synonym: "down-regulation of response to external stimulus" EXACT [] synonym: "downregulation of response to external stimulus" EXACT [] synonym: "inhibition of response to external stimulus" NARROW [] is_a: GO:0032101 ! regulation of response to external stimulus is_a: GO:0048585 ! negative regulation of response to stimulus intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0009605 ! response to external stimulus relationship: negatively_regulates GO:0009605 ! response to external stimulus [Term] id: GO:0032103 name: positive regulation of response to external stimulus namespace: biological_process def: "Any process that activates, maintains or increases the rate of a response to an external stimulus." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate synonym: "activation of response to external stimulus" NARROW [] synonym: "stimulation of response to external stimulus" NARROW [] synonym: "up regulation of response to external stimulus" EXACT [] synonym: "up-regulation of response to external stimulus" EXACT [] synonym: "upregulation of response to external stimulus" EXACT [] is_a: GO:0032101 ! regulation of response to external stimulus is_a: GO:0048584 ! positive regulation of response to stimulus intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0009605 ! response to external stimulus relationship: positively_regulates GO:0009605 ! response to external stimulus [Term] id: GO:0032259 name: methylation namespace: biological_process def: "The process in which a methyl group is covalently attached to a molecule." [GOC:mah] subset: goslim_chembl xref: Reactome:REACT_100463 "Methylation, Rattus norvegicus" xref: Reactome:REACT_104378 "Methylation, Staphylococcus aureus N315" xref: Reactome:REACT_106986 "Methylation, Schizosaccharomyces pombe" xref: Reactome:REACT_107353 "Methylation, Taeniopygia guttata" xref: Reactome:REACT_107808 "Methylation, Caenorhabditis elegans" xref: Reactome:REACT_110691 "Methylation, Gallus gallus" xref: Reactome:REACT_34638 "Methylation, Mus musculus" xref: Reactome:REACT_6946 "Methylation, Homo sapiens" xref: Reactome:REACT_77304 "Methylation, Oryza sativa" xref: Reactome:REACT_78116 "Methylation, Xenopus tropicalis" xref: Reactome:REACT_87183 "Methylation, Drosophila melanogaster" xref: Reactome:REACT_88148 "Methylation, Canis familiaris" xref: Reactome:REACT_90436 "Methylation, Danio rerio" xref: Reactome:REACT_92149 "Methylation, Sus scrofa" xref: Reactome:REACT_92596 "Methylation, Escherichia coli" xref: Reactome:REACT_93357 "Methylation, Mycobacterium tuberculosis" xref: Reactome:REACT_95391 "Methylation, Saccharomyces cerevisiae" xref: Reactome:REACT_98332 "Methylation, Arabidopsis thaliana" xref: Reactome:REACT_99471 "Methylation, Bos taurus" xref: Reactome:REACT_99529 "Methylation, Dictyostelium discoideum" xref: Wikipedia:Methylation is_a: GO:0008152 ! metabolic process [Term] id: GO:0032268 name: regulation of cellular protein metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell." [GOC:mah] synonym: "regulation of cellular protein metabolism" EXACT [] is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0051246 ! regulation of protein metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0044267 ! cellular protein metabolic process relationship: regulates GO:0044267 ! cellular protein metabolic process [Term] id: GO:0032269 name: negative regulation of cellular protein metabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell." [GOC:mah] synonym: "down regulation of cellular protein metabolic process" EXACT [] synonym: "down-regulation of cellular protein metabolic process" EXACT [] synonym: "downregulation of cellular protein metabolic process" EXACT [] synonym: "inhibition of cellular protein metabolic process" NARROW [] synonym: "negative regulation of cellular protein metabolism" EXACT [] is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0032268 ! regulation of cellular protein metabolic process is_a: GO:0051248 ! negative regulation of protein metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0044267 ! cellular protein metabolic process relationship: negatively_regulates GO:0044267 ! cellular protein metabolic process [Term] id: GO:0032270 name: positive regulation of cellular protein metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell." [GOC:mah] synonym: "activation of cellular protein metabolic process" NARROW [] synonym: "positive regulation of cellular protein metabolism" EXACT [] synonym: "stimulation of cellular protein metabolic process" NARROW [] synonym: "up regulation of cellular protein metabolic process" EXACT [] synonym: "up-regulation of cellular protein metabolic process" EXACT [] synonym: "upregulation of cellular protein metabolic process" EXACT [] is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0032268 ! regulation of cellular protein metabolic process is_a: GO:0051247 ! positive regulation of protein metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0044267 ! cellular protein metabolic process relationship: positively_regulates GO:0044267 ! cellular protein metabolic process [Term] id: GO:0032303 name: regulation of icosanoid secretion namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the controlled release of an icosanoid from a cell." [GOC:mah] synonym: "regulation of eicosanoid secretion" EXACT [] is_a: GO:0051046 ! regulation of secretion is_a: GO:2000191 ! regulation of fatty acid transport intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0032309 ! icosanoid secretion relationship: regulates GO:0032309 ! icosanoid secretion [Term] id: GO:0032304 name: negative regulation of icosanoid secretion namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of an icosanoid from a cell." [GOC:mah] synonym: "down regulation of icosanoid secretion" EXACT [] synonym: "down-regulation of icosanoid secretion" EXACT [] synonym: "downregulation of icosanoid secretion" EXACT [] synonym: "inhibition of icosanoid secretion" NARROW [] synonym: "negative regulation of eicosanoid secretion" EXACT [] is_a: GO:0032303 ! regulation of icosanoid secretion is_a: GO:0051048 ! negative regulation of secretion is_a: GO:2000192 ! negative regulation of fatty acid transport intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0032309 ! icosanoid secretion relationship: negatively_regulates GO:0032309 ! icosanoid secretion [Term] id: GO:0032305 name: positive regulation of icosanoid secretion namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the controlled release of an icosanoid from a cell." [GOC:mah] synonym: "activation of icosanoid secretion" NARROW [] synonym: "positive regulation of eicosanoid secretion" EXACT [] synonym: "stimulation of icosanoid secretion" NARROW [] synonym: "up regulation of icosanoid secretion" EXACT [] synonym: "up-regulation of icosanoid secretion" EXACT [] synonym: "upregulation of icosanoid secretion" EXACT [] is_a: GO:0032303 ! regulation of icosanoid secretion is_a: GO:0051047 ! positive regulation of secretion is_a: GO:2000193 ! positive regulation of fatty acid transport intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0032309 ! icosanoid secretion relationship: positively_regulates GO:0032309 ! icosanoid secretion [Term] id: GO:0032309 name: icosanoid secretion namespace: biological_process def: "The controlled release of icosanoids, any of a group of C20 polyunsaturated fatty acids from a cell or a tissue." [GOC:mah] synonym: "eicosanoid secretion" EXACT [] is_a: GO:0046717 ! acid secretion is_a: GO:0071715 ! icosanoid transport [Term] id: GO:0032368 name: regulation of lipid transport namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] is_a: GO:0051049 ! regulation of transport is_a: GO:1905952 ! regulation of lipid localization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006869 ! lipid transport relationship: regulates GO:0006869 ! lipid transport [Term] id: GO:0032369 name: negative regulation of lipid transport namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] synonym: "down regulation of lipid transport" EXACT [] synonym: "down-regulation of lipid transport" EXACT [] synonym: "downregulation of lipid transport" EXACT [] synonym: "inhibition of lipid transport" NARROW [] is_a: GO:0032368 ! regulation of lipid transport is_a: GO:0051051 ! negative regulation of transport is_a: GO:1905953 ! negative regulation of lipid localization intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006869 ! lipid transport relationship: negatively_regulates GO:0006869 ! lipid transport [Term] id: GO:0032370 name: positive regulation of lipid transport namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] synonym: "activation of lipid transport" NARROW [] synonym: "stimulation of lipid transport" NARROW [] synonym: "up regulation of lipid transport" EXACT [] synonym: "up-regulation of lipid transport" EXACT [] synonym: "upregulation of lipid transport" EXACT [] is_a: GO:0032368 ! regulation of lipid transport is_a: GO:0051050 ! positive regulation of transport is_a: GO:1905954 ! positive regulation of lipid localization intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006869 ! lipid transport relationship: positively_regulates GO:0006869 ! lipid transport [Term] id: GO:0032409 name: regulation of transporter activity namespace: biological_process def: "Any process that modulates the activity of a transporter." [GOC:mah] is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0005215 ! transporter activity relationship: regulates GO:0005215 ! transporter activity [Term] id: GO:0032410 name: negative regulation of transporter activity namespace: biological_process def: "Any process that stops or reduces the activity of a transporter." [GOC:mah] synonym: "down regulation of transporter activity" EXACT [] synonym: "down-regulation of transporter activity" EXACT [] synonym: "downregulation of transporter activity" EXACT [] synonym: "inhibition of transporter activity" NARROW [] is_a: GO:0032409 ! regulation of transporter activity is_a: GO:0044092 ! negative regulation of molecular function is_a: GO:0051051 ! negative regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0005215 ! transporter activity relationship: negatively_regulates GO:0005215 ! transporter activity [Term] id: GO:0032411 name: positive regulation of transporter activity namespace: biological_process def: "Any process that activates or increases the activity of a transporter." [GOC:mah] synonym: "activation of transporter activity" NARROW [] synonym: "stimulation of transporter activity" NARROW [] synonym: "up regulation of transporter activity" EXACT [] synonym: "up-regulation of transporter activity" EXACT [] synonym: "upregulation of transporter activity" EXACT [] is_a: GO:0032409 ! regulation of transporter activity is_a: GO:0044093 ! positive regulation of molecular function is_a: GO:0051050 ! positive regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0005215 ! transporter activity relationship: positively_regulates GO:0005215 ! transporter activity [Term] id: GO:0032412 name: regulation of ion transmembrane transporter activity namespace: biological_process def: "Any process that modulates the activity of an ion transporter." [GOC:mah, GOC:tb] synonym: "regulation of ion transporter activity" EXACT [GOC:tb] is_a: GO:0022898 ! regulation of transmembrane transporter activity is_a: GO:0034765 ! regulation of ion transmembrane transport intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0015075 ! ion transmembrane transporter activity relationship: regulates GO:0015075 ! ion transmembrane transporter activity [Term] id: GO:0032413 name: negative regulation of ion transmembrane transporter activity namespace: biological_process def: "Any process that stops or reduces the activity of an ion transporter." [GOC:mah, GOC:tb] synonym: "down regulation of ion transporter activity" EXACT [] synonym: "down-regulation of ion transporter activity" EXACT [] synonym: "downregulation of ion transporter activity" EXACT [] synonym: "inhibition of ion transporter activity" NARROW [] synonym: "negative regulation of ion transporter activity" EXACT [GOC:tb] is_a: GO:0032410 ! negative regulation of transporter activity is_a: GO:0032412 ! regulation of ion transmembrane transporter activity is_a: GO:0034766 ! negative regulation of ion transmembrane transport intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0015075 ! ion transmembrane transporter activity relationship: negatively_regulates GO:0015075 ! ion transmembrane transporter activity [Term] id: GO:0032414 name: positive regulation of ion transmembrane transporter activity namespace: biological_process def: "Any process that activates or increases the activity of an ion transporter." [GOC:mah, GOC:tb] synonym: "activation of ion transporter activity" NARROW [] synonym: "positive regulation of ion transporter activity" EXACT [GOC:tb] synonym: "stimulation of ion transporter activity" NARROW [] synonym: "up regulation of ion transporter activity" EXACT [] synonym: "up-regulation of ion transporter activity" EXACT [] synonym: "upregulation of ion transporter activity" EXACT [] is_a: GO:0032411 ! positive regulation of transporter activity is_a: GO:0032412 ! regulation of ion transmembrane transporter activity is_a: GO:0034767 ! positive regulation of ion transmembrane transport intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0015075 ! ion transmembrane transporter activity relationship: positively_regulates GO:0015075 ! ion transmembrane transporter activity [Term] id: GO:0032501 name: multicellular organismal process namespace: biological_process alt_id: GO:0044707 alt_id: GO:0050874 def: "Any biological process, occurring at the level of a multicellular organism, pertinent to its function." [GOC:curators, GOC:dph, GOC:isa_complete, GOC:tb] subset: goslim_pir synonym: "organismal physiological process" EXACT [] synonym: "single-multicellular organism process" RELATED [] is_a: GO:0008150 ! biological_process created_by: janelomax creation_date: 2012-09-19T16:07:47Z [Term] id: GO:0032502 name: developmental process namespace: biological_process alt_id: GO:0044767 def: "A biological process whose specific outcome is the progression of an integrated living unit: an anatomical structure (which may be a subcellular structure, cell, tissue, or organ), or organism over time from an initial condition to a later condition." [GOC:isa_complete] subset: goslim_agr subset: goslim_aspergillus subset: goslim_pir synonym: "development" NARROW [] synonym: "single-organism developmental process" RELATED [] is_a: GO:0008150 ! biological_process created_by: janelomax creation_date: 2012-12-19T12:21:31Z [Term] id: GO:0032640 name: tumor necrosis factor production namespace: biological_process 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." [GOC:mah] comment: Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). synonym: "TNF production" EXACT [] synonym: "TNF-alpha production" EXACT [] synonym: "tumor necrosis factor-alpha production" EXACT [] is_a: GO:0071706 ! tumor necrosis factor superfamily cytokine production [Term] id: GO:0032680 name: regulation of tumor necrosis factor production namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of tumor necrosis factor production." [GOC:mah] comment: Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). synonym: "regulation of TNF production" EXACT [] synonym: "regulation of TNF-alpha production" EXACT [] synonym: "regulation of tumor necrosis factor-alpha production" EXACT [] is_a: GO:1903555 ! regulation of tumor necrosis factor superfamily cytokine production intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0032640 ! tumor necrosis factor production relationship: regulates GO:0032640 ! tumor necrosis factor production [Term] id: GO:0032720 name: negative regulation of tumor necrosis factor production namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production." [GOC:mah] comment: Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). synonym: "down regulation of tumor necrosis factor production" EXACT [] synonym: "down-regulation of tumor necrosis factor production" EXACT [] synonym: "downregulation of tumor necrosis factor production" EXACT [] synonym: "inhibition of tumor necrosis factor production" NARROW [] synonym: "negative regulation TNF production" EXACT [] synonym: "negative regulation TNF-alpha production" EXACT [] synonym: "negative regulation tumor necrosis factor-alpha production" EXACT [] is_a: GO:0032680 ! regulation of tumor necrosis factor production is_a: GO:1903556 ! negative regulation of tumor necrosis factor superfamily cytokine production intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0032640 ! tumor necrosis factor production relationship: negatively_regulates GO:0032640 ! tumor necrosis factor production [Term] id: GO:0032760 name: positive regulation of tumor necrosis factor production namespace: biological_process def: "Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production." [GOC:mah] comment: Note that this term refers only to the specific, original 'tumor necrosis factor' protein (TNF) and not other members of the tumor necrosis factor superfamily (those with the gene symbol root 'TNFSF'). synonym: "activation of tumor necrosis factor production" NARROW [] synonym: "positive regulation of TNF production" EXACT [] synonym: "positive regulation of TNF-alpha production" EXACT [] synonym: "positive regulation of tumor necrosis factor-alpha production" EXACT [] synonym: "stimulation of tumor necrosis factor production" NARROW [] synonym: "up regulation of tumor necrosis factor production" EXACT [] synonym: "up-regulation of tumor necrosis factor production" EXACT [] synonym: "upregulation of tumor necrosis factor production" EXACT [] is_a: GO:0032680 ! regulation of tumor necrosis factor production is_a: GO:1903557 ! positive regulation of tumor necrosis factor superfamily cytokine production intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0032640 ! tumor necrosis factor production relationship: positively_regulates GO:0032640 ! tumor necrosis factor production [Term] id: GO:0032774 name: RNA biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. Includes polymerization of ribonucleotide monomers. Refers not only to transcription but also to e.g. viral RNA replication." [GOC:mah, GOC:txnOH] comment: Note that, in some cases, viral RNA replication and viral transcription from RNA actually refer to the same process, but may be called differently depending on the focus of a specific research study. synonym: "RNA anabolism" EXACT [] synonym: "RNA biosynthesis" EXACT [] synonym: "RNA formation" EXACT [] synonym: "RNA synthesis" EXACT [] is_a: GO:0009059 ! macromolecule biosynthetic process is_a: GO:0016070 ! RNA metabolic process is_a: GO:0034654 ! nucleobase-containing compound biosynthetic process [Term] id: GO:0032879 name: regulation of localization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location." [GOC:mah] synonym: "regulation of localisation" EXACT [GOC:mah] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0051179 ! localization relationship: regulates GO:0051179 ! localization [Term] id: GO:0032880 name: regulation of protein localization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location." [GOC:dph, GOC:mah, GOC:tb] subset: goslim_chembl synonym: "regulation of protein localisation" EXACT [GOC:mah] is_a: GO:0032879 ! regulation of localization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0008104 ! protein localization relationship: regulates GO:0008104 ! protein localization [Term] id: GO:0032890 name: regulation of organic acid transport namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] is_a: GO:0051049 ! regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0015849 ! organic acid transport relationship: regulates GO:0015849 ! organic acid transport [Term] id: GO:0032891 name: negative regulation of organic acid transport namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] synonym: "down regulation of organic acid transport" EXACT [] synonym: "down-regulation of organic acid transport" EXACT [] synonym: "downregulation of organic acid transport" EXACT [] synonym: "inhibition of organic acid transport" NARROW [] is_a: GO:0032890 ! regulation of organic acid transport is_a: GO:0051051 ! negative regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0015849 ! organic acid transport relationship: negatively_regulates GO:0015849 ! organic acid transport [Term] id: GO:0032892 name: positive regulation of organic acid transport namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the directed movement of organic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] synonym: "activation of organic acid transport" NARROW [] synonym: "stimulation of organic acid transport" NARROW [] synonym: "up regulation of organic acid transport" EXACT [] synonym: "up-regulation of organic acid transport" EXACT [] synonym: "upregulation of organic acid transport" EXACT [] is_a: GO:0032890 ! regulation of organic acid transport is_a: GO:0051050 ! positive regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0015849 ! organic acid transport relationship: positively_regulates GO:0015849 ! organic acid transport [Term] id: GO:0032940 name: secretion by cell namespace: biological_process def: "The controlled release of a substance by a cell." [GOC:mah] synonym: "cellular secretion" EXACT [] xref: Wikipedia:Secretion is_a: GO:0009987 ! cellular process is_a: GO:0046903 ! secretion [Term] id: GO:0032984 name: protein-containing complex disassembly namespace: biological_process alt_id: GO:0034623 alt_id: GO:0043241 def: "The disaggregation of a protein-containing macromolecular complex into its constituent components." [GOC:mah] synonym: "cellular macromolecule complex disassembly" RELATED [] synonym: "macromolecule complex disassembly" RELATED [] synonym: "protein complex disassembly" EXACT [] is_a: GO:0022411 ! cellular component disassembly is_a: GO:0043933 ! protein-containing complex subunit organization [Term] id: GO:0032989 name: cellular component morphogenesis namespace: biological_process def: "The process in which cellular structures, including whole cells or cell parts, are generated and organized." [GOC:dph, GOC:mah, GOC:tb] subset: goslim_pir synonym: "cellular structure morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0009653 ! anatomical structure morphogenesis is_a: GO:0016043 ! cellular component organization is_a: GO:0048869 ! cellular developmental process [Term] id: GO:0032991 name: protein-containing complex namespace: cellular_component alt_id: GO:0043234 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." [GOC:dos, GOC:mah] comment: A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole. subset: goslim_agr subset: goslim_chembl subset: goslim_generic subset: goslim_pir synonym: "macromolecular complex" EXACT [] synonym: "macromolecule complex" EXACT [] synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component [Term] id: GO:0033036 name: macromolecule localization namespace: biological_process def: "Any process in which a macromolecule is transported to, or maintained in, a specific location." [GOC:mah] synonym: "macromolecule localisation" EXACT [GOC:mah] is_a: GO:0051179 ! localization property_value: IAO:0000111 "macromolecule localization" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0033043 name: regulation of organelle organization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of an organelle." [GOC:mah] subset: goslim_yeast synonym: "regulation of organelle organisation" EXACT [GOC:mah] synonym: "regulation of organelle organization and biogenesis" RELATED [GOC:mah] is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006996 ! organelle organization relationship: regulates GO:0006996 ! organelle organization [Term] id: GO:0033044 name: regulation of chromosome organization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of a chromosome." [GOC:mah] synonym: "regulation of chromosome organisation" EXACT [GOC:mah] synonym: "regulation of chromosome organization and biogenesis" RELATED [GOC:mah] is_a: GO:0033043 ! regulation of organelle organization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0051276 ! chromosome organization relationship: regulates GO:0051276 ! chromosome organization [Term] id: GO:0033554 name: cellular response to stress namespace: biological_process 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 the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate is_a: GO:0006950 ! response to stress is_a: GO:0051716 ! cellular response to stimulus [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 property_value: IAO:0000111 "DNA polymerase activity" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0034220 name: ion transmembrane transport namespace: biological_process def: "A process in which an ion is transported across a membrane." [GOC:mah] comment: Note that this term is not intended for use in annotating lateral movement within membranes. synonym: "ion membrane transport" EXACT [] synonym: "transmembrane ion transport" EXACT [GOC:dph, GOC:tb] xref: Reactome:REACT_100497 "Ion channel transport, Rattus norvegicus" xref: Reactome:REACT_101721 "Ion transport by P-type ATPases, Canis familiaris" xref: Reactome:REACT_103924 "Ion transport by P-type ATPases, Taeniopygia guttata" xref: Reactome:REACT_107347 "Ion channel transport, Caenorhabditis elegans" xref: Reactome:REACT_108844 "Ion transport by P-type ATPases, Drosophila melanogaster" xref: Reactome:REACT_109050 "Ion channel transport, Gallus gallus" xref: Reactome:REACT_25149 "Ion transport by P-type ATPases, Homo sapiens" xref: Reactome:REACT_25300 "Ion channel transport, Homo sapiens" xref: Reactome:REACT_25387 "Ligand-gated ion channel transport, Homo sapiens" xref: Reactome:REACT_28672 "Ion transport by P-type ATPases, Arabidopsis thaliana" xref: Reactome:REACT_30601 "Ion channel transport, Danio rerio" xref: Reactome:REACT_31166 "Ion channel transport, Sus scrofa" xref: Reactome:REACT_32763 "Ion channel transport, Plasmodium falciparum" xref: Reactome:REACT_33389 "Ion channel transport, Mycobacterium tuberculosis" xref: Reactome:REACT_34584 "Ion channel transport, Oryza sativa" xref: Reactome:REACT_77153 "Ion channel transport, Arabidopsis thaliana" xref: Reactome:REACT_77267 "Ion channel transport, Taeniopygia guttata" xref: Reactome:REACT_78982 "Ion transport by P-type ATPases, Bos taurus" xref: Reactome:REACT_79679 "Ion transport by P-type ATPases, Xenopus tropicalis" xref: Reactome:REACT_81685 "Ion channel transport, Bos taurus" xref: Reactome:REACT_82102 "Ion channel transport, Canis familiaris" xref: Reactome:REACT_89671 "Ion channel transport, Xenopus tropicalis" xref: Reactome:REACT_89674 "Ion transport by P-type ATPases, Caenorhabditis elegans" xref: Reactome:REACT_89758 "Ion transport by P-type ATPases, Sus scrofa" xref: Reactome:REACT_89890 "Ion transport by P-type ATPases, Oryza sativa" xref: Reactome:REACT_92146 "Ion transport by P-type ATPases, Mus musculus" xref: Reactome:REACT_93475 "Ion transport by P-type ATPases, Rattus norvegicus" xref: Reactome:REACT_94109 "Ion channel transport, Mus musculus" xref: Reactome:REACT_94939 "Ion transport by P-type ATPases, Mycobacterium tuberculosis" xref: Reactome:REACT_94986 "Ion transport by P-type ATPases, Plasmodium falciparum" xref: Reactome:REACT_97506 "Ion transport by P-type ATPases, Danio rerio" xref: Reactome:REACT_97619 "Ion channel transport, Drosophila melanogaster" xref: Reactome:REACT_98518 "Ion transport by P-type ATPases, Gallus gallus" is_a: GO:0006811 ! ion transport is_a: GO:0055085 ! transmembrane transport [Term] id: GO:0034248 name: regulation of cellular amide metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving amides." [GOC:mah] synonym: "regulation of amide metabolism" EXACT [] is_a: GO:0031323 ! regulation of cellular metabolic process is_a: GO:0051171 ! regulation of nitrogen compound metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0043603 ! cellular amide metabolic process relationship: regulates GO:0043603 ! cellular amide metabolic process [Term] id: GO:0034249 name: negative regulation of cellular amide metabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving amides." [GOC:mah] synonym: "negative regulation of amide metabolism" EXACT [] is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0034248 ! regulation of cellular amide metabolic process is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0043603 ! cellular amide metabolic process relationship: negatively_regulates GO:0043603 ! cellular amide metabolic process [Term] id: GO:0034250 name: positive regulation of cellular amide metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving amides." [GOC:mah] synonym: "positive regulation of amide metabolism" EXACT [] is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0034248 ! regulation of cellular amide metabolic process is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0043603 ! cellular amide metabolic process relationship: positively_regulates GO:0043603 ! cellular amide metabolic process [Term] id: GO:0034613 name: cellular protein localization namespace: biological_process alt_id: GO:0016249 def: "Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GOC:mah] synonym: "cellular protein localisation" EXACT [GOC:mah] synonym: "channel localizer activity" NARROW [GOC:mah] is_a: GO:0008104 ! protein localization is_a: GO:0070727 ! cellular macromolecule localization [Term] id: GO:0034622 name: cellular protein-containing complex assembly namespace: biological_process alt_id: GO:0043623 def: "The aggregation, arrangement and bonding together of a set of components to form a protein complex, occurring at the level of an individual cell." [GOC:jl] synonym: "cellular macromolecule complex assembly" RELATED [] synonym: "cellular protein complex assembly" EXACT [] is_a: GO:0065003 ! protein-containing complex assembly [Term] id: GO:0034641 name: cellular nitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving various organic and inorganic nitrogenous compounds, as carried out by individual cells." [GOC:mah] subset: goslim_chembl subset: goslim_generic synonym: "cellular nitrogen compound metabolism" EXACT [] xref: Reactome:REACT_102000 "Metabolism of amino acids and derivatives, Mycobacterium tuberculosis" xref: Reactome:REACT_103710 "Metabolism of amino acids and derivatives, Escherichia coli" xref: Reactome:REACT_107293 "Metabolism of amino acids and derivatives, Arabidopsis thaliana" xref: Reactome:REACT_108179 "Metabolism of amino acids and derivatives, Xenopus tropicalis" xref: Reactome:REACT_109042 "Metabolism of amino acids and derivatives, Sus scrofa" xref: Reactome:REACT_13 "Metabolism of amino acids and derivatives, Homo sapiens" xref: Reactome:REACT_28699 "Metabolism of amino acids and derivatives, Saccharomyces cerevisiae" xref: Reactome:REACT_29108 "Metabolism of amino acids and derivatives, Caenorhabditis elegans" xref: Reactome:REACT_32429 "Metabolism of amino acids and derivatives, Rattus norvegicus" xref: Reactome:REACT_33347 "Metabolism of amino acids and derivatives, Mus musculus" xref: Reactome:REACT_34326 "Metabolism of amino acids and derivatives, Staphylococcus aureus N315" xref: Reactome:REACT_55564 "Metabolism of amino acids and derivatives, Gallus gallus" xref: Reactome:REACT_77741 "Metabolism of amino acids and derivatives, Taeniopygia guttata" xref: Reactome:REACT_82379 "Metabolism of amino acids and derivatives, Bos taurus" xref: Reactome:REACT_86268 "Metabolism of amino acids and derivatives, Drosophila melanogaster" xref: Reactome:REACT_90299 "Metabolism of amino acids and derivatives, Oryza sativa" xref: Reactome:REACT_91959 "Metabolism of amino acids and derivatives, Plasmodium falciparum" xref: Reactome:REACT_93580 "Metabolism of amino acids and derivatives, Danio rerio" xref: Reactome:REACT_95666 "Metabolism of amino acids and derivatives, Canis familiaris" xref: Reactome:REACT_98086 "Metabolism of amino acids and derivatives, Dictyostelium discoideum" xref: Reactome:REACT_99241 "Metabolism of amino acids and derivatives, Schizosaccharomyces pombe" is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0034645 name: cellular macromolecule biosynthetic process namespace: biological_process alt_id: GO:0034961 def: "The chemical reactions and pathways resulting in the formation of a macromolecule, any 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, carried out by individual cells." [CHEBI:33694, GOC:mah] synonym: "cellular biopolymer biosynthetic process" EXACT [GOC:mtg_chebi_dec09] synonym: "cellular macromolecule anabolism" EXACT [GOC:mah] synonym: "cellular macromolecule biosynthesis" EXACT [GOC:mah] synonym: "cellular macromolecule formation" EXACT [GOC:mah] synonym: "cellular macromolecule synthesis" EXACT [GOC:mah] is_a: GO:0009059 ! macromolecule biosynthetic process is_a: GO:0044249 ! cellular biosynthetic process is_a: GO:0044260 ! cellular macromolecule metabolic process [Term] id: GO:0034654 name: nucleobase-containing compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid anabolism" EXACT [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid biosynthesis" EXACT [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid formation" EXACT [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid synthesis" NARROW [] is_a: GO:0006139 ! nucleobase-containing compound metabolic process is_a: GO:0018130 ! heterocycle biosynthetic process is_a: GO:0019438 ! aromatic compound biosynthetic process is_a: GO:0044271 ! cellular nitrogen compound biosynthetic process is_a: GO:1901362 ! organic cyclic compound biosynthetic process [Term] id: GO:0034655 name: nucleobase-containing compound catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:mah] subset: goslim_chembl subset: goslim_generic synonym: "nucleobase, nucleoside, nucleotide and nucleic acid breakdown" EXACT [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolic process" RELATED [GOC:dph, GOC:tb] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid catabolism" EXACT [] synonym: "nucleobase, nucleoside, nucleotide and nucleic acid degradation" EXACT [] is_a: GO:0006139 ! nucleobase-containing compound metabolic process is_a: GO:0019439 ! aromatic compound catabolic process is_a: GO:0044270 ! cellular nitrogen compound catabolic process is_a: GO:0046700 ! heterocycle catabolic process is_a: GO:1901361 ! organic cyclic compound catabolic process [Term] id: GO:0034660 name: ncRNA metabolic process namespace: biological_process def: "The chemical reactions and pathways involving non-coding RNA transcripts (ncRNAs)." [GOC:mah] synonym: "ncRNA metabolism" EXACT [] xref: Reactome:REACT_104424 "Metabolism of non-coding RNA, Sus scrofa" xref: Reactome:REACT_107260 "Metabolism of non-coding RNA, Canis familiaris" xref: Reactome:REACT_11052 "Metabolism of non-coding RNA, Homo sapiens" xref: Reactome:REACT_31743 "Metabolism of non-coding RNA, Rattus norvegicus" xref: Reactome:REACT_34395 "Metabolism of non-coding RNA, Taeniopygia guttata" xref: Reactome:REACT_77416 "Metabolism of non-coding RNA, Gallus gallus" xref: Reactome:REACT_82057 "Metabolism of non-coding RNA, Drosophila melanogaster" xref: Reactome:REACT_87487 "Metabolism of non-coding RNA, Danio rerio" xref: Reactome:REACT_91823 "Metabolism of non-coding RNA, Xenopus tropicalis" xref: Reactome:REACT_92649 "Metabolism of non-coding RNA, Bos taurus" xref: Reactome:REACT_94145 "Metabolism of non-coding RNA, Mus musculus" is_a: GO:0016070 ! RNA metabolic process [Term] id: GO:0034708 name: methyltransferase complex namespace: cellular_component def: "A protein complex that possesses methyltransferase activity." [GOC:mah] is_a: GO:0044424 ! intracellular part is_a: GO:1990234 ! transferase complex [Term] id: GO:0034762 name: regulation of transmembrane transport namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other." [GOC:mah] synonym: "regulation of membrane transport" EXACT [] is_a: GO:0051049 ! regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0055085 ! transmembrane transport relationship: regulates GO:0055085 ! transmembrane transport [Term] id: GO:0034763 name: negative regulation of transmembrane transport namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other." [GOC:mah] synonym: "down regulation of transmembrane transport" EXACT [] synonym: "down-regulation of transmembrane transport" EXACT [] synonym: "downregulation of transmembrane transport" EXACT [] synonym: "inhibition of transmembrane transport" NARROW [] synonym: "negative regulation of membrane transport" EXACT [] is_a: GO:0034762 ! regulation of transmembrane transport is_a: GO:0051051 ! negative regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0055085 ! transmembrane transport relationship: negatively_regulates GO:0055085 ! transmembrane transport [Term] id: GO:0034764 name: positive regulation of transmembrane transport namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the directed movement of a solute from one side of a membrane to the other." [GOC:mah] synonym: "activation of transmembrane transport" NARROW [] synonym: "positive regulation of membrane transport" EXACT [] synonym: "stimulation of transmembrane transport" NARROW [] synonym: "up regulation of transmembrane transport" EXACT [] synonym: "up-regulation of transmembrane transport" EXACT [] synonym: "upregulation of transmembrane transport" EXACT [] is_a: GO:0034762 ! regulation of transmembrane transport is_a: GO:0051050 ! positive regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0055085 ! transmembrane transport relationship: positively_regulates GO:0055085 ! transmembrane transport [Term] id: GO:0034765 name: regulation of ion transmembrane transport namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other." [GOC:mah] synonym: "regulation of ion membrane transport" EXACT [] synonym: "regulation of transmembrane ion transport" EXACT [GOC:dph, GOC:tb] is_a: GO:0034762 ! regulation of transmembrane transport is_a: GO:0043269 ! regulation of ion transport intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0034220 ! ion transmembrane transport relationship: regulates GO:0034220 ! ion transmembrane transport [Term] id: GO:0034766 name: negative regulation of ion transmembrane transport namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other." [GOC:mah] synonym: "down regulation of transmembrane ion transport" EXACT [] synonym: "down-regulation of transmembrane ion transport" EXACT [] synonym: "downregulation of transmembrane ion transport" EXACT [] synonym: "inhibition of transmembrane ion transport" NARROW [] synonym: "negative regulation of ion membrane transport" EXACT [] synonym: "negative regulation of transmembrane ion transport" EXACT [GOC:dph, GOC:tb] is_a: GO:0034763 ! negative regulation of transmembrane transport is_a: GO:0034765 ! regulation of ion transmembrane transport is_a: GO:0043271 ! negative regulation of ion transport intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0034220 ! ion transmembrane transport relationship: negatively_regulates GO:0034220 ! ion transmembrane transport [Term] id: GO:0034767 name: positive regulation of ion transmembrane transport namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the directed movement of ions from one side of a membrane to the other." [GOC:mah] synonym: "activation of transmembrane ion transport" NARROW [] synonym: "positive regulation of ion membrane transport" EXACT [] synonym: "positive regulation of transmembrane ion transport" EXACT [] synonym: "stimulation of transmembrane ion transport" NARROW [] synonym: "up regulation of transmembrane ion transport" EXACT [] synonym: "up-regulation of transmembrane ion transport" EXACT [] synonym: "upregulation of transmembrane ion transport" EXACT [] is_a: GO:0034764 ! positive regulation of transmembrane transport is_a: GO:0034765 ! regulation of ion transmembrane transport is_a: GO:0043270 ! positive regulation of ion transport intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0034220 ! ion transmembrane transport relationship: positively_regulates GO:0034220 ! ion transmembrane transport [Term] id: GO:0035194 name: posttranscriptional gene silencing by RNA namespace: biological_process def: "Any process of posttranscriptional gene inactivation (silencing) mediated by small RNA molecules that may trigger mRNA degradation or negatively regulate translation." [GOC:mah, PMID:15020054, PMID:15066275, PMID:15066283] synonym: "RNA-mediated posttranscriptional gene silencing" EXACT [GOC:dph, GOC:tb] synonym: "sense-PTGS" RELATED [] is_a: GO:0016441 ! posttranscriptional gene silencing is_a: GO:0031047 ! gene silencing by RNA [Term] id: GO:0035690 name: cellular response to drug namespace: biological_process 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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease." [GOC:sl] subset: goslim_chembl is_a: GO:0042493 ! response to drug is_a: GO:0070887 ! cellular response to chemical stimulus created_by: rfoulger creation_date: 2011-02-24T03:37:26Z [Term] id: GO:0036146 name: cellular response to mycotoxin namespace: biological_process 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 mycotoxin stimulus. A mycotoxin is a toxic chemical substance produced by fungi." [GOC:di, PMID:20548963] is_a: GO:0010046 ! response to mycotoxin is_a: GO:0097237 ! cellular response to toxic substance created_by: rfoulger creation_date: 2012-03-12T11:08:22Z [Term] id: GO:0040007 name: growth namespace: biological_process alt_id: GO:0048590 def: "The increase in size or mass of an entire organism, a part of an organism or a cell." [GOC:bf, GOC:ma] comment: See also the biological process term 'cell growth ; GO:0016049'. subset: gocheck_do_not_annotate subset: goslim_chembl subset: goslim_generic subset: goslim_pir subset: goslim_plant synonym: "growth pattern" RELATED [] synonym: "non-developmental growth" RELATED [GOC:mah] is_a: GO:0008150 ! biological_process [Term] id: GO:0040008 name: regulation of growth namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the growth of all or part of an organism so that it occurs at its proper speed, either globally or in a specific part of the organism's development." [GOC:ems, GOC:mah] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0040007 ! growth relationship: regulates GO:0040007 ! growth [Term] id: GO:0040011 name: locomotion namespace: biological_process def: "Self-propelled movement of a cell or organism from one location to another." [GOC:dgh] subset: goslim_chembl subset: goslim_generic subset: goslim_pir is_a: GO:0008150 ! biological_process [Term] id: GO:0040012 name: regulation of locomotion namespace: biological_process def: "Any process that modulates the frequency, rate or extent of locomotion of a cell or organism." [GOC:ems] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0040011 ! locomotion relationship: regulates GO:0040011 ! locomotion [Term] id: GO:0040013 name: negative regulation of locomotion namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of locomotion of a cell or organism." [GOC:go_curators] synonym: "down regulation of locomotion" EXACT [] synonym: "down-regulation of locomotion" EXACT [] synonym: "downregulation of locomotion" EXACT [] synonym: "inhibition of locomotion" NARROW [] is_a: GO:0040012 ! regulation of locomotion is_a: GO:0048519 ! negative regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0040011 ! locomotion relationship: negatively_regulates GO:0040011 ! locomotion [Term] id: GO:0040017 name: positive regulation of locomotion namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of locomotion of a cell or organism." [GOC:go_curators] synonym: "activation of locomotion" NARROW [] synonym: "stimulation of locomotion" NARROW [] synonym: "up regulation of locomotion" EXACT [] synonym: "up-regulation of locomotion" EXACT [] synonym: "upregulation of locomotion" EXACT [] is_a: GO:0040012 ! regulation of locomotion is_a: GO:0048518 ! positive regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0040011 ! locomotion relationship: positively_regulates GO:0040011 ! locomotion [Term] id: GO:0040029 name: regulation of gene expression, epigenetic namespace: biological_process def: "Any process that modulates the frequency, rate or extent of gene expression; the process is mitotically or meiotically heritable, or is stably self-propagated in the cytoplasm of a resting cell, and does not entail a change in DNA sequence." [PMID:10521337, PMID:11498582] subset: goslim_plant is_a: GO:0010468 ! regulation of gene expression [Term] id: GO:0040030 name: regulation of molecular function, epigenetic def: "Any heritable epigenetic process that modulates the frequency, rate or extent of protein function by self-perpetuating conformational conversions of normal proteins in healthy cells. This is distinct from, though mechanistically analogous to, disease states associated with prion propagation and amyloidogenesis. A single protein, if it carries a glutamine/asparagine-rich ('prion') domain, can sometimes stably exist in at least two distinct physical states, each associated with a different phenotype; propagation of one of these traits is achieved by a self-perpetuating change in the protein from one form to the other, mediated by conformational changes in the glutamine/asparagine-rich domain. Prion domains are both modular and transferable to other proteins, on which they can confer a heritable epigenetic alteration of function; existing bioinformatics data indicate that they are rare in non-eukarya, but common in eukarya." [] is_a: GO:0008150 ! biological_process property_value: IAO:0000111 "regulation of molecular function, epigenetic" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0040033 name: negative regulation of translation, ncRNA-mediated namespace: biological_process def: "Any process, mediated by small non-coding RNAs, that stops, prevents or reduces the rate that mRNAs are effectively translated into protein." [GOC:dph, GOC:ems, GOC:tb] synonym: "down regulation of mRNA translation, ncRNA-mediated" EXACT [] synonym: "down-regulation of mRNA translation, ncRNA-mediated" EXACT [] synonym: "downregulation of mRNA translation, ncRNA-mediated" EXACT [] synonym: "inhibition of mRNA translation, ncRNA-mediated" NARROW [] is_a: GO:0017148 ! negative regulation of translation is_a: GO:0045974 ! regulation of translation, ncRNA-mediated [Term] id: GO:0042060 name: wound healing namespace: biological_process def: "The series of events that restore integrity to a damaged tissue, following an injury." [GOC:bf, PMID:15269788] xref: Wikipedia:Wound_healing is_a: GO:0009611 ! response to wounding [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 property_value: IAO:0000111 "T cell receptor complex" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042127 name: regulation of cell proliferation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cell proliferation." [GOC:jl] is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0008283 ! cell proliferation relationship: regulates GO:0008283 ! cell proliferation [Term] id: GO:0042221 name: response to chemical namespace: biological_process 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 chemical stimulus." [GOC:jl] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate subset: goslim_aspergillus subset: goslim_candida subset: goslim_metagenomics subset: goslim_yeast synonym: "response to chemical stimulus" EXACT [GOC:dos] synonym: "response to chemical substance" EXACT [] is_a: GO:0050896 ! response to stimulus [Term] id: GO:0042330 name: taxis namespace: biological_process def: "The directed movement of a motile cell or organism in response to an external stimulus." [GOC:jl, ISBN:0192801023] synonym: "directed movement in response to stimulus" EXACT [] xref: Wikipedia:Taxis is_a: GO:0040011 ! locomotion relationship: part_of GO:0009605 ! response to external stimulus [Term] id: GO:0042391 name: regulation of membrane potential namespace: biological_process def: "Any process that modulates the establishment or extent of a membrane potential, the electric potential existing across any membrane arising from charges in the membrane itself and from the charges present in the media on either side of the membrane." [GOC:jl, GOC:mtg_cardio, GOC:tb, ISBN:0198506732] is_a: GO:0065008 ! regulation of biological quality [Term] id: GO:0042493 name: response to drug namespace: biological_process alt_id: GO:0017035 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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease." [GOC:jl] subset: goslim_candida synonym: "drug resistance" RELATED [] synonym: "drug susceptibility/resistance" RELATED [] is_a: GO:0042221 ! response to chemical [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." [] is_a: GO:0019814 ! immunoglobulin complex is_a: OBI:1110022 ! adaptive immune receptor property_value: IAO:0000111 "immunoglobulin complex, circulating" xsd:string property_value: IAO:0000118 "antibody" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl property_value: OBI:9991118 "antibody" xsd:string [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:0043234 ! protein complex is_a: OBI:0000427 ! enzyme property_value: IAO:0000111 "DNA polymerase complex" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0042710 name: biofilm formation namespace: biological_process def: "A process in which planktonically growing microorganisms grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription." [GOC:di, PMID:11932229] subset: gocheck_do_not_annotate subset: gocheck_do_not_manually_annotate subset: goslim_candida subset: goslim_pir is_a: GO:0044764 ! multi-organism cellular process [Term] id: GO:0042868 name: antisense RNA metabolic process namespace: biological_process def: "The chemical reactions and pathways involving antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis." [GOC:jl] synonym: "antisense RNA metabolism" EXACT [] is_a: GO:0034660 ! ncRNA metabolic process [Term] id: GO:0042886 name: amide transport namespace: biological_process def: "The directed movement of an amide, any compound containing one, two, or three acyl groups attached to a nitrogen atom, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl, ISBN:0198506732] subset: goslim_pir is_a: GO:0071705 ! nitrogen compound transport [Term] id: GO:0042981 name: regulation of apoptotic process namespace: biological_process def: "Any process that modulates the occurrence or rate of cell death by apoptotic process." [GOC:jl, GOC:mtg_apoptosis] comment: This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. synonym: "apoptosis regulator activity" RELATED [] synonym: "regulation of apoptosis" NARROW [] xref: Reactome:REACT_106248 "Regulation of Apoptosis, Mus musculus" xref: Reactome:REACT_109234 "Regulation of Apoptosis, Rattus norvegicus" xref: Reactome:REACT_109339 "Regulation of Apoptosis, Sus scrofa" xref: Reactome:REACT_13648 "Regulation of Apoptosis, Homo sapiens" xref: Reactome:REACT_29911 "Regulation of Apoptosis, Danio rerio" xref: Reactome:REACT_30641 "Regulation of Apoptosis, Drosophila melanogaster" xref: Reactome:REACT_79698 "Regulation of Apoptosis, Taeniopygia guttata" xref: Reactome:REACT_85908 "Regulation of Apoptosis, Bos taurus" xref: Reactome:REACT_86575 "Regulation of Apoptosis, Xenopus tropicalis" xref: Reactome:REACT_95946 "Regulation of Apoptosis, Caenorhabditis elegans" xref: Reactome:REACT_96201 "Regulation of Apoptosis, Canis familiaris" xref: Reactome:REACT_99944 "Regulation of Apoptosis, Gallus gallus" is_a: GO:0043067 ! regulation of programmed cell death intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006915 ! apoptotic process relationship: regulates GO:0006915 ! apoptotic process [Term] id: GO:0043043 name: peptide biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide." [CHEBI:16670, GOC:dph, GOC:jl] synonym: "peptide anabolism" EXACT [] synonym: "peptide biosynthesis" EXACT [] synonym: "peptide formation" EXACT [] synonym: "peptide synthesis" EXACT [] is_a: GO:0006518 ! peptide metabolic process is_a: GO:0043604 ! amide biosynthetic process is_a: GO:1901566 ! organonitrogen compound biosynthetic process [Term] id: GO:0043065 name: positive regulation of apoptotic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process." [GOC:jl, GOC:mtg_apoptosis] comment: This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is positively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. subset: goslim_chembl synonym: "activation of apoptosis" NARROW [] synonym: "positive regulation of apoptosis" NARROW [] synonym: "pro-apoptosis" RELATED [] synonym: "stimulation of apoptosis" NARROW [] synonym: "up regulation of apoptosis" EXACT [] synonym: "up-regulation of apoptosis" EXACT [] synonym: "upregulation of apoptosis" EXACT [] is_a: GO:0042981 ! regulation of apoptotic process is_a: GO:0043068 ! positive regulation of programmed cell death intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006915 ! apoptotic process relationship: positively_regulates GO:0006915 ! apoptotic process [Term] id: GO:0043066 name: negative regulation of apoptotic process namespace: biological_process alt_id: GO:0006916 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process." [GOC:jl, GOC:mtg_apoptosis] comment: This term should only be used when it is not possible to determine which phase or subtype of the apoptotic process is negatively regulated by a gene product. Whenever detailed information is available, the more granular children terms should be used. synonym: "anti-apoptosis" EXACT [] synonym: "apoptosis inhibitor activity" RELATED [] synonym: "down regulation of apoptosis" EXACT [] synonym: "down-regulation of apoptosis" EXACT [] synonym: "downregulation of apoptosis" EXACT [] synonym: "inhibition of apoptosis" NARROW [] synonym: "negative regulation of apoptosis" NARROW [] synonym: "pro-survival" RELATED [] xref: Reactome:REACT_13537 "p75NTR signals via NF-kB, Homo sapiens" xref: Reactome:REACT_29981 "p75NTR signals via NF-kB, Canis familiaris" xref: Reactome:REACT_77563 "p75NTR signals via NF-kB, Sus scrofa" xref: Reactome:REACT_81263 "p75NTR signals via NF-kB, Taeniopygia guttata" xref: Reactome:REACT_83278 "p75NTR signals via NF-kB, Drosophila melanogaster" xref: Reactome:REACT_84567 "p75NTR signals via NF-kB, Gallus gallus" xref: Reactome:REACT_91585 "p75NTR signals via NF-kB, Danio rerio" xref: Reactome:REACT_93662 "p75NTR signals via NF-kB, Rattus norvegicus" xref: Reactome:REACT_95215 "p75NTR signals via NF-kB, Mus musculus" xref: Reactome:REACT_95867 "p75NTR signals via NF-kB, Xenopus tropicalis" xref: Reactome:REACT_98500 "p75NTR signals via NF-kB, Bos taurus" is_a: GO:0042981 ! regulation of apoptotic process is_a: GO:0043069 ! negative regulation of programmed cell death intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006915 ! apoptotic process relationship: negatively_regulates GO:0006915 ! apoptotic process [Term] id: GO:0043067 name: regulation of programmed cell death namespace: biological_process alt_id: GO:0043070 def: "Any process that modulates the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl] synonym: "regulation of non-apoptotic programmed cell death" NARROW [] is_a: GO:0010941 ! regulation of cell death intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0012501 ! programmed cell death relationship: regulates GO:0012501 ! programmed cell death [Term] id: GO:0043068 name: positive regulation of programmed cell death namespace: biological_process alt_id: GO:0043071 def: "Any process that activates or increases the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl] synonym: "activation of programmed cell death" NARROW [] synonym: "positive regulation of non-apoptotic programmed cell death" NARROW [] synonym: "stimulation of programmed cell death" NARROW [] synonym: "up regulation of programmed cell death" EXACT [] synonym: "up-regulation of programmed cell death" EXACT [] synonym: "upregulation of programmed cell death" EXACT [] is_a: GO:0010942 ! positive regulation of cell death is_a: GO:0043067 ! regulation of programmed cell death intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0012501 ! programmed cell death relationship: positively_regulates GO:0012501 ! programmed cell death [Term] id: GO:0043069 name: negative regulation of programmed cell death namespace: biological_process alt_id: GO:0043072 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of programmed cell death, cell death resulting from activation of endogenous cellular processes." [GOC:jl] synonym: "down regulation of programmed cell death" EXACT [] synonym: "down-regulation of programmed cell death" EXACT [] synonym: "downregulation of programmed cell death" EXACT [] synonym: "inhibition of programmed cell death" NARROW [] synonym: "negative regulation of non-apoptotic programmed cell death" NARROW [] is_a: GO:0043067 ! regulation of programmed cell death is_a: GO:0060548 ! negative regulation of cell death intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0012501 ! programmed cell death relationship: negatively_regulates GO:0012501 ! programmed cell death [Term] id: GO:0043085 name: positive regulation of catalytic activity namespace: biological_process alt_id: GO:0048554 def: "Any process that activates or increases the activity of an enzyme." [GOC:ebc, GOC:jl, GOC:tb, GOC:vw] subset: goslim_chembl synonym: "activation of enzyme activity" NARROW [] synonym: "activation of metalloenzyme activity" NARROW [] synonym: "positive regulation of enzyme activity" EXACT [GOC:tb] synonym: "positive regulation of metalloenzyme activity" NARROW [] synonym: "stimulation of enzyme activity" NARROW [] synonym: "stimulation of metalloenzyme activity" NARROW [] synonym: "up regulation of enzyme activity" EXACT [] synonym: "up regulation of metalloenzyme activity" NARROW [] synonym: "up-regulation of enzyme activity" EXACT [] synonym: "up-regulation of metalloenzyme activity" NARROW [] synonym: "upregulation of enzyme activity" EXACT [] synonym: "upregulation of metalloenzyme activity" NARROW [] is_a: GO:0044093 ! positive regulation of molecular function is_a: GO:0050790 ! regulation of catalytic activity intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0003824 ! catalytic activity relationship: positively_regulates GO:0003824 ! catalytic activity [Term] id: GO:0043086 name: negative regulation of catalytic activity namespace: biological_process alt_id: GO:0048553 def: "Any process that stops or reduces the activity of an enzyme." [GOC:ebc, GOC:jl, GOC:tb, GOC:vw] synonym: "down regulation of enzyme activity" EXACT [] synonym: "down regulation of metalloenzyme activity" NARROW [] synonym: "down-regulation of enzyme activity" EXACT [] synonym: "down-regulation of metalloenzyme activity" EXACT [] synonym: "downregulation of enzyme activity" EXACT [] synonym: "downregulation of metalloenzyme activity" NARROW [] synonym: "inhibition of enzyme activity" NARROW [] synonym: "inhibition of metalloenzyme activity" NARROW [] synonym: "negative regulation of enzyme activity" EXACT [GOC:tb] synonym: "negative regulation of metalloenzyme activity" NARROW [] is_a: GO:0044092 ! negative regulation of molecular function is_a: GO:0050790 ! regulation of catalytic activity intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0003824 ! catalytic activity relationship: negatively_regulates GO:0003824 ! catalytic activity [Term] id: GO:0043143 name: regulation of translation by machinery localization namespace: biological_process def: "Any process in which proteins and protein complexes involved in translation are transported to, or maintained in, a specific location." [GOC:jl] synonym: "establishment and maintenance of translational machinery localization" EXACT [] synonym: "establishment and maintenance of translational protein localization" EXACT [] synonym: "regulation of translation by machinery localisation" EXACT [GOC:mah] synonym: "translational machinery localization" EXACT [GOC:dph, GOC:tb] synonym: "translational protein localization" EXACT [] is_a: GO:0006417 ! regulation of translation is_a: GO:0034613 ! cellular protein localization intersection_of: GO:0008104 ! protein localization intersection_of: part_of GO:0006412 ! translation relationship: part_of GO:0006412 ! translation [Term] id: GO:0043170 name: macromolecule metabolic process namespace: biological_process alt_id: GO:0043283 alt_id: GO:0044259 def: "The chemical reactions and pathways involving macromolecules, any 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." [CHEBI:33694, GOC:mah] subset: goslim_pir synonym: "biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "macromolecule metabolism" EXACT [] synonym: "multicellular organismal macromolecule metabolic process" NARROW [] synonym: "organismal macromolecule metabolism" EXACT [] is_a: GO:0071704 ! organic substance metabolic process [Term] id: GO:0043234 name: protein complex def: "A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical." [] is_a: BFO:0000040 ! material entity relationship: has_part PR:000000001 ! protein property_value: IAO:0000111 "protein complex" xsd:string property_value: IAO:0000112 "A ribosome is a protein complex" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043242 name: negative regulation of protein complex disassembly namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components." [GOC:jl] synonym: "down regulation of protein complex disassembly" EXACT [] synonym: "down-regulation of protein complex disassembly" EXACT [] synonym: "downregulation of protein complex disassembly" EXACT [] synonym: "inhibition of protein complex disassembly" NARROW [] is_a: GO:0043244 ! regulation of protein complex disassembly is_a: GO:0051129 ! negative regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0032984 ! protein-containing complex disassembly relationship: negatively_regulates GO:0032984 ! protein-containing complex disassembly [Term] id: GO:0043243 name: positive regulation of protein complex disassembly namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components." [GOC:jl] synonym: "activation of protein complex disassembly" NARROW [] synonym: "stimulation of protein complex disassembly" NARROW [] synonym: "up regulation of protein complex disassembly" EXACT [] synonym: "up-regulation of protein complex disassembly" EXACT [] synonym: "upregulation of protein complex disassembly" EXACT [] is_a: GO:0043244 ! regulation of protein complex disassembly is_a: GO:0051130 ! positive regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0032984 ! protein-containing complex disassembly relationship: positively_regulates GO:0032984 ! protein-containing complex disassembly [Term] id: GO:0043244 name: regulation of protein complex disassembly namespace: biological_process def: "Any process that modulates the frequency, rate or extent of protein complex disassembly, the disaggregation of a protein complex into its constituent components." [GOC:jl] is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0032984 ! protein-containing complex disassembly relationship: regulates GO:0032984 ! protein-containing complex disassembly [Term] id: GO:0043254 name: regulation of protein complex assembly namespace: biological_process def: "Any process that modulates the frequency, rate or extent of protein complex assembly." [GOC:jl] is_a: GO:0044087 ! regulation of cellular component biogenesis is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0065003 ! protein-containing complex assembly relationship: regulates GO:0065003 ! protein-containing complex assembly [Term] id: GO:0043269 name: regulation of ion transport namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl] is_a: GO:0051049 ! regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006811 ! ion transport relationship: regulates GO:0006811 ! ion transport [Term] id: GO:0043270 name: positive regulation of ion transport namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl] synonym: "activation of ion transport" NARROW [] synonym: "stimulation of ion transport" NARROW [] synonym: "up regulation of ion transport" EXACT [] synonym: "up-regulation of ion transport" EXACT [] synonym: "upregulation of ion transport" EXACT [] is_a: GO:0043269 ! regulation of ion transport is_a: GO:0051050 ! positive regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006811 ! ion transport relationship: positively_regulates GO:0006811 ! ion transport [Term] id: GO:0043271 name: negative regulation of ion transport namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl] synonym: "down regulation of ion transport" EXACT [] synonym: "down-regulation of ion transport" EXACT [] synonym: "downregulation of ion transport" EXACT [] synonym: "inhibition of ion transport" NARROW [] is_a: GO:0043269 ! regulation of ion transport is_a: GO:0051051 ! negative regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006811 ! ion transport relationship: negatively_regulates GO:0006811 ! ion transport [Term] id: GO:0043388 name: positive regulation of DNA binding namespace: biological_process def: "Any process that increases the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC:dph, GOC:jl, GOC:tb] synonym: "activation of DNA binding" NARROW [] synonym: "stimulation of DNA binding" NARROW [] synonym: "up regulation of DNA binding" EXACT [] synonym: "up-regulation of DNA binding" EXACT [] synonym: "upregulation of DNA binding" EXACT [] is_a: GO:0051099 ! positive regulation of binding is_a: GO:0051101 ! regulation of DNA binding intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0003677 ! DNA binding relationship: positively_regulates GO:0003677 ! DNA binding [Term] id: GO:0043392 name: negative regulation of DNA binding namespace: biological_process def: "Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC:dph, GOC:jl, GOC:tb] synonym: "down regulation of DNA binding" EXACT [] synonym: "down-regulation of DNA binding" EXACT [] synonym: "downregulation of DNA binding" EXACT [] synonym: "inhibition of DNA binding" NARROW [] is_a: GO:0051100 ! negative regulation of binding is_a: GO:0051101 ! regulation of DNA binding intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0003677 ! DNA binding relationship: negatively_regulates GO:0003677 ! DNA binding [Term] id: GO:0043412 name: macromolecule modification namespace: biological_process def: "The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties." [GOC:go_curators] subset: goslim_pir is_a: GO:0043170 ! macromolecule metabolic process [Term] id: GO:0043414 name: macromolecule methylation namespace: biological_process def: "The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule." [GOC:go_curators] is_a: GO:0032259 ! methylation is_a: GO:0043412 ! macromolecule modification is_a: GO:0044260 ! cellular macromolecule metabolic process [Term] id: GO:0043565 name: sequence-specific DNA binding namespace: molecular_function def: "Interacting selectively and non-covalently with 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." [GOC:jl] synonym: "sequence specific DNA binding" EXACT [] is_a: GO:0003677 ! DNA binding is_a: OBI:0001588 ! binding property_value: IAO:0000111 "sequence-specific DNA binding" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0043603 name: cellular amide metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group, as carried out by individual cells." [CHEBI:32988] subset: goslim_pir synonym: "amide metabolism" EXACT [] is_a: GO:0034641 ! cellular nitrogen compound metabolic process [Term] id: GO:0043604 name: amide biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of an amide, any derivative of an oxoacid in which an acidic hydroxy group has been replaced by an amino or substituted amino group." [CHEBI:32988] is_a: GO:0043603 ! cellular amide metabolic process is_a: GO:0044271 ! cellular nitrogen compound biosynthetic process [Term] id: GO:0043624 name: cellular protein complex disassembly namespace: biological_process def: "The disaggregation of a protein complex into its constituent components, occurring at the level of an individual cell. Protein complexes may have other associated non-protein prosthetic groups, such as nucleic acids, metal ions or carbohydrate groups." [GOC:jl] is_a: GO:0032984 ! protein-containing complex disassembly [Term] id: GO:0043900 name: regulation of multi-organism process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species." [GOC:jl] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0051704 ! multi-organism process relationship: regulates GO:0051704 ! multi-organism process [Term] id: GO:0043901 name: negative regulation of multi-organism process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species." [GOC:jl] is_a: GO:0043900 ! regulation of multi-organism process is_a: GO:0048519 ! negative regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0051704 ! multi-organism process relationship: negatively_regulates GO:0051704 ! multi-organism process [Term] id: GO:0043902 name: positive regulation of multi-organism process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of a multi-organism process, a process in which an organism has an effect on another organism of the same or different species." [GOC:jl] is_a: GO:0043900 ! regulation of multi-organism process is_a: GO:0048518 ! positive regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0051704 ! multi-organism process relationship: positively_regulates GO:0051704 ! multi-organism process [Term] id: GO:0043933 name: protein-containing complex subunit organization namespace: biological_process alt_id: GO:0034600 alt_id: GO:0034621 alt_id: GO:0071822 def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein complex." [GOC:mah] synonym: "cellular macromolecular complex organization" RELATED [] synonym: "cellular macromolecular complex subunit organisation" RELATED [GOC:curators] synonym: "cellular macromolecular complex subunit organization" RELATED [] synonym: "macromolecular complex organization" RELATED [] synonym: "macromolecular complex subunit organisation" RELATED [GOC:curators] synonym: "macromolecular complex subunit organization" RELATED [] synonym: "protein complex subunit organisation" EXACT [GOC:mah] synonym: "protein complex subunit organization" EXACT [] is_a: GO:0016043 ! cellular component organization created_by: midori creation_date: 2010-09-08T10:01:42Z [Term] id: GO:0044030 name: regulation of DNA methylation namespace: biological_process 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." [GOC:jl] is_a: GO:0040030 ! regulation of molecular function, epigenetic is_a: GO:0051052 ! regulation of DNA metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006306 ! DNA methylation relationship: regulates GO:0006306 ! DNA methylation property_value: IAO:0000111 "regulation of DNA methylation" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0044070 name: regulation of anion transport namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of anions, atoms or small molecules with a net negative charge into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl] is_a: GO:0043269 ! regulation of ion transport intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006820 ! anion transport relationship: regulates GO:0006820 ! anion transport [Term] id: GO:0044085 name: cellular component biogenesis namespace: biological_process alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] subset: goslim_pir synonym: "cellular component biogenesis at cellular level" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis [Term] id: GO:0044087 name: regulation of cellular component biogenesis namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component." [GOC:jl] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0044085 ! cellular component biogenesis relationship: regulates GO:0044085 ! cellular component biogenesis [Term] id: GO:0044089 name: positive regulation of cellular component biogenesis namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cellular component biogenesis, a process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component." [GOC:jl] is_a: GO:0044087 ! regulation of cellular component biogenesis is_a: GO:0048518 ! positive regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0044085 ! cellular component biogenesis relationship: positively_regulates GO:0044085 ! cellular component biogenesis [Term] id: GO:0044092 name: negative regulation of molecular function namespace: biological_process def: "Any process that stops or reduces the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GO:jl] is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0003674 ! GO:molecular_function relationship: negatively_regulates GO:0003674 ! GO:molecular_function created_by: jane creation_date: 2009-04-21T04:07:27Z [Term] id: GO:0044093 name: positive regulation of molecular function namespace: biological_process def: "Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GO:jl] is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0003674 ! GO:molecular_function relationship: positively_regulates GO:0003674 ! GO:molecular_function created_by: jane creation_date: 2009-04-21T04:11:06Z [Term] id: GO:0044212 name: transcription regulatory region DNA binding namespace: molecular_function alt_id: GO:0000975 def: "Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors." [GOC:jl, GOC:txnOH, SO:0005836] comment: The word "promoter" is used variously in the literature to describe the core promoter specifically or the entire proximal regulatory region (excluding any distal enhancers) including both the core promoter and the upstream region where activating transcription factors such as Gal4 in S. cerevisiae or catabolite activator protein (CAP) in E. coli bind. To minimize ambiguity in the use of the word "promoter" in GO, we have chosen the phrase "transcription regulatory region" in order to refer to all of the regulatory regions. Regulatory regions in the DNA which control initiation may include the "core promoter" where the basal transcription machinery binds, the "core promoter proximal region" where regulatory factors other than the basal machinery bind, and "enhancer" regions which are typically more distal from the core promoter. There are also additional regulatory regions, in both the DNA and the RNA transcript, which regulate elongation or termination of transcription. ANNOTATION NOTE: Regarding annotation to "transcription regulatory region DNA binding" (GO:0044212) and any of its is_a children, note that annotation to these terms specifies DNA binding only without any statement about transcription factor activity. To make an annotation about a function of transcription factor activity, consider "sequence-specific DNA-binding transcription factor activity" (GO:0003700) or its is_a children which have has_part relationships to the appropriate kind of "transcription regulatory region DNA binding". synonym: "regulatory region DNA binding" BROAD [] is_a: GO:0001067 ! regulatory region nucleic acid binding is_a: GO:0003677 ! DNA binding created_by: kchris creation_date: 2009-11-04T12:58:25Z [Term] id: GO:0044237 name: cellular metabolic process namespace: biological_process def: "The chemical reactions and pathways by which individual cells transform chemical substances." [GOC:go_curators] synonym: "cellular metabolism" EXACT [] synonym: "intermediary metabolism" RELATED [GOC:mah] is_a: GO:0008152 ! metabolic process is_a: GO:0009987 ! cellular process [Term] id: GO:0044238 name: primary metabolic process namespace: biological_process def: "The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [GOC:go_curators, http://www.metacyc.org] subset: goslim_pir synonym: "primary metabolism" EXACT [] is_a: GO:0008152 ! metabolic process [Term] id: GO:0044248 name: cellular catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of substances, carried out by individual cells." [GOC:jl] synonym: "cellular breakdown" EXACT [] synonym: "cellular catabolism" EXACT [] synonym: "cellular degradation" EXACT [] is_a: GO:0009056 ! catabolic process is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0044249 name: cellular biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of substances, carried out by individual cells." [GOC:jl] synonym: "cellular anabolism" EXACT [] synonym: "cellular biosynthesis" EXACT [] synonym: "cellular formation" EXACT [] synonym: "cellular synthesis" EXACT [] is_a: GO:0009058 ! biosynthetic process is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0044260 name: cellular macromolecule metabolic process namespace: biological_process alt_id: GO:0034960 def: "The chemical reactions and pathways involving macromolecules, any 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, as carried out by individual cells." [CHEBI:33694, GOC:mah] synonym: "cellular biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "cellular macromolecule metabolism" EXACT [] is_a: GO:0043170 ! macromolecule metabolic process is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0044265 name: cellular macromolecule catabolic process namespace: biological_process alt_id: GO:0034962 def: "The chemical reactions and pathways resulting in the breakdown of a macromolecule, any large molecule including proteins, nucleic acids and carbohydrates, as carried out by individual cells." [CHEBI:33694, GOC:jl] synonym: "cellular biopolymer catabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "cellular macromolecule breakdown" EXACT [] synonym: "cellular macromolecule catabolism" EXACT [] synonym: "cellular macromolecule degradation" EXACT [] is_a: GO:0009057 ! macromolecule catabolic process is_a: GO:0044248 ! cellular catabolic process is_a: GO:0044260 ! cellular macromolecule metabolic process [Term] id: GO:0044267 name: cellular protein metabolic process namespace: biological_process def: "The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification." [GOC:jl] synonym: "cellular protein metabolism" EXACT [] xref: Reactome:REACT_101554 "Metabolism of proteins, Gallus gallus" xref: Reactome:REACT_102155 "Metabolism of proteins, Arabidopsis thaliana" xref: Reactome:REACT_105825 "Metabolism of proteins, Dictyostelium discoideum" xref: Reactome:REACT_106151 "Metabolism of proteins, Xenopus tropicalis" xref: Reactome:REACT_108005 "Metabolism of proteins, Bos taurus" xref: Reactome:REACT_109022 "Metabolism of proteins, Schizosaccharomyces pombe" xref: Reactome:REACT_17015 "Metabolism of proteins, Homo sapiens" xref: Reactome:REACT_32904 "Metabolism of proteins, Canis familiaris" xref: Reactome:REACT_34473 "Metabolism of proteins, Taeniopygia guttata" xref: Reactome:REACT_80561 "Metabolism of proteins, Escherichia coli" xref: Reactome:REACT_81994 "Metabolism of proteins, Sus scrofa" xref: Reactome:REACT_82523 "Metabolism of proteins, Danio rerio" xref: Reactome:REACT_85873 "Metabolism of proteins, Saccharomyces cerevisiae" xref: Reactome:REACT_86658 "Metabolism of proteins, Drosophila melanogaster" xref: Reactome:REACT_89852 "Metabolism of proteins, Rattus norvegicus" xref: Reactome:REACT_91052 "Metabolism of proteins, Caenorhabditis elegans" xref: Reactome:REACT_93132 "Metabolism of proteins, Mus musculus" xref: Reactome:REACT_96466 "Metabolism of proteins, Plasmodium falciparum" xref: Reactome:REACT_99179 "Metabolism of proteins, Oryza sativa" is_a: GO:0019538 ! protein metabolic process is_a: GO:0044260 ! cellular macromolecule metabolic process [Term] id: GO:0044270 name: cellular nitrogen compound catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of organic and inorganic nitrogenous compounds." [GOC:jl, ISBN:0198506732] synonym: "nitrogen compound breakdown" BROAD [] synonym: "nitrogen compound catabolism" BROAD [] synonym: "nitrogen compound degradation" BROAD [] is_a: GO:0034641 ! cellular nitrogen compound metabolic process is_a: GO:0044248 ! cellular catabolic process [Term] id: GO:0044271 name: cellular nitrogen compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of organic and inorganic nitrogenous compounds." [GOC:jl, ISBN:0198506732] synonym: "nitrogen compound anabolism" BROAD [] synonym: "nitrogen compound biosynthesis" BROAD [] synonym: "nitrogen compound formation" BROAD [] synonym: "nitrogen compound synthesis" BROAD [] is_a: GO:0034641 ! cellular nitrogen compound metabolic process is_a: GO:0044249 ! cellular biosynthetic process [Term] id: GO:0044424 name: intracellular part namespace: cellular_component def: "Any constituent part of the living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm." [GOC:jl] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: goantislim_grouping subset: gocheck_do_not_annotate is_a: GO:0044464 ! cell part intersection_of: GO:0005575 ! cellular_component intersection_of: part_of GO:0005622 ! intracellular relationship: part_of GO:0005622 ! intracellular [Term] id: GO:0044464 name: cell part namespace: cellular_component def: "Any constituent part of a cell, the basic structural and functional unit of all organisms." [GOC:jl] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: goantislim_grouping subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cellular subcomponent" EXACT [NIF_Subcellular:sao628508602] synonym: "protoplast" RELATED [GOC:mah] xref: NIF_Subcellular:sao628508602 is_a: GO:0005575 ! cellular_component intersection_of: GO:0005575 ! cellular_component intersection_of: part_of GO:0005623 ! cell relationship: part_of GO:0005623 ! cell [Term] id: GO:0044728 name: DNA methylation or demethylation namespace: biological_process def: "The process of adding or removing a methyl group from one or more nucleotides within an DNA molecule." [GOC:jl] synonym: "changes in DNA methylation" RELATED [] is_a: GO:0006304 ! DNA modification created_by: janelomax creation_date: 2012-10-24T14:49:41Z [Term] id: GO:0044764 name: multi-organism cellular process namespace: biological_process def: "Any process that is carried out at the cellular level which involves another organism of the same or different species." [GOC:jl] is_a: GO:0009987 ! cellular process is_a: GO:0051704 ! multi-organism process created_by: janelomax creation_date: 2012-12-11T17:00:50Z [Term] id: GO:0045182 name: translation regulator activity namespace: molecular_function def: "Any molecular function involved in the initiation, activation, perpetuation, repression or termination of polypeptide synthesis at the ribosome." [GOC:ai] subset: goslim_aspergillus subset: goslim_candida subset: goslim_pir subset: goslim_plant synonym: "translation factor activity" EXACT [] is_a: GO:0003674 ! GO:molecular_function intersection_of: GO:0003674 ! GO:molecular_function intersection_of: part_of GO:0006417 ! regulation of translation relationship: part_of GO:0006417 ! regulation of translation [Term] id: GO:0045184 name: establishment of protein localization namespace: biological_process def: "The directed movement of a protein to a specific location." [GOC:bf] synonym: "establishment of protein localisation" EXACT [GOC:mah] synonym: "protein positioning" EXACT [] synonym: "protein recruitment" EXACT [] is_a: GO:0008104 ! protein localization is_a: GO:0051234 ! establishment of localization [Term] id: GO:0045727 name: positive regulation of translation namespace: biological_process alt_id: GO:0045946 def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA." [GOC:dph, GOC:go_curators, GOC:tb] synonym: "activation of protein biosynthetic process" NARROW [] synonym: "positive regulation of protein anabolism" EXACT [] synonym: "positive regulation of protein biosynthesis" EXACT [] synonym: "positive regulation of protein biosynthetic process" EXACT [GOC:tb] synonym: "positive regulation of protein formation" EXACT [] synonym: "positive regulation of protein synthesis" EXACT [] synonym: "stimulation of protein biosynthetic process" NARROW [] synonym: "up regulation of protein biosynthetic process" EXACT [] synonym: "up-regulation of protein biosynthetic process" EXACT [] synonym: "upregulation of protein biosynthetic process" EXACT [] xref: Reactome:REACT_6236 "Activated DTOR phosphorylates DS6K, Drosophila melanogaster" is_a: GO:0006417 ! regulation of translation is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process is_a: GO:0010628 ! positive regulation of gene expression is_a: GO:0031328 ! positive regulation of cellular biosynthetic process is_a: GO:0032270 ! positive regulation of cellular protein metabolic process is_a: GO:0034250 ! positive regulation of cellular amide metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006412 ! translation relationship: positively_regulates GO:0006412 ! translation [Term] id: GO:0045740 name: positive regulation of DNA replication namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of DNA replication." [GOC:go_curators] synonym: "activation of DNA replication" NARROW [] synonym: "stimulation of DNA replication" NARROW [] synonym: "up regulation of DNA replication" EXACT [] synonym: "up-regulation of DNA replication" EXACT [] synonym: "upregulation of DNA replication" EXACT [] is_a: GO:0006275 ! regulation of DNA replication is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process is_a: GO:0031328 ! positive regulation of cellular biosynthetic process is_a: GO:0051054 ! positive regulation of DNA metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006260 ! DNA replication relationship: positively_regulates GO:0006260 ! DNA replication [Term] id: GO:0045759 name: negative regulation of action potential namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." [GOC:go_curators] synonym: "down regulation of action potential" EXACT [] synonym: "down-regulation of action potential" EXACT [] synonym: "downregulation of action potential" EXACT [] synonym: "inhibition of action potential" NARROW [] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0098900 ! regulation of action potential intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0001508 ! action potential relationship: negatively_regulates GO:0001508 ! action potential [Term] id: GO:0045760 name: positive regulation of action potential namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." [GOC:go_curators] synonym: "activation of action potential" NARROW [] synonym: "stimulation of action potential" NARROW [] synonym: "up regulation of action potential" EXACT [] synonym: "up-regulation of action potential" EXACT [] synonym: "upregulation of action potential" EXACT [] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0098900 ! regulation of action potential intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0001508 ! action potential relationship: positively_regulates GO:0001508 ! action potential [Term] id: GO:0045892 name: negative regulation of transcription, DNA-templated namespace: biological_process alt_id: GO:0016481 alt_id: GO:0032582 alt_id: GO:0061021 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH] synonym: "down regulation of gene-specific transcription" RELATED [] synonym: "down regulation of transcription, DNA-dependent" EXACT [] synonym: "down-regulation of gene-specific transcription" RELATED [] synonym: "down-regulation of transcription, DNA-dependent" EXACT [] synonym: "downregulation of gene-specific transcription" RELATED [] synonym: "downregulation of transcription, DNA-dependent" EXACT [] synonym: "inhibition of gene-specific transcription" RELATED [] synonym: "inhibition of transcription, DNA-dependent" NARROW [] synonym: "negative regulation of cellular transcription, DNA-dependent" EXACT [] synonym: "negative regulation of gene-specific transcription" RELATED [] synonym: "negative regulation of transcription, DNA-dependent" EXACT [GOC:txnOH] synonym: "transcription repressor activity" RELATED [] is_a: GO:0006355 ! regulation of transcription, DNA-templated is_a: GO:0010629 ! negative regulation of gene expression is_a: GO:1903507 ! negative regulation of nucleic acid-templated transcription is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006351 ! transcription, DNA-templated relationship: negatively_regulates GO:0006351 ! transcription, DNA-templated [Term] id: GO:0045893 name: positive regulation of transcription, DNA-templated namespace: biological_process alt_id: GO:0043193 alt_id: GO:0045941 alt_id: GO:0061020 def: "Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription." [GOC:go_curators, GOC:txnOH] synonym: "activation of gene-specific transcription" RELATED [] synonym: "activation of transcription, DNA-dependent" NARROW [] synonym: "positive regulation of cellular transcription, DNA-dependent" EXACT [] synonym: "positive regulation of gene-specific transcription" RELATED [] synonym: "positive regulation of transcription, DNA-dependent" EXACT [GOC:txnOH] synonym: "stimulation of gene-specific transcription" NARROW [] synonym: "stimulation of transcription, DNA-dependent" NARROW [] synonym: "transcription activator activity" RELATED [] synonym: "up regulation of gene-specific transcription" RELATED [] synonym: "up regulation of transcription, DNA-dependent" EXACT [] synonym: "up-regulation of gene-specific transcription" RELATED [] synonym: "up-regulation of transcription, DNA-dependent" EXACT [] synonym: "upregulation of gene-specific transcription" RELATED [] synonym: "upregulation of transcription, DNA-dependent" EXACT [] is_a: GO:0006355 ! regulation of transcription, DNA-templated is_a: GO:0010628 ! positive regulation of gene expression is_a: GO:1903508 ! positive regulation of nucleic acid-templated transcription intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006351 ! transcription, DNA-templated relationship: positively_regulates GO:0006351 ! transcription, DNA-templated [Term] id: GO:0045900 name: negative regulation of translational elongation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation." [GOC:go_curators] synonym: "down regulation of translational elongation" EXACT [] synonym: "down-regulation of translational elongation" EXACT [] synonym: "downregulation of translational elongation" EXACT [] synonym: "inhibition of translational elongation" NARROW [] is_a: GO:0006448 ! regulation of translational elongation is_a: GO:0017148 ! negative regulation of translation intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006414 ! translational elongation relationship: negatively_regulates GO:0006414 ! translational elongation [Term] id: GO:0045901 name: positive regulation of translational elongation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translational elongation." [GOC:go_curators] synonym: "activation of translational elongation" NARROW [] synonym: "stimulation of translational elongation" NARROW [] synonym: "up regulation of translational elongation" EXACT [] synonym: "up-regulation of translational elongation" EXACT [] synonym: "upregulation of translational elongation" EXACT [] is_a: GO:0006448 ! regulation of translational elongation is_a: GO:0045727 ! positive regulation of translation intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006414 ! translational elongation relationship: positively_regulates GO:0006414 ! translational elongation [Term] id: GO:0045904 name: negative regulation of translational termination namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translational termination." [GOC:go_curators] synonym: "down regulation of translational termination" EXACT [] synonym: "down-regulation of translational termination" EXACT [] synonym: "downregulation of translational termination" EXACT [] synonym: "inhibition of translational termination" NARROW [] is_a: GO:0006449 ! regulation of translational termination is_a: GO:0017148 ! negative regulation of translation is_a: GO:0043242 ! negative regulation of protein complex disassembly intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006415 ! translational termination relationship: negatively_regulates GO:0006415 ! translational termination [Term] id: GO:0045905 name: positive regulation of translational termination namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translational termination." [GOC:go_curators] synonym: "activation of translational termination" NARROW [] synonym: "stimulation of translational termination" NARROW [] synonym: "up regulation of translational termination" EXACT [] synonym: "up-regulation of translational termination" EXACT [] synonym: "upregulation of translational termination" EXACT [] is_a: GO:0006449 ! regulation of translational termination is_a: GO:0043243 ! positive regulation of protein complex disassembly is_a: GO:0045727 ! positive regulation of translation intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006415 ! translational termination relationship: positively_regulates GO:0006415 ! translational termination [Term] id: GO:0045926 name: negative regulation of growth namespace: biological_process def: "Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism." [GOC:go_curators] synonym: "down regulation of growth" EXACT [] synonym: "down-regulation of growth" EXACT [] synonym: "downregulation of growth" EXACT [] synonym: "inhibition of growth" NARROW [] is_a: GO:0040008 ! regulation of growth is_a: GO:0048519 ! negative regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0040007 ! growth relationship: negatively_regulates GO:0040007 ! growth [Term] id: GO:0045927 name: positive regulation of growth namespace: biological_process def: "Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism." [GOC:go_curators] synonym: "activation of growth" NARROW [] synonym: "stimulation of growth" NARROW [] synonym: "up regulation of growth" EXACT [] synonym: "up-regulation of growth" EXACT [] synonym: "upregulation of growth" EXACT [] is_a: GO:0040008 ! regulation of growth is_a: GO:0048518 ! positive regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0040007 ! growth relationship: positively_regulates GO:0040007 ! growth [Term] id: GO:0045934 name: negative regulation of nucleobase-containing compound metabolic process namespace: biological_process def: "Any cellular process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] synonym: "down regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "down-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "downregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "inhibition of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" NARROW [] synonym: "negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] synonym: "negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process is_a: GO:0031324 ! negative regulation of cellular metabolic process is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006139 ! nucleobase-containing compound metabolic process relationship: negatively_regulates GO:0006139 ! nucleobase-containing compound metabolic process [Term] id: GO:0045935 name: positive regulation of nucleobase-containing compound metabolic process namespace: biological_process def: "Any cellular process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nucleobases, nucleosides, nucleotides and nucleic acids." [GOC:go_curators] synonym: "activation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" NARROW [] synonym: "positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" RELATED [GOC:dph, GOC:tb] synonym: "positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism" EXACT [] synonym: "stimulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" NARROW [] synonym: "up regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "up-regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] synonym: "upregulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process" EXACT [] is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process is_a: GO:0031325 ! positive regulation of cellular metabolic process is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006139 ! nucleobase-containing compound metabolic process relationship: positively_regulates GO:0006139 ! nucleobase-containing compound metabolic process [Term] id: GO:0045947 name: negative regulation of translational initiation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation." [GOC:go_curators] synonym: "down regulation of translational initiation" EXACT [] synonym: "down-regulation of translational initiation" EXACT [] synonym: "downregulation of translational initiation" EXACT [] synonym: "inhibition of translational initiation" NARROW [] is_a: GO:0006446 ! regulation of translational initiation is_a: GO:0017148 ! negative regulation of translation intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006413 ! translational initiation relationship: negatively_regulates GO:0006413 ! translational initiation [Term] id: GO:0045948 name: positive regulation of translational initiation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of translational initiation." [GOC:go_curators] synonym: "activation of translational initiation" NARROW [] synonym: "stimulation of translational initiation" NARROW [] synonym: "up regulation of translational initiation" EXACT [] synonym: "up-regulation of translational initiation" EXACT [] synonym: "upregulation of translational initiation" EXACT [] is_a: GO:0006446 ! regulation of translational initiation is_a: GO:0045727 ! positive regulation of translation intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006413 ! translational initiation relationship: positively_regulates GO:0006413 ! translational initiation [Term] id: GO:0045974 name: regulation of translation, ncRNA-mediated namespace: biological_process def: "Any process, mediated by small non-coding RNAs, that modulates the frequency, rate or extent that mRNAs are effectively translated into protein." [GOC:dph, GOC:go_curators, GOC:tb] is_a: GO:0006417 ! regulation of translation [Term] id: GO:0046483 name: heterocycle metabolic process namespace: biological_process def: "The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [CHEBI:5686, ISBN:0198506732] subset: goslim_pir synonym: "heterocycle metabolism" EXACT [] is_a: GO:0044237 ! cellular metabolic process [Term] id: GO:0046677 name: response to antibiotic namespace: biological_process 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 an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms." [GOC:ai, GOC:ef] subset: goslim_chembl synonym: "antibiotic susceptibility/resistance" RELATED [] is_a: GO:0042221 ! response to chemical [Term] id: GO:0046700 name: heterocycle catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings)." [GOC:ai] synonym: "heterocycle breakdown" EXACT [] synonym: "heterocycle catabolism" EXACT [] synonym: "heterocycle degradation" EXACT [] is_a: GO:0044248 ! cellular catabolic process is_a: GO:0046483 ! heterocycle metabolic process [Term] id: GO:0046717 name: acid secretion namespace: biological_process def: "The controlled release of acid by a cell or a tissue." [GOC:ai] is_a: GO:0046903 ! secretion [Term] id: GO:0046903 name: secretion namespace: biological_process def: "The controlled release of a substance by a cell or a tissue." [GOC:ai] subset: goslim_pir is_a: GO:0006810 ! transport [Term] id: GO:0046942 name: carboxylic acid transport namespace: biological_process def: "The directed movement of carboxylic acids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carboxylic acids are organic acids containing one or more carboxyl (COOH) groups or anions (COO-)." [GOC:ai] is_a: GO:0015711 ! organic anion transport is_a: GO:0015849 ! organic acid transport [Term] id: GO:0048518 name: positive regulation of biological process namespace: biological_process alt_id: GO:0043119 def: "Any process that activates or increases the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] subset: gocheck_do_not_annotate synonym: "activation of biological process" NARROW [] synonym: "positive regulation of physiological process" EXACT [] synonym: "stimulation of biological process" NARROW [] synonym: "up regulation of biological process" EXACT [] synonym: "up-regulation of biological process" EXACT [] synonym: "upregulation of biological process" EXACT [] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0008150 ! biological_process relationship: positively_regulates GO:0008150 ! biological_process [Term] id: GO:0048519 name: negative regulation of biological process namespace: biological_process alt_id: GO:0043118 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:jid] subset: gocheck_do_not_annotate synonym: "down regulation of biological process" EXACT [] synonym: "down-regulation of biological process" EXACT [] synonym: "downregulation of biological process" EXACT [] synonym: "inhibition of biological process" NARROW [] synonym: "negative regulation of physiological process" EXACT [] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0008150 ! biological_process relationship: negatively_regulates GO:0008150 ! biological_process [Term] id: GO:0048522 name: positive regulation of cellular process namespace: biological_process alt_id: GO:0051242 def: "Any process that activates or increases the frequency, rate or extent of a cellular process, any of those 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." [GOC:jid] synonym: "activation of cellular process" NARROW [] synonym: "positive regulation of cellular physiological process" EXACT [] synonym: "stimulation of cellular process" NARROW [] synonym: "up regulation of cellular process" EXACT [] synonym: "up-regulation of cellular process" EXACT [] synonym: "upregulation of cellular process" EXACT [] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0009987 ! cellular process relationship: positively_regulates GO:0009987 ! cellular process [Term] id: GO:0048523 name: negative regulation of cellular process namespace: biological_process alt_id: GO:0051243 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a cellular process, any of those 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." [GOC:jid] synonym: "down regulation of cellular process" EXACT [] synonym: "down-regulation of cellular process" EXACT [] synonym: "downregulation of cellular process" EXACT [] synonym: "inhibition of cellular process" NARROW [] synonym: "negative regulation of cellular physiological process" EXACT [] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0009987 ! cellular process relationship: negatively_regulates GO:0009987 ! cellular process [Term] id: GO:0048532 name: anatomical structure arrangement namespace: biological_process def: "The process that gives rise to the configuration of the constituent parts of an anatomical structure. This process pertains to the physical shaping of a rudimentary structure. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:go_curators] synonym: "anatomical structure organization" BROAD [] synonym: "anatomical structure structural organization" EXACT [] synonym: "organization of an anatomical structure" EXACT [] synonym: "structural organization" EXACT [] is_a: GO:0032502 ! developmental process relationship: part_of GO:0009653 ! anatomical structure morphogenesis [Term] id: GO:0048583 name: regulation of response to stimulus namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a response to a stimulus. Response to stimulus is 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." [GOC:jid] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0050896 ! response to stimulus relationship: regulates GO:0050896 ! response to stimulus [Term] id: GO:0048584 name: positive regulation of response to stimulus namespace: biological_process def: "Any process that activates, maintains or increases the rate of a response to a stimulus. Response to stimulus is 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." [GOC:jid] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate synonym: "activation of response to stimulus" NARROW [] synonym: "stimulation of response to stimulus" NARROW [] synonym: "up regulation of response to stimulus" EXACT [] synonym: "up-regulation of response to stimulus" EXACT [] synonym: "upregulation of response to stimulus" EXACT [] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0050896 ! response to stimulus relationship: positively_regulates GO:0050896 ! response to stimulus [Term] id: GO:0048585 name: negative regulation of response to stimulus namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a response to a stimulus. Response to stimulus is 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." [GOC:jid] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate synonym: "down regulation of response to stimulus" EXACT [] synonym: "down-regulation of response to stimulus" EXACT [] synonym: "downregulation of response to stimulus" EXACT [] synonym: "inhibition of response to stimulus" NARROW [] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0050896 ! response to stimulus relationship: negatively_regulates GO:0050896 ! response to stimulus [Term] id: GO:0048646 name: anatomical structure formation involved in morphogenesis namespace: biological_process def: "The developmental process pertaining to the initial formation of an anatomical structure from unspecified parts. This process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the structural rudiment is recognizable. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GOC:dph, GOC:jid, GOC:tb] comment: Note that, for example, the formation of a pseudopod in an amoeba would not be considered formation involved in morphogenesis because it would not be thought of as the formation of an anatomical structure that was part of the shaping of the amoeba during its development. The formation of an axon from a neuron would be considered the formation of an anatomical structure involved in morphogenesis because it contributes to the creation of the form of the neuron in a developmental sense. subset: goslim_chembl subset: goslim_generic synonym: "formation of an anatomical structure involved in morphogenesis" EXACT [GOC:dph, GOC:tb] is_a: GO:0032502 ! developmental process relationship: part_of GO:0009653 ! anatomical structure morphogenesis [Term] id: GO:0048856 name: anatomical structure development namespace: biological_process def: "The biological process whose specific outcome is the progression of an anatomical structure from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure, whatever form that may be including its natural destruction. An anatomical structure is any biological entity that occupies space and is distinguished from its surroundings. Anatomical structures can be macroscopic such as a carpel, or microscopic such as an acrosome." [GO_REF:0000021, GOC:mtg_15jun06] comment: This term was added by GO_REF:0000021. subset: goslim_chembl subset: goslim_generic synonym: "development of an anatomical structure" EXACT [] is_a: GO:0032502 ! developmental process [Term] id: GO:0048869 name: cellular developmental process namespace: biological_process def: "A biological process whose specific outcome is the progression of a cell over time from an initial condition to a later condition." [GOC:isa_complete] is_a: GO:0009987 ! cellular process is_a: GO:0032502 ! developmental process [Term] id: GO:0048870 name: cell motility namespace: biological_process def: "Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another." [GOC:dgh, GOC:dph, GOC:isa_complete, GOC:mlg] subset: goslim_chembl subset: goslim_generic synonym: "cell locomotion" EXACT [] synonym: "cell movement" RELATED [] synonym: "movement of a cell" EXACT [] is_a: GO:0006928 ! movement of cell or subcellular component is_a: GO:0040011 ! locomotion relationship: part_of GO:0051674 ! localization of cell [Term] id: GO:0050482 name: arachidonic acid secretion namespace: biological_process def: "The controlled release of arachidonic acid from a cell or a tissue." [GOC:ai] comment: This term should be used to annotate release of arachidonic acid from the cell. For the hydrolytic release of arachidonic acid from a phospholipid, consider instead annotating to 'phospholipase A2 activity ; GO:0004623'. is_a: GO:0032309 ! icosanoid secretion is_a: GO:1903963 ! arachidonate transport [Term] id: GO:0050663 name: cytokine secretion namespace: biological_process def: "The regulated release of cytokines from a cell. Cytokines are any of a group of proteins that function to control the survival, growth and differentiation of tissues and cells, and which have autocrine and paracrine activity." [GOC:ai, GOC:bf, ISBN:0198599471] synonym: "interferon secretion" NARROW [GOC:add, GOC:mah] synonym: "interleukin secretion" NARROW [GOC:add, GOC:mah, http://wiki.geneontology.org/index.php/Why_isn%27t_interleukin_in_GO%3F] is_a: GO:0009306 ! protein secretion relationship: part_of GO:0001816 ! cytokine production [Term] id: GO:0050707 name: regulation of cytokine secretion namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the regulated release of cytokines from a cell." [GOC:ai] is_a: GO:0001817 ! regulation of cytokine production is_a: GO:0050708 ! regulation of protein secretion intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0050663 ! cytokine secretion relationship: regulates GO:0050663 ! cytokine secretion [Term] id: GO:0050708 name: regulation of protein secretion namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the controlled release of a protein from a cell." [GOC:ai] is_a: GO:0002791 ! regulation of peptide secretion is_a: GO:0051223 ! regulation of protein transport is_a: GO:1903530 ! regulation of secretion by cell intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0009306 ! protein secretion relationship: regulates GO:0009306 ! protein secretion [Term] id: GO:0050709 name: negative regulation of protein secretion namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a protein from a cell." [GOC:ai] synonym: "down regulation of protein secretion" EXACT [] synonym: "down-regulation of protein secretion" EXACT [] synonym: "downregulation of protein secretion" EXACT [] synonym: "inhibition of protein secretion" NARROW [] is_a: GO:0002792 ! negative regulation of peptide secretion is_a: GO:0050708 ! regulation of protein secretion is_a: GO:0051224 ! negative regulation of protein transport is_a: GO:1903531 ! negative regulation of secretion by cell intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0009306 ! protein secretion relationship: negatively_regulates GO:0009306 ! protein secretion [Term] id: GO:0050710 name: negative regulation of cytokine secretion namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of cytokines from a cell." [GOC:ai] synonym: "down regulation of cytokine secretion" EXACT [] synonym: "down-regulation of cytokine secretion" EXACT [] synonym: "downregulation of cytokine secretion" EXACT [] synonym: "inhibition of cytokine secretion" NARROW [] is_a: GO:0001818 ! negative regulation of cytokine production is_a: GO:0050707 ! regulation of cytokine secretion is_a: GO:0050709 ! negative regulation of protein secretion intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0050663 ! cytokine secretion relationship: negatively_regulates GO:0050663 ! cytokine secretion [Term] id: GO:0050714 name: positive regulation of protein secretion namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell." [GOC:ai] synonym: "activation of protein secretion" NARROW [] synonym: "stimulation of protein secretion" NARROW [] synonym: "up regulation of protein secretion" EXACT [] synonym: "up-regulation of protein secretion" EXACT [] synonym: "upregulation of protein secretion" EXACT [] is_a: GO:0002793 ! positive regulation of peptide secretion is_a: GO:0050708 ! regulation of protein secretion is_a: GO:0051222 ! positive regulation of protein transport is_a: GO:1903532 ! positive regulation of secretion by cell intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0009306 ! protein secretion relationship: positively_regulates GO:0009306 ! protein secretion [Term] id: GO:0050715 name: positive regulation of cytokine secretion namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the regulated release of cytokines from a cell." [GOC:ai] synonym: "activation of cytokine secretion" NARROW [] synonym: "stimulation of cytokine secretion" NARROW [] synonym: "up regulation of cytokine secretion" EXACT [] synonym: "up-regulation of cytokine secretion" EXACT [] synonym: "upregulation of cytokine secretion" EXACT [] is_a: GO:0001819 ! positive regulation of cytokine production is_a: GO:0050707 ! regulation of cytokine secretion is_a: GO:0050714 ! positive regulation of protein secretion intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0050663 ! cytokine secretion relationship: positively_regulates GO:0050663 ! cytokine secretion [Term] id: GO:0050789 name: regulation of biological process namespace: biological_process alt_id: GO:0050791 def: "Any process that modulates the frequency, rate or extent of a biological process. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule." [GOC:ai, GOC:go_curators] subset: gocheck_do_not_annotate subset: goslim_agr subset: goslim_aspergillus subset: goslim_candida subset: goslim_pir synonym: "regulation of physiological process" EXACT [] is_a: GO:0065007 ! biological regulation intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0008150 ! biological_process relationship: regulates GO:0008150 ! biological_process [Term] id: GO:0050790 name: regulation of catalytic activity namespace: biological_process alt_id: GO:0048552 def: "Any process that modulates the activity of an enzyme." [GOC:ai, GOC:ebc, GOC:vw] subset: goslim_chembl synonym: "regulation of enzyme activity" EXACT [] synonym: "regulation of metalloenzyme activity" NARROW [] is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0003824 ! catalytic activity relationship: regulates GO:0003824 ! catalytic activity [Term] id: GO:0050793 name: regulation of developmental process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of development, the biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:go_curators] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0032502 ! developmental process relationship: regulates GO:0032502 ! developmental process [Term] id: GO:0050794 name: regulation of cellular process namespace: biological_process alt_id: GO:0051244 def: "Any process that modulates the frequency, rate or extent of a cellular process, any of those 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." [GOC:go_curators] synonym: "regulation of cellular physiological process" EXACT [] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0009987 ! cellular process relationship: regulates GO:0009987 ! cellular process [Term] id: GO:0050896 name: response to stimulus namespace: biological_process alt_id: GO:0051869 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." [GOC:ai, GOC:bf] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate subset: goslim_agr subset: goslim_mouse subset: goslim_pir synonym: "physiological response to stimulus" EXACT [] is_a: GO:0008150 ! biological_process property_value: IAO:0000111 "response to stimulus" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0050920 name: regulation of chemotaxis namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient." [GOC:ai] is_a: GO:0032101 ! regulation of response to external stimulus is_a: GO:0040012 ! regulation of locomotion intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006935 ! chemotaxis relationship: regulates GO:0006935 ! chemotaxis [Term] id: GO:0050921 name: positive regulation of chemotaxis namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient." [GOC:ai] synonym: "activation of chemotaxis" NARROW [] synonym: "stimulation of chemotaxis" NARROW [] synonym: "up regulation of chemotaxis" EXACT [] synonym: "up-regulation of chemotaxis" EXACT [] synonym: "upregulation of chemotaxis" EXACT [] is_a: GO:0032103 ! positive regulation of response to external stimulus is_a: GO:0040017 ! positive regulation of locomotion is_a: GO:0050920 ! regulation of chemotaxis intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006935 ! chemotaxis relationship: positively_regulates GO:0006935 ! chemotaxis [Term] id: GO:0050922 name: negative regulation of chemotaxis namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a motile cell or organism in response to a specific chemical concentration gradient." [GOC:ai] synonym: "down regulation of chemotaxis" EXACT [] synonym: "down-regulation of chemotaxis" EXACT [] synonym: "downregulation of chemotaxis" EXACT [] synonym: "inhibition of chemotaxis" NARROW [] is_a: GO:0032102 ! negative regulation of response to external stimulus is_a: GO:0040013 ! negative regulation of locomotion is_a: GO:0050920 ! regulation of chemotaxis intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006935 ! chemotaxis relationship: negatively_regulates GO:0006935 ! chemotaxis [Term] id: GO:0051046 name: regulation of secretion namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the controlled release of a substance from a cell or a tissue." [GOC:ai] is_a: GO:0051049 ! regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0046903 ! secretion relationship: regulates GO:0046903 ! secretion [Term] id: GO:0051047 name: positive regulation of secretion namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the controlled release of a substance from a cell or a tissue." [GOC:ai] synonym: "activation of secretion" NARROW [] synonym: "stimulation of secretion" NARROW [] synonym: "up regulation of secretion" EXACT [] synonym: "up-regulation of secretion" EXACT [] synonym: "upregulation of secretion" EXACT [] is_a: GO:0051046 ! regulation of secretion is_a: GO:0051050 ! positive regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0046903 ! secretion relationship: positively_regulates GO:0046903 ! secretion [Term] id: GO:0051048 name: negative regulation of secretion namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the controlled release of a substance from a cell or a tissue." [GOC:ai] synonym: "down regulation of secretion" EXACT [] synonym: "down-regulation of secretion" EXACT [] synonym: "downregulation of secretion" EXACT [] synonym: "inhibition of secretion" NARROW [] is_a: GO:0051046 ! regulation of secretion is_a: GO:0051051 ! negative regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0046903 ! secretion relationship: negatively_regulates GO:0046903 ! secretion [Term] id: GO:0051049 name: regulation of transport namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] subset: goslim_yeast is_a: GO:0032879 ! regulation of localization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006810 ! transport relationship: regulates GO:0006810 ! transport [Term] id: GO:0051050 name: positive regulation of transport namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] synonym: "activation of transport" NARROW [] synonym: "stimulation of transport" NARROW [] synonym: "up regulation of transport" EXACT [] synonym: "up-regulation of transport" EXACT [] synonym: "upregulation of transport" EXACT [] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0051049 ! regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006810 ! transport relationship: positively_regulates GO:0006810 ! transport [Term] id: GO:0051051 name: negative regulation of transport namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] synonym: "down regulation of transport" EXACT [] synonym: "down-regulation of transport" EXACT [] synonym: "downregulation of transport" EXACT [] synonym: "inhibition of transport" NARROW [] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0051049 ! regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006810 ! transport relationship: negatively_regulates GO:0006810 ! transport [Term] id: GO:0051052 name: regulation of DNA metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving DNA." [GOC:ai] subset: goslim_yeast synonym: "regulation of DNA metabolism" EXACT [] is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006259 ! DNA metabolic process relationship: regulates GO:0006259 ! DNA metabolic process [Term] id: GO:0051053 name: negative regulation of DNA metabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving DNA." [GOC:ai] synonym: "down regulation of DNA metabolic process" EXACT [] synonym: "down-regulation of DNA metabolic process" EXACT [] synonym: "downregulation of DNA metabolic process" EXACT [] synonym: "inhibition of DNA metabolic process" NARROW [] synonym: "negative regulation of DNA metabolism" EXACT [] is_a: GO:0010605 ! negative regulation of macromolecule metabolic process is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process is_a: GO:0051052 ! regulation of DNA metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006259 ! DNA metabolic process relationship: negatively_regulates GO:0006259 ! DNA metabolic process [Term] id: GO:0051054 name: positive regulation of DNA metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving DNA." [GOC:ai] synonym: "activation of DNA metabolic process" NARROW [] synonym: "positive regulation of DNA metabolism" EXACT [] synonym: "stimulation of DNA metabolic process" NARROW [] synonym: "up regulation of DNA metabolic process" EXACT [] synonym: "up-regulation of DNA metabolic process" EXACT [] synonym: "upregulation of DNA metabolic process" EXACT [] is_a: GO:0010604 ! positive regulation of macromolecule metabolic process is_a: GO:0045935 ! positive regulation of nucleobase-containing compound metabolic process is_a: GO:0051052 ! regulation of DNA metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006259 ! DNA metabolic process relationship: positively_regulates GO:0006259 ! DNA metabolic process [Term] id: GO:0051093 name: negative regulation of developmental process namespace: biological_process def: "Any process that stops, prevents or reduces the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:ai] synonym: "down regulation of developmental process" EXACT [] synonym: "down-regulation of developmental process" EXACT [] synonym: "downregulation of developmental process" EXACT [] synonym: "inhibition of developmental process" NARROW [] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0032502 ! developmental process relationship: negatively_regulates GO:0032502 ! developmental process [Term] id: GO:0051094 name: positive regulation of developmental process namespace: biological_process def: "Any process that activates or increases the rate or extent of development, the biological process whose specific outcome is the progression of an organism over time from an initial condition (e.g. a zygote, or a young adult) to a later condition (e.g. a multicellular animal or an aged adult)." [GOC:ai] synonym: "activation of developmental process" NARROW [] synonym: "stimulation of developmental process" NARROW [] synonym: "up regulation of developmental process" EXACT [] synonym: "up-regulation of developmental process" EXACT [] synonym: "upregulation of developmental process" EXACT [] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0032502 ! developmental process relationship: positively_regulates GO:0032502 ! developmental process [Term] id: GO:0051098 name: regulation of binding namespace: biological_process def: "Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule." [GOC:ai] is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0005488 ! binding relationship: regulates GO:0005488 ! binding [Term] id: GO:0051099 name: positive regulation of binding namespace: biological_process def: "Any process that activates or increases the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule." [GOC:ai] synonym: "activation of binding" NARROW [] synonym: "stimulation of binding" NARROW [] synonym: "up regulation of binding" EXACT [] synonym: "up-regulation of binding" EXACT [] synonym: "upregulation of binding" EXACT [] is_a: GO:0044093 ! positive regulation of molecular function is_a: GO:0051098 ! regulation of binding intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0005488 ! binding relationship: positively_regulates GO:0005488 ! binding [Term] id: GO:0051100 name: negative regulation of binding namespace: biological_process def: "Any process that stops or reduces the rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule." [GOC:ai] synonym: "down regulation of binding" EXACT [] synonym: "down-regulation of binding" EXACT [] synonym: "downregulation of binding" EXACT [] synonym: "inhibition of binding" NARROW [] is_a: GO:0044092 ! negative regulation of molecular function is_a: GO:0051098 ! regulation of binding intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0005488 ! binding relationship: negatively_regulates GO:0005488 ! binding [Term] id: GO:0051101 name: regulation of DNA binding namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid)." [GOC:ai, GOC:dph, GOC:tb] is_a: GO:0051098 ! regulation of binding intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0003677 ! DNA binding relationship: regulates GO:0003677 ! DNA binding [Term] id: GO:0051128 name: regulation of cellular component organization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:ai] synonym: "regulation of cell organisation" RELATED [GOC:mah] synonym: "regulation of cell organization" RELATED [GOC:mah] synonym: "regulation of cellular component organisation" EXACT [GOC:curators] synonym: "regulation of cellular component organization and biogenesis" RELATED [GOC:mah] is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0016043 ! cellular component organization relationship: regulates GO:0016043 ! cellular component organization [Term] id: GO:0051129 name: negative regulation of cellular component organization namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:ai] synonym: "down regulation of cell organization" EXACT [] synonym: "down-regulation of cell organization" EXACT [] synonym: "downregulation of cell organization" EXACT [] synonym: "inhibition of cell organization" NARROW [] synonym: "negative regulation of cell organisation" RELATED [GOC:mah] synonym: "negative regulation of cellular component organization and biogenesis" RELATED [GOC:mah] is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0016043 ! cellular component organization relationship: negatively_regulates GO:0016043 ! cellular component organization [Term] id: GO:0051130 name: positive regulation of cellular component organization namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of cell structures, including the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope." [GOC:ai] synonym: "activation of cell organization" NARROW [] synonym: "positive regulation of cell organisation" EXACT [] synonym: "positive regulation of cellular component organization and biogenesis" RELATED [GOC:mah] synonym: "stimulation of cell organization" NARROW [] synonym: "up regulation of cell organization" EXACT [] synonym: "up-regulation of cell organization" EXACT [] synonym: "upregulation of cell organization" EXACT [] is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0051128 ! regulation of cellular component organization intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0016043 ! cellular component organization relationship: positively_regulates GO:0016043 ! cellular component organization [Term] id: GO:0051171 name: regulation of nitrogen compound metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] synonym: "regulation of nitrogen metabolic process" EXACT [GOC:tb] synonym: "regulation of nitrogen metabolism" EXACT [] is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006807 ! nitrogen compound metabolic process relationship: regulates GO:0006807 ! nitrogen compound metabolic process [Term] id: GO:0051172 name: negative regulation of nitrogen compound metabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] synonym: "down regulation of nitrogen metabolic process" EXACT [] synonym: "down-regulation of nitrogen metabolic process" EXACT [] synonym: "downregulation of nitrogen metabolic process" EXACT [] synonym: "inhibition of nitrogen metabolic process" NARROW [] synonym: "negative regulation of nitrogen metabolic process" EXACT [GOC:tb] synonym: "negative regulation of nitrogen metabolism" EXACT [] is_a: GO:0009892 ! negative regulation of metabolic process is_a: GO:0051171 ! regulation of nitrogen compound metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006807 ! nitrogen compound metabolic process relationship: negatively_regulates GO:0006807 ! nitrogen compound metabolic process [Term] id: GO:0051173 name: positive regulation of nitrogen compound metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving nitrogen or nitrogenous compounds." [GOC:ai, GOC:tb] synonym: "activation of nitrogen metabolic process" NARROW [] synonym: "positive regulation of nitrogen metabolic process" EXACT [GOC:tb] synonym: "positive regulation of nitrogen metabolism" EXACT [] synonym: "stimulation of nitrogen metabolic process" NARROW [] synonym: "up regulation of nitrogen metabolic process" EXACT [] synonym: "up-regulation of nitrogen metabolic process" EXACT [] synonym: "upregulation of nitrogen metabolic process" EXACT [] is_a: GO:0009893 ! positive regulation of metabolic process is_a: GO:0051171 ! regulation of nitrogen compound metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006807 ! nitrogen compound metabolic process relationship: positively_regulates GO:0006807 ! nitrogen compound metabolic process [Term] id: GO:0051179 name: localization namespace: biological_process alt_id: GO:1902578 def: "Any process in which a cell, a substance, or a cellular entity, such as a protein complex or organelle, is transported, tethered to or otherwise maintained in a specific location. In the case of substances, localization may also be achieved via selective degradation." [GOC:ai, GOC:dos] subset: goslim_pir synonym: "establishment and maintenance of cellular component location" NARROW [] synonym: "establishment and maintenance of localization" EXACT [] synonym: "establishment and maintenance of position" EXACT [] synonym: "establishment and maintenance of substance location" NARROW [] synonym: "establishment and maintenance of substrate location" NARROW [] synonym: "localisation" EXACT [GOC:mah] synonym: "single organism localization" RELATED [GOC:TermGenie] synonym: "single-organism localization" RELATED [] is_a: GO:0008150 ! biological_process created_by: jl creation_date: 2013-12-18T13:51:04Z [Term] id: GO:0051222 name: positive regulation of protein transport namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] synonym: "activation of protein transport" NARROW [] synonym: "stimulation of protein transport" NARROW [] synonym: "up regulation of protein transport" EXACT [] synonym: "up-regulation of protein transport" EXACT [] synonym: "upregulation of protein transport" EXACT [] is_a: GO:0051050 ! positive regulation of transport is_a: GO:0051223 ! regulation of protein transport is_a: GO:1904951 ! positive regulation of establishment of protein localization intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0015031 ! protein transport relationship: positively_regulates GO:0015031 ! protein transport [Term] id: GO:0051223 name: regulation of protein transport namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] is_a: GO:0070201 ! regulation of establishment of protein localization is_a: GO:0090087 ! regulation of peptide transport intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0015031 ! protein transport relationship: regulates GO:0015031 ! protein transport [Term] id: GO:0051224 name: negative regulation of protein transport namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of a protein into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] synonym: "down regulation of protein transport" EXACT [] synonym: "down-regulation of protein transport" EXACT [] synonym: "downregulation of protein transport" EXACT [] synonym: "inhibition of protein transport" NARROW [] is_a: GO:0051051 ! negative regulation of transport is_a: GO:0051223 ! regulation of protein transport is_a: GO:1904950 ! negative regulation of establishment of protein localization intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0015031 ! protein transport relationship: negatively_regulates GO:0015031 ! protein transport [Term] id: GO:0051234 name: establishment of localization namespace: biological_process def: "Any process that localizes a substance or cellular component. This may occur via movement, tethering or selective degradation." [GOC:ai, GOC:dos] subset: goslim_agr subset: goslim_mouse subset: goslim_pir synonym: "establishment of localisation" EXACT [GOC:mah] is_a: GO:0051179 ! localization [Term] id: GO:0051239 name: regulation of multicellular organismal process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a multicellular organismal process, the processes pertinent to the function of a multicellular organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai, GOC:dph, GOC:tb] is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0032501 ! multicellular organismal process relationship: regulates GO:0032501 ! multicellular organismal process [Term] id: GO:0051240 name: positive regulation of multicellular organismal process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of an organismal process, any of the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai] synonym: "activation of multicellular organismal process" NARROW [] synonym: "stimulation of multicellular organismal process" NARROW [] synonym: "up regulation of multicellular organismal process" EXACT [] synonym: "up-regulation of multicellular organismal process" EXACT [] synonym: "upregulation of multicellular organismal process" EXACT [] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0032501 ! multicellular organismal process relationship: positively_regulates GO:0032501 ! multicellular organismal process [Term] id: GO:0051241 name: negative regulation of multicellular organismal process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of an organismal process, the processes pertinent to the function of an organism above the cellular level; includes the integrated processes of tissues and organs." [GOC:ai] synonym: "down regulation of multicellular organismal process" EXACT [] synonym: "down-regulation of multicellular organismal process" EXACT [] synonym: "downregulation of multicellular organismal process" EXACT [] synonym: "inhibition of multicellular organismal process" NARROW [] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0051239 ! regulation of multicellular organismal process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0032501 ! multicellular organismal process relationship: negatively_regulates GO:0032501 ! multicellular organismal process [Term] id: GO:0051246 name: regulation of protein metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving a protein." [GOC:ai] synonym: "regulation of protein metabolism" EXACT [] is_a: GO:0051171 ! regulation of nitrogen compound metabolic process is_a: GO:0060255 ! regulation of macromolecule metabolic process is_a: GO:0080090 ! regulation of primary metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0019538 ! protein metabolic process relationship: regulates GO:0019538 ! protein metabolic process [Term] id: GO:0051247 name: positive regulation of protein metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein." [GOC:ai] synonym: "activation of protein metabolic process" NARROW [] synonym: "positive regulation of protein metabolism" EXACT [] synonym: "stimulation of protein metabolic process" NARROW [] synonym: "up regulation of protein metabolic process" EXACT [] synonym: "up-regulation of protein metabolic process" EXACT [] synonym: "upregulation of protein metabolic process" EXACT [] is_a: GO:0010604 ! positive regulation of macromolecule metabolic process is_a: GO:0051173 ! positive regulation of nitrogen compound metabolic process is_a: GO:0051246 ! regulation of protein metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0019538 ! protein metabolic process relationship: positively_regulates GO:0019538 ! protein metabolic process [Term] id: GO:0051248 name: negative regulation of protein metabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of chemical reactions and pathways involving a protein." [GOC:ai] synonym: "down regulation of protein metabolic process" EXACT [] synonym: "down-regulation of protein metabolic process" EXACT [] synonym: "downregulation of protein metabolic process" EXACT [] synonym: "inhibition of protein metabolic process" NARROW [] synonym: "negative regulation of protein metabolism" EXACT [] is_a: GO:0010605 ! negative regulation of macromolecule metabolic process is_a: GO:0051172 ! negative regulation of nitrogen compound metabolic process is_a: GO:0051246 ! regulation of protein metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0019538 ! protein metabolic process relationship: negatively_regulates GO:0019538 ! protein metabolic process [Term] id: GO:0051252 name: regulation of RNA metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving RNA." [GOC:ai] synonym: "regulation of RNA metabolism" EXACT [] is_a: GO:0019219 ! regulation of nucleobase-containing compound metabolic process is_a: GO:0060255 ! regulation of macromolecule metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0016070 ! RNA metabolic process relationship: regulates GO:0016070 ! RNA metabolic process [Term] id: GO:0051253 name: negative regulation of RNA metabolic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving RNA." [GOC:ai] synonym: "down regulation of RNA metabolic process" EXACT [] synonym: "down-regulation of RNA metabolic process" EXACT [] synonym: "downregulation of RNA metabolic process" EXACT [] synonym: "inhibition of RNA metabolic process" NARROW [] synonym: "negative regulation of RNA metabolism" EXACT [] is_a: GO:0010605 ! negative regulation of macromolecule metabolic process is_a: GO:0045934 ! negative regulation of nucleobase-containing compound metabolic process is_a: GO:0051252 ! regulation of RNA metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0016070 ! RNA metabolic process relationship: negatively_regulates GO:0016070 ! RNA metabolic process [Term] id: GO:0051254 name: positive regulation of RNA metabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving RNA." [GOC:ai] synonym: "activation of RNA metabolic process" NARROW [] synonym: "positive regulation of RNA metabolism" EXACT [] synonym: "stimulation of RNA metabolic process" NARROW [] synonym: "up regulation of RNA metabolic process" EXACT [] synonym: "up-regulation of RNA metabolic process" EXACT [] synonym: "upregulation of RNA metabolic process" EXACT [] is_a: GO:0010604 ! positive regulation of macromolecule metabolic process is_a: GO:0045935 ! positive regulation of nucleobase-containing compound metabolic process is_a: GO:0051252 ! regulation of RNA metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0016070 ! RNA metabolic process relationship: positively_regulates GO:0016070 ! RNA metabolic process [Term] id: GO:0051270 name: regulation of cellular component movement namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl] synonym: "regulation of cell movement" RELATED [] synonym: "regulation of cellular component motion" EXACT [GOC:mah] is_a: GO:0032879 ! regulation of localization is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006928 ! movement of cell or subcellular component relationship: regulates GO:0006928 ! movement of cell or subcellular component [Term] id: GO:0051271 name: negative regulation of cellular component movement namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl] synonym: "down regulation of cell motility" EXACT [] synonym: "down-regulation of cell motility" EXACT [] synonym: "downregulation of cell motility" EXACT [] synonym: "inhibition of cell motility" NARROW [] synonym: "negative regulation of cell movement" RELATED [] synonym: "negative regulation of cellular component motion" EXACT [GOC:mah] is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0051270 ! regulation of cellular component movement intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006928 ! movement of cell or subcellular component relationship: negatively_regulates GO:0006928 ! movement of cell or subcellular component [Term] id: GO:0051272 name: positive regulation of cellular component movement namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of the movement of a cellular component." [GOC:ai, GOC:dph, GOC:jl] synonym: "activation of cell motility" NARROW [] synonym: "positive regulation of cell movement" RELATED [] synonym: "positive regulation of cellular component motion" EXACT [GOC:mah] synonym: "stimulation of cell motility" NARROW [] synonym: "up regulation of cell motility" EXACT [] synonym: "up-regulation of cell motility" EXACT [] synonym: "upregulation of cell motility" EXACT [] is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0051270 ! regulation of cellular component movement intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006928 ! movement of cell or subcellular component relationship: positively_regulates GO:0006928 ! movement of cell or subcellular component [Term] id: GO:0051276 name: chromosome organization namespace: biological_process alt_id: GO:0007001 alt_id: GO:0051277 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." [GOC:ai, GOC:dph, GOC:jl, GOC:mah] subset: goslim_chembl subset: goslim_generic subset: goslim_pir synonym: "chromosome organisation" EXACT [] synonym: "chromosome organization and biogenesis" RELATED [GOC:mah] synonym: "maintenance of genome integrity" RELATED [] synonym: "nuclear genome maintenance" RELATED [] is_a: GO:0006996 ! organelle organization property_value: IAO:0000111 "chromosome organization" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0051336 name: regulation of hydrolase activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [EC:3.-.-.-, GOC:ai] synonym: "hydrolase regulator" EXACT [] is_a: GO:0050790 ! regulation of catalytic activity intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0016787 ! hydrolase activity relationship: regulates GO:0016787 ! hydrolase activity [Term] id: GO:0051345 name: positive regulation of hydrolase activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds." [GOC:ai] synonym: "activation of hydrolase activity" NARROW [] synonym: "hydrolase activator" EXACT [] synonym: "stimulation of hydrolase activity" NARROW [] synonym: "up regulation of hydrolase activity" EXACT [] synonym: "up-regulation of hydrolase activity" EXACT [] synonym: "upregulation of hydrolase activity" EXACT [] is_a: GO:0043085 ! positive regulation of catalytic activity is_a: GO:0051336 ! regulation of hydrolase activity intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0016787 ! hydrolase activity relationship: positively_regulates GO:0016787 ! hydrolase activity [Term] id: GO:0051346 name: negative regulation of hydrolase activity namespace: biological_process def: "Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds." [GOC:ai] synonym: "down regulation of hydrolase activity" EXACT [] synonym: "down-regulation of hydrolase activity" EXACT [] synonym: "downregulation of hydrolase activity" EXACT [] synonym: "hydrolase inhibitor" EXACT [] synonym: "inhibition of hydrolase activity" NARROW [] is_a: GO:0043086 ! negative regulation of catalytic activity is_a: GO:0051336 ! regulation of hydrolase activity intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0016787 ! hydrolase activity relationship: negatively_regulates GO:0016787 ! hydrolase activity [Term] id: GO:0051641 name: cellular localization namespace: biological_process alt_id: GO:1902580 def: "A cellular localization process whereby a substance or cellular entity, such as a protein complex or organelle, is transported to, and/or maintained in, a specific location within a cell including the localization of substances or cellular entities to the cell membrane." [GOC:tb, GOC:vw] subset: goslim_pir synonym: "cellular localisation" EXACT [GOC:mah] synonym: "establishment and maintenance of cellular localization" EXACT [] synonym: "establishment and maintenance of localization in cell or cell membrane" EXACT [] synonym: "intracellular localization" NARROW [] synonym: "localization within cell" NARROW [] synonym: "single organism cellular localization" EXACT [GOC:TermGenie] synonym: "single-organism cellular localization" RELATED [] is_a: GO:0051179 ! localization created_by: jl creation_date: 2013-12-18T14:04:32Z [Term] id: GO:0051674 name: localization of cell namespace: biological_process def: "Any process in which a cell is transported to, and/or maintained in, a specific location." [GOC:ai] synonym: "cell localization" EXACT [] synonym: "establishment and maintenance of cell localization" EXACT [] synonym: "establishment and maintenance of localization of cell" EXACT [] synonym: "localisation of cell" EXACT [GOC:mah] is_a: GO:0051179 ! localization [Term] id: GO:0051704 name: multi-organism process namespace: biological_process alt_id: GO:0051706 def: "A biological process which involves another organism of the same or different species." [GOC:jl] subset: goslim_pir synonym: "interaction between organisms" EXACT [] synonym: "physiological interaction between organisms" EXACT [] synonym: "physiological interaction with other organism" EXACT [] is_a: GO:0008150 ! biological_process [Term] id: GO:0051716 name: cellular response to stimulus namespace: biological_process 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. The process begins with detection of the stimulus by a cell and ends with a change in state or activity or the cell." [GOC:bf, GOC:jl] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate is_a: GO:0009987 ! cellular process is_a: GO:0050896 ! response to stimulus [Term] id: GO:0055085 name: transmembrane transport namespace: biological_process def: "The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other." [GOC:dph, GOC:jid] comment: Transmembrane transport requires transport of a solute across a lipid bilayer. Note that transport through the nuclear pore complex is not transmembrane because the nuclear membrane is a double membrane and is not traversed. For transport through the nuclear pore, consider instead the term 'nucleocytoplasmic transport ; GO:0006913' and its children. Note also that this term is not intended for use in annotating lateral movement within membranes. subset: goslim_chembl subset: goslim_generic subset: goslim_pombe subset: goslim_yeast synonym: "membrane transport" EXACT [] xref: Reactome:REACT_100480 "SLC-mediated transmembrane transport, Taeniopygia guttata" xref: Reactome:REACT_101577 "SLC-mediated transmembrane transport, Caenorhabditis elegans" xref: Reactome:REACT_101877 "SLC-mediated transmembrane transport, Escherichia coli" xref: Reactome:REACT_101975 "SLC-mediated transmembrane transport, Sus scrofa" xref: Reactome:REACT_102348 "Transmembrane transport of small molecules, Staphylococcus aureus N315" xref: Reactome:REACT_102897 "Transmembrane transport of small molecules, Caenorhabditis elegans" xref: Reactome:REACT_102974 "SLC-mediated transmembrane transport, Canis familiaris" xref: Reactome:REACT_104555 "SLC-mediated transmembrane transport, Xenopus tropicalis" xref: Reactome:REACT_108243 "SLC-mediated transmembrane transport, Staphylococcus aureus N315" xref: Reactome:REACT_109832 "Transmembrane transport of small molecules, Plasmodium falciparum" xref: Reactome:REACT_110770 "ABC-family proteins mediated transport, Mus musculus" xref: Reactome:REACT_114546 "ABC-family proteins mediated transport, Staphylococcus aureus N315" xref: Reactome:REACT_114763 "ABC-family proteins mediated transport, Escherichia coli" xref: Reactome:REACT_114890 "ABC-family proteins mediated transport, Plasmodium falciparum" xref: Reactome:REACT_115378 "ABC-family proteins mediated transport, Mycobacterium tuberculosis" xref: Reactome:REACT_15480 "ABC-family proteins mediated transport, Homo sapiens" xref: Reactome:REACT_15518 "Transmembrane transport of small molecules, Homo sapiens" xref: Reactome:REACT_19118 "SLC-mediated transmembrane transport, Homo sapiens" xref: Reactome:REACT_29093 "ABC-family proteins mediated transport, Taeniopygia guttata" xref: Reactome:REACT_29184 "SLC-mediated transmembrane transport, Gallus gallus" xref: Reactome:REACT_29635 "Transmembrane transport of small molecules, Canis familiaris" xref: Reactome:REACT_30969 "ABC-family proteins mediated transport, Canis familiaris" xref: Reactome:REACT_32055 "Transmembrane transport of small molecules, Saccharomyces cerevisiae" xref: Reactome:REACT_32223 "Transmembrane transport of small molecules, Rattus norvegicus" xref: Reactome:REACT_32423 "SLC-mediated transmembrane transport, Bos taurus" xref: Reactome:REACT_32713 "ABC-family proteins mediated transport, Sus scrofa" xref: Reactome:REACT_33571 "SLC-mediated transmembrane transport, Danio rerio" xref: Reactome:REACT_61245 "Transmembrane transport of small molecules, Bos taurus" xref: Reactome:REACT_79086 "SLC-mediated transmembrane transport, Plasmodium falciparum" xref: Reactome:REACT_79921 "SLC-mediated transmembrane transport, Saccharomyces cerevisiae" xref: Reactome:REACT_80022 "ABC-family proteins mediated transport, Bos taurus" xref: Reactome:REACT_80510 "ABC-family proteins mediated transport, Rattus norvegicus" xref: Reactome:REACT_80848 "ABC-family proteins mediated transport, Schizosaccharomyces pombe" xref: Reactome:REACT_80977 "ABC-family proteins mediated transport, Caenorhabditis elegans" xref: Reactome:REACT_81024 "Transmembrane transport of small molecules, Oryza sativa" xref: Reactome:REACT_81153 "SLC-mediated transmembrane transport, Mus musculus" xref: Reactome:REACT_82725 "SLC-mediated transmembrane transport, Rattus norvegicus" xref: Reactome:REACT_83770 "Transmembrane transport of small molecules, Escherichia coli" xref: Reactome:REACT_86135 "ABC-family proteins mediated transport, Oryza sativa" xref: Reactome:REACT_86409 "Transmembrane transport of small molecules, Drosophila melanogaster" xref: Reactome:REACT_86576 "Transmembrane transport of small molecules, Schizosaccharomyces pombe" xref: Reactome:REACT_87124 "SLC-mediated transmembrane transport, Oryza sativa" xref: Reactome:REACT_88059 "ABC-family proteins mediated transport, Xenopus tropicalis" xref: Reactome:REACT_88521 "Transmembrane transport of small molecules, Taeniopygia guttata" xref: Reactome:REACT_88894 "Transmembrane transport of small molecules, Gallus gallus" xref: Reactome:REACT_89376 "SLC-mediated transmembrane transport, Schizosaccharomyces pombe" xref: Reactome:REACT_91272 "ABC-family proteins mediated transport, Arabidopsis thaliana" xref: Reactome:REACT_91803 "SLC-mediated transmembrane transport, Mycobacterium tuberculosis" xref: Reactome:REACT_92006 "Transmembrane transport of small molecules, Mycobacterium tuberculosis" xref: Reactome:REACT_92624 "ABC-family proteins mediated transport, Gallus gallus" xref: Reactome:REACT_93747 "Transmembrane transport of small molecules, Dictyostelium discoideum" xref: Reactome:REACT_94160 "Transmembrane transport of small molecules, Mus musculus" xref: Reactome:REACT_94393 "ABC-family proteins mediated transport, Drosophila melanogaster" xref: Reactome:REACT_94944 "ABC-family proteins mediated transport, Danio rerio" xref: Reactome:REACT_94972 "SLC-mediated transmembrane transport, Dictyostelium discoideum" xref: Reactome:REACT_96633 "Transmembrane transport of small molecules, Sus scrofa" xref: Reactome:REACT_96636 "SLC-mediated transmembrane transport, Arabidopsis thaliana" xref: Reactome:REACT_97365 "Transmembrane transport of small molecules, Arabidopsis thaliana" xref: Reactome:REACT_97867 "ABC-family proteins mediated transport, Saccharomyces cerevisiae" xref: Reactome:REACT_98509 "Transmembrane transport of small molecules, Xenopus tropicalis" xref: Reactome:REACT_98716 "SLC-mediated transmembrane transport, Drosophila melanogaster" xref: Reactome:REACT_99579 "Transmembrane transport of small molecules, Danio rerio" xref: Reactome:REACT_99829 "ABC-family proteins mediated transport, Dictyostelium discoideum" is_a: GO:0006810 ! transport [Term] id: GO:0060147 name: regulation of posttranscriptional gene silencing namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism." [GOC:dph] is_a: GO:0060968 ! regulation of gene silencing intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0016441 ! posttranscriptional gene silencing relationship: regulates GO:0016441 ! posttranscriptional gene silencing [Term] id: GO:0060148 name: positive regulation of posttranscriptional gene silencing namespace: biological_process def: "Any process that increases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism." [GOC:dph] is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0060147 ! regulation of posttranscriptional gene silencing intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0016441 ! posttranscriptional gene silencing relationship: positively_regulates GO:0016441 ! posttranscriptional gene silencing [Term] id: GO:0060149 name: negative regulation of posttranscriptional gene silencing namespace: biological_process def: "Any process that decreases the frequency, rate or extent of the inactivation of gene expression by a posttranscriptional mechanism." [GOC:dph] is_a: GO:0060147 ! regulation of posttranscriptional gene silencing is_a: GO:0060969 ! negative regulation of gene silencing intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0016441 ! posttranscriptional gene silencing relationship: negatively_regulates GO:0016441 ! posttranscriptional gene silencing [Term] id: GO:0060194 name: regulation of antisense RNA transcription namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA." [GOC:dph, GOC:jp, GOC:tb, PMID:18075583] is_a: GO:0006355 ! regulation of transcription, DNA-templated intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0009300 ! antisense RNA transcription relationship: regulates GO:0009300 ! antisense RNA transcription [Term] id: GO:0060195 name: negative regulation of antisense RNA transcription namespace: biological_process def: "Any process that decreases the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA." [GOC:dph, GOC:tb, PMID:18075583] is_a: GO:0045892 ! negative regulation of transcription, DNA-templated is_a: GO:0060194 ! regulation of antisense RNA transcription intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0009300 ! antisense RNA transcription relationship: negatively_regulates GO:0009300 ! antisense RNA transcription [Term] id: GO:0060196 name: positive regulation of antisense RNA transcription namespace: biological_process def: "Any process that increases the frequency, rate or extent of the synthesis of antisense RNA, an RNA molecule complementary in sequence to another RNA or DNA molecule, which, by binding the latter, acts to inhibit its function and/or completion of synthesis, on a template of DNA." [GOC:dph, GOC:tb, PMID:18075583] is_a: GO:0045893 ! positive regulation of transcription, DNA-templated is_a: GO:0060194 ! regulation of antisense RNA transcription intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0009300 ! antisense RNA transcription relationship: positively_regulates GO:0009300 ! antisense RNA transcription [Term] id: GO:0060255 name: regulation of macromolecule metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways involving macromolecules, any 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." [GOC:dph, GOC:tb] is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0043170 ! macromolecule metabolic process relationship: regulates GO:0043170 ! macromolecule metabolic process [Term] id: GO:0060326 name: cell chemotaxis namespace: biological_process def: "The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis)." [GOC:dph] is_a: GO:0006935 ! chemotaxis is_a: GO:0016477 ! cell migration relationship: part_of GO:0070887 ! cellular response to chemical stimulus [Term] id: GO:0060341 name: regulation of cellular localization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a process in which a cell, a substance, or a cellular entity is transported to, or maintained in a specific location within or in the membrane of a cell." [GOC:dph, GOC:tb] synonym: "regulation of cellular localisation" EXACT [GOC:mah] is_a: GO:0032879 ! regulation of localization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0051641 ! cellular localization relationship: regulates GO:0051641 ! cellular localization [Term] id: GO:0060491 name: regulation of cell projection assembly namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of cell projection assembly." [GOC:dph, GOC:tb] synonym: "regulation of cell projection formation" RELATED [GOC:dph, GOC:tb] is_a: GO:0031344 ! regulation of cell projection organization is_a: GO:0044087 ! regulation of cellular component biogenesis intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0030031 ! cell projection assembly relationship: regulates GO:0030031 ! cell projection assembly [Term] id: GO:0060548 name: negative regulation of cell death namespace: biological_process def: "Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death." [GOC:BHF, GOC:dph, GOC:tb] is_a: GO:0010941 ! regulation of cell death is_a: GO:0048523 ! negative regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0008219 ! cell death relationship: negatively_regulates GO:0008219 ! cell death created_by: dph creation_date: 2009-04-13T01:56:10Z [Term] id: GO:0060561 name: apoptotic process involved in morphogenesis namespace: biological_process def: "Any apoptotic process that contributes to the shaping of an anatomical structure." [GOC:dph, GOC:mtg_apoptosis] synonym: "apoptosis involved in development" RELATED [] synonym: "apoptosis involved in morphogenesis" NARROW [] synonym: "morphogenetic apoptosis" RELATED [GOC:dph] is_a: GO:1902742 ! apoptotic process involved in development intersection_of: GO:0006915 ! apoptotic process intersection_of: part_of GO:0009653 ! anatomical structure morphogenesis relationship: part_of GO:0009653 ! anatomical structure morphogenesis created_by: dph creation_date: 2009-04-28T09:17:27Z [Term] id: GO:0060966 name: regulation of gene silencing by RNA namespace: biological_process def: "Any process that regulates the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes." [GOC:dph, GOC:tb] is_a: GO:0060968 ! regulation of gene silencing intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0031047 ! gene silencing by RNA relationship: regulates GO:0031047 ! gene silencing by RNA created_by: dph creation_date: 2009-10-05T03:17:02Z [Term] id: GO:0060967 name: negative regulation of gene silencing by RNA namespace: biological_process def: "Any process that decreases the rate, frequency, or extent of gene silencing by RNA. Gene silencing by RNA is the process in which RNA molecules inactivate expression of target genes." [GOC:dph, GOC:tb] is_a: GO:0060966 ! regulation of gene silencing by RNA is_a: GO:0060969 ! negative regulation of gene silencing intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0031047 ! gene silencing by RNA relationship: negatively_regulates GO:0031047 ! gene silencing by RNA created_by: dph creation_date: 2009-10-05T03:21:05Z [Term] id: GO:0060968 name: regulation of gene silencing namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation." [GOC:dph, GOC:tb] is_a: GO:0010468 ! regulation of gene expression is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0016458 ! gene silencing relationship: regulates GO:0016458 ! gene silencing created_by: dph creation_date: 2009-10-05T03:23:56Z [Term] id: GO:0060969 name: negative regulation of gene silencing namespace: biological_process def: "Any process that decreases the rate, frequency, or extent of gene silencing, the transcriptional or post-transcriptional process carried out at the cellular level that results in long-term gene inactivation." [GOC:dph, GOC:tb] is_a: GO:0010628 ! positive regulation of gene expression is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0060968 ! regulation of gene silencing intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0016458 ! gene silencing relationship: negatively_regulates GO:0016458 ! gene silencing created_by: dph creation_date: 2009-10-05T03:26:19Z [Term] id: GO:0061041 name: regulation of wound healing namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury." [GOC:BHF, GOC:dph] is_a: GO:1903034 ! regulation of response to wounding intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0042060 ! wound healing relationship: regulates GO:0042060 ! wound healing created_by: dph creation_date: 2010-02-25T10:14:37Z [Term] id: GO:0061045 name: negative regulation of wound healing namespace: biological_process def: "Any process that decreases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury." [GOC:dph] is_a: GO:0032102 ! negative regulation of response to external stimulus is_a: GO:0061041 ! regulation of wound healing is_a: GO:1903035 ! negative regulation of response to wounding intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0042060 ! wound healing relationship: negatively_regulates GO:0042060 ! wound healing created_by: dph creation_date: 2010-02-25T10:33:30Z [Term] id: GO:0061478 name: response to platelet aggregation inhibitor namespace: biological_process 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 platelet aggregation inhibitor stimulus." [GOC:dph] is_a: GO:0042493 ! response to drug created_by: dph creation_date: 2012-11-07T09:09:37Z [Term] id: GO:0065003 name: protein-containing complex assembly namespace: biological_process alt_id: GO:0006461 def: "The aggregation, arrangement and bonding together of a set of macromolecules to form a protein-containing complex." [GOC:jl] subset: goslim_chembl subset: goslim_generic subset: goslim_metagenomics subset: goslim_pir subset: goslim_pombe synonym: "chaperone activity" RELATED [] synonym: "macromolecular complex assembly" RELATED [] synonym: "macromolecule complex assembly" RELATED [] synonym: "protein complex assembly" RELATED [] synonym: "protein complex formation" RELATED [] is_a: GO:0022607 ! cellular component assembly is_a: GO:0043933 ! protein-containing complex subunit organization [Term] id: GO:0065007 name: biological regulation namespace: biological_process def: "Any process that modulates a measurable attribute of any biological process, quality or function." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw] subset: gocheck_do_not_annotate subset: goslim_pir synonym: "regulation" BROAD [] is_a: GO:0008150 ! biological_process [Term] id: GO:0065008 name: regulation of biological quality namespace: biological_process def: "Any process that modulates a qualitative or quantitative trait of a biological quality. A biological quality is a measurable attribute of an organism or part of an organism, such as size, mass, shape, color, etc." [GOC:dph, GOC:isa_complete, GOC:mah, GOC:pr, GOC:vw] subset: goslim_pir synonym: "regulation of biological attribute" EXACT [] synonym: "regulation of biological characteristic" EXACT [] is_a: GO:0065007 ! biological regulation [Term] id: GO:0065009 name: regulation of molecular function namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GOC:isa_complete] subset: gocheck_do_not_annotate subset: goslim_agr subset: goslim_pir synonym: "regulation of a molecular function" EXACT [] is_a: GO:0065007 ! biological regulation intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0003674 ! GO:molecular_function relationship: regulates GO:0003674 ! GO:molecular_function [Term] id: GO:0070201 name: regulation of establishment of protein localization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of a protein to a specific location." [GOC:BHF, GOC:mah] synonym: "regulation of establishment of protein localisation" EXACT [GOC:mah] is_a: GO:0032880 ! regulation of protein localization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0045184 ! establishment of protein localization relationship: regulates GO:0045184 ! establishment of protein localization [Term] id: GO:0070549 name: negative regulation of translation involved in RNA interference namespace: biological_process def: "A process of negative regulation of translation that is mediated by the association of small interfering RNAs (siRNAs) with a cognate target mRNA." [GOC:mah, PMID:18771919] synonym: "down regulation of translation involved in RNA interference" EXACT [GOC:mah] synonym: "down-regulation of translation involved in RNA interference" EXACT [GOC:mah] synonym: "downregulation of translation involved in RNA interference" EXACT [GOC:mah] synonym: "inhibition of translation involved in RNA interference" NARROW [GOC:mah] synonym: "RNA interference, negative regulation of translation" EXACT [GOC:mah] is_a: GO:0040033 ! negative regulation of translation, ncRNA-mediated intersection_of: GO:0017148 ! negative regulation of translation intersection_of: part_of GO:0016246 ! RNA interference relationship: part_of GO:0016246 ! RNA interference [Term] id: GO:0070727 name: cellular macromolecule localization namespace: biological_process def: "Any process in which a macromolecule is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GOC:mah] synonym: "cellular macromolecule localisation" EXACT [GOC:mah] is_a: GO:0033036 ! macromolecule localization is_a: GO:0051641 ! cellular localization created_by: midori creation_date: 2009-06-16T04:08:29Z [Term] id: GO:0070887 name: cellular response to chemical stimulus namespace: biological_process 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 chemical stimulus." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate is_a: GO:0042221 ! response to chemical is_a: GO:0051716 ! cellular response to stimulus created_by: midori creation_date: 2009-08-27T04:41:45Z [Term] id: GO:0071310 name: cellular response to organic substance namespace: biological_process 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 an organic substance stimulus." [GOC:mah] is_a: GO:0010033 ! response to organic substance is_a: GO:0070887 ! cellular response to chemical stimulus created_by: midori creation_date: 2009-12-10T04:46:04Z [Term] id: GO:0071407 name: cellular response to organic cyclic compound namespace: biological_process 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 an organic cyclic compound stimulus." [GOC:mah] synonym: "cellular response to organic cyclic substance" EXACT [GOC:mah] is_a: GO:0014070 ! response to organic cyclic compound is_a: GO:0071310 ! cellular response to organic substance created_by: midori creation_date: 2009-12-14T02:55:58Z [Term] id: GO:0071417 name: cellular response to organonitrogen compound namespace: biological_process 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 an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond." [CHEBI:35352, GOC:mah] synonym: "cellular response to organic nitrogen" EXACT [GOC:mah] is_a: GO:0010243 ! response to organonitrogen compound is_a: GO:0071310 ! cellular response to organic substance is_a: GO:0071495 ! cellular response to endogenous stimulus is_a: GO:1901699 ! cellular response to nitrogen compound created_by: midori creation_date: 2009-12-14T04:07:27Z [Term] id: GO:0071495 name: cellular response to endogenous stimulus namespace: biological_process 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 arising within the organism." [GOC:mah] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate is_a: GO:0009719 ! response to endogenous stimulus created_by: midori creation_date: 2009-12-18T02:25:40Z [Term] id: GO:0071702 name: organic substance transport namespace: biological_process def: "The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon." [CHEBI:50860, GOC:mah] is_a: GO:0006810 ! transport created_by: midori creation_date: 2010-03-08T02:15:14Z [Term] id: GO:0071704 name: organic substance metabolic process namespace: biological_process def: "The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon." [CHEBI:50860, GOC:mah] synonym: "organic molecular entity metabolic process" EXACT [] synonym: "organic molecular entity metabolism" EXACT [] synonym: "organic substance metabolism" EXACT [] is_a: GO:0008152 ! metabolic process created_by: midori creation_date: 2010-03-08T03:32:18Z [Term] id: GO:0071705 name: nitrogen compound transport namespace: biological_process def: "The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [CHEBI:51143, GOC:mah] is_a: GO:0006810 ! transport created_by: midori creation_date: 2010-03-08T03:56:28Z [Term] id: GO:0071706 name: tumor necrosis factor superfamily cytokine production namespace: biological_process 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." [GOC:add] synonym: "TNF superfamily production" RELATED [GOC:rv] synonym: "TNFSF cytokine production" EXACT [GOC:add] is_a: GO:0001816 ! cytokine production created_by: midori creation_date: 2010-03-09T02:40:35Z [Term] id: GO:0071715 name: icosanoid transport namespace: biological_process def: "The directed movement of icosanoids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Icosanoids are unsaturated C20 fatty acids and skeletally related compounds." [CHEBI:23899, GOC:mah] synonym: "eicosanoid transport" EXACT [GOC:sl] is_a: GO:0046942 ! carboxylic acid transport is_a: GO:1901571 ! fatty acid derivative transport created_by: midori creation_date: 2010-03-10T02:47:22Z [Term] id: GO:0071826 name: ribonucleoprotein complex subunit organization namespace: biological_process def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a ribonucleoprotein complex." [GOC:mah] synonym: "protein-RNA complex subunit organization" EXACT [GOC:mah] synonym: "ribonucleoprotein complex subunit organisation" EXACT [GOC:mah] synonym: "RNA-protein complex subunit organization" EXACT [GOC:mah] is_a: GO:0043933 ! protein-containing complex subunit organization created_by: midori creation_date: 2010-09-08T10:10:35Z [Term] id: GO:0071840 name: cellular component organization or biogenesis namespace: biological_process alt_id: GO:0071841 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, arrangement of constituent parts, or disassembly of a cellular component." [GOC:mah] subset: goslim_metagenomics synonym: "cellular component organisation or biogenesis" EXACT [GOC:mah] synonym: "cellular component organisation or biogenesis at cellular level" EXACT [GOC:mah] synonym: "cellular component organization or biogenesis at cellular level" EXACT [] is_a: GO:0008150 ! biological_process created_by: midori creation_date: 2010-09-10T01:39:16Z [Term] id: GO:0071897 name: DNA biosynthetic process namespace: biological_process def: "The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one." [GOC:mah] synonym: "DNA anabolism" EXACT [GOC:mah] synonym: "DNA biosynthesis" EXACT [GOC:mah] synonym: "DNA formation" EXACT [GOC:mah] synonym: "DNA synthesis" EXACT [GOC:mah] is_a: GO:0006259 ! DNA metabolic process is_a: GO:0034645 ! cellular macromolecule biosynthetic process is_a: GO:0034654 ! nucleobase-containing compound biosynthetic process created_by: midori creation_date: 2010-09-15T02:14:33Z [Term] id: GO:0072749 name: cellular response to cytochalasin B namespace: biological_process 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 cytochalasin B stimulus." [GOC:mah] is_a: GO:0035690 ! cellular response to drug is_a: GO:0036146 ! cellular response to mycotoxin is_a: GO:0071407 ! cellular response to organic cyclic compound is_a: GO:0071417 ! cellular response to organonitrogen compound is_a: GO:1901328 ! response to cytochalasin B is_a: GO:1901701 ! cellular response to oxygen-containing compound created_by: midori creation_date: 2012-08-31T12:37:15Z [Term] id: GO:0080090 name: regulation of primary metabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the chemical reactions and pathways within a cell or an organism involving those compounds formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism." [PMID:19211694] is_a: GO:0019222 ! regulation of metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0044238 ! primary metabolic process relationship: regulates GO:0044238 ! primary metabolic process created_by: donghui creation_date: 2009-04-22T04:30:52Z [Term] id: GO:0080134 name: regulation of response to stress namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a response to stress. Response to stress is 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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:dhl] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006950 ! response to stress relationship: regulates GO:0006950 ! response to stress created_by: donghui creation_date: 2009-05-06T04:51:28Z [Term] id: GO:0080135 name: regulation of cellular response to stress namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a cellular response to stress. Cellular response to stress is 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 the organism is under stress. The stress is usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:dhl] is_a: GO:0050794 ! regulation of cellular process is_a: GO:0080134 ! regulation of response to stress intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0033554 ! cellular response to stress relationship: regulates GO:0033554 ! cellular response to stress created_by: donghui creation_date: 2009-05-06T05:02:52Z [Term] id: GO:0090087 name: regulation of peptide transport namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:tb] is_a: GO:0051049 ! regulation of transport intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0015833 ! peptide transport relationship: regulates GO:0015833 ! peptide transport created_by: tanyaberardini creation_date: 2009-10-23T11:21:38Z [Term] id: GO:0090237 name: regulation of arachidonic acid secretion namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of arachidonic acid secretion, the controlled release of arachidonic acid from a cell or a tissue." [GOC:dph, GOC:tb] is_a: GO:0032303 ! regulation of icosanoid secretion intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0050482 ! arachidonic acid secretion relationship: regulates GO:0050482 ! arachidonic acid secretion created_by: tanyaberardini creation_date: 2010-01-20T03:32:22Z [Term] id: GO:0090238 name: positive regulation of arachidonic acid secretion namespace: biological_process def: "Any process that increases the rate, frequency, or extent of arachidonic acid secretion, the controlled release of arachidonic acid from a cell or a tissue." [GOC:BHF, GOC:dph, GOC:tb] is_a: GO:0032305 ! positive regulation of icosanoid secretion is_a: GO:0090237 ! regulation of arachidonic acid secretion intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0050482 ! arachidonic acid secretion relationship: positively_regulates GO:0050482 ! arachidonic acid secretion created_by: tanyaberardini creation_date: 2010-01-20T03:32:22Z [Term] id: GO:0090303 name: positive regulation of wound healing namespace: biological_process def: "Any process that increases the rate, frequency, or extent of the series of events that restore integrity to a damaged tissue, following an injury." [GOC:BHF] is_a: GO:0061041 ! regulation of wound healing is_a: GO:1903036 ! positive regulation of response to wounding intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0042060 ! wound healing relationship: positively_regulates GO:0042060 ! wound healing created_by: tanyaberardini creation_date: 2010-03-22T02:12:03Z [Term] id: GO:0090304 name: nucleic acid metabolic process namespace: biological_process def: "Any cellular metabolic process involving nucleic acids." [GOC:dph, GOC:tb] is_a: GO:0006139 ! nucleobase-containing compound metabolic process is_a: GO:0043170 ! macromolecule metabolic process created_by: tanyaberardini creation_date: 2010-04-07T10:18:47Z [Term] id: GO:0090305 name: nucleic acid phosphodiester bond hydrolysis namespace: biological_process def: "The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis." [GOC:dph, GOC:tb] synonym: "nucleic acid cleavage" EXACT [GOC:dph, GOC:tb] is_a: GO:0090304 ! nucleic acid metabolic process created_by: tanyaberardini creation_date: 2010-04-07T10:26:30Z [Term] id: GO:0090342 name: regulation of cell aging namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan." [GOC:BHF, GOC:dph, GOC:tb] is_a: GO:0050793 ! regulation of developmental process is_a: GO:0050794 ! regulation of cellular process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0007569 ! cell aging relationship: regulates GO:0007569 ! cell aging created_by: tanyaberardini creation_date: 2010-06-02T10:12:37Z [Term] id: GO:0090343 name: positive regulation of cell aging namespace: biological_process def: "Any process that increases the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan." [GOC:BHF, GOC:dph, GOC:tb] is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0051094 ! positive regulation of developmental process is_a: GO:0090342 ! regulation of cell aging intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0007569 ! cell aging relationship: positively_regulates GO:0007569 ! cell aging created_by: tanyaberardini creation_date: 2010-06-02T10:12:37Z [Term] id: GO:0090344 name: negative regulation of cell aging namespace: biological_process def: "Any process that decreases the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan." [GOC:BHF, GOC:dph, GOC:tb] is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0051093 ! negative regulation of developmental process is_a: GO:0090342 ! regulation of cell aging intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0007569 ! cell aging relationship: negatively_regulates GO:0007569 ! cell aging created_by: tanyaberardini creation_date: 2010-06-02T10:12:37Z [Term] id: GO:0090592 name: DNA synthesis involved in DNA replication namespace: biological_process def: "Synthesis of DNA that is a part of the process of duplicating one or more molecules of DNA." [GOC:vw] is_a: GO:0071897 ! DNA biosynthetic process intersection_of: GO:0071897 ! DNA biosynthetic process intersection_of: part_of GO:0006260 ! DNA replication relationship: part_of GO:0006260 ! DNA replication created_by: tanyaberardini creation_date: 2014-06-06T13:54:36Z [Term] id: GO:0097159 name: organic cyclic compound binding namespace: molecular_function def: "Interacting selectively and non-covalently with an organic cyclic compound, any molecular entity that contains carbon arranged in a cyclic molecular structure." [CHEBI:33832, GOC:sjw, PMID:7583672] is_a: GO:0005488 ! binding created_by: paola creation_date: 2011-09-23T02:31:01Z [Term] id: GO:0097190 name: apoptotic signaling pathway namespace: biological_process alt_id: GO:0008624 def: "A series of molecular signals which triggers the apoptotic death of a cell. The pathway starts with reception of a signal, and ends when the execution phase of apoptosis is triggered." [GOC:mtg_apoptosis] comment: This term can be used to annotate gene products involved in apoptotic events happening downstream of the cross-talk point between the extrinsic and intrinsic apoptotic pathways. The cross-talk starts when caspase-8 cleaves Bid and truncated Bid interacts with mitochondria. From this point on it is not possible to distinguish between extrinsic and intrinsic pathways. synonym: "apoptotic signalling pathway" EXACT [GOC:mah] synonym: "induction of apoptosis by extracellular signals" EXACT [] xref: Reactome:REACT_101039 "Ceramide signalling, Canis familiaris" xref: Reactome:REACT_101287 "Death Receptor Signalling, Xenopus tropicalis" xref: Reactome:REACT_101722 "FasL/ CD95L signaling, Rattus norvegicus" xref: Reactome:REACT_102105 "FASL binds FAS Receptor, Taeniopygia guttata" xref: Reactome:REACT_102682 "Ceramide signalling, Bos taurus" xref: Reactome:REACT_103565 "Death Receptor Signalling, Danio rerio" xref: Reactome:REACT_104430 "Ceramide signalling, Gallus gallus" xref: Reactome:REACT_104446 "Death Receptor Signalling, Bos taurus" xref: Reactome:REACT_104880 "Cell death signalling via NRAGE, NRIF and NADE, Drosophila melanogaster" xref: Reactome:REACT_105789 "Cell death signalling via NRAGE, NRIF and NADE, Canis familiaris" xref: Reactome:REACT_1059 "Extrinsic Pathway for Apoptosis, Homo sapiens" xref: Reactome:REACT_106019 "Ceramide signalling, Caenorhabditis elegans" xref: Reactome:REACT_106417 "Cell death signalling via NRAGE, NRIF and NADE, Oryza sativa" xref: Reactome:REACT_107145 "FASL binds FAS Receptor, Rattus norvegicus" xref: Reactome:REACT_107277 "Cell death signalling via NRAGE, NRIF and NADE, Rattus norvegicus" xref: Reactome:REACT_108226 "Ceramide signalling, Rattus norvegicus" xref: Reactome:REACT_108738 "FASL binds FAS Receptor, Canis familiaris" xref: Reactome:REACT_108954 "Cell death signalling via NRAGE, NRIF and NADE, Sus scrofa" xref: Reactome:REACT_110327 "FASL binds FAS Receptor, Gallus gallus" xref: Reactome:REACT_110777 "Extrinsic Pathway for Apoptosis, Canis familiaris" xref: Reactome:REACT_113012 "Extrinsic Pathway for Apoptosis, Caenorhabditis elegans" xref: Reactome:REACT_113720 "FasL/ CD95L signaling, Xenopus tropicalis" xref: Reactome:REACT_114928 "Cell death signalling via NRAGE, NRIF and NADE, Dictyostelium discoideum" xref: Reactome:REACT_115331 "FASL binds FAS Receptor, Xenopus tropicalis" xref: Reactome:REACT_13720 "Cell death signalling via NRAGE, NRIF and NADE, Homo sapiens" xref: Reactome:REACT_13806 "Ceramide signalling, Homo sapiens" xref: Reactome:REACT_1426 "FASL binds FAS Receptor, Homo sapiens" xref: Reactome:REACT_1619 "Death Receptor Signalling, Homo sapiens" xref: Reactome:REACT_28136 "Death Receptor Signalling, Taeniopygia guttata" xref: Reactome:REACT_30777 "Death Receptor Signalling, Sus scrofa" xref: Reactome:REACT_32035 "FasL/ CD95L signaling, Danio rerio" xref: Reactome:REACT_33023 "Ceramide signalling, Xenopus tropicalis" xref: Reactome:REACT_33363 "Death Receptor Signalling, Gallus gallus" xref: Reactome:REACT_47012 "Death Receptor Signalling, Mus musculus" xref: Reactome:REACT_78512 "Ceramide signalling, Taeniopygia guttata" xref: Reactome:REACT_78709 "Ceramide signalling, Drosophila melanogaster" xref: Reactome:REACT_79738 "Extrinsic Pathway for Apoptosis, Xenopus tropicalis" xref: Reactome:REACT_81353 "Ceramide signalling, Mus musculus" xref: Reactome:REACT_81381 "FasL/ CD95L signaling, Gallus gallus" xref: Reactome:REACT_82611 "Cell death signalling via NRAGE, NRIF and NADE, Taeniopygia guttata" xref: Reactome:REACT_83750 "Extrinsic Pathway for Apoptosis, Gallus gallus" xref: Reactome:REACT_84151 "Extrinsic Pathway for Apoptosis, Bos taurus" xref: Reactome:REACT_85830 "Cell death signalling via NRAGE, NRIF and NADE, Danio rerio" xref: Reactome:REACT_86320 "Cell death signalling via NRAGE, NRIF and NADE, Gallus gallus" xref: Reactome:REACT_86807 "Death Receptor Signalling, Canis familiaris" xref: Reactome:REACT_88410 "Cell death signalling via NRAGE, NRIF and NADE, Schizosaccharomyces pombe" xref: Reactome:REACT_88562 "Ceramide signalling, Danio rerio" xref: Reactome:REACT_89305 "FASL binds FAS Receptor, Bos taurus" xref: Reactome:REACT_89421 "Cell death signalling via NRAGE, NRIF and NADE, Xenopus tropicalis" xref: Reactome:REACT_900 "FasL/ CD95L signaling, Homo sapiens" xref: Reactome:REACT_90409 "Ceramide signalling, Schizosaccharomyces pombe" xref: Reactome:REACT_90414 "Cell death signalling via NRAGE, NRIF and NADE, Arabidopsis thaliana" xref: Reactome:REACT_90980 "FasL/ CD95L signaling, Canis familiaris" xref: Reactome:REACT_91488 "Cell death signalling via NRAGE, NRIF and NADE, Bos taurus" xref: Reactome:REACT_92659 "Extrinsic Pathway for Apoptosis, Sus scrofa" xref: Reactome:REACT_92947 "Extrinsic Pathway for Apoptosis, Danio rerio" xref: Reactome:REACT_93354 "Ceramide signalling, Sus scrofa" xref: Reactome:REACT_93927 "Cell death signalling via NRAGE, NRIF and NADE, Caenorhabditis elegans" xref: Reactome:REACT_94832 "Ceramide signalling, Saccharomyces cerevisiae" xref: Reactome:REACT_94837 "Extrinsic Pathway for Apoptosis, Taeniopygia guttata" xref: Reactome:REACT_95750 "FASL binds FAS Receptor, Danio rerio" xref: Reactome:REACT_95777 "FasL/ CD95L signaling, Taeniopygia guttata" xref: Reactome:REACT_96066 "Death Receptor Signalling, Rattus norvegicus" xref: Reactome:REACT_96229 "Extrinsic Pathway for Apoptosis, Rattus norvegicus" xref: Reactome:REACT_96867 "Cell death signalling via NRAGE, NRIF and NADE, Saccharomyces cerevisiae" xref: Reactome:REACT_97301 "Extrinsic Pathway for Apoptosis, Mus musculus" xref: Reactome:REACT_98119 "Cell death signalling via NRAGE, NRIF and NADE, Mus musculus" xref: Reactome:REACT_98804 "FasL/ CD95L signaling, Bos taurus" xref: Reactome:REACT_99367 "FASL binds FAS Receptor, Mus musculus" xref: Reactome:REACT_99865 "FasL/ CD95L signaling, Mus musculus" is_a: GO:0007165 ! signal transduction relationship: part_of GO:0006915 ! apoptotic process created_by: paola creation_date: 2011-11-23T09:30:23Z [Term] id: GO:0097194 name: execution phase of apoptosis namespace: biological_process def: "A stage of the apoptotic process that starts with the controlled breakdown of the cell through the action of effector caspases or other effector molecules (e.g. cathepsins, calpains etc.). Key steps of the execution phase are rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died." [GOC:mtg_apoptosis, PMID:21760595] synonym: "apoptosis" NARROW [] synonym: "execution phase of apoptotic process" EXACT [] is_a: GO:0009987 ! cellular process relationship: has_part GO:0032060 ! bleb assembly relationship: part_of GO:0006915 ! apoptotic process created_by: paola creation_date: 2011-11-23T09:45:24Z [Term] id: GO:0097237 name: cellular response to toxic substance namespace: biological_process 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 toxic stimulus." [GOC:pr] is_a: GO:0009636 ! response to toxic substance is_a: GO:0070887 ! cellular response to chemical stimulus created_by: paola creation_date: 2012-02-02T12:23:31Z [Term] id: GO:0097458 name: neuron part def: "Any constituent part of a neuron, the basic cellular unit of nervous tissue. A typical neuron consists of a cell body (often called the soma), an axon, and dendrites. Their purpose is to receive, conduct, and transmit impulses in the nervous system." [] is_a: GO:0005575 ! cellular_component property_value: IAO:0000111 "neuron part" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/go.owl [Term] id: GO:0097659 name: nucleic acid-templated transcription namespace: biological_process def: "The cellular synthesis of RNA on a template of nucleic acid (DNA or RNA)." [GOC:pr, GOC:txnOH, GOC:vw] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: gocheck_do_not_manually_annotate subset: goslim_mouse is_a: GO:0032774 ! RNA biosynthetic process created_by: paola creation_date: 2014-10-01T13:49:27Z [Term] id: GO:0098900 name: regulation of action potential namespace: biological_process def: "Any process that modulates the frequency, rate or extent of action potential creation, propagation or termination. This typically occurs via modulation of the activity or expression of voltage-gated ion channels." [GOC:dos, GOC:dph, GOC:go_curators, GOC:tb, ISBN:978-0-07-139011-8] comment: The ion channels through which current flows during an action potential should be annotated to the process 'action potential'. Gene products involved in modulating the characteristics of an action potential via changing the expression levels or the activity of these channels (e.g. modulating their kinetics or voltage sensitivity) should be annotated to this regulation term. is_a: GO:0042391 ! regulation of membrane potential is_a: GO:0050789 ! regulation of biological process intersection_of: GO:0050789 ! regulation of biological process intersection_of: regulates GO:0001508 ! action potential relationship: regulates GO:0001508 ! action potential [Term] id: GO:0120031 name: plasma membrane bounded cell projection assembly namespace: biological_process def: "Formation of a prolongation or process extending and that is bounded by plasma membrane, e.g. a cilium, lamellipodium, or axon." [GOC:krc] is_a: GO:0030031 ! cell projection assembly is_a: GO:0120036 ! plasma membrane bounded cell projection organization created_by: kchris creation_date: 2017-04-24T23:56:08Z [Term] id: GO:0120032 name: regulation of plasma membrane bounded cell projection assembly namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of plasma membrane bounded cell projection assembly." [GOC:krc] is_a: GO:0060491 ! regulation of cell projection assembly is_a: GO:0120035 ! regulation of plasma membrane bounded cell projection organization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0120031 ! plasma membrane bounded cell projection assembly relationship: regulates GO:0120031 ! plasma membrane bounded cell projection assembly created_by: kchris creation_date: 2017-04-26T04:27:04Z [Term] id: GO:0120033 name: negative regulation of plasma membrane bounded cell projection assembly namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of plasma membrane bounded cell projection assembly." [GOC:krc] is_a: GO:0031345 ! negative regulation of cell projection organization is_a: GO:0120032 ! regulation of plasma membrane bounded cell projection assembly intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0120031 ! plasma membrane bounded cell projection assembly relationship: negatively_regulates GO:0120031 ! plasma membrane bounded cell projection assembly created_by: kchris creation_date: 2017-04-26T04:34:31Z [Term] id: GO:0120034 name: positive regulation of plasma membrane bounded cell projection assembly namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of plasma membrane bounded cell projection assembly." [GOC:krc] is_a: GO:0031346 ! positive regulation of cell projection organization is_a: GO:0044089 ! positive regulation of cellular component biogenesis is_a: GO:0120032 ! regulation of plasma membrane bounded cell projection assembly intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0120031 ! plasma membrane bounded cell projection assembly relationship: positively_regulates GO:0120031 ! plasma membrane bounded cell projection assembly created_by: kchris creation_date: 2017-04-26T04:34:45Z [Term] id: GO:0120035 name: regulation of plasma membrane bounded cell projection organization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a process involved in the formation, arrangement of constituent parts, or disassembly of plasma membrane bounded cell projections." [GOC:krc] is_a: GO:0031344 ! regulation of cell projection organization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0120036 ! plasma membrane bounded cell projection organization relationship: regulates GO:0120036 ! plasma membrane bounded cell projection organization created_by: kchris creation_date: 2017-04-26T16:02:06Z [Term] id: GO:0120036 name: plasma membrane bounded cell projection organization namespace: biological_process def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a plasma membrane bounded prolongation or process extending from a cell, e.g. a cilium or axon." [GOC:krc] is_a: GO:0030030 ! cell projection organization created_by: kchris creation_date: 2017-04-26T16:07:02Z [Term] id: GO:0140097 name: catalytic activity, acting on DNA namespace: molecular_function def: "Catalytic activity that acts to modify DNA." [GOC:pdt] comment: https://github.com/geneontology/go-ontology/issues/14225 is_a: GO:0003824 ! catalytic activity created_by: pg creation_date: 2017-09-14T12:03:51Z [Term] id: GO:1900117 name: regulation of execution phase of apoptosis namespace: biological_process def: "Any process that modulates the frequency, rate or extent of execution phase of apoptosis." [GOC:mtg_apoptosis, GOC:TermGenie] is_a: GO:0042981 ! regulation of apoptotic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0097194 ! execution phase of apoptosis relationship: regulates GO:0097194 ! execution phase of apoptosis created_by: pr creation_date: 2012-02-22T11:26:20Z [Term] id: GO:1900118 name: negative regulation of execution phase of apoptosis namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of execution phase of apoptosis." [GOC:mtg_apoptosis, GOC:TermGenie] synonym: "down regulation of execution phase of apoptosis" EXACT [GOC:TermGenie] synonym: "down-regulation of execution phase of apoptosis" EXACT [GOC:TermGenie] synonym: "downregulation of execution phase of apoptosis" EXACT [GOC:TermGenie] synonym: "inhibition of execution phase of apoptosis" NARROW [GOC:TermGenie] is_a: GO:0043066 ! negative regulation of apoptotic process is_a: GO:1900117 ! regulation of execution phase of apoptosis intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0097194 ! execution phase of apoptosis relationship: negatively_regulates GO:0097194 ! execution phase of apoptosis created_by: pr creation_date: 2012-02-22T11:26:24Z [Term] id: GO:1900119 name: positive regulation of execution phase of apoptosis namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of execution phase of apoptosis." [GOC:mtg_apoptosis, GOC:TermGenie] synonym: "activation of execution phase of apoptosis" NARROW [GOC:TermGenie] synonym: "up regulation of execution phase of apoptosis" EXACT [GOC:TermGenie] synonym: "up-regulation of execution phase of apoptosis" EXACT [GOC:TermGenie] synonym: "upregulation of execution phase of apoptosis" EXACT [GOC:TermGenie] is_a: GO:0043065 ! positive regulation of apoptotic process is_a: GO:1900117 ! regulation of execution phase of apoptosis intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0097194 ! execution phase of apoptosis relationship: positively_regulates GO:0097194 ! execution phase of apoptosis created_by: pr creation_date: 2012-02-22T11:26:27Z [Term] id: GO:1900139 name: negative regulation of arachidonic acid secretion namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of arachidonic acid secretion." [GOC:TermGenie] synonym: "down regulation of arachidonic acid secretion" EXACT [GOC:TermGenie] synonym: "down-regulation of arachidonic acid secretion" EXACT [GOC:TermGenie] synonym: "downregulation of arachidonic acid secretion" EXACT [GOC:TermGenie] synonym: "inhibition of arachidonic acid secretion" NARROW [GOC:TermGenie] is_a: GO:0032304 ! negative regulation of icosanoid secretion is_a: GO:0090237 ! regulation of arachidonic acid secretion intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0050482 ! arachidonic acid secretion relationship: negatively_regulates GO:0050482 ! arachidonic acid secretion created_by: rph creation_date: 2012-03-01T09:21:19Z [Term] id: GO:1900368 name: regulation of RNA interference namespace: biological_process def: "Any process that modulates the frequency, rate or extent of RNA interference." [GOC:kmv, GOC:TermGenie, PMID:22412382] synonym: "regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "regulation of RNAi" EXACT [GOC:TermGenie] is_a: GO:0060147 ! regulation of posttranscriptional gene silencing is_a: GO:0060966 ! regulation of gene silencing by RNA intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0016246 ! RNA interference relationship: regulates GO:0016246 ! RNA interference created_by: kmv creation_date: 2012-04-13T08:28:39Z [Term] id: GO:1900369 name: negative regulation of RNA interference namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of RNA interference." [GOC:kmv, GOC:TermGenie, PMID:22412382] synonym: "down regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "down regulation of RNA interference" EXACT [GOC:TermGenie] synonym: "down regulation of RNAi" EXACT [GOC:TermGenie] synonym: "down-regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "down-regulation of RNA interference" EXACT [GOC:TermGenie] synonym: "down-regulation of RNAi" EXACT [GOC:TermGenie] synonym: "downregulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "downregulation of RNA interference" EXACT [GOC:TermGenie] synonym: "downregulation of RNAi" EXACT [GOC:TermGenie] synonym: "inhibition of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "inhibition of RNA interference" NARROW [GOC:TermGenie] synonym: "inhibition of RNAi" EXACT [GOC:TermGenie] synonym: "negative regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "negative regulation of RNAi" EXACT [GOC:TermGenie] is_a: GO:0060149 ! negative regulation of posttranscriptional gene silencing is_a: GO:0060967 ! negative regulation of gene silencing by RNA is_a: GO:1900368 ! regulation of RNA interference intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0016246 ! RNA interference relationship: negatively_regulates GO:0016246 ! RNA interference created_by: kmv creation_date: 2012-04-13T08:28:50Z [Term] id: GO:1900370 name: positive regulation of RNA interference namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of RNA interference." [GOC:kmv, GOC:TermGenie, PMID:22412382] synonym: "activation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "activation of RNA interference" NARROW [GOC:TermGenie] synonym: "activation of RNAi" EXACT [GOC:TermGenie] synonym: "positive regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "positive regulation of RNAi" EXACT [GOC:TermGenie] synonym: "up regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "up regulation of RNA interference" EXACT [GOC:TermGenie] synonym: "up regulation of RNAi" EXACT [GOC:TermGenie] synonym: "up-regulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "up-regulation of RNA interference" EXACT [GOC:TermGenie] synonym: "up-regulation of RNAi" EXACT [GOC:TermGenie] synonym: "upregulation of posttranscriptional gene silencing by siRNA" EXACT [GOC:TermGenie] synonym: "upregulation of RNA interference" EXACT [GOC:TermGenie] synonym: "upregulation of RNAi" EXACT [GOC:TermGenie] is_a: GO:0060148 ! positive regulation of posttranscriptional gene silencing is_a: GO:1900368 ! regulation of RNA interference intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0016246 ! RNA interference relationship: positively_regulates GO:0016246 ! RNA interference created_by: kmv creation_date: 2012-04-13T08:29:00Z [Term] id: GO:1901190 name: regulation of formation of translation initiation ternary complex namespace: biological_process def: "Any process that modulates the frequency, rate or extent of formation of translation initiation ternary complex." [GOC:TermGenie] synonym: "regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] is_a: GO:0006446 ! regulation of translational initiation is_a: GO:0043254 ! regulation of protein complex assembly intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0001677 ! formation of translation initiation ternary complex relationship: regulates GO:0001677 ! formation of translation initiation ternary complex created_by: ss creation_date: 2012-07-25T02:26:58Z [Term] id: GO:1901191 name: negative regulation of formation of translation initiation ternary complex namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of formation of translation initiation ternary complex." [GOC:TermGenie] synonym: "down regulation of formation of translation initiation ternary complex" EXACT [GOC:TermGenie] synonym: "down regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "down-regulation of formation of translation initiation ternary complex" EXACT [GOC:TermGenie] synonym: "down-regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "downregulation of formation of translation initiation ternary complex" EXACT [GOC:TermGenie] synonym: "downregulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "inhibition of formation of translation initiation ternary complex" NARROW [GOC:TermGenie] synonym: "inhibition of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "negative regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] is_a: GO:0031333 ! negative regulation of protein complex assembly is_a: GO:0045947 ! negative regulation of translational initiation is_a: GO:1901190 ! regulation of formation of translation initiation ternary complex intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0001677 ! formation of translation initiation ternary complex relationship: negatively_regulates GO:0001677 ! formation of translation initiation ternary complex created_by: ss creation_date: 2012-07-25T02:27:21Z [Term] id: GO:1901192 name: positive regulation of formation of translation initiation ternary complex namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of formation of translation initiation ternary complex." [GOC:TermGenie] synonym: "activation of formation of translation initiation ternary complex" NARROW [GOC:TermGenie] synonym: "activation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "positive regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "up regulation of formation of translation initiation ternary complex" EXACT [GOC:TermGenie] synonym: "up regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "up-regulation of formation of translation initiation ternary complex" EXACT [GOC:TermGenie] synonym: "up-regulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] synonym: "upregulation of formation of translation initiation ternary complex" EXACT [GOC:TermGenie] synonym: "upregulation of translation initiation ternary complex assembly" EXACT [GOC:TermGenie] is_a: GO:0031334 ! positive regulation of protein complex assembly is_a: GO:0045948 ! positive regulation of translational initiation is_a: GO:1901190 ! regulation of formation of translation initiation ternary complex intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0001677 ! formation of translation initiation ternary complex relationship: positively_regulates GO:0001677 ! formation of translation initiation ternary complex created_by: ss creation_date: 2012-07-25T02:27:29Z [Term] id: GO:1901328 name: response to cytochalasin B namespace: biological_process 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 cytochalasin B stimulus." [GOC:TermGenie] is_a: GO:0010046 ! response to mycotoxin is_a: GO:0010243 ! response to organonitrogen compound is_a: GO:0014070 ! response to organic cyclic compound is_a: GO:0061478 ! response to platelet aggregation inhibitor is_a: GO:1901700 ! response to oxygen-containing compound created_by: mah creation_date: 2012-08-30T16:36:35Z [Term] id: GO:1901360 name: organic cyclic compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organic cyclic compound." [GOC:TermGenie] synonym: "organic cyclic compound metabolism" EXACT [GOC:TermGenie] is_a: GO:0071704 ! organic substance metabolic process created_by: bf creation_date: 2012-09-14T09:03:51Z [Term] id: GO:1901361 name: organic cyclic compound catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of organic cyclic compound." [GOC:TermGenie] synonym: "organic cyclic compound breakdown" EXACT [GOC:TermGenie] synonym: "organic cyclic compound catabolism" EXACT [GOC:TermGenie] synonym: "organic cyclic compound degradation" EXACT [GOC:TermGenie] is_a: GO:1901360 ! organic cyclic compound metabolic process is_a: GO:1901575 ! organic substance catabolic process created_by: bf creation_date: 2012-09-14T09:05:04Z [Term] id: GO:1901362 name: organic cyclic compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of organic cyclic compound." [GOC:TermGenie] synonym: "organic cyclic compound anabolism" EXACT [GOC:TermGenie] synonym: "organic cyclic compound biosynthesis" EXACT [GOC:TermGenie] synonym: "organic cyclic compound formation" EXACT [GOC:TermGenie] synonym: "organic cyclic compound synthesis" EXACT [GOC:TermGenie] is_a: GO:1901360 ! organic cyclic compound metabolic process is_a: GO:1901576 ! organic substance biosynthetic process created_by: bf creation_date: 2012-09-14T09:05:22Z [Term] id: GO:1901363 name: heterocyclic compound binding namespace: molecular_function def: "Interacting selectively and non-covalently with heterocyclic compound." [GOC:TermGenie] is_a: GO:0005488 ! binding created_by: bf creation_date: 2012-09-14T13:53:50Z [Term] id: GO:1901564 name: organonitrogen compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving organonitrogen compound." [GOC:pr, GOC:TermGenie] synonym: "organonitrogen compound metabolism" EXACT [GOC:TermGenie] is_a: GO:0006807 ! nitrogen compound metabolic process is_a: GO:0071704 ! organic substance metabolic process created_by: pr creation_date: 2012-11-04T15:17:52Z [Term] id: GO:1901566 name: organonitrogen compound biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of organonitrogen compound." [GOC:pr, GOC:TermGenie] synonym: "organonitrogen compound anabolism" EXACT [GOC:TermGenie] synonym: "organonitrogen compound biosynthesis" EXACT [GOC:TermGenie] synonym: "organonitrogen compound formation" EXACT [GOC:TermGenie] synonym: "organonitrogen compound synthesis" EXACT [GOC:TermGenie] is_a: GO:1901564 ! organonitrogen compound metabolic process is_a: GO:1901576 ! organic substance biosynthetic process created_by: pr creation_date: 2012-11-04T15:18:00Z [Term] id: GO:1901571 name: fatty acid derivative transport namespace: biological_process def: "The directed movement of a fatty acid derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:pr, GOC:TermGenie] is_a: GO:0071702 ! organic substance transport created_by: pr creation_date: 2012-11-04T17:13:49Z [Term] id: GO:1901575 name: organic substance catabolic process namespace: biological_process def: "The chemical reactions and pathways resulting in the breakdown of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] synonym: "organic molecular entity breakdown" EXACT [GOC:TermGenie] synonym: "organic molecular entity catabolic process" EXACT [] synonym: "organic molecular entity catabolism" EXACT [GOC:TermGenie] synonym: "organic molecular entity degradation" EXACT [GOC:TermGenie] synonym: "organic substance breakdown" EXACT [] synonym: "organic substance catabolism" EXACT [] synonym: "organic substance degradation" EXACT [] is_a: GO:0009056 ! catabolic process is_a: GO:0071704 ! organic substance metabolic process created_by: pr creation_date: 2012-11-05T11:04:36Z [Term] id: GO:1901576 name: organic substance biosynthetic process namespace: biological_process def: "The chemical reactions and pathways resulting in the formation of an organic substance, any molecular entity containing carbon." [GOC:pr, GOC:TermGenie] synonym: "organic molecular entity anabolism" EXACT [GOC:TermGenie] synonym: "organic molecular entity biosynthesis" EXACT [GOC:TermGenie] synonym: "organic molecular entity biosynthetic process" EXACT [] synonym: "organic molecular entity formation" EXACT [GOC:TermGenie] synonym: "organic molecular entity synthesis" EXACT [GOC:TermGenie] synonym: "organic substance anabolism" EXACT [] synonym: "organic substance biosynthesis" EXACT [] synonym: "organic substance formation" EXACT [] synonym: "organic substance synthesis" EXACT [] is_a: GO:0009058 ! biosynthetic process is_a: GO:0071704 ! organic substance metabolic process created_by: pr creation_date: 2012-11-05T11:04:40Z [Term] id: GO:1901698 name: response to nitrogen compound namespace: biological_process 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 nitrogen compound stimulus." [GOC:pr, GOC:TermGenie] synonym: "response to nitrogen molecular entity" EXACT [] is_a: GO:0042221 ! response to chemical created_by: pr creation_date: 2012-12-13T15:06:08Z [Term] id: GO:1901699 name: cellular response to nitrogen compound namespace: biological_process 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 nitrogen compound stimulus." [GOC:pr, GOC:TermGenie] synonym: "cellular response to nitrogen molecular entity" EXACT [] is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1901698 ! response to nitrogen compound created_by: pr creation_date: 2012-12-13T15:06:13Z [Term] id: GO:1901700 name: response to oxygen-containing compound namespace: biological_process 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 an oxygen-containing compound stimulus." [GOC:pr, GOC:TermGenie] synonym: "response to oxygen molecular entity" EXACT [] is_a: GO:0042221 ! response to chemical created_by: pr creation_date: 2012-12-13T15:11:37Z [Term] id: GO:1901701 name: cellular response to oxygen-containing compound namespace: biological_process 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 an oxygen-containing compound stimulus." [GOC:pr, GOC:TermGenie] synonym: "cellular response to oxygen molecular entity" EXACT [] is_a: GO:0070887 ! cellular response to chemical stimulus is_a: GO:1901700 ! response to oxygen-containing compound created_by: pr creation_date: 2012-12-13T15:11:42Z [Term] id: GO:1902337 name: regulation of apoptotic process involved in morphogenesis namespace: biological_process def: "Any process that modulates the frequency, rate or extent of apoptotic process involved in morphogenesis." [GOC:sart, GOC:TermGenie, PMID:12202035] synonym: "regulation of apoptosis involved in development" RELATED [GOC:TermGenie] synonym: "regulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] synonym: "regulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] is_a: GO:0022603 ! regulation of anatomical structure morphogenesis is_a: GO:1904748 ! regulation of apoptotic process involved in development intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0060561 ! apoptotic process involved in morphogenesis relationship: regulates GO:0060561 ! apoptotic process involved in morphogenesis created_by: sart creation_date: 2013-07-29T15:03:16Z [Term] id: GO:1902338 name: negative regulation of apoptotic process involved in morphogenesis namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in morphogenesis." [GOC:sart, GOC:TermGenie, PMID:12202035] synonym: "down regulation of apoptosis involved in development" RELATED [GOC:TermGenie] synonym: "down regulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] synonym: "down regulation of apoptotic process involved in morphogenesis" EXACT [GOC:TermGenie] synonym: "down regulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] synonym: "down-regulation of apoptosis involved in development" RELATED [GOC:TermGenie] synonym: "down-regulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] synonym: "down-regulation of apoptotic process involved in morphogenesis" EXACT [GOC:TermGenie] synonym: "down-regulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] synonym: "downregulation of apoptosis involved in development" RELATED [GOC:TermGenie] synonym: "downregulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] synonym: "downregulation of apoptotic process involved in morphogenesis" EXACT [GOC:TermGenie] synonym: "downregulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] synonym: "inhibition of apoptosis involved in development" RELATED [GOC:TermGenie] synonym: "inhibition of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] synonym: "inhibition of apoptotic process involved in morphogenesis" NARROW [GOC:TermGenie] synonym: "inhibition of morphogenetic apoptosis" RELATED [GOC:TermGenie] synonym: "negative regulation of apoptosis involved in development" RELATED [GOC:TermGenie] synonym: "negative regulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] synonym: "negative regulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] is_a: GO:1902337 ! regulation of apoptotic process involved in morphogenesis is_a: GO:1904746 ! negative regulation of apoptotic process involved in development intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0060561 ! apoptotic process involved in morphogenesis relationship: negatively_regulates GO:0060561 ! apoptotic process involved in morphogenesis created_by: sart creation_date: 2013-07-29T15:03:25Z [Term] id: GO:1902339 name: positive regulation of apoptotic process involved in morphogenesis namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of apoptotic process involved in morphogenesis." [GOC:sart, GOC:TermGenie, PMID:12202035] synonym: "activation of apoptosis involved in development" RELATED [GOC:TermGenie] synonym: "activation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] synonym: "activation of apoptotic process involved in morphogenesis" NARROW [GOC:TermGenie] synonym: "activation of morphogenetic apoptosis" RELATED [GOC:TermGenie] synonym: "positive regulation of apoptosis involved in development" RELATED [GOC:TermGenie] synonym: "positive regulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] synonym: "positive regulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] synonym: "up regulation of apoptosis involved in development" RELATED [GOC:TermGenie] synonym: "up regulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] synonym: "up regulation of apoptotic process involved in morphogenesis" EXACT [GOC:TermGenie] synonym: "up regulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] synonym: "up-regulation of apoptosis involved in development" RELATED [GOC:TermGenie] synonym: "up-regulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] synonym: "up-regulation of apoptotic process involved in morphogenesis" EXACT [GOC:TermGenie] synonym: "up-regulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] synonym: "upregulation of apoptosis involved in development" RELATED [GOC:TermGenie] synonym: "upregulation of apoptosis involved in morphogenesis" NARROW [GOC:TermGenie] synonym: "upregulation of apoptotic process involved in morphogenesis" EXACT [GOC:TermGenie] synonym: "upregulation of morphogenetic apoptosis" RELATED [GOC:TermGenie] is_a: GO:1902337 ! regulation of apoptotic process involved in morphogenesis is_a: GO:1904747 ! positive regulation of apoptotic process involved in development intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0060561 ! apoptotic process involved in morphogenesis relationship: positively_regulates GO:0060561 ! apoptotic process involved in morphogenesis created_by: sart creation_date: 2013-07-29T15:03:33Z [Term] id: GO:1902494 name: catalytic complex namespace: cellular_component def: "A protein complex which is capable of catalytic activity." [GOC:bhm, GOC:TermGenie, PMID:8077207] subset: goslim_metagenomics synonym: "enzyme complex" EXACT [GOC:bhm, GOC:jl] is_a: GO:0032991 ! protein-containing complex created_by: bhm creation_date: 2013-11-13T16:18:47Z [Term] id: GO:1902510 name: regulation of apoptotic DNA fragmentation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of apoptotic DNA fragmentation." [GOC:hjd, GOC:TermGenie, PMID:15572351, PMID:15723341] comment: DNA fragmentation in response to apoptotic signals is achieved through the activity of apoptotic nucleases (see GO:0006309 'apoptotic DNA fragmentation'). Gene products involved in compartmentalization of such nucleases and in activation or repression of their enzymatic activity should be annotated to the regulation term GO:1902510 'regulation of apoptotic DNA fragmentation' or to one of its children (see PMID:15723341). synonym: "regulation of chromatinolysis" BROAD [GOC:TermGenie] synonym: "regulation of DNA catabolic process during apoptosis" EXACT [GOC:TermGenie] synonym: "regulation of DNA catabolism during apoptosis" EXACT [GOC:TermGenie] synonym: "regulation of DNA fragmentation" BROAD [GOC:TermGenie] synonym: "regulation of DNA fragmentation involved in apoptotic nuclear change" EXACT [GOC:TermGenie] synonym: "regulation of endonucleolytic DNA catabolic process involved in apoptosis" EXACT [GOC:TermGenie] is_a: GO:0051128 ! regulation of cellular component organization is_a: GO:1900117 ! regulation of execution phase of apoptosis is_a: GO:1903624 ! regulation of DNA catabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006309 ! apoptotic DNA fragmentation relationship: regulates GO:0006309 ! apoptotic DNA fragmentation created_by: hjd creation_date: 2013-11-15T18:28:32Z [Term] id: GO:1902511 name: negative regulation of apoptotic DNA fragmentation namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic DNA fragmentation." [GOC:hjd, GOC:TermGenie, PMID:15572351] synonym: "down regulation of apoptotic DNA fragmentation" EXACT [GOC:TermGenie] synonym: "down regulation of DNA catabolic process during apoptosis" EXACT [GOC:TermGenie] synonym: "down regulation of DNA catabolism during apoptosis" EXACT [GOC:TermGenie] synonym: "down regulation of DNA fragmentation involved in apoptotic nuclear change" EXACT [GOC:TermGenie] synonym: "down regulation of endonucleolytic DNA catabolic process involved in apoptosis" EXACT [GOC:TermGenie] synonym: "down-regulation of apoptotic DNA fragmentation" EXACT [GOC:TermGenie] synonym: "down-regulation of DNA catabolic process during apoptosis" EXACT [GOC:TermGenie] synonym: "down-regulation of DNA catabolism during apoptosis" EXACT [GOC:TermGenie] synonym: "down-regulation of DNA fragmentation involved in apoptotic nuclear change" EXACT [GOC:TermGenie] synonym: "down-regulation of endonucleolytic DNA catabolic process involved in apoptosis" EXACT [GOC:TermGenie] synonym: "downregulation of apoptotic DNA fragmentation" EXACT [GOC:TermGenie] synonym: "downregulation of DNA catabolic process during apoptosis" EXACT [GOC:TermGenie] synonym: "downregulation of DNA catabolism during apoptosis" EXACT [GOC:TermGenie] synonym: "downregulation of DNA fragmentation involved in apoptotic nuclear change" EXACT [GOC:TermGenie] synonym: "downregulation of endonucleolytic DNA catabolic process involved in apoptosis" EXACT [GOC:TermGenie] synonym: "inhibition of apoptotic DNA fragmentation" NARROW [GOC:TermGenie] synonym: "inhibition of DNA catabolic process during apoptosis" NARROW [GOC:TermGenie] synonym: "inhibition of DNA catabolism during apoptosis" NARROW [GOC:TermGenie] synonym: "inhibition of DNA fragmentation involved in apoptotic nuclear change" NARROW [GOC:TermGenie] synonym: "inhibition of endonucleolytic DNA catabolic process involved in apoptosis" NARROW [GOC:TermGenie] synonym: "negative regulation of DNA catabolic process during apoptosis" EXACT [GOC:TermGenie] synonym: "negative regulation of DNA catabolism during apoptosis" EXACT [GOC:TermGenie] synonym: "negative regulation of DNA fragmentation involved in apoptotic nuclear change" EXACT [GOC:TermGenie] synonym: "negative regulation of endonucleolytic DNA catabolic process involved in apoptosis" EXACT [GOC:TermGenie] is_a: GO:0051129 ! negative regulation of cellular component organization is_a: GO:1900118 ! negative regulation of execution phase of apoptosis is_a: GO:1902510 ! regulation of apoptotic DNA fragmentation is_a: GO:1903625 ! negative regulation of DNA catabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006309 ! apoptotic DNA fragmentation relationship: negatively_regulates GO:0006309 ! apoptotic DNA fragmentation created_by: hjd creation_date: 2013-11-15T18:28:41Z [Term] id: GO:1902512 name: positive regulation of apoptotic DNA fragmentation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of apoptotic DNA fragmentation." [GOC:hjd, GOC:TermGenie, PMID:15572351] synonym: "activation of apoptotic DNA fragmentation" NARROW [GOC:TermGenie] synonym: "activation of DNA catabolic process during apoptosis" NARROW [GOC:TermGenie] synonym: "activation of DNA catabolism during apoptosis" NARROW [GOC:TermGenie] synonym: "activation of DNA fragmentation involved in apoptotic nuclear change" NARROW [GOC:TermGenie] synonym: "activation of endonucleolytic DNA catabolic process involved in apoptosis" NARROW [GOC:TermGenie] synonym: "positive regulation of DNA catabolic process during apoptosis" EXACT [GOC:TermGenie] synonym: "positive regulation of DNA catabolism during apoptosis" EXACT [GOC:TermGenie] synonym: "positive regulation of DNA fragmentation involved in apoptotic nuclear change" EXACT [GOC:TermGenie] synonym: "positive regulation of endonucleolytic DNA catabolic process involved in apoptosis" EXACT [GOC:TermGenie] synonym: "up regulation of apoptotic DNA fragmentation" EXACT [GOC:TermGenie] synonym: "up regulation of DNA catabolic process during apoptosis" EXACT [GOC:TermGenie] synonym: "up regulation of DNA catabolism during apoptosis" EXACT [GOC:TermGenie] synonym: "up regulation of DNA fragmentation involved in apoptotic nuclear change" EXACT [GOC:TermGenie] synonym: "up regulation of endonucleolytic DNA catabolic process involved in apoptosis" EXACT [GOC:TermGenie] synonym: "up-regulation of apoptotic DNA fragmentation" EXACT [GOC:TermGenie] synonym: "up-regulation of DNA catabolic process during apoptosis" EXACT [GOC:TermGenie] synonym: "up-regulation of DNA catabolism during apoptosis" EXACT [GOC:TermGenie] synonym: "up-regulation of DNA fragmentation involved in apoptotic nuclear change" EXACT [GOC:TermGenie] synonym: "up-regulation of endonucleolytic DNA catabolic process involved in apoptosis" EXACT [GOC:TermGenie] synonym: "upregulation of apoptotic DNA fragmentation" EXACT [GOC:TermGenie] synonym: "upregulation of DNA catabolic process during apoptosis" EXACT [GOC:TermGenie] synonym: "upregulation of DNA catabolism during apoptosis" EXACT [GOC:TermGenie] synonym: "upregulation of DNA fragmentation involved in apoptotic nuclear change" EXACT [GOC:TermGenie] synonym: "upregulation of endonucleolytic DNA catabolic process involved in apoptosis" EXACT [GOC:TermGenie] is_a: GO:0051130 ! positive regulation of cellular component organization is_a: GO:1900119 ! positive regulation of execution phase of apoptosis is_a: GO:1902510 ! regulation of apoptotic DNA fragmentation is_a: GO:1903626 ! positive regulation of DNA catabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006309 ! apoptotic DNA fragmentation relationship: positively_regulates GO:0006309 ! apoptotic DNA fragmentation created_by: hjd creation_date: 2013-11-15T18:28:50Z [Term] id: GO:1902679 name: negative regulation of RNA biosynthetic process namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process." [GO:jl, GO_REF:0000058, GOC:TermGenie] synonym: "down regulation of RNA anabolism" EXACT [GOC:TermGenie] synonym: "down regulation of RNA biosynthesis" EXACT [GOC:TermGenie] synonym: "down regulation of RNA biosynthetic process" EXACT [GOC:TermGenie] synonym: "down regulation of RNA formation" EXACT [GOC:TermGenie] synonym: "down regulation of RNA synthesis" EXACT [GOC:TermGenie] synonym: "down-regulation of RNA anabolism" EXACT [GOC:TermGenie] synonym: "down-regulation of RNA biosynthesis" EXACT [GOC:TermGenie] synonym: "down-regulation of RNA biosynthetic process" EXACT [GOC:TermGenie] synonym: "down-regulation of RNA formation" EXACT [GOC:TermGenie] synonym: "down-regulation of RNA synthesis" EXACT [GOC:TermGenie] synonym: "downregulation of RNA anabolism" EXACT [GOC:TermGenie] synonym: "downregulation of RNA biosynthesis" EXACT [GOC:TermGenie] synonym: "downregulation of RNA biosynthetic process" EXACT [GOC:TermGenie] synonym: "downregulation of RNA formation" EXACT [GOC:TermGenie] synonym: "downregulation of RNA synthesis" EXACT [GOC:TermGenie] synonym: "inhibition of RNA anabolism" NARROW [GOC:TermGenie] synonym: "inhibition of RNA biosynthesis" NARROW [GOC:TermGenie] synonym: "inhibition of RNA biosynthetic process" NARROW [GOC:TermGenie] synonym: "inhibition of RNA formation" NARROW [GOC:TermGenie] synonym: "inhibition of RNA synthesis" NARROW [GOC:TermGenie] synonym: "negative regulation of RNA anabolism" EXACT [GOC:TermGenie] synonym: "negative regulation of RNA biosynthesis" EXACT [GOC:TermGenie] synonym: "negative regulation of RNA formation" EXACT [GOC:TermGenie] synonym: "negative regulation of RNA synthesis" EXACT [GOC:TermGenie] is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process is_a: GO:0031327 ! negative regulation of cellular biosynthetic process is_a: GO:0051253 ! negative regulation of RNA metabolic process is_a: GO:2001141 ! regulation of RNA biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0032774 ! RNA biosynthetic process relationship: negatively_regulates GO:0032774 ! RNA biosynthetic process created_by: jl creation_date: 2014-02-05T16:32:01Z [Term] id: GO:1902680 name: positive regulation of RNA biosynthetic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of RNA biosynthetic process." [GO:jl, GO_REF:0000058, GOC:TermGenie] synonym: "activation of RNA anabolism" NARROW [GOC:TermGenie] synonym: "activation of RNA biosynthesis" NARROW [GOC:TermGenie] synonym: "activation of RNA biosynthetic process" NARROW [GOC:TermGenie] synonym: "activation of RNA formation" NARROW [GOC:TermGenie] synonym: "activation of RNA synthesis" NARROW [GOC:TermGenie] synonym: "positive regulation of RNA anabolism" EXACT [GOC:TermGenie] synonym: "positive regulation of RNA biosynthesis" EXACT [GOC:TermGenie] synonym: "positive regulation of RNA formation" EXACT [GOC:TermGenie] synonym: "positive regulation of RNA synthesis" EXACT [GOC:TermGenie] synonym: "up regulation of RNA anabolism" EXACT [GOC:TermGenie] synonym: "up regulation of RNA biosynthesis" EXACT [GOC:TermGenie] synonym: "up regulation of RNA biosynthetic process" EXACT [GOC:TermGenie] synonym: "up regulation of RNA formation" EXACT [GOC:TermGenie] synonym: "up regulation of RNA synthesis" EXACT [GOC:TermGenie] synonym: "up-regulation of RNA anabolism" EXACT [GOC:TermGenie] synonym: "up-regulation of RNA biosynthesis" EXACT [GOC:TermGenie] synonym: "up-regulation of RNA biosynthetic process" EXACT [GOC:TermGenie] synonym: "up-regulation of RNA formation" EXACT [GOC:TermGenie] synonym: "up-regulation of RNA synthesis" EXACT [GOC:TermGenie] synonym: "upregulation of RNA anabolism" EXACT [GOC:TermGenie] synonym: "upregulation of RNA biosynthesis" EXACT [GOC:TermGenie] synonym: "upregulation of RNA biosynthetic process" EXACT [GOC:TermGenie] synonym: "upregulation of RNA formation" EXACT [GOC:TermGenie] synonym: "upregulation of RNA synthesis" EXACT [GOC:TermGenie] is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process is_a: GO:0031328 ! positive regulation of cellular biosynthetic process is_a: GO:0051254 ! positive regulation of RNA metabolic process is_a: GO:2001141 ! regulation of RNA biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0032774 ! RNA biosynthetic process relationship: positively_regulates GO:0032774 ! RNA biosynthetic process created_by: jl creation_date: 2014-02-05T16:32:10Z [Term] id: GO:1902742 name: apoptotic process involved in development namespace: biological_process def: "Any apoptotic process that is involved in anatomical structure development." [GO_REF:0000060, GOC:mtg_apoptosis, GOC:pg, GOC:TermGenie] synonym: "activation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "activation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "apoptosis activator activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "apoptosis activator activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "apoptosis signaling involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "apoptosis signaling involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "apoptotic cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "apoptotic cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "apoptotic process involved in anatomical structure development" EXACT [] synonym: "apoptotic process involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "apoptotic program involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "apoptotic program involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "apoptotic programmed cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "apoptotic programmed cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "commitment to apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "commitment to apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "induction of apoptosis by p53 involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "induction of apoptosis by p53 involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "induction of apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "induction of apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "programmed cell death by apoptosis involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "programmed cell death by apoptosis involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "signaling (initiator) caspase activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "signaling (initiator) caspase activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "type I programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "type I programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: part_of GO:0048856 ! anatomical structure development relationship: part_of GO:0048856 ! anatomical structure development created_by: pr creation_date: 2014-02-28T13:09:43Z [Term] id: GO:1903034 name: regulation of response to wounding namespace: biological_process def: "Any process that modulates the frequency, rate or extent of response to wounding." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:19164535] synonym: "regulation of physiological response to wounding" EXACT [GOC:TermGenie] is_a: GO:0080134 ! regulation of response to stress intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0009611 ! response to wounding relationship: regulates GO:0009611 ! response to wounding created_by: kmv creation_date: 2014-05-18T01:28:46Z [Term] id: GO:1903035 name: negative regulation of response to wounding namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of response to wounding." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:19164535] synonym: "down regulation of physiological response to wounding" EXACT [GOC:TermGenie] synonym: "down regulation of response to wounding" EXACT [GOC:TermGenie] synonym: "down-regulation of physiological response to wounding" EXACT [GOC:TermGenie] synonym: "down-regulation of response to wounding" EXACT [GOC:TermGenie] synonym: "downregulation of physiological response to wounding" EXACT [GOC:TermGenie] synonym: "downregulation of response to wounding" EXACT [GOC:TermGenie] synonym: "inhibition of physiological response to wounding" NARROW [GOC:TermGenie] synonym: "inhibition of response to wounding" NARROW [GOC:TermGenie] synonym: "negative regulation of physiological response to wounding" EXACT [GOC:TermGenie] is_a: GO:0048585 ! negative regulation of response to stimulus is_a: GO:1903034 ! regulation of response to wounding intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0009611 ! response to wounding relationship: negatively_regulates GO:0009611 ! response to wounding created_by: kmv creation_date: 2014-05-18T01:28:52Z [Term] id: GO:1903036 name: positive regulation of response to wounding namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of response to wounding." [GO_REF:0000058, GOC:kmv, GOC:TermGenie, pmid:19164535] synonym: "activation of physiological response to wounding" NARROW [GOC:TermGenie] synonym: "activation of response to wounding" NARROW [GOC:TermGenie] synonym: "positive regulation of physiological response to wounding" EXACT [GOC:TermGenie] synonym: "up regulation of physiological response to wounding" EXACT [GOC:TermGenie] synonym: "up regulation of response to wounding" EXACT [GOC:TermGenie] synonym: "up-regulation of physiological response to wounding" EXACT [GOC:TermGenie] synonym: "up-regulation of response to wounding" EXACT [GOC:TermGenie] synonym: "upregulation of physiological response to wounding" EXACT [GOC:TermGenie] synonym: "upregulation of response to wounding" EXACT [GOC:TermGenie] is_a: GO:0048584 ! positive regulation of response to stimulus is_a: GO:1903034 ! regulation of response to wounding intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0009611 ! response to wounding relationship: positively_regulates GO:0009611 ! response to wounding created_by: kmv creation_date: 2014-05-18T01:28:58Z [Term] id: GO:1903353 name: regulation of nucleus organization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of nucleus organization." [GO_REF:0000058, GOC:TermGenie, PMID:16943282] synonym: "regulation of nuclear morphology" RELATED [GOC:TermGenie] synonym: "regulation of nuclear organisation" EXACT [GOC:TermGenie] synonym: "regulation of nuclear organization" EXACT [GOC:TermGenie] synonym: "regulation of nuclear organization and biogenesis" RELATED [GOC:TermGenie] synonym: "regulation of nucleus organization and biogenesis" RELATED [GOC:TermGenie] is_a: GO:0033043 ! regulation of organelle organization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006997 ! nucleus organization relationship: regulates GO:0006997 ! nucleus organization created_by: hjd creation_date: 2014-08-20T19:36:16Z [Term] id: GO:1903506 name: regulation of nucleic acid-templated transcription namespace: biological_process def: "Any process that modulates the frequency, rate or extent of nucleic acid-templated transcription." [GO_REF:0000058, GOC:pr, GOC:TermGenie, GOC:txnOH, GOC:vw] is_a: GO:2001141 ! regulation of RNA biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0097659 ! nucleic acid-templated transcription relationship: regulates GO:0097659 ! nucleic acid-templated transcription created_by: pr creation_date: 2014-10-01T14:44:47Z [Term] id: GO:1903507 name: negative regulation of nucleic acid-templated transcription namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription." [GO_REF:0000058, GOC:pr, GOC:TermGenie, GOC:txnOH, GOC:vw] synonym: "down regulation of nucleic acid-templated transcription" EXACT [GOC:TermGenie] synonym: "down-regulation of nucleic acid-templated transcription" EXACT [GOC:TermGenie] synonym: "downregulation of nucleic acid-templated transcription" EXACT [GOC:TermGenie] synonym: "inhibition of nucleic acid-templated transcription" NARROW [GOC:TermGenie] is_a: GO:1902679 ! negative regulation of RNA biosynthetic process is_a: GO:1903506 ! regulation of nucleic acid-templated transcription intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0097659 ! nucleic acid-templated transcription relationship: negatively_regulates GO:0097659 ! nucleic acid-templated transcription created_by: pr creation_date: 2014-10-01T14:44:56Z [Term] id: GO:1903508 name: positive regulation of nucleic acid-templated transcription namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of nucleic acid-templated transcription." [GO_REF:0000058, GOC:pr, GOC:TermGenie, GOC:txnOH, GOC:vw] synonym: "activation of nucleic acid-templated transcription" NARROW [GOC:TermGenie] synonym: "up regulation of nucleic acid-templated transcription" EXACT [GOC:TermGenie] synonym: "up-regulation of nucleic acid-templated transcription" EXACT [GOC:TermGenie] synonym: "upregulation of nucleic acid-templated transcription" EXACT [GOC:TermGenie] is_a: GO:1902680 ! positive regulation of RNA biosynthetic process is_a: GO:1903506 ! regulation of nucleic acid-templated transcription intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0097659 ! nucleic acid-templated transcription relationship: positively_regulates GO:0097659 ! nucleic acid-templated transcription created_by: pr creation_date: 2014-10-01T14:45:04Z [Term] id: GO:1903530 name: regulation of secretion by cell namespace: biological_process def: "Any process that modulates the frequency, rate or extent of secretion by cell." [GO_REF:0000058, GOC:pm, GOC:TermGenie, PMID:12130530] synonym: "regulation of cellular secretion" EXACT [GOC:TermGenie] is_a: GO:0050794 ! regulation of cellular process is_a: GO:0051046 ! regulation of secretion intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0032940 ! secretion by cell relationship: regulates GO:0032940 ! secretion by cell created_by: pm creation_date: 2014-10-08T13:24:59Z [Term] id: GO:1903531 name: negative regulation of secretion by cell namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of secretion by cell." [GO_REF:0000058, GOC:pm, GOC:TermGenie, PMID:12130530] synonym: "down regulation of cellular secretion" EXACT [GOC:TermGenie] synonym: "down regulation of secretion by cell" EXACT [GOC:TermGenie] synonym: "down-regulation of cellular secretion" EXACT [GOC:TermGenie] synonym: "down-regulation of secretion by cell" EXACT [GOC:TermGenie] synonym: "downregulation of cellular secretion" EXACT [GOC:TermGenie] synonym: "downregulation of secretion by cell" EXACT [GOC:TermGenie] synonym: "inhibition of cellular secretion" NARROW [GOC:TermGenie] synonym: "inhibition of secretion by cell" NARROW [GOC:TermGenie] synonym: "negative regulation of cellular secretion" EXACT [GOC:TermGenie] is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0051048 ! negative regulation of secretion is_a: GO:1903530 ! regulation of secretion by cell intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0032940 ! secretion by cell relationship: negatively_regulates GO:0032940 ! secretion by cell created_by: pm creation_date: 2014-10-08T13:25:08Z [Term] id: GO:1903532 name: positive regulation of secretion by cell namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of secretion by cell." [GO_REF:0000058, GOC:pm, GOC:TermGenie, PMID:12130530] synonym: "activation of cellular secretion" NARROW [GOC:TermGenie] synonym: "activation of secretion by cell" NARROW [GOC:TermGenie] synonym: "positive regulation of cellular secretion" EXACT [GOC:TermGenie] synonym: "up regulation of cellular secretion" EXACT [GOC:TermGenie] synonym: "up regulation of secretion by cell" EXACT [GOC:TermGenie] synonym: "up-regulation of cellular secretion" EXACT [GOC:TermGenie] synonym: "up-regulation of secretion by cell" EXACT [GOC:TermGenie] synonym: "upregulation of cellular secretion" EXACT [GOC:TermGenie] synonym: "upregulation of secretion by cell" EXACT [GOC:TermGenie] is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0051047 ! positive regulation of secretion is_a: GO:1903530 ! regulation of secretion by cell intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0032940 ! secretion by cell relationship: positively_regulates GO:0032940 ! secretion by cell created_by: pm creation_date: 2014-10-08T13:25:17Z [Term] id: GO:1903555 name: regulation of tumor necrosis factor superfamily cytokine production namespace: biological_process def: "Any process that modulates the frequency, rate or extent of tumor necrosis factor superfamily cytokine production." [GO_REF:0000058, GOC:TermGenie, PMID:24187568] synonym: "regulation of TNF superfamily production" RELATED [GOC:TermGenie] synonym: "regulation of TNFSF cytokine production" EXACT [GOC:TermGenie] is_a: GO:0001817 ! regulation of cytokine production intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0071706 ! tumor necrosis factor superfamily cytokine production relationship: regulates GO:0071706 ! tumor necrosis factor superfamily cytokine production created_by: pga creation_date: 2014-10-21T10:26:05Z [Term] id: GO:1903556 name: negative regulation of tumor necrosis factor superfamily cytokine production namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor superfamily cytokine production." [GO_REF:0000058, GOC:TermGenie, PMID:24187568] synonym: "down regulation of TNF superfamily production" RELATED [GOC:TermGenie] synonym: "down regulation of TNFSF cytokine production" EXACT [GOC:TermGenie] synonym: "down regulation of tumor necrosis factor superfamily cytokine production" EXACT [GOC:TermGenie] synonym: "down-regulation of TNF superfamily production" RELATED [GOC:TermGenie] synonym: "down-regulation of TNFSF cytokine production" EXACT [GOC:TermGenie] synonym: "down-regulation of tumor necrosis factor superfamily cytokine production" EXACT [GOC:TermGenie] synonym: "downregulation of TNF superfamily production" RELATED [GOC:TermGenie] synonym: "downregulation of TNFSF cytokine production" EXACT [GOC:TermGenie] synonym: "downregulation of tumor necrosis factor superfamily cytokine production" EXACT [GOC:TermGenie] synonym: "inhibition of TNF superfamily production" RELATED [GOC:TermGenie] synonym: "inhibition of TNFSF cytokine production" NARROW [GOC:TermGenie] synonym: "inhibition of tumor necrosis factor superfamily cytokine production" NARROW [GOC:TermGenie] synonym: "negative regulation of TNF superfamily production" RELATED [GOC:TermGenie] synonym: "negative regulation of TNFSF cytokine production" EXACT [GOC:TermGenie] is_a: GO:0001818 ! negative regulation of cytokine production is_a: GO:1903555 ! regulation of tumor necrosis factor superfamily cytokine production intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0071706 ! tumor necrosis factor superfamily cytokine production relationship: negatively_regulates GO:0071706 ! tumor necrosis factor superfamily cytokine production created_by: pga creation_date: 2014-10-21T10:26:14Z [Term] id: GO:1903557 name: positive regulation of tumor necrosis factor superfamily cytokine production namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of tumor necrosis factor superfamily cytokine production." [GO_REF:0000058, GOC:TermGenie, PMID:24187568] synonym: "activation of TNF superfamily production" RELATED [GOC:TermGenie] synonym: "activation of TNFSF cytokine production" NARROW [GOC:TermGenie] synonym: "activation of tumor necrosis factor superfamily cytokine production" NARROW [GOC:TermGenie] synonym: "positive regulation of TNF superfamily production" RELATED [GOC:TermGenie] synonym: "positive regulation of TNFSF cytokine production" EXACT [GOC:TermGenie] synonym: "up regulation of TNF superfamily production" RELATED [GOC:TermGenie] synonym: "up regulation of TNFSF cytokine production" EXACT [GOC:TermGenie] synonym: "up regulation of tumor necrosis factor superfamily cytokine production" EXACT [GOC:TermGenie] synonym: "up-regulation of TNF superfamily production" RELATED [GOC:TermGenie] synonym: "up-regulation of TNFSF cytokine production" EXACT [GOC:TermGenie] synonym: "up-regulation of tumor necrosis factor superfamily cytokine production" EXACT [GOC:TermGenie] synonym: "upregulation of TNF superfamily production" RELATED [GOC:TermGenie] synonym: "upregulation of TNFSF cytokine production" EXACT [GOC:TermGenie] synonym: "upregulation of tumor necrosis factor superfamily cytokine production" EXACT [GOC:TermGenie] is_a: GO:0001819 ! positive regulation of cytokine production is_a: GO:1903555 ! regulation of tumor necrosis factor superfamily cytokine production intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0071706 ! tumor necrosis factor superfamily cytokine production relationship: positively_regulates GO:0071706 ! tumor necrosis factor superfamily cytokine production created_by: pga creation_date: 2014-10-21T10:26:23Z [Term] id: GO:1903624 name: regulation of DNA catabolic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA catabolic process." [GO_REF:0000058, GOC:TermGenie, PMID:2001740] synonym: "regulation of DNA breakdown" EXACT [GOC:TermGenie] synonym: "regulation of DNA catabolism" EXACT [GOC:TermGenie] synonym: "regulation of DNA degradation" EXACT [GOC:TermGenie] is_a: GO:0031329 ! regulation of cellular catabolic process is_a: GO:0051052 ! regulation of DNA metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006308 ! DNA catabolic process relationship: regulates GO:0006308 ! DNA catabolic process created_by: sl creation_date: 2014-11-19T22:36:35Z [Term] id: GO:1903625 name: negative regulation of DNA catabolic process namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of DNA catabolic process." [GO_REF:0000058, GOC:TermGenie, PMID:2001740] synonym: "down regulation of DNA breakdown" EXACT [GOC:TermGenie] synonym: "down regulation of DNA catabolic process" EXACT [GOC:TermGenie] synonym: "down regulation of DNA catabolism" EXACT [GOC:TermGenie] synonym: "down regulation of DNA degradation" EXACT [GOC:TermGenie] synonym: "down-regulation of DNA breakdown" EXACT [GOC:TermGenie] synonym: "down-regulation of DNA catabolic process" EXACT [GOC:TermGenie] synonym: "down-regulation of DNA catabolism" EXACT [GOC:TermGenie] synonym: "down-regulation of DNA degradation" EXACT [GOC:TermGenie] synonym: "downregulation of DNA breakdown" EXACT [GOC:TermGenie] synonym: "downregulation of DNA catabolic process" EXACT [GOC:TermGenie] synonym: "downregulation of DNA catabolism" EXACT [GOC:TermGenie] synonym: "downregulation of DNA degradation" EXACT [GOC:TermGenie] synonym: "inhibition of DNA breakdown" NARROW [GOC:TermGenie] synonym: "inhibition of DNA catabolic process" NARROW [GOC:TermGenie] synonym: "inhibition of DNA catabolism" NARROW [GOC:TermGenie] synonym: "inhibition of DNA degradation" NARROW [GOC:TermGenie] synonym: "negative regulation of DNA breakdown" EXACT [GOC:TermGenie] synonym: "negative regulation of DNA catabolism" EXACT [GOC:TermGenie] synonym: "negative regulation of DNA degradation" EXACT [GOC:TermGenie] is_a: GO:0031330 ! negative regulation of cellular catabolic process is_a: GO:0051053 ! negative regulation of DNA metabolic process is_a: GO:1903624 ! regulation of DNA catabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006308 ! DNA catabolic process relationship: negatively_regulates GO:0006308 ! DNA catabolic process created_by: sl creation_date: 2014-11-19T22:36:43Z [Term] id: GO:1903626 name: positive regulation of DNA catabolic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of DNA catabolic process." [GO_REF:0000058, GOC:TermGenie, PMID:2001740] synonym: "activation of DNA breakdown" NARROW [GOC:TermGenie] synonym: "activation of DNA catabolic process" NARROW [GOC:TermGenie] synonym: "activation of DNA catabolism" NARROW [GOC:TermGenie] synonym: "activation of DNA degradation" NARROW [GOC:TermGenie] synonym: "positive regulation of DNA breakdown" EXACT [GOC:TermGenie] synonym: "positive regulation of DNA catabolism" EXACT [GOC:TermGenie] synonym: "positive regulation of DNA degradation" EXACT [GOC:TermGenie] synonym: "up regulation of DNA breakdown" EXACT [GOC:TermGenie] synonym: "up regulation of DNA catabolic process" EXACT [GOC:TermGenie] synonym: "up regulation of DNA catabolism" EXACT [GOC:TermGenie] synonym: "up regulation of DNA degradation" EXACT [GOC:TermGenie] synonym: "up-regulation of DNA breakdown" EXACT [GOC:TermGenie] synonym: "up-regulation of DNA catabolic process" EXACT [GOC:TermGenie] synonym: "up-regulation of DNA catabolism" EXACT [GOC:TermGenie] synonym: "up-regulation of DNA degradation" EXACT [GOC:TermGenie] synonym: "upregulation of DNA breakdown" EXACT [GOC:TermGenie] synonym: "upregulation of DNA catabolic process" EXACT [GOC:TermGenie] synonym: "upregulation of DNA catabolism" EXACT [GOC:TermGenie] synonym: "upregulation of DNA degradation" EXACT [GOC:TermGenie] is_a: GO:0031331 ! positive regulation of cellular catabolic process is_a: GO:0051054 ! positive regulation of DNA metabolic process is_a: GO:1903624 ! regulation of DNA catabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006308 ! DNA catabolic process relationship: positively_regulates GO:0006308 ! DNA catabolic process created_by: sl creation_date: 2014-11-19T22:36:51Z [Term] id: GO:1903792 name: negative regulation of anion transport namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of anion transport." [GO_REF:0000058, GOC:TermGenie, PMID:11336802] synonym: "down regulation of anion transport" EXACT [GOC:TermGenie] synonym: "down-regulation of anion transport" EXACT [GOC:TermGenie] synonym: "downregulation of anion transport" EXACT [GOC:TermGenie] synonym: "inhibition of anion transport" NARROW [GOC:TermGenie] is_a: GO:0043271 ! negative regulation of ion transport is_a: GO:0044070 ! regulation of anion transport intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006820 ! anion transport relationship: negatively_regulates GO:0006820 ! anion transport created_by: sl creation_date: 2015-01-12T21:50:20Z [Term] id: GO:1903793 name: positive regulation of anion transport namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of anion transport." [GO_REF:0000058, GOC:TermGenie, PMID:11336802] synonym: "activation of anion transport" NARROW [GOC:TermGenie] synonym: "up regulation of anion transport" EXACT [GOC:TermGenie] synonym: "up-regulation of anion transport" EXACT [GOC:TermGenie] synonym: "upregulation of anion transport" EXACT [GOC:TermGenie] is_a: GO:0043270 ! positive regulation of ion transport is_a: GO:0044070 ! regulation of anion transport intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006820 ! anion transport relationship: positively_regulates GO:0006820 ! anion transport created_by: sl creation_date: 2015-01-12T21:50:30Z [Term] id: GO:1903827 name: regulation of cellular protein localization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GO_REF:0000058, GOC:TermGenie, GOC:vw] synonym: "regulation of cellular protein localisation" EXACT [GOC:TermGenie] synonym: "regulation of channel localizer activity" NARROW [GOC:TermGenie] is_a: GO:0032880 ! regulation of protein localization is_a: GO:0060341 ! regulation of cellular localization intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0034613 ! cellular protein localization relationship: regulates GO:0034613 ! cellular protein localization created_by: jl creation_date: 2015-01-20T14:32:14Z [Term] id: GO:1903828 name: negative regulation of cellular protein localization namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GO_REF:0000058, GOC:TermGenie, GOC:vw] synonym: "down regulation of cellular protein localisation" EXACT [GOC:TermGenie] synonym: "down regulation of cellular protein localization" EXACT [GOC:TermGenie] synonym: "down regulation of channel localizer activity" NARROW [GOC:TermGenie] synonym: "down-regulation of cellular protein localisation" EXACT [GOC:TermGenie] synonym: "down-regulation of cellular protein localization" EXACT [GOC:TermGenie] synonym: "down-regulation of channel localizer activity" NARROW [GOC:TermGenie] synonym: "downregulation of cellular protein localisation" EXACT [GOC:TermGenie] synonym: "downregulation of cellular protein localization" EXACT [GOC:TermGenie] synonym: "downregulation of channel localizer activity" NARROW [GOC:TermGenie] synonym: "inhibition of cellular protein localisation" NARROW [GOC:TermGenie] synonym: "inhibition of cellular protein localization" NARROW [GOC:TermGenie] synonym: "inhibition of channel localizer activity" NARROW [GOC:TermGenie] synonym: "negative regulation of cellular protein localisation" EXACT [GOC:TermGenie] synonym: "negative regulation of channel localizer activity" NARROW [GOC:TermGenie] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:1903827 ! regulation of cellular protein localization intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0034613 ! cellular protein localization relationship: negatively_regulates GO:0034613 ! cellular protein localization created_by: jl creation_date: 2015-01-20T14:32:24Z [Term] id: GO:1903829 name: positive regulation of cellular protein localization namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cellular protein localization. Cellular protein localization is any process in which a protein is transported to, and/or maintained in, a specific location and encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell." [GO_REF:0000058, GOC:TermGenie, GOC:vw] synonym: "activation of cellular protein localisation" NARROW [GOC:TermGenie] synonym: "activation of cellular protein localization" NARROW [GOC:TermGenie] synonym: "activation of channel localizer activity" NARROW [GOC:TermGenie] synonym: "positive regulation of cellular protein localisation" EXACT [GOC:TermGenie] synonym: "positive regulation of channel localizer activity" NARROW [GOC:TermGenie] synonym: "up regulation of cellular protein localisation" EXACT [GOC:TermGenie] synonym: "up regulation of cellular protein localization" EXACT [GOC:TermGenie] synonym: "up regulation of channel localizer activity" NARROW [GOC:TermGenie] synonym: "up-regulation of cellular protein localisation" EXACT [GOC:TermGenie] synonym: "up-regulation of cellular protein localization" EXACT [GOC:TermGenie] synonym: "up-regulation of channel localizer activity" NARROW [GOC:TermGenie] synonym: "upregulation of cellular protein localisation" EXACT [GOC:TermGenie] synonym: "upregulation of cellular protein localization" EXACT [GOC:TermGenie] synonym: "upregulation of channel localizer activity" NARROW [GOC:TermGenie] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:1903827 ! regulation of cellular protein localization intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0034613 ! cellular protein localization relationship: positively_regulates GO:0034613 ! cellular protein localization created_by: jl creation_date: 2015-01-20T14:32:33Z [Term] id: GO:1903963 name: arachidonate transport namespace: biological_process def: "The directed movement of an arachidonate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GO_REF:0000065, GOC:bhm, GOC:TermGenie, PMID:15642721] synonym: "arachidonic acid transport" EXACT [] is_a: GO:0015909 ! long-chain fatty acid transport is_a: GO:0071715 ! icosanoid transport created_by: bhm creation_date: 2015-02-25T16:06:14Z [Term] id: GO:1904170 name: regulation of bleb assembly namespace: biological_process def: "Any process that modulates the frequency, rate or extent of bleb assembly." [GO_REF:0000058, GOC:als, GOC:TermGenie, PMID:25651887] synonym: "regulation of cell blebbing" EXACT [GOC:TermGenie] is_a: GO:0120032 ! regulation of plasma membrane bounded cell projection assembly intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0032060 ! bleb assembly relationship: regulates GO:0032060 ! bleb assembly created_by: als creation_date: 2015-04-23T09:32:19Z [Term] id: GO:1904171 name: negative regulation of bleb assembly namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of bleb assembly." [GO_REF:0000058, GOC:als, GOC:TermGenie, PMID:25651887] synonym: "down regulation of bleb assembly" EXACT [GOC:TermGenie] synonym: "down regulation of cell blebbing" EXACT [GOC:TermGenie] synonym: "down-regulation of bleb assembly" EXACT [GOC:TermGenie] synonym: "down-regulation of cell blebbing" EXACT [GOC:TermGenie] synonym: "downregulation of bleb assembly" EXACT [GOC:TermGenie] synonym: "downregulation of cell blebbing" EXACT [GOC:TermGenie] synonym: "inhibition of bleb assembly" NARROW [GOC:TermGenie] synonym: "inhibition of cell blebbing" NARROW [GOC:TermGenie] synonym: "negative regulation of cell blebbing" EXACT [GOC:TermGenie] is_a: GO:0120033 ! negative regulation of plasma membrane bounded cell projection assembly is_a: GO:1904170 ! regulation of bleb assembly intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0032060 ! bleb assembly relationship: negatively_regulates GO:0032060 ! bleb assembly created_by: als creation_date: 2015-04-23T09:32:25Z [Term] id: GO:1904172 name: positive regulation of bleb assembly namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of bleb assembly." [GO_REF:0000058, GOC:als, GOC:TermGenie, PMID:25651887] synonym: "activation of bleb assembly" NARROW [GOC:TermGenie] synonym: "activation of cell blebbing" NARROW [GOC:TermGenie] synonym: "positive regulation of cell blebbing" EXACT [GOC:TermGenie] synonym: "up regulation of bleb assembly" EXACT [GOC:TermGenie] synonym: "up regulation of cell blebbing" EXACT [GOC:TermGenie] synonym: "up-regulation of bleb assembly" EXACT [GOC:TermGenie] synonym: "up-regulation of cell blebbing" EXACT [GOC:TermGenie] synonym: "upregulation of bleb assembly" EXACT [GOC:TermGenie] synonym: "upregulation of cell blebbing" EXACT [GOC:TermGenie] is_a: GO:0120034 ! positive regulation of plasma membrane bounded cell projection assembly is_a: GO:1904170 ! regulation of bleb assembly intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0032060 ! bleb assembly relationship: positively_regulates GO:0032060 ! bleb assembly created_by: als creation_date: 2015-04-23T09:32:31Z [Term] id: GO:1904467 name: regulation of tumor necrosis factor secretion namespace: biological_process def: "Any process that modulates the frequency, rate or extent of tumor necrosis factor secretion." [GO_REF:0000058, GOC:TermGenie, PMID:15560120] synonym: "regulation of cachectin secretion" EXACT [GOC:TermGenie] synonym: "regulation of TNF secretion" EXACT [GOC:TermGenie] synonym: "regulation of TNF superfamily, member 2 secretion" EXACT [GOC:TermGenie] synonym: "regulation of TNF-alpha secretion" EXACT [GOC:TermGenie] synonym: "regulation of Tnfa secretion" EXACT [GOC:TermGenie] synonym: "regulation of tumor necrosis factor alpha secretion" EXACT [GOC:TermGenie] synonym: "regulation of tumor necrosis factor ligand superfamily member 2 secretion" EXACT [GOC:TermGenie] is_a: GO:0032680 ! regulation of tumor necrosis factor production is_a: GO:0050707 ! regulation of cytokine secretion intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:1990774 ! tumor necrosis factor secretion relationship: regulates GO:1990774 ! tumor necrosis factor secretion created_by: sl creation_date: 2015-07-09T19:50:02Z [Term] id: GO:1904468 name: negative regulation of tumor necrosis factor secretion namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of tumor necrosis factor secretion." [GO_REF:0000058, GOC:TermGenie, PMID:15560120] synonym: "down regulation of cachectin secretion" EXACT [GOC:TermGenie] synonym: "down regulation of TNF secretion" EXACT [GOC:TermGenie] synonym: "down regulation of TNF superfamily, member 2 secretion" EXACT [GOC:TermGenie] synonym: "down regulation of TNF-alpha secretion" EXACT [GOC:TermGenie] synonym: "down regulation of Tnfa secretion" EXACT [GOC:TermGenie] synonym: "down regulation of tumor necrosis factor alpha secretion" EXACT [GOC:TermGenie] synonym: "down regulation of tumor necrosis factor ligand superfamily member 2 secretion" EXACT [GOC:TermGenie] synonym: "down regulation of tumor necrosis factor secretion" EXACT [GOC:TermGenie] synonym: "down-regulation of cachectin secretion" EXACT [GOC:TermGenie] synonym: "down-regulation of TNF secretion" EXACT [GOC:TermGenie] synonym: "down-regulation of TNF superfamily, member 2 secretion" EXACT [GOC:TermGenie] synonym: "down-regulation of TNF-alpha secretion" EXACT [GOC:TermGenie] synonym: "down-regulation of Tnfa secretion" EXACT [GOC:TermGenie] synonym: "down-regulation of tumor necrosis factor alpha secretion" EXACT [GOC:TermGenie] synonym: "down-regulation of tumor necrosis factor ligand superfamily member 2 secretion" EXACT [GOC:TermGenie] synonym: "down-regulation of tumor necrosis factor secretion" EXACT [GOC:TermGenie] synonym: "downregulation of cachectin secretion" EXACT [GOC:TermGenie] synonym: "downregulation of TNF secretion" EXACT [GOC:TermGenie] synonym: "downregulation of TNF superfamily, member 2 secretion" EXACT [GOC:TermGenie] synonym: "downregulation of TNF-alpha secretion" EXACT [GOC:TermGenie] synonym: "downregulation of Tnfa secretion" EXACT [GOC:TermGenie] synonym: "downregulation of tumor necrosis factor alpha secretion" EXACT [GOC:TermGenie] synonym: "downregulation of tumor necrosis factor ligand superfamily member 2 secretion" EXACT [GOC:TermGenie] synonym: "downregulation of tumor necrosis factor secretion" EXACT [GOC:TermGenie] synonym: "inhibition of cachectin secretion" NARROW [GOC:TermGenie] synonym: "inhibition of TNF secretion" NARROW [GOC:TermGenie] synonym: "inhibition of TNF superfamily, member 2 secretion" NARROW [GOC:TermGenie] synonym: "inhibition of TNF-alpha secretion" NARROW [GOC:TermGenie] synonym: "inhibition of Tnfa secretion" NARROW [GOC:TermGenie] synonym: "inhibition of tumor necrosis factor alpha secretion" NARROW [GOC:TermGenie] synonym: "inhibition of tumor necrosis factor ligand superfamily member 2 secretion" NARROW [GOC:TermGenie] synonym: "inhibition of tumor necrosis factor secretion" NARROW [GOC:TermGenie] synonym: "negative regulation of cachectin secretion" EXACT [GOC:TermGenie] synonym: "negative regulation of TNF secretion" EXACT [GOC:TermGenie] synonym: "negative regulation of TNF superfamily, member 2 secretion" EXACT [GOC:TermGenie] synonym: "negative regulation of TNF-alpha secretion" EXACT [GOC:TermGenie] synonym: "negative regulation of Tnfa secretion" EXACT [GOC:TermGenie] synonym: "negative regulation of tumor necrosis factor alpha secretion" EXACT [GOC:TermGenie] synonym: "negative regulation of tumor necrosis factor ligand superfamily member 2 secretion" EXACT [GOC:TermGenie] is_a: GO:0032720 ! negative regulation of tumor necrosis factor production is_a: GO:0050710 ! negative regulation of cytokine secretion is_a: GO:1904467 ! regulation of tumor necrosis factor secretion intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:1990774 ! tumor necrosis factor secretion relationship: negatively_regulates GO:1990774 ! tumor necrosis factor secretion created_by: sl creation_date: 2015-07-09T19:50:08Z [Term] id: GO:1904469 name: positive regulation of tumor necrosis factor secretion namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of tumor necrosis factor secretion." [GO_REF:0000058, GOC:TermGenie, PMID:15560120] synonym: "activation of cachectin secretion" NARROW [GOC:TermGenie] synonym: "activation of TNF secretion" NARROW [GOC:TermGenie] synonym: "activation of TNF superfamily, member 2 secretion" NARROW [GOC:TermGenie] synonym: "activation of TNF-alpha secretion" NARROW [GOC:TermGenie] synonym: "activation of Tnfa secretion" NARROW [GOC:TermGenie] synonym: "activation of tumor necrosis factor alpha secretion" NARROW [GOC:TermGenie] synonym: "activation of tumor necrosis factor ligand superfamily member 2 secretion" NARROW [GOC:TermGenie] synonym: "activation of tumor necrosis factor secretion" NARROW [GOC:TermGenie] synonym: "positive regulation of cachectin secretion" EXACT [GOC:TermGenie] synonym: "positive regulation of TNF secretion" EXACT [GOC:TermGenie] synonym: "positive regulation of TNF superfamily, member 2 secretion" EXACT [GOC:TermGenie] synonym: "positive regulation of TNF-alpha secretion" EXACT [GOC:TermGenie] synonym: "positive regulation of Tnfa secretion" EXACT [GOC:TermGenie] synonym: "positive regulation of tumor necrosis factor alpha secretion" EXACT [GOC:TermGenie] synonym: "positive regulation of tumor necrosis factor ligand superfamily member 2 secretion" EXACT [GOC:TermGenie] synonym: "up regulation of cachectin secretion" EXACT [GOC:TermGenie] synonym: "up regulation of TNF secretion" EXACT [GOC:TermGenie] synonym: "up regulation of TNF superfamily, member 2 secretion" EXACT [GOC:TermGenie] synonym: "up regulation of TNF-alpha secretion" EXACT [GOC:TermGenie] synonym: "up regulation of Tnfa secretion" EXACT [GOC:TermGenie] synonym: "up regulation of tumor necrosis factor alpha secretion" EXACT [GOC:TermGenie] synonym: "up regulation of tumor necrosis factor ligand superfamily member 2 secretion" EXACT [GOC:TermGenie] synonym: "up regulation of tumor necrosis factor secretion" EXACT [GOC:TermGenie] synonym: "up-regulation of cachectin secretion" EXACT [GOC:TermGenie] synonym: "up-regulation of TNF secretion" EXACT [GOC:TermGenie] synonym: "up-regulation of TNF superfamily, member 2 secretion" EXACT [GOC:TermGenie] synonym: "up-regulation of TNF-alpha secretion" EXACT [GOC:TermGenie] synonym: "up-regulation of Tnfa secretion" EXACT [GOC:TermGenie] synonym: "up-regulation of tumor necrosis factor alpha secretion" EXACT [GOC:TermGenie] synonym: "up-regulation of tumor necrosis factor ligand superfamily member 2 secretion" EXACT [GOC:TermGenie] synonym: "up-regulation of tumor necrosis factor secretion" EXACT [GOC:TermGenie] synonym: "upregulation of cachectin secretion" EXACT [GOC:TermGenie] synonym: "upregulation of TNF secretion" EXACT [GOC:TermGenie] synonym: "upregulation of TNF superfamily, member 2 secretion" EXACT [GOC:TermGenie] synonym: "upregulation of TNF-alpha secretion" EXACT [GOC:TermGenie] synonym: "upregulation of Tnfa secretion" EXACT [GOC:TermGenie] synonym: "upregulation of tumor necrosis factor alpha secretion" EXACT [GOC:TermGenie] synonym: "upregulation of tumor necrosis factor ligand superfamily member 2 secretion" EXACT [GOC:TermGenie] synonym: "upregulation of tumor necrosis factor secretion" EXACT [GOC:TermGenie] is_a: GO:0032760 ! positive regulation of tumor necrosis factor production is_a: GO:0050715 ! positive regulation of cytokine secretion is_a: GO:1904467 ! regulation of tumor necrosis factor secretion intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:1990774 ! tumor necrosis factor secretion relationship: positively_regulates GO:1990774 ! tumor necrosis factor secretion created_by: sl creation_date: 2015-07-09T19:50:14Z [Term] id: GO:1904746 name: negative regulation of apoptotic process involved in development namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic process involved in development." [GO_REF:0000058, GOC:TermGenie, PMID:22801495] comment: U4PR86 in PMID:22801495 inferred from mutant phenotype synonym: "down regulation of activation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "down regulation of activation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "down regulation of apoptosis activator activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "down regulation of apoptosis activator activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "down regulation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "down regulation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "down regulation of apoptosis signaling involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "down regulation of apoptosis signaling involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "down regulation of apoptotic cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "down regulation of apoptotic cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "down regulation of apoptotic process involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "down regulation of apoptotic process involved in development" EXACT [GOC:TermGenie] synonym: "down regulation of apoptotic process involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "down regulation of apoptotic program involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "down regulation of apoptotic program involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "down regulation of apoptotic programmed cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "down regulation of apoptotic programmed cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "down regulation of commitment to apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "down regulation of commitment to apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "down regulation of induction of apoptosis by p53 involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "down regulation of induction of apoptosis by p53 involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "down regulation of induction of apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "down regulation of induction of apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "down regulation of programmed cell death by apoptosis involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "down regulation of programmed cell death by apoptosis involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "down regulation of signaling (initiator) caspase activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "down regulation of signaling (initiator) caspase activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "down regulation of type I programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "down regulation of type I programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "down-regulation of activation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "down-regulation of activation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "down-regulation of apoptosis activator activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "down-regulation of apoptosis activator activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "down-regulation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "down-regulation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "down-regulation of apoptosis signaling involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "down-regulation of apoptosis signaling involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "down-regulation of apoptotic cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "down-regulation of apoptotic cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "down-regulation of apoptotic process involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "down-regulation of apoptotic process involved in development" EXACT [GOC:TermGenie] synonym: "down-regulation of apoptotic process involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "down-regulation of apoptotic program involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "down-regulation of apoptotic program involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "down-regulation of apoptotic programmed cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "down-regulation of apoptotic programmed cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "down-regulation of commitment to apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "down-regulation of commitment to apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "down-regulation of induction of apoptosis by p53 involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "down-regulation of induction of apoptosis by p53 involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "down-regulation of induction of apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "down-regulation of induction of apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "down-regulation of programmed cell death by apoptosis involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "down-regulation of programmed cell death by apoptosis involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "down-regulation of signaling (initiator) caspase activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "down-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "down-regulation of type I programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "down-regulation of type I programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "downregulation of activation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "downregulation of activation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "downregulation of apoptosis activator activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "downregulation of apoptosis activator activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "downregulation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "downregulation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "downregulation of apoptosis signaling involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "downregulation of apoptosis signaling involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "downregulation of apoptotic cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "downregulation of apoptotic cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "downregulation of apoptotic process involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "downregulation of apoptotic process involved in development" EXACT [GOC:TermGenie] synonym: "downregulation of apoptotic process involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "downregulation of apoptotic program involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "downregulation of apoptotic program involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "downregulation of apoptotic programmed cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "downregulation of apoptotic programmed cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "downregulation of commitment to apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "downregulation of commitment to apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "downregulation of induction of apoptosis by p53 involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "downregulation of induction of apoptosis by p53 involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "downregulation of induction of apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "downregulation of induction of apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "downregulation of programmed cell death by apoptosis involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "downregulation of programmed cell death by apoptosis involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "downregulation of signaling (initiator) caspase activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "downregulation of signaling (initiator) caspase activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "downregulation of type I programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "downregulation of type I programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "inhibition of activation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "inhibition of activation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "inhibition of apoptosis activator activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "inhibition of apoptosis activator activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "inhibition of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "inhibition of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "inhibition of apoptosis signaling involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "inhibition of apoptosis signaling involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "inhibition of apoptotic cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "inhibition of apoptotic cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "inhibition of apoptotic process involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "inhibition of apoptotic process involved in development" NARROW [GOC:TermGenie] synonym: "inhibition of apoptotic process involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "inhibition of apoptotic program involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "inhibition of apoptotic program involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "inhibition of apoptotic programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "inhibition of apoptotic programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "inhibition of commitment to apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "inhibition of commitment to apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "inhibition of induction of apoptosis by p53 involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "inhibition of induction of apoptosis by p53 involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "inhibition of induction of apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "inhibition of induction of apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "inhibition of programmed cell death by apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "inhibition of programmed cell death by apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "inhibition of signaling (initiator) caspase activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "inhibition of signaling (initiator) caspase activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "inhibition of type I programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "inhibition of type I programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "negative regulation of activation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "negative regulation of activation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "negative regulation of apoptosis activator activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "negative regulation of apoptosis activator activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "negative regulation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "negative regulation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "negative regulation of apoptosis signaling involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "negative regulation of apoptosis signaling involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "negative regulation of apoptotic cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "negative regulation of apoptotic cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "negative regulation of apoptotic process involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "negative regulation of apoptotic process involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "negative regulation of apoptotic program involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "negative regulation of apoptotic program involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "negative regulation of apoptotic programmed cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "negative regulation of apoptotic programmed cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "negative regulation of commitment to apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "negative regulation of commitment to apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "negative regulation of induction of apoptosis by p53 involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "negative regulation of induction of apoptosis by p53 involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "negative regulation of induction of apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "negative regulation of induction of apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "negative regulation of programmed cell death by apoptosis involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "negative regulation of programmed cell death by apoptosis involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "negative regulation of signaling (initiator) caspase activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "negative regulation of signaling (initiator) caspase activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "negative regulation of type I programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "negative regulation of type I programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] is_a: GO:0043066 ! negative regulation of apoptotic process is_a: GO:0051093 ! negative regulation of developmental process is_a: GO:1904748 ! regulation of apoptotic process involved in development intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:1902742 ! apoptotic process involved in development relationship: negatively_regulates GO:1902742 ! apoptotic process involved in development created_by: es creation_date: 2015-10-19T14:12:27Z [Term] id: GO:1904747 name: positive regulation of apoptotic process involved in development namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of apoptotic process involved in development." [GO_REF:0000058, GOC:TermGenie, PMID:22801495] comment: U4PR86 in PMID:22801495 inferred from mutant phenotype synonym: "activation of activation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "activation of activation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "activation of apoptosis activator activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "activation of apoptosis activator activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "activation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "activation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "activation of apoptosis signaling involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "activation of apoptosis signaling involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "activation of apoptotic cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "activation of apoptotic cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "activation of apoptotic process involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "activation of apoptotic process involved in development" NARROW [GOC:TermGenie] synonym: "activation of apoptotic process involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "activation of apoptotic program involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "activation of apoptotic program involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "activation of apoptotic programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "activation of apoptotic programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "activation of commitment to apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "activation of commitment to apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "activation of induction of apoptosis by p53 involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "activation of induction of apoptosis by p53 involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "activation of induction of apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "activation of induction of apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "activation of programmed cell death by apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "activation of programmed cell death by apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "activation of signaling (initiator) caspase activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "activation of signaling (initiator) caspase activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "activation of type I programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "activation of type I programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "positive regulation of activation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "positive regulation of activation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "positive regulation of apoptosis activator activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "positive regulation of apoptosis activator activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "positive regulation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "positive regulation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "positive regulation of apoptosis signaling involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "positive regulation of apoptosis signaling involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "positive regulation of apoptotic cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "positive regulation of apoptotic cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "positive regulation of apoptotic process involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "positive regulation of apoptotic process involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "positive regulation of apoptotic program involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "positive regulation of apoptotic program involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "positive regulation of apoptotic programmed cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "positive regulation of apoptotic programmed cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "positive regulation of commitment to apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "positive regulation of commitment to apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "positive regulation of induction of apoptosis by p53 involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "positive regulation of induction of apoptosis by p53 involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "positive regulation of induction of apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "positive regulation of induction of apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "positive regulation of programmed cell death by apoptosis involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "positive regulation of programmed cell death by apoptosis involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "positive regulation of signaling (initiator) caspase activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "positive regulation of signaling (initiator) caspase activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "positive regulation of type I programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "positive regulation of type I programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "up regulation of activation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "up regulation of activation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "up regulation of apoptosis activator activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "up regulation of apoptosis activator activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "up regulation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "up regulation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "up regulation of apoptosis signaling involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "up regulation of apoptosis signaling involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "up regulation of apoptotic cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "up regulation of apoptotic cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "up regulation of apoptotic process involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "up regulation of apoptotic process involved in development" EXACT [GOC:TermGenie] synonym: "up regulation of apoptotic process involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "up regulation of apoptotic program involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "up regulation of apoptotic program involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "up regulation of apoptotic programmed cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "up regulation of apoptotic programmed cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "up regulation of commitment to apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "up regulation of commitment to apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "up regulation of induction of apoptosis by p53 involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "up regulation of induction of apoptosis by p53 involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "up regulation of induction of apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "up regulation of induction of apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "up regulation of programmed cell death by apoptosis involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "up regulation of programmed cell death by apoptosis involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "up regulation of signaling (initiator) caspase activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "up regulation of signaling (initiator) caspase activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "up regulation of type I programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "up regulation of type I programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "up-regulation of activation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "up-regulation of activation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "up-regulation of apoptosis activator activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "up-regulation of apoptosis activator activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "up-regulation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "up-regulation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "up-regulation of apoptosis signaling involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "up-regulation of apoptosis signaling involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "up-regulation of apoptotic cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "up-regulation of apoptotic cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "up-regulation of apoptotic process involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "up-regulation of apoptotic process involved in development" EXACT [GOC:TermGenie] synonym: "up-regulation of apoptotic process involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "up-regulation of apoptotic program involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "up-regulation of apoptotic program involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "up-regulation of apoptotic programmed cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "up-regulation of apoptotic programmed cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "up-regulation of commitment to apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "up-regulation of commitment to apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "up-regulation of induction of apoptosis by p53 involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "up-regulation of induction of apoptosis by p53 involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "up-regulation of induction of apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "up-regulation of induction of apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "up-regulation of programmed cell death by apoptosis involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "up-regulation of programmed cell death by apoptosis involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "up-regulation of signaling (initiator) caspase activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "up-regulation of signaling (initiator) caspase activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "up-regulation of type I programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "up-regulation of type I programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "upregulation of activation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "upregulation of activation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "upregulation of apoptosis activator activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "upregulation of apoptosis activator activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "upregulation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "upregulation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "upregulation of apoptosis signaling involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "upregulation of apoptosis signaling involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "upregulation of apoptotic cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "upregulation of apoptotic cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "upregulation of apoptotic process involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "upregulation of apoptotic process involved in development" EXACT [GOC:TermGenie] synonym: "upregulation of apoptotic process involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "upregulation of apoptotic program involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "upregulation of apoptotic program involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "upregulation of apoptotic programmed cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "upregulation of apoptotic programmed cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "upregulation of commitment to apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "upregulation of commitment to apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "upregulation of induction of apoptosis by p53 involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "upregulation of induction of apoptosis by p53 involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "upregulation of induction of apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "upregulation of induction of apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "upregulation of programmed cell death by apoptosis involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "upregulation of programmed cell death by apoptosis involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "upregulation of signaling (initiator) caspase activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "upregulation of signaling (initiator) caspase activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "upregulation of type I programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "upregulation of type I programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] is_a: GO:0043065 ! positive regulation of apoptotic process is_a: GO:0051094 ! positive regulation of developmental process is_a: GO:1904748 ! regulation of apoptotic process involved in development intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:1902742 ! apoptotic process involved in development relationship: positively_regulates GO:1902742 ! apoptotic process involved in development created_by: es creation_date: 2015-10-19T14:12:34Z [Term] id: GO:1904748 name: regulation of apoptotic process involved in development namespace: biological_process def: "Any process that modulates the frequency, rate or extent of apoptotic process involved in development." [GO_REF:0000058, GOC:TermGenie, PMID:22801495] comment: Q10943 in PMID:22801495, inferred from mutant phenotype synonym: "regulation of activation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "regulation of activation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "regulation of apoptosis activator activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "regulation of apoptosis activator activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "regulation of apoptosis involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "regulation of apoptosis involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "regulation of apoptosis signaling involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "regulation of apoptosis signaling involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "regulation of apoptotic cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "regulation of apoptotic cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "regulation of apoptotic process involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "regulation of apoptotic process involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "regulation of apoptotic program involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "regulation of apoptotic program involved in development of an anatomical structure" NARROW [GOC:TermGenie] synonym: "regulation of apoptotic programmed cell death involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "regulation of apoptotic programmed cell death involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "regulation of commitment to apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "regulation of commitment to apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "regulation of induction of apoptosis by p53 involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "regulation of induction of apoptosis by p53 involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "regulation of induction of apoptosis involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "regulation of induction of apoptosis involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "regulation of programmed cell death by apoptosis involved in anatomical structure development" EXACT [GOC:TermGenie] synonym: "regulation of programmed cell death by apoptosis involved in development of an anatomical structure" EXACT [GOC:TermGenie] synonym: "regulation of signaling (initiator) caspase activity involved in anatomical structure development" RELATED [GOC:TermGenie] synonym: "regulation of signaling (initiator) caspase activity involved in development of an anatomical structure" RELATED [GOC:TermGenie] synonym: "regulation of type I programmed cell death involved in anatomical structure development" NARROW [GOC:TermGenie] synonym: "regulation of type I programmed cell death involved in development of an anatomical structure" NARROW [GOC:TermGenie] is_a: GO:0042981 ! regulation of apoptotic process is_a: GO:0050793 ! regulation of developmental process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:1902742 ! apoptotic process involved in development relationship: regulates GO:1902742 ! apoptotic process involved in development created_by: es creation_date: 2015-10-19T15:02:28Z [Term] id: GO:1904796 name: regulation of core promoter binding namespace: biological_process def: "Any process that modulates the frequency, rate or extent of core promoter binding." [GO_REF:0000059, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:22723415] is_a: GO:0050789 {is_inferred="true"} ! regulation of biological process is_a: GO:2000677 ! regulation of transcription regulatory region DNA binding intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0001047 ! core promoter binding relationship: regulates GO:0001047 ! core promoter binding created_by: nc creation_date: 2015-11-09T12:32:23Z [Term] id: GO:1904797 name: negative regulation of core promoter binding namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of core promoter binding." [GO_REF:0000059, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:22723415] synonym: "down regulation of core promoter binding" EXACT [GOC:TermGenie] synonym: "down-regulation of core promoter binding" EXACT [GOC:TermGenie] synonym: "downregulation of core promoter binding" EXACT [GOC:TermGenie] synonym: "inhibition of core promoter binding" NARROW [GOC:TermGenie] is_a: GO:0048519 {is_inferred="true"} ! negative regulation of biological process is_a: GO:1904796 ! regulation of core promoter binding is_a: GO:2000678 ! negative regulation of transcription regulatory region DNA binding intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0001047 ! core promoter binding relationship: negatively_regulates GO:0001047 ! core promoter binding created_by: nc creation_date: 2015-11-09T12:32:31Z [Term] id: GO:1904798 name: positive regulation of core promoter binding namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of core promoter binding." [GO_REF:0000059, GOC:BHF, GOC:BHF_telomere, GOC:nc, GOC:TermGenie, PMID:22723415] synonym: "activation of core promoter binding" NARROW [GOC:TermGenie] synonym: "up regulation of core promoter binding" EXACT [GOC:TermGenie] synonym: "up-regulation of core promoter binding" EXACT [GOC:TermGenie] synonym: "upregulation of core promoter binding" EXACT [GOC:TermGenie] is_a: GO:0048518 {is_inferred="true"} ! positive regulation of biological process is_a: GO:1904796 ! regulation of core promoter binding is_a: GO:2000679 ! positive regulation of transcription regulatory region DNA binding intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0001047 ! core promoter binding relationship: positively_regulates GO:0001047 ! core promoter binding created_by: nc creation_date: 2015-11-09T12:32:38Z [Term] id: GO:1904950 name: negative regulation of establishment of protein localization namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of establishment of protein localization." [GO_REF:0000058, GOC:TermGenie, PMID:22761445] synonym: "down regulation of establishment of protein localisation" EXACT [GOC:TermGenie] synonym: "down regulation of establishment of protein localization" EXACT [GOC:TermGenie] synonym: "down regulation of protein positioning" EXACT [GOC:TermGenie] synonym: "down regulation of protein recruitment" EXACT [GOC:TermGenie] synonym: "down-regulation of establishment of protein localisation" EXACT [GOC:TermGenie] synonym: "down-regulation of establishment of protein localization" EXACT [GOC:TermGenie] synonym: "down-regulation of protein positioning" EXACT [GOC:TermGenie] synonym: "down-regulation of protein recruitment" EXACT [GOC:TermGenie] synonym: "downregulation of establishment of protein localisation" EXACT [GOC:TermGenie] synonym: "downregulation of establishment of protein localization" EXACT [GOC:TermGenie] synonym: "downregulation of protein positioning" EXACT [GOC:TermGenie] synonym: "downregulation of protein recruitment" EXACT [GOC:TermGenie] synonym: "inhibition of establishment of protein localisation" NARROW [GOC:TermGenie] synonym: "inhibition of establishment of protein localization" NARROW [GOC:TermGenie] synonym: "inhibition of protein positioning" NARROW [GOC:TermGenie] synonym: "inhibition of protein recruitment" NARROW [GOC:TermGenie] synonym: "negative regulation of establishment of protein localisation" EXACT [GOC:TermGenie] synonym: "negative regulation of protein positioning" EXACT [GOC:TermGenie] synonym: "negative regulation of protein recruitment" EXACT [GOC:TermGenie] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:0070201 ! regulation of establishment of protein localization intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0045184 ! establishment of protein localization relationship: negatively_regulates GO:0045184 ! establishment of protein localization created_by: mec creation_date: 2016-02-05T09:59:24Z [Term] id: GO:1904951 name: positive regulation of establishment of protein localization namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of establishment of protein localization." [GO_REF:0000058, GOC:TermGenie, PMID:22761445] synonym: "activation of establishment of protein localisation" NARROW [GOC:TermGenie] synonym: "activation of establishment of protein localization" NARROW [GOC:TermGenie] synonym: "activation of protein positioning" NARROW [GOC:TermGenie] synonym: "activation of protein recruitment" NARROW [GOC:TermGenie] synonym: "positive regulation of establishment of protein localisation" EXACT [GOC:TermGenie] synonym: "positive regulation of protein positioning" EXACT [GOC:TermGenie] synonym: "positive regulation of protein recruitment" EXACT [GOC:TermGenie] synonym: "up regulation of establishment of protein localisation" EXACT [GOC:TermGenie] synonym: "up regulation of establishment of protein localization" EXACT [GOC:TermGenie] synonym: "up regulation of protein positioning" EXACT [GOC:TermGenie] synonym: "up regulation of protein recruitment" EXACT [GOC:TermGenie] synonym: "up-regulation of establishment of protein localisation" EXACT [GOC:TermGenie] synonym: "up-regulation of establishment of protein localization" EXACT [GOC:TermGenie] synonym: "up-regulation of protein positioning" EXACT [GOC:TermGenie] synonym: "up-regulation of protein recruitment" EXACT [GOC:TermGenie] synonym: "upregulation of establishment of protein localisation" EXACT [GOC:TermGenie] synonym: "upregulation of establishment of protein localization" EXACT [GOC:TermGenie] synonym: "upregulation of protein positioning" EXACT [GOC:TermGenie] synonym: "upregulation of protein recruitment" EXACT [GOC:TermGenie] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:0070201 ! regulation of establishment of protein localization intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0045184 ! establishment of protein localization relationship: positively_regulates GO:0045184 ! establishment of protein localization created_by: mec creation_date: 2016-02-05T09:59:32Z [Term] id: GO:1905642 name: negative regulation of DNA methylation namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of DNA methylation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:27336847] synonym: "down regulation of DNA methylation" EXACT [GOC:TermGenie] synonym: "down-regulation of DNA methylation" EXACT [GOC:TermGenie] synonym: "downregulation of DNA methylation" EXACT [GOC:TermGenie] synonym: "inhibition of DNA methylation" NARROW [GOC:TermGenie] is_a: GO:0044030 ! regulation of DNA methylation is_a: GO:0051053 ! negative regulation of DNA metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006306 ! DNA methylation relationship: negatively_regulates GO:0006306 ! DNA methylation created_by: bc creation_date: 2016-11-04T16:43:13Z [Term] id: GO:1905643 name: positive regulation of DNA methylation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of DNA methylation." [GO_REF:0000058, GOC:bc, GOC:PARL, GOC:TermGenie, PMID:27336847] synonym: "activation of DNA methylation" NARROW [GOC:TermGenie] synonym: "up regulation of DNA methylation" EXACT [GOC:TermGenie] synonym: "up-regulation of DNA methylation" EXACT [GOC:TermGenie] synonym: "upregulation of DNA methylation" EXACT [GOC:TermGenie] is_a: GO:0044030 ! regulation of DNA methylation is_a: GO:0051054 ! positive regulation of DNA metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006306 ! DNA methylation relationship: positively_regulates GO:0006306 ! DNA methylation created_by: bc creation_date: 2016-11-04T16:43:22Z [Term] id: GO:1905952 name: regulation of lipid localization namespace: biological_process def: "Any process that modulates the frequency, rate or extent of lipid localization." [GO_REF:0000058, GOC:TermGenie, PMID:17564681] synonym: "regulation of lipid localisation" EXACT [GOC:TermGenie] is_a: GO:0032879 ! regulation of localization intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0010876 ! lipid localization relationship: regulates GO:0010876 ! lipid localization created_by: rozaru creation_date: 2017-02-21T12:12:22Z [Term] id: GO:1905953 name: negative regulation of lipid localization namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of lipid localization." [GO_REF:0000058, GOC:TermGenie, PMID:17564681] synonym: "down regulation of lipid localisation" EXACT [GOC:TermGenie] synonym: "down regulation of lipid localization" EXACT [GOC:TermGenie] synonym: "down-regulation of lipid localisation" EXACT [GOC:TermGenie] synonym: "down-regulation of lipid localization" EXACT [GOC:TermGenie] synonym: "downregulation of lipid localisation" EXACT [GOC:TermGenie] synonym: "downregulation of lipid localization" EXACT [GOC:TermGenie] synonym: "inhibition of lipid localisation" NARROW [GOC:TermGenie] synonym: "inhibition of lipid localization" NARROW [GOC:TermGenie] synonym: "negative regulation of lipid localisation" EXACT [GOC:TermGenie] is_a: GO:0048519 ! negative regulation of biological process is_a: GO:1905952 ! regulation of lipid localization intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0010876 ! lipid localization relationship: negatively_regulates GO:0010876 ! lipid localization created_by: rozaru creation_date: 2017-02-21T12:12:41Z [Term] id: GO:1905954 name: positive regulation of lipid localization namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of lipid localization." [GO_REF:0000058, GOC:TermGenie, PMID:17564681] synonym: "activation of lipid localisation" NARROW [GOC:TermGenie] synonym: "activation of lipid localization" NARROW [GOC:TermGenie] synonym: "positive regulation of lipid localisation" EXACT [GOC:TermGenie] synonym: "up regulation of lipid localisation" EXACT [GOC:TermGenie] synonym: "up regulation of lipid localization" EXACT [GOC:TermGenie] synonym: "up-regulation of lipid localisation" EXACT [GOC:TermGenie] synonym: "up-regulation of lipid localization" EXACT [GOC:TermGenie] synonym: "upregulation of lipid localisation" EXACT [GOC:TermGenie] synonym: "upregulation of lipid localization" EXACT [GOC:TermGenie] is_a: GO:0048518 ! positive regulation of biological process is_a: GO:1905952 ! regulation of lipid localization intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0010876 ! lipid localization relationship: positively_regulates GO:0010876 ! lipid localization created_by: rozaru creation_date: 2017-02-21T12:12:49Z [Term] id: GO:1990234 name: transferase complex namespace: cellular_component def: "A protein complex capable of catalyzing the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor)." [GOC:bhm, PMID:16540464] is_a: GO:1902494 ! catalytic complex created_by: bhm creation_date: 2013-11-12T13:20:12Z [Term] id: GO:1990774 name: tumor necrosis factor secretion namespace: biological_process def: "The regulated release of tumor necrosis factor from a cell. 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." [PMID:15560120] synonym: "cachectin secretion" EXACT [] synonym: "TNF secretion" EXACT [] synonym: "TNF superfamily, member 2 secretion" EXACT [] synonym: "TNF-alpha secretion" EXACT [] synonym: "Tnfa secretion" EXACT [] synonym: "tumor necrosis factor alpha secretion" EXACT [] synonym: "tumor necrosis factor ligand superfamily member 2 secretion" EXACT [] is_a: GO:0050663 ! cytokine secretion relationship: part_of GO:0032640 ! tumor necrosis factor production created_by: sl creation_date: 2015-06-15T22:59:26Z [Term] id: GO:2000112 name: regulation of cellular macromolecule biosynthetic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cellular macromolecule biosynthetic process." [GOC:obol] synonym: "regulation of cellular biopolymer biosynthetic process" EXACT [GOC:obol] synonym: "regulation of cellular macromolecule anabolism" EXACT [GOC:obol] synonym: "regulation of cellular macromolecule biosynthesis" EXACT [GOC:obol] synonym: "regulation of cellular macromolecule formation" EXACT [GOC:obol] synonym: "regulation of cellular macromolecule synthesis" EXACT [GOC:obol] is_a: GO:0010556 ! regulation of macromolecule biosynthetic process is_a: GO:0031326 ! regulation of cellular biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0034645 ! cellular macromolecule biosynthetic process relationship: regulates GO:0034645 ! cellular macromolecule biosynthetic process created_by: tanyaberardini creation_date: 2010-09-15T08:55:45Z [Term] id: GO:2000113 name: negative regulation of cellular macromolecule biosynthetic process namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cellular macromolecule biosynthetic process." [GOC:obol] synonym: "negative regulation of cellular biopolymer biosynthetic process" EXACT [GOC:obol] synonym: "negative regulation of cellular macromolecule anabolism" EXACT [GOC:obol] synonym: "negative regulation of cellular macromolecule biosynthesis" EXACT [GOC:obol] synonym: "negative regulation of cellular macromolecule formation" EXACT [GOC:obol] synonym: "negative regulation of cellular macromolecule synthesis" EXACT [GOC:obol] is_a: GO:0010558 ! negative regulation of macromolecule biosynthetic process is_a: GO:0031327 ! negative regulation of cellular biosynthetic process is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0034645 ! cellular macromolecule biosynthetic process relationship: negatively_regulates GO:0034645 ! cellular macromolecule biosynthetic process created_by: tanyaberardini creation_date: 2010-09-15T08:55:48Z [Term] id: GO:2000145 name: regulation of cell motility namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cell motility." [GOC:mah] synonym: "regulation of cell locomotion" EXACT [GOC:obol] synonym: "regulation of cell movement" RELATED [GOC:obol] synonym: "regulation of movement of a cell" EXACT [GOC:obol] is_a: GO:0040012 ! regulation of locomotion is_a: GO:0051270 ! regulation of cellular component movement intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0048870 ! cell motility relationship: regulates GO:0048870 ! cell motility created_by: midori creation_date: 2010-10-01T09:41:21Z [Term] id: GO:2000146 name: negative regulation of cell motility namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of cell motility." [GOC:mah] synonym: "negative regulation of cell locomotion" EXACT [GOC:obol] synonym: "negative regulation of cell movement" RELATED [GOC:obol] synonym: "negative regulation of movement of a cell" EXACT [GOC:obol] is_a: GO:0040013 ! negative regulation of locomotion is_a: GO:0051271 ! negative regulation of cellular component movement is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0048870 ! cell motility relationship: negatively_regulates GO:0048870 ! cell motility created_by: midori creation_date: 2010-10-01T09:41:26Z [Term] id: GO:2000147 name: positive regulation of cell motility namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cell motility." [GOC:mah] synonym: "positive regulation of cell locomotion" EXACT [GOC:obol] synonym: "positive regulation of cell movement" RELATED [GOC:obol] synonym: "positive regulation of movement of a cell" EXACT [GOC:obol] is_a: GO:0040017 ! positive regulation of locomotion is_a: GO:0051272 ! positive regulation of cellular component movement is_a: GO:2000145 ! regulation of cell motility intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0048870 ! cell motility relationship: positively_regulates GO:0048870 ! cell motility created_by: midori creation_date: 2010-10-01T09:41:30Z [Term] id: GO:2000191 name: regulation of fatty acid transport namespace: biological_process def: "Any process that modulates the frequency, rate or extent of fatty acid transport." [GOC:BHF] is_a: GO:0032368 ! regulation of lipid transport is_a: GO:0032890 ! regulation of organic acid transport is_a: GO:0044070 ! regulation of anion transport intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0015908 ! fatty acid transport relationship: regulates GO:0015908 ! fatty acid transport created_by: rl creation_date: 2010-10-18T10:37:13Z [Term] id: GO:2000192 name: negative regulation of fatty acid transport namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of fatty acid transport." [GOC:BHF] is_a: GO:0032369 ! negative regulation of lipid transport is_a: GO:0032891 ! negative regulation of organic acid transport is_a: GO:1903792 ! negative regulation of anion transport is_a: GO:2000191 ! regulation of fatty acid transport intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0015908 ! fatty acid transport relationship: negatively_regulates GO:0015908 ! fatty acid transport created_by: rl creation_date: 2010-10-18T10:37:15Z [Term] id: GO:2000193 name: positive regulation of fatty acid transport namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of fatty acid transport." [GOC:BHF] is_a: GO:0032370 ! positive regulation of lipid transport is_a: GO:0032892 ! positive regulation of organic acid transport is_a: GO:1903793 ! positive regulation of anion transport is_a: GO:2000191 ! regulation of fatty acid transport intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0015908 ! fatty acid transport relationship: positively_regulates GO:0015908 ! fatty acid transport created_by: rl creation_date: 2010-10-18T10:37:17Z [Term] id: GO:2000278 name: regulation of DNA biosynthetic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of DNA biosynthetic process." [GOC:obol] synonym: "regulation of DNA anabolism" EXACT [GOC:obol] synonym: "regulation of DNA biosynthesis" EXACT [GOC:obol] synonym: "regulation of DNA formation" EXACT [GOC:obol] synonym: "regulation of DNA synthesis" EXACT [GOC:obol] is_a: GO:0051052 ! regulation of DNA metabolic process is_a: GO:2000112 ! regulation of cellular macromolecule biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0071897 ! DNA biosynthetic process relationship: regulates GO:0071897 ! DNA biosynthetic process created_by: yaf creation_date: 2010-12-08T04:48:15Z [Term] id: GO:2000279 name: negative regulation of DNA biosynthetic process namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of DNA biosynthetic process." [GOC:obol] synonym: "negative regulation of DNA anabolism" EXACT [GOC:obol] synonym: "negative regulation of DNA biosynthesis" EXACT [GOC:obol] synonym: "negative regulation of DNA formation" EXACT [GOC:obol] synonym: "negative regulation of DNA synthesis" EXACT [GOC:obol] is_a: GO:0051053 ! negative regulation of DNA metabolic process is_a: GO:2000113 ! negative regulation of cellular macromolecule biosynthetic process is_a: GO:2000278 ! regulation of DNA biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0071897 ! DNA biosynthetic process relationship: negatively_regulates GO:0071897 ! DNA biosynthetic process created_by: yaf creation_date: 2010-12-08T04:48:20Z [Term] id: GO:2000573 name: positive regulation of DNA biosynthetic process namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process." [GOC:obol] synonym: "positive regulation of DNA anabolism" EXACT [GOC:obol] synonym: "positive regulation of DNA biosynthesis" EXACT [GOC:obol] synonym: "positive regulation of DNA formation" EXACT [GOC:obol] synonym: "positive regulation of DNA synthesis" EXACT [GOC:obol] is_a: GO:0010557 ! positive regulation of macromolecule biosynthetic process is_a: GO:0031328 ! positive regulation of cellular biosynthetic process is_a: GO:0051054 ! positive regulation of DNA metabolic process is_a: GO:2000278 ! regulation of DNA biosynthetic process intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0071897 ! DNA biosynthetic process relationship: positively_regulates GO:0071897 ! DNA biosynthetic process created_by: yaf creation_date: 2011-04-04T10:01:20Z [Term] id: GO:2000677 name: regulation of transcription regulatory region DNA binding namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transcription regulatory region DNA binding." [GOC:obol] is_a: GO:0051101 ! regulation of DNA binding intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0044212 ! transcription regulatory region DNA binding relationship: regulates GO:0044212 ! transcription regulatory region DNA binding created_by: yaf creation_date: 2011-05-09T03:28:11Z [Term] id: GO:2000678 name: negative regulation of transcription regulatory region DNA binding namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of transcription regulatory region DNA binding." [GOC:obol] is_a: GO:0043392 ! negative regulation of DNA binding is_a: GO:2000677 ! regulation of transcription regulatory region DNA binding intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0044212 ! transcription regulatory region DNA binding relationship: negatively_regulates GO:0044212 ! transcription regulatory region DNA binding created_by: yaf creation_date: 2011-05-09T03:28:14Z [Term] id: GO:2000679 name: positive regulation of transcription regulatory region DNA binding namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transcription regulatory region DNA binding." [GOC:obol] is_a: GO:0043388 ! positive regulation of DNA binding is_a: GO:2000677 ! regulation of transcription regulatory region DNA binding intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0044212 ! transcription regulatory region DNA binding relationship: positively_regulates GO:0044212 ! transcription regulatory region DNA binding created_by: yaf creation_date: 2011-05-09T03:28:17Z [Term] id: GO:2001020 name: regulation of response to DNA damage stimulus namespace: biological_process def: "Any process that modulates the frequency, rate or extent of response to DNA damage stimulus." [GOC:obol] synonym: "regulation of cellular DNA damage response" EXACT [GOC:obol] synonym: "regulation of cellular response to DNA damage stimulus" EXACT [GOC:obol] synonym: "regulation of DNA damage response" EXACT [GOC:obol] synonym: "regulation of response to genotoxic stress" EXACT [GOC:obol] is_a: GO:0080135 ! regulation of cellular response to stress intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0006974 ! cellular response to DNA damage stimulus relationship: regulates GO:0006974 ! cellular response to DNA damage stimulus created_by: yaf creation_date: 2011-08-19T10:20:25Z [Term] id: GO:2001021 name: negative regulation of response to DNA damage stimulus namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of response to DNA damage stimulus." [GOC:obol] synonym: "negative regulation of cellular DNA damage response" EXACT [GOC:obol] synonym: "negative regulation of cellular response to DNA damage stimulus" EXACT [GOC:obol] synonym: "negative regulation of DNA damage response" EXACT [GOC:obol] synonym: "negative regulation of response to genotoxic stress" EXACT [GOC:obol] is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:0048585 ! negative regulation of response to stimulus is_a: GO:2001020 ! regulation of response to DNA damage stimulus intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0006974 ! cellular response to DNA damage stimulus relationship: negatively_regulates GO:0006974 ! cellular response to DNA damage stimulus created_by: yaf creation_date: 2011-08-19T10:20:29Z [Term] id: GO:2001022 name: positive regulation of response to DNA damage stimulus namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of response to DNA damage stimulus." [GOC:obol] synonym: "positive regulation of cellular DNA damage response" EXACT [GOC:obol] synonym: "positive regulation of cellular response to DNA damage stimulus" EXACT [GOC:obol] synonym: "positive regulation of DNA damage response" EXACT [GOC:obol] synonym: "positive regulation of response to genotoxic stress" EXACT [GOC:obol] is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:0048584 ! positive regulation of response to stimulus is_a: GO:2001020 ! regulation of response to DNA damage stimulus intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0006974 ! cellular response to DNA damage stimulus relationship: positively_regulates GO:0006974 ! cellular response to DNA damage stimulus created_by: yaf creation_date: 2011-08-19T10:20:33Z [Term] id: GO:2001023 name: regulation of response to drug namespace: biological_process def: "Any process that modulates the frequency, rate or extent of response to drug." [GOC:obol] synonym: "regulation of drug resistance" RELATED [GOC:obol] synonym: "regulation of drug susceptibility/resistance" RELATED [GOC:obol] is_a: GO:0048583 ! regulation of response to stimulus intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0042493 ! response to drug relationship: regulates GO:0042493 ! response to drug created_by: yaf creation_date: 2011-08-19T01:47:20Z [Term] id: GO:2001024 name: negative regulation of response to drug namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of response to drug." [GOC:obol] synonym: "negative regulation of drug resistance" RELATED [GOC:obol] synonym: "negative regulation of drug susceptibility/resistance" RELATED [GOC:obol] is_a: GO:0048585 ! negative regulation of response to stimulus is_a: GO:2001023 ! regulation of response to drug intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0042493 ! response to drug relationship: negatively_regulates GO:0042493 ! response to drug created_by: yaf creation_date: 2011-08-19T01:47:24Z [Term] id: GO:2001025 name: positive regulation of response to drug namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of response to drug." [GOC:obol] synonym: "positive regulation of drug resistance" RELATED [GOC:obol] synonym: "positive regulation of drug susceptibility/resistance" RELATED [GOC:obol] is_a: GO:0048584 ! positive regulation of response to stimulus is_a: GO:2001023 ! regulation of response to drug intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0042493 ! response to drug relationship: positively_regulates GO:0042493 ! response to drug created_by: yaf creation_date: 2011-08-19T01:47:27Z [Term] id: GO:2001038 name: regulation of cellular response to drug namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cellular response to drug." [GOC:obol] is_a: GO:0050794 ! regulation of cellular process is_a: GO:2001023 ! regulation of response to drug intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0035690 ! cellular response to drug relationship: regulates GO:0035690 ! cellular response to drug created_by: yaf creation_date: 2011-08-27T04:12:19Z [Term] id: GO:2001039 name: negative regulation of cellular response to drug namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of cellular response to drug." [GOC:obol] is_a: GO:0048523 ! negative regulation of cellular process is_a: GO:2001024 ! negative regulation of response to drug is_a: GO:2001038 ! regulation of cellular response to drug intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0035690 ! cellular response to drug relationship: negatively_regulates GO:0035690 ! cellular response to drug created_by: yaf creation_date: 2011-08-27T04:12:23Z [Term] id: GO:2001040 name: positive regulation of cellular response to drug namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cellular response to drug." [GOC:obol] is_a: GO:0048522 ! positive regulation of cellular process is_a: GO:2001025 ! positive regulation of response to drug is_a: GO:2001038 ! regulation of cellular response to drug intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0035690 ! cellular response to drug relationship: positively_regulates GO:0035690 ! cellular response to drug created_by: yaf creation_date: 2011-08-27T04:12:25Z [Term] id: GO:2001141 name: regulation of RNA biosynthetic process namespace: biological_process def: "Any process that modulates the frequency, rate or extent of RNA biosynthetic process." [GOC:dph] synonym: "regulation of RNA anabolism" EXACT [GOC:obol] synonym: "regulation of RNA biosynthesis" EXACT [GOC:obol] synonym: "regulation of RNA formation" EXACT [GOC:obol] synonym: "regulation of RNA synthesis" EXACT [GOC:obol] is_a: GO:0010556 ! regulation of macromolecule biosynthetic process is_a: GO:0031326 ! regulation of cellular biosynthetic process is_a: GO:0051252 ! regulation of RNA metabolic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0032774 ! RNA biosynthetic process relationship: regulates GO:0032774 ! RNA biosynthetic process created_by: dph creation_date: 2011-10-17T11:36:25Z [Term] id: GO:2001233 name: regulation of apoptotic signaling pathway namespace: biological_process def: "Any process that modulates the frequency, rate or extent of apoptotic signaling pathway." [GOC:mtg_apoptosis] synonym: "regulation of apoptotic signalling pathway" EXACT [GOC:mah] is_a: GO:0009966 ! regulation of signal transduction is_a: GO:0042981 ! regulation of apoptotic process intersection_of: GO:0008150 ! biological_process intersection_of: regulates GO:0097190 ! apoptotic signaling pathway relationship: regulates GO:0097190 ! apoptotic signaling pathway created_by: pr creation_date: 2011-11-24T01:20:49Z [Term] id: GO:2001234 name: negative regulation of apoptotic signaling pathway namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of apoptotic signaling pathway." [GOC:mtg_apoptosis] synonym: "negative regulation of apoptotic signalling pathway" EXACT [GOC:mah] is_a: GO:0009968 ! negative regulation of signal transduction is_a: GO:0043066 ! negative regulation of apoptotic process is_a: GO:2001233 ! regulation of apoptotic signaling pathway intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0097190 ! apoptotic signaling pathway relationship: negatively_regulates GO:0097190 ! apoptotic signaling pathway created_by: pr creation_date: 2011-11-24T01:20:54Z [Term] id: GO:2001235 name: positive regulation of apoptotic signaling pathway namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway." [GOC:mtg_apoptosis] synonym: "positive regulation of apoptotic signalling pathway" EXACT [GOC:mah] is_a: GO:0009967 ! positive regulation of signal transduction is_a: GO:0043065 ! positive regulation of apoptotic process is_a: GO:2001233 ! regulation of apoptotic signaling pathway intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0097190 ! apoptotic signaling pathway relationship: positively_regulates GO:0097190 ! apoptotic signaling pathway created_by: pr creation_date: 2011-11-24T01:20:58Z [Term] id: GO:2001251 name: negative regulation of chromosome organization namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of chromosome organization." [GOC:obol] synonym: "negative regulation of chromosome organisation" EXACT [GOC:obol] synonym: "negative regulation of chromosome organization and biogenesis" RELATED [GOC:obol] synonym: "negative regulation of maintenance of genome integrity" RELATED [GOC:obol] synonym: "negative regulation of nuclear genome maintenance" RELATED [GOC:obol] is_a: GO:0010639 ! negative regulation of organelle organization is_a: GO:0033044 ! regulation of chromosome organization intersection_of: GO:0008150 ! biological_process intersection_of: negatively_regulates GO:0051276 ! chromosome organization relationship: negatively_regulates GO:0051276 ! chromosome organization created_by: yaf creation_date: 2011-12-02T02:01:20Z [Term] id: GO:2001252 name: positive regulation of chromosome organization namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of chromosome organization." [GOC:obol] synonym: "positive regulation of chromosome organisation" EXACT [GOC:obol] synonym: "positive regulation of chromosome organization and biogenesis" RELATED [GOC:obol] synonym: "positive regulation of maintenance of genome integrity" RELATED [GOC:obol] synonym: "positive regulation of nuclear genome maintenance" RELATED [GOC:obol] is_a: GO:0010638 ! positive regulation of organelle organization is_a: GO:0033044 ! regulation of chromosome organization intersection_of: GO:0008150 ! biological_process intersection_of: positively_regulates GO:0051276 ! chromosome organization relationship: positively_regulates GO:0051276 ! chromosome organization created_by: yaf creation_date: 2011-12-02T02:01:26Z [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 property_value: IAO:0000111 "measurement unit label" xsd:string property_value: IAO:0000112 "Examples of measurement unit labels are liters, inches, weight per volume." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2009-03-16: provenance: a term measurement unit was\nproposed for OBI (OBI_0000176) , edited by Chris Stoeckert and\nCristian Cocos, and subsequently moved to IAO where the objective for\nwhich the original term was defined was satisfied with the definition\nof this, different, term." xsd:string property_value: IAO:0000116 "2009-03-16: review of this term done during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify this definition please notify OBI." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string [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." [] is_a: IAO:0000033 ! directive information entity property_value: IAO:0000111 "objective specification" xsd:string property_value: IAO:0000112 "In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2009-03-16: original definition when imported from OBI read: \"objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed.\"" xsd:string property_value: IAO:0000116 "2014-03-31: In the example of usage (\"In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction\") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that." xsd:string property_value: IAO:0000116 "Answers the question, why did you do this experiment?" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Barry Smith" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000118 "goal specification" xsd:string property_value: IAO:0000119 "OBI Plan and Planned Process/Roles Branch" xsd:string property_value: IAO:0000119 "OBI_0000217" xsd:string [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 property_value: IAO:0000112 "Pour the contents of flask 1 into flask 2" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "OBI Plan and Planned Process branch" xsd:string [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 property_value: IAO:0000111 "datum label" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n xsd:string property_value: IAO:0000117 "GROUP: IAO" xsd:string property_value: IAO:0000232 "9/22/11 BP: changed the rdfs:label for this class from 'label' to 'datum label' to convey that this class is not intended to cover all kinds of labels (stickers, radiolabels, etc.), and not even all kind of textual labels, but rather the kind of labels occuring in a datum. \n" xsd:string [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 property_value: IAO:0000111 "software" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "see sourceforge tracker discussion at http://sourceforge.net/tracker/index.php?func=detail&aid=1958818&group_id=177891&atid=886178" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000119 "GROUP: OBI" xsd:string [Term] id: IAO:0000015 name: information carrier def: "A quality of an information bearer that imparts the information content" [] is_a: BFO:0000019 ! quality intersection_of: BFO:0000019 ! quality intersection_of: RO:0000059 IAO:0000030 ! concretizes information content entity property_value: IAO:0000111 "information carrier" xsd:string property_value: IAO:0000112 "In the case of a printed paperback novel the physicality of the ink and of the paper form part of the information bearer. The qualities of appearing black and having a certain pattern for the ink and appearing white for the paper form part of the information carrier in this case." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "12/15/09: There is a concern that some ways that carry information may be processes rather than qualities, such as in a 'delayed wave carrier'." xsd:string property_value: IAO:0000116 "2014-03-10: We are not certain that all information carriers are qualities. There was a discussion of dropping it." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string [Term] id: IAO:0000027 name: data item def: "a data item is 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." [] is_a: IAO:0000030 ! information content entity property_value: IAO:0000111 "data item" xsd:string property_value: IAO:0000112 "Data items include counts of things, analyte concentrations, and statistical summaries." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers." xsd:string property_value: IAO:0000116 "2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum." xsd:string property_value: IAO:0000116 "2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym." xsd:string property_value: IAO:0000116 "2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/" xsd:string property_value: IAO:0000116 "JAR: datum -- well, this will be very tricky to define, but maybe some \ninformation-like stuff that might be put into a computer and that is \nmeant, by someone, to denote and/or to be interpreted by some \nprocess... I would include lists, tables, sentences... I think I might \ndefer to Barry, or to Brian Cantwell Smith\n\nJAR: A data item is an approximately justified approximately true approximate belief" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON: Jonathan Rees" xsd:string property_value: IAO:0000118 "data" xsd:string [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 relationship: IAO:0000136 BFO:0000001 ! is about entity property_value: IAO:0000111 "information content entity" xsd:string property_value: IAO:0000112 "Examples of information content entites include journal articles, data, graphical layouts, and graphs." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2014-03-10: The use of \"thing\" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ)." xsd:string property_value: IAO:0000116 "information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).\n\nPrevious. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity." xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000119 "OBI_0000142" xsd:string [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 relationship: OBI:0001938 OBI:0001931 ! has value specification scalar value specification property_value: IAO:0000112 "10 feet. 3 ml." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2009-03-16: we decided to keep datum singular in scalar measurement datum, as in\nthis case we explicitly refer to the singular form" xsd:string property_value: IAO:0000116 "Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string [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 relationship: IAO:0000136 BFO:0000017 ! is about realizable entity property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was \"is the specification of a process that can be concretized and realized by an actor\" with alternative term \"instruction\".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string property_value: IAO:0000116 "2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it." xsd:string property_value: IAO:0000116 "8/6/2009 Alan Ruttenberg: Changed label from \"information entity about a realizable\" after discussions at ICBO" xsd:string property_value: IAO:0000116 "Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string [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 property_value: IAO:0000111 "dot plot" xsd:string property_value: IAO:0000112 "Dot plot of SSC-H and FSC-H." xsd:string property_value: IAO:0000114 IAO:0000002 property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000123" xsd:string [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 property_value: IAO:0000111 "graph" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000240" xsd:string [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 property_value: IAO:0000111 "algorithm" xsd:string property_value: IAO:0000112 "PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)" xsd:string property_value: IAO:0000119 "OBI_0000270" xsd:string [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 property_value: IAO:0000111 "curation status specification" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)" xsd:string property_value: IAO:0000117 "PERSON:Bill Bug" xsd:string property_value: IAO:0000119 GROUP:OBI: xsd:string property_value: IAO:0000119 "OBI_0000266" xsd:string [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 property_value: IAO:0000111 "data format specification" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "2009-03-16: provenance: term imported from OBI_0000187, which had original definition \"A data format specification is a plan which organizes\ninformation. Example: The ISO document specifying what encompasses an\nXML document; The instructions in a XSD file\"" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: IAO:0000119 "OBI_0000187" xsd:string [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 property_value: IAO:0000111 "data set" xsd:string property_value: IAO:0000112 "Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves)." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type" xsd:string property_value: IAO:0000116 "2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction." xsd:string property_value: IAO:0000117 "person:Allyson Lister" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000042" xsd:string [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 property_value: IAO:0000111 "image" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000117 person:Allyson xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000030" xsd:string [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 property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [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 relationship: has_part IAO:0000005 ! objective specification relationship: has_part IAO:0000007 ! action specification property_value: IAO:0000111 "plan specification" xsd:string property_value: IAO:0000112 "PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was \" a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan\". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term." xsd:string property_value: IAO:0000116 "2014-03-31: A plan specification can have other parts, such as conditional specifications." xsd:string property_value: IAO:0000116 "Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved" xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "OBI Plan and Planned Process branch" xsd:string property_value: IAO:0000119 "OBI_0000344" xsd:string [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 relationship: OBI:0001938 OBI:0001933 ! has value specification value specification property_value: IAO:0000111 "measurement datum" xsd:string property_value: IAO:0000112 "Examples of measurement data are the recoding of the weight of a mouse as {40,mass,\"grams\"}, the recording of an observation of the behavior of the mouse {,process,\"agitated\"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2/2/2009 is_specified_output of some assay?" xsd:string property_value: IAO:0000117 "person:Chris Stoeckert" xsd:string property_value: IAO:0000119 group:OBI xsd:string property_value: IAO:0000119 "OBI_0000305" xsd:string [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 property_value: IAO:0000111 "material information bearer" xsd:string property_value: IAO:0000112 "a brain" xsd:string property_value: IAO:0000112 "a hard drive" xsd:string property_value: IAO:0000112 "A page of a paperback novel with writing on it. The paper itself is a material information bearer, the pattern of ink is the information carrier." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "GROUP: IAO" xsd:string [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 property_value: IAO:0000111 "histogram" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000119 GROUP:OBI xsd:string [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 property_value: IAO:0000111 "heatmap" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000119 GROUP:OBI xsd:string [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 property_value: IAO:0000111 "dendrogram" xsd:string property_value: IAO:0000112 "Dendrograms are often used in computational biology to\nillustrate the clustering of genes." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Dendrogram" xsd:string [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." [] is_a: IAO:0000038 ! graph property_value: IAO:0000111 "scatter plot" xsd:string property_value: IAO:0000112 "Comparison of gene expression values in two samples can be displayed in a scatter plot" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:James Malone" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000118 "scattergraph" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Scatterplot" xsd:string [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 property_value: IAO:0000111 "obsolescence reason specification" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "The creation of this class has been inspired in part by Werner Ceusters' paper, Applying evolutionary terminology auditing to the Gene Ontology." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string [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 property_value: IAO:0000111 "figure" xsd:string property_value: IAO:0000112 "Any picture, diagram or table" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [Term] id: IAO:0000309 name: diagram def: "A figure that expresses one or more propositions" [] is_a: IAO:0000308 ! figure property_value: IAO:0000111 "diagram" xsd:string property_value: IAO:0000112 "A molecular structure ribbon cartoon showing helices, turns and sheets and their relations to each other in space." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [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 property_value: IAO:0000111 "document" xsd:string property_value: IAO:0000112 "A journal article, patent application, laboratory notebook, or a book" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Lawrence Hunter" xsd:string [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 property_value: IAO:0000112 "The Basic Formal Ontology ontology makes a distinction between Universals and defined classes, where the formal are \"natural kinds\" and the latter arbitrary collections of entities." xsd:string property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Barry Smith, Werner Ceusters" xsd:string [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 relationship: IAO:0000039 UO:0000003 ! has measurement unit label time unit relationship: IAO:0000413 BFO:0000015 ! is duration of process property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "2009/09/28 Alan Ruttenberg. Fucoidan-use-case" xsd:string property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string [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." [] is_a: IAO:0000038 ! graph property_value: IAO:0000111 "line graph" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON:Melanie Courtot" xsd:string property_value: IAO:0000118 "line chart" xsd:string property_value: IAO:0000119 GROUP:OBI xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Line_chart" xsd:string [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 property_value: IAO:0000111 "infection" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ido.owl [Term] id: NCBITaxon:10239 name: Viruses is_a: OBI:0100026 ! organism property_value: IAO:0000111 "Viruses" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:117571 name: Euteleostomi is_a: NCBITaxon:7742 ! Vertebrata property_value: IAO:0000111 "Euteleostomi" xsd:string property_value: IAO:0000118 "bony vertebrates" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:2 name: Bacteria is_a: OBI:0100026 ! organism property_value: IAO:0000111 "Bacteria" xsd:string property_value: IAO:0000118 "eubacteria" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:2157 name: Archaea is_a: OBI:0100026 ! organism property_value: IAO:0000111 "Archaea" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:2759 name: Eukaryota is_a: OBI:0100026 ! organism property_value: IAO:0000111 "Eukaryota" xsd:string property_value: IAO:0000118 "eucaryotes" xsd:string property_value: IAO:0000118 "eukaryotes" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:314146 name: Euarchontoglires is_a: NCBITaxon:40674 ! Mammalia property_value: IAO:0000111 "Euarchontoglires" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:32523 name: Tetrapoda is_a: NCBITaxon:117571 ! Euteleostomi property_value: IAO:0000111 "Tetrapoda" xsd:string property_value: IAO:0000118 "tetrapods" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:32524 name: Amniota is_a: NCBITaxon:32523 ! Tetrapoda property_value: IAO:0000111 "Amniota" xsd:string property_value: IAO:0000118 "amniotes" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:33154 name: Opisthokonta is_a: NCBITaxon:2759 ! Eukaryota property_value: IAO:0000111 "Opisthokonta" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:33213 name: Bilateria is_a: NCBITaxon:33154 ! Opisthokonta property_value: IAO:0000111 "Bilateria" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:40674 name: Mammalia is_a: NCBITaxon:32524 ! Amniota property_value: IAO:0000111 "Mammalia" xsd:string property_value: IAO:0000118 "mammals" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:7742 name: Vertebrata is_a: NCBITaxon:33213 ! Bilateria property_value: IAO:0000111 "Vertebrata " xsd:string property_value: IAO:0000118 "Vertebrata" xsd:string property_value: IAO:0000118 "vertebrates" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: NCBITaxon:9606 name: Homo sapiens is_a: NCBITaxon:314146 ! Euarchontoglires property_value: IAO:0000111 "Homo sapiens" xsd:string property_value: IAO:0000118 "human" xsd:string property_value: IAO:0000118 "human being" xsd:string property_value: IAO:0000118 "man" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ncbitaxon.owl [Term] id: OBI:0000011 name: planned process def: "A processual entity that realizes a plan which is the concretization of a plan specification." [] is_a: BFO:0000015 ! process property_value: IAO:0000111 "planned process" xsd:string property_value: IAO:0000111 "planned process" xsd:string property_value: IAO:0000112 "Injecting mice with a vaccine in order to test its efficacy" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.)" xsd:string property_value: IAO:0000116 "We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some \nobjectives is a planned process." xsd:string property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "branch derived" xsd:string property_value: IAO:0000232 "6/11/9: Edited at workshop. Used to include: is initiated by an agent" xsd:string property_value: IAO:0000232 "This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call)" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: OBI:0000014 name: regulator role def: "a regulatory role involved with making and/or enforcing relevant legislation and governmental orders" [] is_a: OBI:0000017 ! regulatory role property_value: IAO:0000111 "regulator role" xsd:string property_value: IAO:0000112 "Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person:Jennifer Fostel" xsd:string property_value: IAO:0000118 "regulator" xsd:string property_value: IAO:0000119 "OBI" xsd:string [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 property_value: IAO:0000111 "biological feature identification objective" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Jennifer Fostel" xsd:string [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 property_value: IAO:0000111 "regulatory role" xsd:string property_value: IAO:0000112 "Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "GROUP: Role branch" xsd:string property_value: IAO:0000119 "OBI, CDISC" xsd:string property_value: IAO:0000232 "govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent" xsd:string [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." [] is_a: OBI:0000947 ! service provider role property_value: IAO:0000111 "material supplier role" xsd:string property_value: IAO:0000112 "Jackson Labs is an organization which provide mice as experimental material" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "Supplier role is a special kind of service, e.g. biobank" xsd:string property_value: IAO:0000117 "PERSON:Jennifer Fostel" xsd:string property_value: IAO:0000118 "material provider role" xsd:string property_value: IAO:0000118 "supplier" xsd:string [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." [] is_a: IAO:0000100 ! data set property_value: IAO:0000111 "classified data set" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: James Malone" xsd:string property_value: IAO:0000117 "PERSON: Monnie McGee" xsd:string property_value: IAO:0000118 "data set with assigned class labels" xsd:string [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." [] is_a: BFO:0000023 ! role relationship: RO:0000052 BFO:0000040 ! inheres in material entity property_value: IAO:0000111 "reference substance role" xsd:string property_value: IAO:0000112 "Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person:Jennifer Fostel" xsd:string property_value: IAO:0000118 "reference substance" xsd:string property_value: IAO:0000119 "OBI" xsd:string [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 relationship: has_part OBI:0000967 ! container property_value: IAO:0000111 "chromatography column" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Column_chromatography xsd:string property_value: IAO:0000232 "open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178" xsd:string [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 property_value: IAO:0000111 "xenotransplantation" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 intersection_of: BFO:0000040 ! material entity intersection_of: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing property_value: IAO:0000111 "processed material" xsd:string property_value: IAO:0000112 "Examples include gel matrices, filter paper, parafilm and buffer solutions, mass spectrometer, tissue samples" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string [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." [] is_a: OBI:0000832 ! measurement device is_a: OBI:0000932 ! material separation device is_a: OBI:0002089 ! physical store relationship: RO:0000085 OBI:0000370 ! has function contain function relationship: RO:0000085 OBI:0000372 ! has function material separation function relationship: RO:0000085 OBI:0000401 ! has function environment control function relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "chromatography device" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000118 "chromatography instrument" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Chromatography xsd:string property_value: IAO:0000232 "open tracker https://sourceforge.net/tracker/index.php?func=detail&aid=2881353&group_id=177891&atid=886178" xsd:string [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 relationship: has_part OBI:0000345 ! mass analyzer relationship: has_part OBI:0000361 ! ion source relationship: has_part OBI:0000364 ! ion detector relationship: RO:0000053 OBI:0000654 ! bearer of device setting relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "mass spectrometer" xsd:string property_value: IAO:0000112 "LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Mass_spectrometry xsd:string [Term] id: OBI:0000057 name: allotransplantation def: "is the transplantation of organs between members of the same species." [] is_a: OBI:0000105 ! transplantation property_value: IAO:0000111 "allotransplantation" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [Term] id: OBI:0000059 name: gamma counter def: "A processed material which measures gamma radiation" [] is_a: OBI:0000832 ! measurement device relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "gamma counter" xsd:string property_value: IAO:0000112 "A Geiger counter" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Gamma_counter xsd:string [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 relationship: BFO:0000054 OBI:0000070 ! realized in assay relationship: RO:0000052 BFO:0000040 ! inheres in material entity property_value: IAO:0000111 "evaluant role" xsd:string property_value: IAO:0000112 "When a specimen of blood is assayed for glucose concentration, the blood has the evaluant role. When measuring the mass of a mouse, the evaluant is the mouse. When measuring the time of DNA replication, the evaluant is the DNA. When measuring the intensity of light on a surface, the evaluant is the light source." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "examples of features that could be described in an evaluant: quality.... e.g. \"contains 10 pg/ml IL2\", or \"no glucose detected\")" xsd:string property_value: IAO:0000116 "Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputting blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)" xsd:string property_value: IAO:0000117 "GROUP: Role Branch" xsd:string property_value: IAO:0000119 "OBI" xsd:string property_value: IAO:0000232 "Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term." xsd:string [Term] id: OBI:0000070 name: assay def: "A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies." [] is_a: OBI:0000011 ! planned process disjoint_from: OBI:0200000 ! data transformation relationship: BFO:0000055 OBI:0000067 ! realizes evaluant role property_value: IAO:0000111 "assay" xsd:string property_value: IAO:0000112 "Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. " xsd:string property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000118 "measuring" xsd:string property_value: IAO:0000118 "scientific observation" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: OBI:0001847 "study assay" xsd:string property_value: OBI:9991118 "any method" xsd:string [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 property_value: IAO:0000111 "culture medium" xsd:string property_value: IAO:0000112 "A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "changed from a role to a processed material based on on Aug 22, 2011 dev call. Details see the tracker item: http://sourceforge.net/tracker/?func=detail&aid=3325270&group_id=177891&atid=886178\nModification made by JZ." xsd:string property_value: IAO:0000117 "Person: Jennifer Fostel, Jie Zheng" xsd:string property_value: IAO:0000119 "OBI" xsd:string [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). is_a: BFO:0000023 ! role property_value: IAO:0000111 "reagent role" xsd:string property_value: IAO:0000112 "Buffer, dye, a catalyst, a solvating agent." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Matthew Brush" xsd:string property_value: IAO:0000118 "reagent" xsd:string property_value: IAO:0000119 "PERSON:Matthew Brush" xsd:string property_value: IAO:0000232 "Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term.\n\nMay 28 2013. Updated definition taken from ReO based on discussions initiated in Philly 2011 workshop. Former defnition described a narrower view of reagents in chemistry that restricts bearers of the role to be chemical entities (\"a role played by a molecular entity used to produce a chemical reaction to detect, measure, or produce other substances\"). Updated definition allows for broader view of reagents in the domain of biomedical research to include larger materials that have parts that participate chemically in a molecular reaction or interaction.\n" xsd:string [Term] id: OBI:0000094 name: material processing def: "A planned process which results in physical changes in a specified input material" [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 BFO:0000040 ! has_specified_output material entity relationship: OBI:0000299 OBI:0000047 ! has_specified_output processed material property_value: IAO:0000111 "material processing" xsd:string property_value: IAO:0000112 "A cell lysis, production of a cloning vector, creating a buffer." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Frank Gibson" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca Serra" xsd:string property_value: IAO:0000118 "material transformation" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 relationship: BFO:0000054 OBI:0000471 ! realized in study design execution property_value: IAO:0000111 "study subject role" xsd:string property_value: IAO:0000112 "Human subjects in a clinical trial, rats in a toxicogenomics study, tissue cutlures subjected to drug tests, fish observed in an ecotoxicology study. \nParasite example: people are infected with a parasite which is then extracted; the particpant under investigation could be the parasite, the people, or a population of which the people are members, depending on the nature of the study.\nLake example: a lake could realize this role in an investigation that assays pollution levels in samples of water taken from the lake." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "A participant can realize both \"specimen role\" and \"participant under investigation role\" at the same time. However \"participant under investigation role\" is distinct from \"specimen role\", since a specimen could somehow be involved in an investigation without being the thing that is under investigation." xsd:string property_value: IAO:0000117 "GROUP: Role Branch" xsd:string property_value: IAO:0000119 "OBI" xsd:string property_value: IAO:0000232 "Following OBI call November 2012,26th:\n \n1. it was decided there was no need for moving the children class and making them siblings of study subject role.\n2. it also settles the disambiguation about 'study subject'. This is about the individual participating in the investigation/study, Not the 'topic' (as in 'toxicity study') of the investigation/study\n\nThis note closes the issue and validates the class definition to be part of the OBI core\neditor = PRS\n" xsd:string [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 relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "transplantation" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 property_value: IAO:0000111 "specimen role" xsd:string property_value: IAO:0000112 "liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role." xsd:string property_value: IAO:0000116 "blood taken from animal: animal continues in study, whereas blood has role specimen.\nsomething taken from study subject, leaves the study and becomes the specimen." xsd:string property_value: IAO:0000116 "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string property_value: IAO:0000116 "parasite example\n- when parasite in people we study people, people are subjects and parasites are specimen\n- when parasite extracted, they become subject in the following study\nspecimen can later be subject." xsd:string property_value: IAO:0000117 "GROUP: Role Branch" xsd:string property_value: IAO:0000119 "OBI" xsd:string [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 property_value: IAO:0000111 "sequence feature identification objective" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Jennifer Fostel" xsd:string [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 property_value: IAO:0000111 "intervention design" xsd:string property_value: IAO:0000112 "PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Philppe Rocca-Serra" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 property_value: IAO:0000111 "molecular feature identification objective" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Jennifer Fostel" xsd:string [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 relationship: OBI:0000293 OBI:0000079 ! has_specified_input culture medium relationship: OBI:0000299 OBI:0100060 ! has_specified_output cultured cell population relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "cell co-culturing" xsd:string property_value: IAO:0000112 "Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [Term] id: OBI:0000164 name: 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 relationship: OBI:0000312 OBI:0600064 ! is_specified_output_of recombinant vector cloning relationship: OBI:0000643 OBI:0000731 ! has grain recombinant vector property_value: IAO:0000111 "cDNA library" xsd:string property_value: IAO:0000112 "PMID:6110205. collection of cDNA derived from mouse splenocytes." xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Luisa Montecchi" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "GROUP: PSI" xsd:string property_value: IAO:0000232 "PRS: 22022008. class moved under population,\nmodification of definition and replacement of biomaterials in previous definition with 'material'\naddition of has_role restriction" xsd:string [Term] id: OBI:0000185 name: imaging assay def: "An imaging assay is an assay to produce a picture of an entity. definition_source: OBI." [] is_a: OBI:0000070 ! assay relationship: OBI:0000299 IAO:0000101 ! has_specified_output image relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective property_value: IAO:0000111 "imaging assay" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [Term] id: OBI:0000192 name: microtiter plate def: "A microtiter_plate is a flat plate with multiple wells used as small test tubes." [] is_a: OBI:0000967 ! container relationship: RO:0000085 OBI:0000370 ! has function contain function property_value: IAO:0000111 "microtiter plate" xsd:string property_value: IAO:0000112 "A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000118 "microplate" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Microtiter_plate xsd:string [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 property_value: IAO:0000111 "radioactivity detection" xsd:string property_value: IAO:0000112 "Placing the evaluant input material close to a scintillation counter which emits light upon being hit with alpha/beta/gamma radiation and counting the frequency of light blasts to determine the radioactivity of the input material." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PlanAndPlannedProcess Branch, IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 property_value: IAO:0000111 "cellular feature identification objective" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Jennifer Fostel" xsd:string [Term] id: OBI:0000231 name: enzymatic cleavage def: "enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme" [] is_a: OBI:0000094 ! material processing relationship: OBI:0000293 OBI:0100051 ! has_specified_input specimen relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "enzymatic cleavage" xsd:string property_value: IAO:0000112 "Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 property_value: IAO:0000111 "organization" xsd:string property_value: IAO:0000112 "PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:\n\n1) there are organization_member_roles (president, treasurer, branch\neditor), with individual persons as bearers\n\n2) there are organization_roles (employer, owner, vendor, patent holder)\n\n3) an organization has a charter / rules / bylaws, which specify what roles\nthere are, how they should be realized, and how to modify the\ncharter/rules/bylaws themselves.\n\nIt is debatable what the organization itself is (some kind of dependent\ncontinuant or an aggregate of people). This also determines who/what the\nbearer of organization_roles' are. My personal favorite is still to define\norganization as a kind of 'legal entity', but thinking it through leads to\nall kinds of questions that are clearly outside the scope of OBI.\n\nInterestingly enough, it does not seem to matter much where we place\norganization itself, as long as we can subclass it (University, Corporation,\nGovernment Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,\nW3C, University of Oklahoma), and have it play roles.\n\nThis leads to my proposal: We define organization through the statements 1 -\n3 above, but without an 'is a' statement for now. We can leave it in its\ncurrent place in the is_a hierarchy (material entity) or move it up to\n'continuant'. We leave further clarifications to BFO, and close this issue\nfor now." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000117 "PERSON: Susanna Sansone" xsd:string property_value: IAO:0000119 "GROUP: OBI" xsd:string [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 relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "artificially induced nucleic acid hybridization" xsd:string property_value: IAO:0000112 "www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 relationship: OBI:0000299 CHEBI:16991 ! has_specified_output deoxyribonucleic acid property_value: IAO:0000111 "DNA extraction" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 property_value: IAO:0000111 "organism feature identification objective" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Jennifer Fostel" xsd:string [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." [] is_a: IAO:0000104 ! plan specification property_value: IAO:0000111 "protocol" xsd:string property_value: IAO:0000112 "PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)" xsd:string property_value: OBI:0001847 "study protocol" xsd:string [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 relationship: BFO:0000055 OBI:0000319 ! realizes material to be added role relationship: BFO:0000055 OBI:0000444 ! realizes target of material addition role property_value: IAO:0000111 "adding a material entity into a target" xsd:string property_value: IAO:0000112 "Injecting a drug into a mouse. Adding IL-2 to a cell culture. Adding NaCl into water." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "Class was renamed from 'administering substance', as this is commonly used only for additions into organisms." xsd:string property_value: IAO:0000117 "BP" xsd:string property_value: IAO:0000119 "branch derived" xsd:string [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 relationship: BFO:0000054 OBI:0000443 ! realized in analyte assay property_value: IAO:0000111 "analyte role" xsd:string property_value: IAO:0000112 "Glucose in blood (measured in an assay to determine the concentration of glucose)." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "interestingly, an analyte is still an analyte even if it is not detected. for this reason it does not bear a specified input role" xsd:string property_value: IAO:0000116 "pH (technically the inverse log of [H+]) may be considered a quality; this remains to be tested." xsd:string property_value: IAO:0000116 "qualities such as weight, color are not assayed but measured, so they do not fall into this category." xsd:string property_value: IAO:0000117 "GROUP: Role Branch" xsd:string property_value: IAO:0000119 "OBI" xsd:string property_value: IAO:0000232 "Feb 10, 2009. changes after discussion at OBI Consortium Workshop Feb 2-6, 2009. accepted as core term." xsd:string [Term] id: OBI:0000288 name: protein-protein interaction detection def: "An assay with the objective to determine interactions between proteins, such as protein-protein binding." [] is_a: OBI:0000070 ! assay property_value: IAO:0000111 "protein-protein interaction detection" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "20091101, Bjoern Peters: This class may be overly broad. Lot's of assays would seem to classify under it, and I have the feeling that the intend would be to limit this to determining protein-protein interactions as they occur within an organism, rather than e.g. peptide:MHC binding assays." xsd:string [Term] id: OBI:0000291 name: transcription factor binding site assay def: "An assay with objective to find DNA region specifically recognized by proteins that function as transcription factors" [] is_a: OBI:0001146 ! binding assay property_value: IAO:0000111 "transcription factor binding site identification" xsd:string property_value: IAO:0000112 "Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.\nFunct Integr Genomics. 2007 Oct;7(4):335-45. Epub 2007 Jul 19. PMID: 17638031" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "JZ: add equivalent axiom for classification\nadd alternative term 'TF binding' which was used in BCBC database" xsd:string property_value: IAO:0000116 "JZ: fixed inconsistency issue and relabel the term\nsee tracker: https://sourceforge.net/p/obi/obi-terms/767/" xsd:string property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "TF binding" xsd:string property_value: IAO:0000119 "OBI" xsd:string [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" [] is_a: OBI:0000047 ! processed material relationship: OBI:0000312 OBI:0302905 ! is_specified_output_of elution property_value: IAO:0000111 "eluate" xsd:string property_value: IAO:0000112 "Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "need to add restriction to indicate: has_part some (material entity has_role mobile phase)\nneed to add mobile phase as role" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "eluted material" xsd:string property_value: IAO:0000119 "OBI Bionaterial" xsd:string [Term] id: OBI:0000319 name: material to be added role def: "material to be added role is a protocol participant role realized by a material which is added into a material bearing the target of material addition role in a material addition process" [] is_a: BFO:0000023 ! role property_value: IAO:0000111 "material to be added role" xsd:string property_value: IAO:0000112 "drug added to a buffer contained in a tube; substance injected into an animal;" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Role Branch" xsd:string property_value: IAO:0000119 "OBI" xsd:string property_value: IAO:0000232 "9 March 09 from discussion with PA branch" xsd:string [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 relationship: OBI:0000293 OBI:0100066 ! has_specified_input organ section relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective relationship: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective relationship: RO:0000057 OBI:0400168 ! has participant microtome property_value: IAO:0000111 "histological sample preparation" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 relationship: RO:0000085 OBI:0000372 ! has function material separation function relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "mass analyzer" xsd:string property_value: IAO:0000112 "The mass analyzer of the Voyager-DE(tm) STR Biospectrometry Workstation" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "PERSON: Daniel Schober" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer xsd:string [Term] id: OBI:0000361 name: ion source def: "An ion source is a device that is part of a mass\nspectrometer that ionizes the material under analysis. The ions are\nthen transported by magnetic or electric fields to the mass analyzer.\nTechniques for ionization have been key to determining what types of\nsamples can be analyzed by mass spectrometry. Electron ionization and\nchemical ionization are used for gases and vapors. In chemical\nionization sources, the material is ionized by chemical ion-molecule\nreactions during collisions in the source. Two techniques often used\nwith liquid and solid biological samples include electrospray\nionization (due to John Fenn PMID 2675315.) and matrix-assisted laser\ndesorption/ionization (MALDI, due to M. Karas and F. Hillenkamp\n(Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson\n(Editor) (ISBN 0-941901-31-9)))." [] is_a: OBI:0000968 ! device relationship: RO:0000085 OBI:0000385 ! has function ionization function property_value: IAO:0000111 "ion source" xsd:string property_value: IAO:0000112 "The ion source of a Voyager-DE??? STR Biospectrometry Workstation" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source xsd:string [Term] id: OBI:0000364 name: ion detector def: "An ion detector is a device that measures and records\nthe charge induced or current produced when an ion passes by or hits a\nsurface. \n\nExample: In a scanning instrument the signal produced in the detector\nduring the course of the scan versus where the instrument is in the\nscan (at what m/Q) will produce a mass spectrum, a record of ions as a\nfunction of m/Q." [] is_a: OBI:0000832 ! measurement device relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "ion detector" xsd:string property_value: IAO:0000112 "The ion detector of the Voyager-DE(tm) STR Biospectrometry Workstation" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Mass_spectrometry#Detector xsd:string [Term] id: OBI:0000366 name: metabolite profiling def: "metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism" [] is_a: OBI:0000070 ! assay relationship: OBI:0000293 OBI:0100051 ! has_specified_input specimen relationship: OBI:0000299 IAO:0000109 ! has_specified_output measurement datum relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective property_value: IAO:0000111 "metabolite profiling" xsd:string property_value: IAO:0000112 "Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "metabolite assay" xsd:string property_value: IAO:0000119 "OBI" xsd:string [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 property_value: IAO:0000111 "light emission function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string [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 property_value: IAO:0000111 "magnify function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string [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 property_value: IAO:0000111 "contain function" xsd:string property_value: IAO:0000112 "A syringe, a beaker" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string [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 property_value: IAO:0000111 "heat function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string [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 property_value: IAO:0000111 "material separation function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string [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 property_value: IAO:0000111 "excitation function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string [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 property_value: IAO:0000111 "synthesizing function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string [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 property_value: IAO:0000111 "perturb function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Perturbation_biology xsd:string [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 property_value: IAO:0000111 "filter function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Frank Gibson" xsd:string [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 property_value: IAO:0000111 "mechanical function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Mechanical_work xsd:string [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." [] is_a: OBI:0000391 ! energy supply function property_value: IAO:0000111 "electricity supply function" xsd:string property_value: IAO:0000112 "the function of supplying current during a neuroscience experiment." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000118 "power supply" xsd:string [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 property_value: IAO:0000111 "ionization function" xsd:string property_value: IAO:0000112 "The ion source in amass spectrometer" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Ionization xsd:string [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 property_value: IAO:0000111 "cool function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string [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 property_value: IAO:0000111 "energy supply function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Frank Gibson" xsd:string [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 relationship: BFO:0000054 OBI:0001007 ! realized in image creation relationship: RO:0000052 OBI:0000398 ! inheres in image creation device property_value: IAO:0000111 "image acquisition function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Frank Gibson" xsd:string [Term] id: OBI:0000398 name: image creation device def: "An image creation device is a device which captures a digitized image of an object" [] is_a: OBI:0000832 ! measurement device intersection_of: OBI:0000968 ! device intersection_of: RO:0000085 OBI:0000397 ! has function image acquisition function property_value: IAO:0000111 "image acquisition device" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000118 "image acquisition device" xsd:string property_value: IAO:0000119 sep:00096 xsd:string [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 property_value: IAO:0000111 "solid support function" xsd:string property_value: IAO:0000112 "Taped, glued, pinned, dried or molecularly bonded to a solid support" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string [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 property_value: IAO:0000111 "environment control function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bill Bug" xsd:string property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string [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 property_value: IAO:0000111 "sort function" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string [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 intersection_of: CHEBI:4705 ! double-stranded DNA intersection_of: OBI:0000312 OBI:0000415 ! is_specified_output_of polymerase chain reaction property_value: IAO:0000111 "PCR product" xsd:string property_value: IAO:0000112 "PCR products are the results of amplifcation process. Detection of a PCR products is used to detect DNA and RNA." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "We are using PCR and not the written out words, as this is the most common used." xsd:string property_value: IAO:0000117 "GROUP: OBI BIomaterial Branch" xsd:string property_value: IAO:0000119 "GROUP: OBI BIomaterial Branch" xsd:string [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 relationship: BFO:0000054 OBI:0000415 ! realized in polymerase chain reaction relationship: RO:0000052 CHEBI:33696 ! inheres in nucleic acid property_value: IAO:0000111 "nucleic acid template role" xsd:string property_value: IAO:0000112 "a model or standard for making comparisons; wordnet.princeton.edu/perl/webwn 19 feb 2009" xsd:string property_value: IAO:0000114 IAO:0000123 [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 relationship: BFO:0000054 OBI:0600064 ! realized in recombinant vector cloning relationship: RO:0000052 CHEBI:33696 ! inheres in nucleic acid property_value: IAO:0000111 "cloning vector role" xsd:string property_value: IAO:0000112 "pBluescript plays the role of a cloning vector" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "JZ: related tracker: https://sourceforge.net/p/obi/obi-terms/102/" xsd:string property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string [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." [] is_a: OBI:0600058 ! enzymatic amplification relationship: OBI:0000293 CHEBI:16991 ! has_specified_input deoxyribonucleic acid relationship: OBI:0000299 OBI:0000406 ! has_specified_output PCR product relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "polymerase chain reaction" xsd:string property_value: IAO:0000112 "Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "OBI Plan" xsd:string property_value: IAO:0000118 "PCR" xsd:string property_value: IAO:0000119 "adapted from wikipedai" xsd:string [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 property_value: IAO:0000111 "cloning insert role" xsd:string property_value: IAO:0000114 IAO:0000121 property_value: IAO:0000116 "Feb 20, 2009. from Wikipedia: cloning of any DNA fragment essentially involves four steps: DNA fragmentation with restriction endonucleases, ligation of DNA fragments to a vector, transfection, and screening/selection. There are multiple processes involved, it is not just \"cloning process\"" xsd:string property_value: IAO:0000117 "GROUP: Role branch" xsd:string property_value: IAO:0000119 "OBII and Wikipedia" xsd:string [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 property_value: IAO:0000111 "reverse transcriptase" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "person:Melanie Courtot" xsd:string property_value: IAO:0000119 group:OBI xsd:string [Term] id: OBI:0000423 name: extract def: "an extract is a material entity which results from an extraction process" [] is_a: OBI:0000047 ! processed material relationship: OBI:0000312 OBI:0302884 ! is_specified_output_of extraction property_value: IAO:0000111 "extract" xsd:string property_value: IAO:0000112 "Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "extracted material" xsd:string property_value: IAO:0000119 "GROUP: OBI Biomatrial Branch" xsd:string [Term] id: OBI:0000424 name: transcription profiling assay def: "An assay which aims to provide information about gene expression and transcription activity using ribonucleic acids collected from a material entity using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot" [] is_a: OBI:0000443 ! analyte assay intersection_of: OBI:0000070 ! assay intersection_of: OBI:0000417 OBI:0001331 ! achieves_planned_objective transcription profiling identification objective property_value: IAO:0000111 "transcription profiling assay" xsd:string property_value: IAO:0000112 "Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "gene expression profiling" xsd:string property_value: IAO:0000119 "OBI" xsd:string property_value: OBI:0001847 "transcription profiling" xsd:string [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 property_value: IAO:0000111 "enzyme" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "MC: known issue: enzyme doesn't classify under material entity for now as it isn't stated that anything\nthat has_part some material entity is a material entity. If we add as equivalent classes to material entity has_part some material entity and part_of some material entity (each one in his own necessary and sufficient block) Pellet in P3 doesn't classify any more." xsd:string property_value: IAO:0000117 "person: Melanie Courtot" xsd:string property_value: IAO:0000119 GROUP:OBI xsd:string [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 relationship: has_part CHEBI:28619 ! acrylamide relationship: OBI:0000312 OBI:0302890 ! is_specified_output_of polymerization property_value: IAO:0000111 "polyacrylamide gel" xsd:string property_value: IAO:0000112 "Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "GROUP: OBI Biomaterial Branch" xsd:string [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 property_value: IAO:0000111 "adding material objective" xsd:string property_value: IAO:0000112 "creating a mouse infected with LCM virus" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "BP" xsd:string [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\ntechniques and instruments can be used to produce information about sequence variation at particular genomic positions." [] is_a: OBI:0000443 ! analyte assay relationship: OBI:0000299 OBI:0001305 ! has_specified_output genotype information relationship: OBI:0000417 OBI:0000113 ! achieves_planned_objective sequence feature identification objective property_value: IAO:0000111 "genotyping assay" xsd:string property_value: IAO:0000112 "High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "genotype profiling, SNP genotyping" xsd:string property_value: IAO:0000119 "OBI Biomaterial" xsd:string property_value: OBI:0001847 "SNP analysis" xsd:string [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 property_value: IAO:0000111 "analyte measurement objective" xsd:string property_value: IAO:0000112 "The objective to measure the concentration of glucose in a blood sample" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000119 "PPPB branch" xsd:string [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 relationship: OBI:0000312 OBI:0302890 ! is_specified_output_of polymerization property_value: IAO:0000111 "agarose gel" xsd:string property_value: IAO:0000112 "Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "GROUP: OBI Biomaterial Branch" xsd:string [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 property_value: IAO:0000111 "assay objective" xsd:string property_value: IAO:0000112 "the objective to determine the weight of a mouse." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PPPB branch" xsd:string property_value: IAO:0000119 "PPPB branch" xsd:string [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 relationship: BFO:0000055 OBI:0000275 ! realizes analyte role relationship: OBI:0000299 IAO:0000109 ! has_specified_output measurement datum property_value: IAO:0000111 "analyte assay" xsd:string property_value: IAO:0000112 "example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2013-09-23: simplify equivalent axiom" xsd:string property_value: IAO:0000116 "logical def modified to remove expression below, as some analyte assays report below the level of detection, and therefore not a scalar measurement datum, replaced by measurement datum\n\nand \n('has measurement unit label' some 'measurement unit label') and \n('is quality measurement of' some 'molecular concentration'))" xsd:string property_value: IAO:0000116 "Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement." xsd:string property_value: IAO:0000117 "PERSON:Bjoern Peters, Helen Parkinson, Philippe Rocca-Serra, Alan Ruttenberg" xsd:string property_value: IAO:0000119 "PERSON:Bjoern Peters\nPERSON:Helen Parkinson\nPERSON:Philippe Rocca-Serra\nPERSON:Alan Ruttenberg\nGROUP:OBI Planned process branch" xsd:string [Term] id: OBI:0000444 name: target of material addition role def: "target of material addition role is a role realized by an entity into which a material is added in a material addition process" [] is_a: BFO:0000023 ! role relationship: BFO:0000054 OBI:0000274 ! realized in adding a material entity into a target relationship: RO:0000052 BFO:0000040 ! inheres in material entity property_value: IAO:0000111 "target of material addition role" xsd:string property_value: IAO:0000112 "peritoneum of an animal receiving an interperitoneal injection; solution in a tube receiving additional material; location of absorbed material following a dermal application." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "From Branch discussion with BP, AR, MC -- there is a need for the recipient to interact with the administered material. for example, a tooth receiving a filling was not considered to be a target role." xsd:string property_value: IAO:0000117 "GROUP: Role Branch" xsd:string property_value: IAO:0000119 "OBI" xsd:string [Term] id: OBI:0000447 name: intra cellular electrophysiology recording def: "An intracellular electrophysiology recording is a process where the recording location of the electrode is intracellular" [] is_a: OBI:0000070 ! assay relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective property_value: IAO:0000111 "intra cellular electrophysiology recording" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Frank Gibson" xsd:string property_value: IAO:0000119 "PERSON: Frank Gibson" xsd:string [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 intersection_of: OBI:0000245 ! organization intersection_of: RO:0000087 OBI:0000014 ! has role regulator role property_value: IAO:0000111 "regulatory agency" xsd:string property_value: IAO:0000112 "The US Environmental Protection Agency" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string property_value: IAO:0000119 "WEB: en.wikipedia.org/wiki/Regulator" xsd:string [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 relationship: RO:0000079 OBI:0000047 ! function of processed material property_value: IAO:0000111 "measure function" xsd:string property_value: IAO:0000112 "A glucometer measures blood glucose concentration, the glucometer has a measure function." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Daniel Schober" xsd:string property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON:Frank Gibson" xsd:string [Term] id: OBI:0000454 name: extracellular electrophysiology recording def: "An extracellular electrophysiology recording is process where the recording location of the electrode is extracellular and data" [] is_a: OBI:0000070 ! assay relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective property_value: IAO:0000111 "extracellular electrophysiology recording" xsd:string property_value: IAO:0000112 "The recording of a spike train in the caudate nucleus of a monkey where the electrodes are extra cellular, i.e. not in the neuron" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Frank Gibson, Helen Parkinson" xsd:string property_value: IAO:0000119 "PERSON: Frank Gibson" xsd:string [Term] id: OBI:0000456 name: material transformation objective def: "an objective specifiction that creates an specific output object from input materials." [] is_a: IAO:0000005 ! objective specification property_value: IAO:0000111 "material transformation objective" xsd:string property_value: IAO:0000112 "The objective to create a mouse infected with LCM virus. The objective to create a defined solution of PBS." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Frank Gibson" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "artifact creation objective" xsd:string property_value: IAO:0000119 "GROUP: OBI PlanAndPlannedProcess Branch" xsd:string [Term] id: OBI:0000457 name: manufacturing def: "Manufacturing is a process with the intent to produce a processed material which will have a function for future use. A person or organization (having manufacturer role) is a participant in this process" [] is_a: OBI:0000094 ! material processing relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 OBI:0000047 ! has_specified_output processed material property_value: IAO:0000111 "manufacturing" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "Manufacturing implies reproducibility and responsibility AR" xsd:string property_value: IAO:0000116 "This includes a single scientist making a processed material for personal use." xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Frank Gibson" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "GROUP: OBI PlanAndPlannedProcess Branch" xsd:string [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 property_value: IAO:0000111 "manufacturing objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Frank Gibson" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "GROUP: OBI PlanAndPlannedProcess Branch" xsd:string [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 it and measuring the mass-to-charge ratio of the resulting particles." [] is_a: OBI:0000070 ! assay intersection_of: OBI:0000070 ! assay intersection_of: OBI:0000293 OBI:0000049 {all_some="true"} ! has_specified_input mass spectrometer property_value: IAO:0000111 "mass spectrometry assay" xsd:string property_value: IAO:0000112 "Identification of a proteins cut out from a 2D gel by cleaving it into peptides using trypsin digestion using electrospray ionizatino to ensure the peptides are charged, and accelerating them with an electro magnetic field in which the flight path is determined by the mass / charge ratio of the peptides. Comparing the mass/charge ratio of peptides in the proteins with databases of protein sequences allows to identify which protein gave rise to the peptides." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "Philippe Rocca-Serra" xsd:string [Term] id: OBI:0000471 name: study design execution def: "a planned process that carries out a study design" [] is_a: OBI:0000011 ! planned process property_value: IAO:0000111 "study design execution" xsd:string property_value: IAO:0000112 "injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired." xsd:string property_value: IAO:0000119 "branch derived" xsd:string property_value: IAO:0000232 "6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation." xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [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 property_value: IAO:0000111 "affinity column" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string property_value: IAO:0000119 GROUP: xsd:string property_value: IAO:0000119 http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01094 xsd:string [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 property_value: IAO:0000111 "gel filtration column" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string property_value: IAO:0000119 GROUP: xsd:string property_value: IAO:0000119 http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01104 xsd:string [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." [] is_a: OBI:0600058 ! enzymatic amplification relationship: OBI:0000293 CHEBI:33697 ! has_specified_input ribonucleic acid relationship: OBI:0000299 OBI:0000406 ! has_specified_output PCR product property_value: IAO:0000111 "reverse transcribed polymerase chain reaction" xsd:string property_value: IAO:0000112 "Harmonisation of multi-centre real-time reverse-transcribed PCR results of a candidate prognostic marker in breast cancer: an EU-FP6 supported study of members of the EORTC - PathoBiology Group.\n\nSpan PN, Sieuwerts AM, Heuvel JJ, Spyratos F, Duffy MJ, Eppenberger-Castori S, Vacher S, O'Brien K, McKiernan E, Pierce A, Vuaroqueaux V, Foekens JA, Sweep FC, Martens JW.\nEur J Cancer. 2009 Jan;45(1):74-81. PMID: 19008094" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "3/21/10, BP:Modified definition to clarify that this is not the assay, but the material transformation" xsd:string property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "reverse transcription polymerase chain reaction" xsd:string property_value: IAO:0000118 "RT-PCR" xsd:string [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 relationship: BFO:0000054 OBI:0000457 ! realized in manufacturing property_value: IAO:0000111 "manufacturer role" xsd:string property_value: IAO:0000112 "With respect to The Accuri C6 Flow Cytometer System, the organization Accuri bears the role manufacturer role. With respect to a transformed line of tissue culture cells derived by a specific lab, the lab whose personnel isolated the cll line bears the role manufacturer role. With respect to a specific antibody produced by an individual scientist, the scientist who purifies, characterizes and distributes the anitbody bears the role manufacturer role." xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "GROUP: Role Branch" xsd:string property_value: IAO:0000119 "OBI" xsd:string [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" [] is_a: BFO:0000040 ! material entity relationship: OBI:0000643 CHEBI:23367 ! has grain molecular entity relationship: OBI:0000643 CHEBI:23367 ! has grain molecular entity property_value: IAO:0000111 "scattered molecular aggregate" xsd:string property_value: IAO:0000112 "the sodium and chloride ions in a glass of salt water" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000118 "Collective" xsd:string property_value: IAO:0000119 "Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. With inspiration from the paper Granularity, scale and collectivity: When size does and does not matter, Alan Recto, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349" xsd:string [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 property_value: IAO:0000111 "chromatography consumable" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string property_value: IAO:0000119 GROUP: xsd:string property_value: IAO:0000119 http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01115 xsd:string property_value: IAO:0000232 "chromatography device" xsd:string [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 property_value: IAO:0000111 "size exclusion column" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Daniel Schober" xsd:string property_value: IAO:0000119 GROUP: xsd:string property_value: IAO:0000119 http://msi-ontology.sourceforge.net/ontology/CHROM.owl#msi_01100 xsd:string [Term] id: OBI:0000623 name: NMR spectroscopy def: "NMR spectroscopy is a process which 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." [] is_a: OBI:0000070 ! assay relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective property_value: IAO:0000111 "NMR spectroscopy" xsd:string property_value: IAO:0000112 "Metabolic profiling studies on the toxicological effects of realgar in rats by (1)H NMR spectroscopy. Wei L, Liao P, Wu H, Li X, Pei F, Li W, Wu Y. Toxicol Appl Pharmacol. 2008 Nov 25. PMID: 19073202" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "Nuclear magnetic resonance spectroscopy" xsd:string property_value: IAO:0000119 "adapted from Wikipedia" xsd:string [Term] id: OBI:0000626 name: DNA sequencing def: "DNA sequencing is a sequencing process which uses deoxyribonucleic acid as input and results in a the creation of DNA sequence information artifact using a DNA sequencer instrument." [] is_a: OBI:0600047 ! sequencing assay relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective relationship: RO:0000057 OBI:0400103 ! has participant DNA sequencer property_value: IAO:0000111 "DNA sequencing" xsd:string property_value: IAO:0000112 "Genomic deletions of OFD1 account for 23% of oral-facial-digital type 1 syndrome after negative DNA sequencing. Thauvin-Robinet C, Franco B, Saugier-Veber P, Aral B, Gigot N, Donzel A, Van Maldergem L, Bieth E, Layet V, Mathieu M, Teebi A, Lespinasse J, Callier P, Mugneret F, Masurel-Paulet A, Gautier E, Huet F, Teyssier JR, Tosi M, Frébourg T, Faivre L. Hum Mutat. 2008 Nov 19. PMID: 19023858" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "OBI Branch derived" xsd:string property_value: OBI:0001847 "nucleotide sequencing" xsd:string [Term] id: OBI:0000630 name: hematology def: "hematology is a process studying blood and blood producing organs relying on a variety of techniques and instruments" [] is_a: OBI:0000070 ! assay relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective property_value: IAO:0000111 "hematology" xsd:string property_value: IAO:0000112 "Co-associations between insulin sensitivity and measures of liver function, subclinical inflammation, and hematology. \nGodsland IF, Johnston DG. \nMetabolism. 2008 Sep;57(9):1190-7. \nPMID: 18702943" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "blood analysis, haematology" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [Term] id: OBI:0000634 name: DNA methylation profiling assay def: "an assay which aims to provide information about 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." [] is_a: OBI:0000443 ! analyte assay is_a: OBI:0002020 ! epigenetic modification assay relationship: OBI:0000417 OBI:0001234 ! achieves_planned_objective epigenetic modification identification objective property_value: IAO:0000111 "DNA methylation profiling assay" xsd:string property_value: IAO:0000112 "Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Reinders J, Delucinge Vivier C, Theiler G, Chollet D, Descombes P, Paszkowski J. \nGenome Res. 2008 Mar;18(3):469-76. Epub 2008 Jan 24. PMID: 18218979" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: OBI:0001847 "DNA methylation profiling" xsd:string [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 union_of: OBI:0000678 ! portioning objective union_of: OBI:0000681 ! separation into different composition objective property_value: IAO:0000111 "material separation objective" xsd:string property_value: IAO:0000112 "The objective to obtain multiple aliquots of an enzyme preparation. The objective to obtain cells contained in a sample of blood." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PPPB branch" xsd:string property_value: IAO:0000119 "PPPB branch" xsd:string [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." [] is_a: IAO:0000100 ! data set property_value: IAO:0000111 "clustered data set" xsd:string property_value: IAO:0000112 "A clustered data set is the output of a K means clustering data transformation" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: James Malone" xsd:string property_value: IAO:0000117 "PERSON: Monnie McGee" xsd:string property_value: IAO:0000118 "data set with assigned discovered class labels" xsd:string property_value: IAO:0000232 "AR thinks could be a data item instead" xsd:string [Term] id: OBI:0000650 name: differential expression analysis data transformation def: "A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of" [] is_a: OBI:0200000 ! data transformation property_value: IAO:0000111 "differential expression analysis data transformation" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000117 "Monnie McGee" xsd:string property_value: IAO:0000119 WEB: xsd:string [Term] id: OBI:0000651 name: urine specimen def: "a portion of urine collected from an organism" [] is_a: OBI:0001479 ! specimen from organism relationship: OBI:0000312 OBI:0600005 ! is_specified_output_of collecting specimen from organism relationship: RO:0000087 OBI:0000112 ! has role specimen role relationship: RO:0001000 UBERON:0001088 ! derives from urine property_value: IAO:0000111 "urine specimen" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "4/10/2011BP: It seems to me that the editor notes refer to a previous version, and are no longer relevant. " xsd:string property_value: IAO:0000116 "are we happy calling collection of urine a material separation?" xsd:string property_value: IAO:0000116 "This could be instead a kind of collection of secreted stuff. Among secreted stuff there is passive, and active. urine is secreted, passiv. lavage is secreted, active" xsd:string [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 relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 BFO:0000040 ! has_specified_output material entity property_value: IAO:0000111 "material combination" xsd:string property_value: IAO:0000112 "Mixing two fluids. Adding salt into water. Injecting a mouse with PBS." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "created at workshop as parent class for 'adding material into target', which is asymmetric, while combination encompasses all addition processes." xsd:string property_value: IAO:0000117 "bp" xsd:string property_value: IAO:0000119 "bp" xsd:string [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 relationship: RO:0000052 OBI:0000047 ! inheres in processed material property_value: IAO:0000111 "device setting" xsd:string property_value: IAO:0000112 "Examples, 300V for 4 hours, 200mvolts, 37degrees.A knob set a 300 V is the device setting, the protocol stating to set the instrument to 300V is a device setting specification" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "There is some question of whether 'device setting' is really best modelled as a quality. To be revisited after assay terms have been worked through. See https://github.com/obi-ontology/obi/issues/133" xsd:string property_value: IAO:0000117 "PERSON: Frank Gibson" xsd:string [Term] id: OBI:0000659 name: specimen collection process def: "A planned process with the objective of collecting a specimen." [] is_a: OBI:0000011 ! planned process intersection_of: OBI:0000011 ! planned process intersection_of: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 OBI:0100051 ! has_specified_output specimen property_value: IAO:0000111 "specimen collection process" xsd:string property_value: IAO:0000112 "drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "label changed to 'specimen collection process' on 10/27/2014, details see tracker:\nhttp://sourceforge.net/p/obi/obi-terms/716/" xsd:string property_value: IAO:0000116 "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string property_value: IAO:0000116 "Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role." xsd:string property_value: IAO:0000116 "Philly2013: The specimen_role for the specimen is created during the specimen collection process." xsd:string property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000118 "specimen collection" xsd:string property_value: IAO:0000232 "5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession" xsd:string property_value: IAO:0000232 "6/9/09: used at workshop" xsd:string [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." [] is_a: OBI:0200000 ! data transformation property_value: IAO:0000111 "class prediction data transformation" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "supervised classification data transformation" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [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 property_value: IAO:0000111 "BrdU incorporation assay" xsd:string property_value: IAO:0000112 "The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of BrdU." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 relationship: has_part OBI:0000201 ! radioactivity detection property_value: IAO:0000111 "tritiated thymidine incorporation assay" xsd:string property_value: IAO:0000112 "The measurement of T cell proliferation as a response to a viral peptide by culturing T cells stimulated with APCs and peptide in the presence of tritiated thymidine, and using a scintillation counter to detect the radioactivity." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 intersection_of: OBI:0000312 OBI:0600005 ! is_specified_output_of collecting specimen from organism intersection_of: RO:0000087 OBI:0000740 ! has role material sample role relationship: RO:0001000 UBERON:0000465 ! derives from material anatomical entity property_value: IAO:0000111 "sample from organism" xsd:string property_value: IAO:0000114 IAO:0000002 property_value: IAO:0000116 "5/29: This is a helper class for now" xsd:string property_value: IAO:0000116 "we need to work on this: Is taking a urine sample a material separation process? If not, we will need to specify what 'taking a sample from organism' entails. We can argue that the objective to obtain a urine sample from a patient is enough to call it a material separation process, but it could dilute what material separation was supposed to be about." xsd:string [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 property_value: IAO:0000111 "portioning objective" xsd:string property_value: IAO:0000112 "The objective to obtain multiple aliquots of an enzyme preparation." xsd:string property_value: IAO:0000114 IAO:0000123 [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 property_value: IAO:0000111 "separation into different composition objective" xsd:string property_value: IAO:0000112 "The objective to obtain cells contained in a sample of blood." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "We should be using has the grain relations or concentrations to distinguish the portioning and other sub-objectives" xsd:string [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 property_value: IAO:0000111 "specimen collection objective" xsd:string property_value: IAO:0000112 "The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "Bjoern Peters" xsd:string [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 relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 OBI:0302729 ! has_specified_output chemical solution relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective relationship: OBI:0000417 OBI:0000686 ! achieves_planned_objective material combination objective property_value: IAO:0000111 "creating a mixture of molecules in solution" xsd:string property_value: IAO:0000112 "The production of PBS" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "PERSON: Helen Parkinson" xsd:string [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 property_value: IAO:0000111 "material combination objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PPPB branch" xsd:string property_value: IAO:0000119 "bp" xsd:string [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 relationship: OBI:0000293 GO:0042571 ! has_specified_input immunoglobulin complex, circulating relationship: OBI:0000417 OBI:0000639 ! achieves_planned_objective material separation objective property_value: IAO:0000111 "immunoprecipitation" xsd:string property_value: IAO:0000112 "PMID: 19419533. Arabidopsis RNA immunoprecipitation. Terzi LC, Simpson GG. Plant J. 2009 Jul;59(1):163-8." xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "OBI plan and planned process branch" xsd:string [Term] id: OBI:0000699 name: survival assessment def: "Survival assessment is an assay that measures the occurrence of death events in one or more organisms that are monitored over time" [] is_a: OBI:0000070 ! assay relationship: OBI:0000293 OBI:0100026 ! has_specified_input organism relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective property_value: IAO:0000111 "survival assessment" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "Need to point out more specifically that survival / death is measured." xsd:string [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." [] is_a: OBI:0000663 ! class prediction data transformation relationship: OBI:0000417 OBI:0200179 ! achieves_planned_objective class prediction objective property_value: IAO:0000111 "support vector machine" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Ryan Brinkman" xsd:string property_value: IAO:0000118 "SVM" xsd:string property_value: IAO:0000119 "PERSON: Ryan Brinkman" xsd:string [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 property_value: IAO:0000111 "decision tree induction objective" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "James Malone" xsd:string [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 property_value: IAO:0000111 "decision tree building data transformation" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [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." [] is_a: OBI:0000094 ! material processing relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "library preparation" xsd:string property_value: IAO:0000112 "PMID: 19570239. Construction and analysis of cotton (Gossypium arboreum L.) drought-related cDNA library. Zhang L, Li FG, Liu CL, Zhang CJ, Zhang XY. BMC Res Notes. 2009 Jul 2;2:120." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "library construction" xsd:string [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 property_value: IAO:0000111 "GenePattern software" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Person:Helen Parkinson" xsd:string property_value: IAO:0000119 "WEB: http://www.broadinstitute.org/cancer/software/genepattern/" xsd:string [Term] id: OBI:0000716 name: ChIP-seq assay def: "an assay which aims at identifying protein binding sites in genomic DNA and determining how protein may regulate gene transcription by relying on immunoprecipitation of DNA bound protein, creation of a library of corresponding DNA fragments (either single or paired-end fragments) and subsequent sequencing using parallelized sequencing methods." [] is_a: OBI:0001956 ! assay using chromatin immunoprecipitation is_a: OBI:0002020 ! epigenetic modification assay is_a: OBI:0600047 ! sequencing assay relationship: has_part OBI:0000626 ! DNA sequencing relationship: has_part OBI:0000690 ! immunoprecipitation relationship: has_part OBI:0000711 ! library preparation relationship: OBI:0000299 OBI:0001573 ! has_specified_output DNA sequence data relationship: OBI:0000417 OBI:0001234 ! achieves_planned_objective epigenetic modification identification objective relationship: OBI:0000417 OBI:0001398 ! achieves_planned_objective protein and DNA interaction identification objective relationship: RO:0000057 OBI:0400103 ! has participant DNA sequencer property_value: IAO:0000111 "ChIP-seq assay" xsd:string property_value: IAO:0000112 "PMID: 19275939\nChIP-seq: using high-throughput sequencing to discover protein-DNA interactions.\nSchmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT.\nMethods. 2009 Jul;48(3):240-8. Epub 2009 Mar 9." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "chromatin immunoprecipitation sequencing assay" xsd:string property_value: IAO:0000119 "adapted from Wikipedia" xsd:string property_value: IAO:0000232 "made some modification based on the discussion on 2011/4/4 obi dev call, using DNA sequencing instead of union of some specific DNA sequencing processes" xsd:string [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" [] is_a: OBI:0000047 ! processed material property_value: IAO:0000111 "paired-end library" xsd:string property_value: IAO:0000112 "PMID: 19339662. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Res. 2009 Apr;19(4):521-32. Fullwood MJ, Wei CL, Liu ET, Ruan Y." xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "mate-paired library" xsd:string property_value: IAO:0000118 "paired-end tag (PET) library" xsd:string property_value: IAO:0000119 "adapted from information provided by Solid web site" xsd:string [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 property_value: IAO:0000111 "peak matching" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Ryan Brinkman" xsd:string property_value: IAO:0000119 "PERSON: Ryan Brinkman" xsd:string [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." [] is_a: OBI:0200171 ! partitioning data transformation is_a: OBI:0200175 ! class discovery data transformation relationship: OBI:0000299 OBI:0000648 ! has_specified_output clustered data set relationship: OBI:0000417 OBI:0200172 ! achieves_planned_objective partitioning objective relationship: OBI:0000417 OBI:0200178 ! achieves_planned_objective class discovery objective property_value: IAO:0000111 "k-nearest neighbors" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "k-NN" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [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 intersection_of: BFO:0000040 ! material entity intersection_of: OBI:0000312 OBI:0600064 ! is_specified_output_of recombinant vector cloning property_value: IAO:0000111 "recombinant vector" xsd:string property_value: IAO:0000114 IAO:0000123 [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" [] is_a: OBI:0000047 ! processed material property_value: IAO:0000111 "single fragment library" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "fragment library" xsd:string [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 intersection_of: BFO:0000040 ! material entity intersection_of: RO:0000087 OBI:0000411 ! has role cloning vector role relationship: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing property_value: IAO:0000111 "cloning vector" xsd:string property_value: IAO:0000114 IAO:0000123 [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 property_value: IAO:0000111 "material sample role" xsd:string property_value: IAO:0000112 "a role borne by a portion of blood taken to represent all the blood in an organism; the role borne by a population of humans with HIV enrolled in a study taken to represent patients with HIV in general." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "7/13/09: Note that this is a relational role: between the sample taken and the 'sampled' material of which the sample is thought to be representative off." xsd:string [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" [] is_a: OBI:0000659 ! specimen collection process intersection_of: OBI:0000659 ! specimen collection process intersection_of: OBI:0000293 BFO:0000040 ! has_specified_input material entity intersection_of: OBI:0000299 OBI:0000747 ! has_specified_output material sample property_value: IAO:0000111 "material sampling process" xsd:string property_value: IAO:0000114 IAO:0000123 [Term] id: OBI:0000747 name: material sample def: "A material entity that has the material sample role" [] is_a: OBI:0100051 ! specimen intersection_of: BFO:0000040 ! material entity intersection_of: RO:0000087 OBI:0000740 ! has role material sample role property_value: IAO:0000111 "material sample" xsd:string property_value: IAO:0000112 "blood drawn from patient to measure his systemic glucose level. A population of humans with HIV enrolled in a study taken to represent patients with HIV in general." xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "OBI: workshop" xsd:string property_value: IAO:0000118 "sample population" xsd:string property_value: OBI:0001847 "sample" xsd:string [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." [] is_a: OBI:0000707 ! decision tree building data transformation relationship: OBI:0000417 OBI:0000704 ! achieves_planned_objective decision tree induction objective property_value: IAO:0000111 "CART" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "classification and regression trees" xsd:string property_value: IAO:0000119 "BOOK: David J. Hand, Heikki Mannila and Padhraic Smyth (2001) Principles of Data Mining." xsd:string [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" [] is_a: IAO:0000033 ! directive information entity relationship: part_of OBI:0500000 ! study design property_value: IAO:0000111 "independent variable specification" xsd:string property_value: IAO:0000112 "In a study in which gene expression is measured in patients between 8 month to 4 years old that have mild or severe malaria and in which the hypothesis is that gene expression in that age group is a function of disease status, disease status is the independent variable." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2/2/2009 Original definition - In the design of experiments, independent variables are those whose values are controlled or selected by the person experimenting (experimenter) 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." xsd:string property_value: IAO:0000116 "In the Philly 2013 workshop the label was chosen to distinguish it from \"dependent variable\" as used in statistical modelling. See: http://en.wikipedia.org/wiki/Statistical_modeling" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000118 "experimental factor" xsd:string property_value: IAO:0000118 "independent variable" xsd:string property_value: IAO:0000119 "Web: http://en.wikipedia.org/wiki/Dependent_and_independent_variables" xsd:string property_value: IAO:0000232 "2009-03-16: work has been done on this term during during the OBI workshop winter 2009 and the current definition was considered acceptable for use in OBI. If there is a need to modify thisdefinition please notify OBI." xsd:string property_value: OBI:0001847 "study factor" xsd:string [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 property_value: IAO:0000111 "survival rate" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Oliver He" xsd:string property_value: IAO:0000119 "adapted from wikipedia\nhttp://en.wikipedia.org/wiki/Survival_rate" xsd:string [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 property_value: IAO:0000111 "statistical model validation" xsd:string property_value: IAO:0000112 "Using the expression levels of 20 proteins to predict whether a cancer patient will respond to a drug. A practical goal would be to determine which subset of the 20 features should be used to produce the best predictive model. - wikipedia" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Helen Parkinson" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Cross-validation_%28statistics%29 xsd:string [Term] id: OBI:0000794 name: transcription factor binding site comment: PLace_holder for sequence ontology term is_a: OBI:0000905 ! sequence feature annotation property_value: IAO:0000111 "transcription factor binding site" xsd:string property_value: IAO:0000114 IAO:0000002 property_value: IAO:0000119 SO:0000235 xsd:string [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" [] is_a: OBI:0000681 ! separation into different composition objective property_value: IAO:0000111 "purification objective" xsd:string property_value: IAO:0000112 "the objective to obtain a pure fraction of a specific peptide when running an HPLC on a crude synthesis of peptides." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string property_value: IAO:0000118 "isolation objective" xsd:string property_value: IAO:0000119 "BP" xsd:string property_value: IAO:0000232 "10/14/09, BP: This should be linked to the 'purified' 'currently conferred quality" xsd:string [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 relationship: OBI:0000299 CHEBI:23367 ! has_specified_output molecular entity relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "cross linking" xsd:string property_value: IAO:0000112 "cross linking can be used as a probe to link proteins together, to check protein protein interactions" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Cross-link xsd:string [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 property_value: IAO:0000111 "material maintenance objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000119 "PERSON: Bjoern Peters" xsd:string [Term] id: OBI:0000807 name: presentation of stimulus def: "a planned process in which an organism is exposed to some stimulus with the intent to invoke an action" [] is_a: OBI:0000011 ! planned process property_value: IAO:0000111 "presentation of stimulus" xsd:string property_value: IAO:0000112 "The presentation of a flashing light to a monkey during reward training" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Helen Parkinson, Jessica Turner, Dirk Derom" xsd:string property_value: IAO:0000118 "stimulation of organism" xsd:string property_value: IAO:0000119 "Helen Parkinson, Jessica Turner, Dirk Derom" xsd:string [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 intersection_of: CHEBI:16991 ! deoxyribonucleic acid intersection_of: OBI:0000312 OBI:0600058 ! is_specified_output_of enzymatic amplification property_value: IAO:0000111 "amplified DNA" xsd:string property_value: IAO:0000112 "Amplied DNA created by PCR" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Alan Ruttenberg" xsd:string [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 property_value: IAO:0000111 "primary structure of DNA macromolecule" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "placeholder for SO" xsd:string property_value: IAO:0000117 "BP et al" xsd:string [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." [] is_a: OBI:0000832 ! measurement device relationship: OBI:0000304 OBI:0000245 ! is_manufactured_by organization relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "micro electrode" xsd:string property_value: IAO:0000112 "A micro-electrode recording device used to record extracellular action potentialsin monkey caudate nucleus" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Helen Parkinson, Jessica Turner, Dirk Derom" xsd:string property_value: IAO:0000118 "micro electrode measuring device" xsd:string property_value: IAO:0000119 "Jessica Turner, Dirk Derom" xsd:string [Term] id: OBI:0000832 name: measurement device def: "A device in which a measure function inheres." [] is_a: OBI:0000968 ! device intersection_of: OBI:0000968 ! device intersection_of: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "measurement device" xsd:string property_value: IAO:0000112 "A ruler, a microarray scanner, a Geiger counter." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "GROUP:OBI Philly workshop" xsd:string property_value: IAO:0000119 "OBI" xsd:string [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 property_value: IAO:0000111 "high molecular weight DNA extract" xsd:string property_value: IAO:0000112 "Extraction of chromosomal DNA from mammalian cells by first isolating nucei" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Chris Stoeckert" xsd:string property_value: IAO:0000119 "OBI" xsd:string [Term] id: OBI:0000835 name: manufacturer def: "A person or organization that has a manufacturer role" [] is_a: BFO:0000040 ! material entity property_value: IAO:0000111 "manufacturer" xsd:string property_value: IAO:0000114 IAO:0000123 [Term] id: OBI:0000838 name: material maintenance def: "a process with that achieves the objective to maintain some or all of the characteristics of an input material over time" [] is_a: OBI:0000011 ! planned process property_value: IAO:0000111 "material maintenance" xsd:string property_value: IAO:0000114 IAO:0000123 [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 property_value: IAO:0000111 "primary structure of RNA molecule" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Person:Bjoern Peters" xsd:string [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 property_value: IAO:0000111 "polyA RNA extraction" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert" xsd:string property_value: IAO:0000117 "Person: Jie Zheng" xsd:string property_value: IAO:0000119 "UPenn Group" xsd:string [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 relationship: RO:0000052 CHEBI:33696 ! inheres in nucleic acid property_value: IAO:0000111 "complementary nucleotide probe role" xsd:string property_value: IAO:0000112 "A primer in a PCR reaction. A probe on an Affymetrix chip." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string [Term] id: OBI:0000860 name: northern blot analysis def: "a northern blot analysis is an assay allowing monitoring presence of gene transcripts by hybridizing labeled RNA or DNA probes against messenger RNAs isolated from tissue or cell cultures, resolved on denaturing agarose gel, transfered by blotting procedure to a nitrocellulose or nylon membrane and immobilized by cross linking or baking to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager" [] is_a: OBI:0000443 ! analyte assay relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective property_value: IAO:0000111 "northern blot analysis" xsd:string property_value: IAO:0000112 "PMID: 18428227. Analysis of RNA by northern blot hybridization.\nBrown T, Mackey K. Curr Protoc Hum Genet. 2001 Nov;Appendix 3:Appendix 3K." xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "2010-01-31: Philippe Rocca-Serra: Need to add a restriction taking into account probe and transcript information" xsd:string property_value: IAO:0000117 "Person: Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "northern blot" xsd:string [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 relationship: OBI:0000312 OBI:0000848 ! is_specified_output_of polyA RNA extraction property_value: IAO:0000111 "polyA RNA extract" xsd:string property_value: IAO:0000112 "Preparation of polyA RNA by cellulose-bound oligo-dT (Aviv, H., Leder, P. 1972. Purification of biologically active globin messenger RNA by chromatography on oligothymidylic acid-cellulose. Proc. Nat. Acad. Sci. USA 69, 1408-1412.)" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "UPenn Group" xsd:string [Term] id: OBI:0000870 name: single-nucleotide-resolution nucleic acid structure mapping assay def: "is an assay which aims to provide 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 property_value: IAO:0000111 "single-nucleotide-resolution nucleic acid structure mapping assay" xsd:string property_value: IAO:0000112 "" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2010-01-31: Philippe Rocca-Serra: OBI needs to review 'structure assay' as currently defined. Need to get feedback from Kevin Clancy." xsd:string property_value: IAO:0000117 "Person: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "RNAO" xsd:string [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 property_value: IAO:0000111 "pre-mortem specimen" xsd:string property_value: IAO:0000112 "material obtained through a liver biopsy from a human patient" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "MO_705 premortem" xsd:string [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 property_value: IAO:0000111 "detection of specific nucleic acid polymers with complementary probes" xsd:string property_value: IAO:0000112 "Primer based PCR assay, Norther blot, Southern Blot, and RNAse protection assays." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 relationship: OBI:0000312 OBI:0666666 ! is_specified_output_of RNA extraction relationship: OBI:0000643 CHEBI:33697 ! has grain ribonucleic acid property_value: IAO:0000111 "RNA extract" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "Group: UPenn Group" xsd:string [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 property_value: IAO:0000111 "cell-cell killing assay" xsd:string property_value: IAO:0000112 "Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 property_value: IAO:0000111 "in vivo cell killing assay" xsd:string property_value: IAO:0000112 "Labeling two populations of cells with different levels of CFSE, pusling one population with an influenza peptide, injecting the cells into a mouse, and recoving cells 24 hours later. By comparing the recovery rate of cells with different CFSE labeling, it is possible to determine if there was specific killing of peptide pulsed target cells." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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:0001237 ! quality of a single physical entity property_value: IAO:0000111 "secondary structure of sequence macromolecule" xsd:string property_value: IAO:0000114 IAO:0000002 property_value: IAO:0000116 "2010-01-31: Philippe Rocca-Serra: This is a placeholder to allow work on 'nucleic acid mapping assay' in collaboration with RNAOntology group. Need to liaise with SO" xsd:string property_value: IAO:0000117 "Person: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "Wikipedia" xsd:string [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 property_value: IAO:0000111 "cell proliferation assay" xsd:string property_value: IAO:0000112 "Measuring the amount of tritiated thymidine incorporated by dividing cells as a proxy for cell proliferation." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:0000892 name: Southern blot analysis def: "Southern blot analysis is a an assay used in molecular biology to assert the presence/absence status of a specific DNA sequence in DNA samples. DNA samples to be assayed are first digested by restriction enzymes, fragments are then resolved by gel electrophoresis following by a blotting ensuring transfer to nitrocellulose or nylon membrane. Immobilization of DNA fragments to the membrane is achieved by UV crosslinking and/or baking. Probes raised against the specific sequences are then hybridized to the membrane. Detection of hybridization signals is carried out by immunofluorescence or radioactivity measurements using photographic films or digital imaging devices such as Phosphor Imager." [] is_a: OBI:0000443 ! analyte assay relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective property_value: IAO:0000111 "Southern blot analysis" xsd:string property_value: IAO:0000112 "PMID: 9452032. Germline mutations detected in the von Hippel-Lindau disease tumor suppressor gene by Southern blot and direct genomic DNA sequencing. Li C, Weber G, Ekman P, Lagercrantz J, Norlen BJ, Akerström G, Nordenskjöld M, Bergerheim US. Hum Mutat. 1998;Suppl 1:S31-3." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2010-01-31: Philippe Rocca-Serra:\nneed extra work on 'labeled probe'" xsd:string property_value: IAO:0000116 "2010-01-31: Philippe Rocca-Serra: \ndeparture from naming convention as the assay is named after Edwin Southern." xsd:string property_value: IAO:0000117 "Person: Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "Southern blot" xsd:string property_value: IAO:0000119 "OBI & Wikipedia" xsd:string [Term] id: OBI:0000893 name: real time polymerase chain reaction assay def: "A laboratory technique based on the PCR, which is used to\namplify and simultaneously quantify a specific DNA\nmolecule based on the use of complementary probes/primers. It enables\nboth detection and quantification (as absolute number of copies or relative\namount when normalized to DNA input or additional normalizing genes) of one\nor more specific sequences in a DNA sample." [] is_a: OBI:0000070 ! assay relationship: has_part OBI:0000415 ! polymerase chain reaction property_value: IAO:0000111 "real time polymerase chain reaction assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "person: Bjoern Peters" xsd:string property_value: IAO:0000117 "person: Melanie Courtot" xsd:string property_value: IAO:0000118 "kinetic polymerase chain reaction" xsd:string property_value: IAO:0000118 "Q-PCR" xsd:string property_value: IAO:0000118 "qPCR" xsd:string property_value: IAO:0000118 "quantitative real time polymerase chain reaction" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Real-time_polymerase_chain_reaction" xsd:string property_value: OBI:0001847 "real time PCR" xsd:string [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 property_value: IAO:0000111 "post mortem specimen" xsd:string property_value: IAO:0000112 "the spleen taken from a dead mouse" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "MO_416 postmortem" xsd:string [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 property_value: IAO:0000111 "in vitro cell killing assay" xsd:string property_value: IAO:0000112 "Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to tissue culture plates, and 1:2 serial dilutions of effectors were made. After a 4-h incubation of the effector cells with the target cells, supernatants were collected and counted with the LKB 1272 Clinigamma counter. Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 property_value: IAO:0000111 "sequence feature annotation" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "Bjoern Peters" xsd:string [Term] id: OBI:0000911 name: real time reverse-transcription polymerase chain reaction assay def: "Is_a PCR real time preceded by a reverse transcription step (reverse transcription step = an RNA strand is reverse transcribed into its DNA complement using the enzyme reverse transcriptase)" [] is_a: OBI:0000070 ! assay property_value: IAO:0000111 "real time reverse-transcription polymerase chain reaction assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000118 "qRT-PCR" xsd:string property_value: IAO:0000118 "RRT-PCR" xsd:string property_value: IAO:0000118 "RT-rt PCR" xsd:string [Term] id: OBI:0000912 name: X-ray crystallography assay def: "A 3D 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:0600045 ! 3D structure determination assay property_value: IAO:0000111 "X-ray crystallography assay" xsd:string property_value: IAO:0000112 "Crystallizing an antibody:antigen complex, and recording the diffraction pattern of a synchrotron beam, and assembling the 3d complex structure based on homologous complexes." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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:0001146 ! binding assay relationship: OBI:0000293 CL:0000000 ! has_specified_input cell property_value: IAO:0000111 "promoter activity detection by reporter gene assay" xsd:string property_value: IAO:0000112 "A T cell hybridoma in which the beta-galactosidase gene (lacZ) was inserted under the control of the IL-2 promoter, is detected by adding the X-gal substrate which when cleaved by lacZ results in detectable blue color." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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." [] is_a: OBI:0001977 ! cytometry assay intersection_of: OBI:0001977 ! cytometry assay intersection_of: has_part OBI:0001501 ! fluorescence detection assay intersection_of: OBI:0000293 OBI:0400044 {all_some="true"} ! has_specified_input flow cytometer property_value: IAO:0000111 "flow cytometry assay" xsd:string property_value: IAO:0000112 "Using a flow cytometer to quantitate the percent of CD3 positive cells in a population by labeling them with a FITC tagged anti-CD3 antibody." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 relationship: OBI:0000643 CHEBI:33697 ! has grain ribonucleic acid property_value: IAO:0000111 "labeled RNA extract" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "Need to find out if we consider labeled nucleotides still nucleotides. It is after consulting with ChEBI group.\nAdded duirng Mar 1, 2010 dev call" xsd:string property_value: IAO:0000117 "Group: OBI group" xsd:string property_value: IAO:0000119 "Group: OBI group" xsd:string [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 intersection_of: OBI:0100051 ! specimen intersection_of: has_part REO:0000280 ! molecular label intersection_of: OBI:0000312 OBI:0600038 ! is_specified_output_of addition of molecular label property_value: IAO:0000111 "labeled specimen" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "added during call 3/1/2010" xsd:string property_value: IAO:0000117 "OBI group" xsd:string [Term] id: OBI:0000925 name: infectious agent def: "is a material entity bearing the disposition to infect an organism" [] is_a: OBI:0100026 ! organism property_value: IAO:0000111 "infectious agent" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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." [] is_a: OBI:0000832 ! measurement device relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "calorimeter" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string property_value: IAO:0000118 "calorimetry instrument?" xsd:string property_value: IAO:0000119 http://chemistry.about.com/od/chemistryglossary/a/calorimeterdef.htm xsd:string [Term] id: OBI:0000931 name: study intervention def: "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 relationship: OBI:0000293 OBI:0100051 ! has_specified_input specimen relationship: OBI:0000299 OBI:0100051 ! has_specified_output specimen property_value: IAO:0000111 "study intervention" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000119 "GROUP: OBI" xsd:string [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 property_value: IAO:0000111 "material separation device" xsd:string property_value: IAO:0000112 "flow cytometer" xsd:string property_value: IAO:0000114 IAO:0000123 [Term] id: OBI:0000944 name: handedness assay def: "A handedness assay 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." [] is_a: OBI:0000070 ! assay property_value: IAO:0000111 "handedness assay" xsd:string property_value: IAO:0000112 "The Edinburgh handedness assay is a specific method of determing handedness" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Helen Parkinson" xsd:string property_value: IAO:0000118 "handedness test" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Handedness xsd:string [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 relationship: BFO:0000054 OBI:0000011 ! realized in planned process property_value: IAO:0000111 "service provider role" xsd:string property_value: IAO:0000112 "Jackson Lab provides experimental animals, EBI provides training on databases, a core facility provides access to a DNA sequencer." xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON:Helen Parkinson" xsd:string [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 intersection_of: OBI:0000047 ! processed material intersection_of: OBI:0100051 ! specimen property_value: IAO:0000111 "processed specimen" xsd:string property_value: IAO:0000112 "A tissue sample that has been sliced and stained for a histology study.\nA blood specimen that has been centrifuged to obtain the white blood cells." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "Bjoern Peters" xsd:string [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 property_value: IAO:0000111 "categorical label" xsd:string property_value: IAO:0000112 "The labels 'positive' vs. 'negative', or 'left handed', 'right handed', 'ambidexterous', or 'strongly binding', 'weakly binding' , 'not binding', or '+++', '++', '+', '-' etc. form scales of categorical labels. " xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "Bjoern Peters" xsd:string [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 property_value: IAO:0000111 "in live cell assay" xsd:string property_value: IAO:0000114 IAO:0000123 [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." [] is_a: OBI:0000070 ! assay property_value: IAO:0000111 "in live organism assay" xsd:string property_value: IAO:0000112 "Measuring the rate in which cells that are pulsed with a peptide are killed inside a mouse by peptide specific cytotoxic T cells." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string property_value: IAO:0000118 "in vivo assay" xsd:string [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 property_value: IAO:0000111 "container" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "03/21/2010: Added to allow classification of children (similar to what we want to do for 'measurement device'. Lookint at what classifies here, we may want to reconsider a contain function assigned to a part of an entity is necessarily also a function of the whole (e.g. is a centrifuge a container because it has test tubes as parts?)" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string [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." [] is_a: OBI:0000047 ! processed material relationship: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing relationship: RO:0000085 BFO:0000034 ! has function function property_value: IAO:0000111 "device" xsd:string property_value: IAO:0000112 "A voltmeter is a measurement device which is intended to perform some measure function." xsd:string property_value: IAO:0000112 "An autoclave is a device that sterlizes instruments or contaminated waste by applying high temperature and pressure." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2012-12-17 JAO: In common lab usage, there is a distinction made between devices and reagents that is difficult to model. Therefore we have chosen to specifically exclude reagents from the definition of \"device\", and are enumerating the types of roles that a reagent can perform.\n\n2013-6-5 MHB: The following clarifications are outcomes of the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For example:\n\n(1) An HPLC machine is considered a device, but has a column that holds a stationary phase resin as an operational component. This resin qualifies as a device if it participates purely in size exclusion, but bears a reagent role that is realized in the running of a column if it interacts electrostatically or chemically with the evaluant. The container the resin is in (“the column”) considered alone is a device. So the entire column as well as the entire HPLC machine are devices that have a reagent as an operating part.\n\n(2) A pH meter is a device, but its electrode component bears a reagent role in virtue of its interacting directly with the evaluant in execution of an assay.\n\n(3) A gel running box is a device that has a metallic lead as a component that participates in a chemical reaction with the running buffer when a charge is passed through it. This metallic lead is considered to have a reagent role as a component of this device realized in the running of a gel.\n\nIn the examples above, a reagent is an operational component of a device, but the device itself does not realize a reagent role (as bearing a reagent role is not transitive across the part_of relation). In this way, the asserted disjointness between a reagent and device holds, as both roles are never realized in the same bearer during execution of an assay. " xsd:string property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string property_value: IAO:0000118 "instrument" xsd:string property_value: IAO:0000119 "OBI development call 2012-12-17." xsd:string [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.\n" [] is_a: IAO:0000109 ! measurement datum property_value: IAO:0000111 "sequence data" xsd:string property_value: IAO:0000112 "example of usage: the representation of a nucleotide sequence in FASTA format used for a sequence similarity search." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person:Chris Stoeckert" xsd:string property_value: IAO:0000119 "GROUP: OBI" xsd:string [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:0001499 ! fluorescence detection binding assay is_a: OBI:0001977 ! cytometry assay property_value: IAO:0000111 "cell-cell binding detection by flow cytometry assay" xsd:string property_value: IAO:0000112 "Staining a B cell with PE and staining a T cell with FITC, incubating them together with a peptide, and counting the number of co-stained conjugates." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 property_value: IAO:0000111 "in container assay" xsd:string property_value: IAO:0000114 IAO:0000123 [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 property_value: IAO:0000111 "growth condition intervention design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000119 "MO_588 growth_condition_design" xsd:string [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 property_value: IAO:0000111 "PCR instrument" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "03/21/2010: Added because it is unclear if the thermal cycler definition is intentionally broader than PCR instrument. Contacted Melanie and Trish about this. Definitions and use of alternative terms need to be made consistent." xsd:string property_value: IAO:0000117 "" xsd:string [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 property_value: IAO:0000111 "electron microscope" xsd:string property_value: IAO:0000114 IAO:0000123 [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 property_value: IAO:0000111 "growth environment" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "Right now this may be incomplete. Should also cover e.g. sound, light as well." xsd:string property_value: IAO:0000117 "PERSON:Richard Scheuermann, Jie Zheng, Bjoern Peters" xsd:string property_value: IAO:0000119 "OBI group" xsd:string [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 property_value: IAO:0000111 "questionnaire" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "JT: It plays a role in collecting data that could be fleshed out more; but I'm thinking it is, in itself, an edited document. \nJZ: based on textual definition of edited document, it can be defined as N&S. I prefer to leave questionnaire as a document now. We can add more restrictions in the future and use that to determine it is an edited document or not. " xsd:string property_value: IAO:0000116 "Need to clarify if this is a document or a directive information entity (or what their connection is))" xsd:string property_value: IAO:0000117 "PERSON: Jessica Turner" xsd:string property_value: IAO:0000119 "Merriam-Webster" xsd:string [Term] id: OBI:0001007 name: image creation def: "A planned process that captures an image of an object." [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 IAO:0000101 ! has_specified_output image property_value: IAO:0000111 "image acquisition" xsd:string property_value: IAO:0000112 "Taking a polaroid picture of a patients skin lesion; Using a digital camera to take a picture of a gel" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000118 "image acquisition" xsd:string [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 relationship: OBI:0000312 OBI:0666667 ! is_specified_output_of nucleic acid extraction relationship: OBI:0000643 CHEBI:33696 ! has grain nucleic acid relationship: RO:0000087 OBI:0000112 ! has role specimen role property_value: IAO:0000111 "nucleic acid extract" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "UPenn Group" xsd:string [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 which relies on proteins acting as enzymatic probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study." [] is_a: OBI:0000870 ! single-nucleotide-resolution nucleic acid structure mapping assay property_value: IAO:0000111 "single-nucleotide-resolution nucleic acid structure mapping assay using enzymatic probing" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Person: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "RNAO and OBI" xsd:string [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 which relies on small chemical compounds acting as chemical probes in order to produce measurement information which one interpreted provide structural information about the RNA species under study." [] is_a: OBI:0000870 ! single-nucleotide-resolution nucleic acid structure mapping assay property_value: IAO:0000111 "single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Person: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "RNAO and OBI" xsd:string [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 intersection_of: OBI:0001146 ! binding assay intersection_of: OBI:0000299 OBI:0001144 ! has_specified_output binding constant property_value: IAO:0000111 "binding constant determination assay" xsd:string property_value: IAO:0000112 "Determination of KD value for an antibody binding a protein using a BIACORE assay. " xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum" xsd:string [Term] id: OBI:0001032 name: light emission device def: "a device which has a function to emit light." [] is_a: OBI:0000968 ! device property_value: IAO:0000111 "light emission device" xsd:string property_value: IAO:0000112 "A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics)" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person:Helen Parkinson" xsd:string property_value: IAO:0000119 "OBI" xsd:string [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 property_value: IAO:0000111 "perturbation device" xsd:string property_value: IAO:0000112 "" xsd:string property_value: IAO:0000112 "A homogenizer is a perturbation device." xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Helen Parkinson" xsd:string property_value: IAO:0000119 "OBI Vancouver workshop 2010" xsd:string property_value: IAO:0000119 "PERSON: Helen Parkinson" xsd:string [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 property_value: IAO:0000111 "environmental control device" xsd:string property_value: IAO:0000112 "A growth chamber is an environmental control device." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Helen Parkinson" xsd:string property_value: IAO:0000119 "OBI" xsd:string [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 relationship: OBI:0000312 OBI:0000257 ! is_specified_output_of DNA extraction relationship: OBI:0000643 CHEBI:16991 ! has grain deoxyribonucleic acid property_value: IAO:0000111 "DNA extract" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Jie Zheng" xsd:string property_value: IAO:0000119 "Group: UPenn group" xsd:string [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 relationship: RO:0000085 OBI:0000372 ! has function material separation function property_value: IAO:0000111 "electrophoresis system" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Erik Segerdell" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Category:Electrophoresis xsd:string [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 property_value: IAO:0000111 "high performance liquid chromatography instrument" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Erik Segerdell" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/High_performance_liquid_chromatography xsd:string [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 relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "confocal microscope" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Erik Segerdell" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Confocal_microscopy xsd:string [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 relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "patch clamp device" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Erik Segerdell" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Patch_clamp xsd:string [Term] id: OBI:0001121 name: gel electrophoresis system def: "A device that moves charged particles through a medium by using an electric field induced by electrodes." [] is_a: OBI:0001053 ! electrophoresis system property_value: IAO:0000111 "gel electrophoresis system" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Erik Segerdell" xsd:string property_value: IAO:0000118 "electrophoresis system" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Category:Electrophoresis xsd:string [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 relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "voltage clamp device" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Erik Segerdell" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Voltage_clamp xsd:string [Term] id: OBI:0001138 name: X-ray source def: "A device that is used to generate X-rays." [] is_a: OBI:0000968 ! device relationship: RO:0000085 OBI:0000374 ! has function excitation function property_value: IAO:0000111 "X-ray source" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Erik Segerdell" xsd:string property_value: IAO:0000118 "x-ray generator" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/X-ray_generator xsd:string [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 property_value: IAO:0000111 "liquid chromatography instrument" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Matthew Brush" xsd:string property_value: IAO:0000119 "PERSON: Matthew Brush" xsd:string [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." [] is_a: OBI:0000924 ! labeled specimen relationship: OBI:0000643 CHEBI:33696 ! has grain nucleic acid property_value: IAO:0000111 "labeled nucleic acid extract" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Jie Zheng" xsd:string property_value: IAO:0000118 "labeled extract" xsd:string property_value: IAO:0000119 "MO_221 labeledExtract" xsd:string property_value: OBI:0001847 "labeled extract" xsd:string [Term] id: OBI:0001144 name: binding constant def: "A binding datum about the disposition of two or more material entities to form complexes which comes in the form of a scalar and unit that are utilized in equations that model the binding process" [] is_a: OBI:0001181 ! binding datum union_of: OBI:0001536 ! equilibrium dissociation constant (KD) union_of: OBI:0001548 ! equilibrium association constant (KA) union_of: OBI:0001571 ! equilibrium dissociation constant (KD) approximated by IC50 union_of: OBI:0001581 ! equilibrium dissociation constant (KD) approximated by EC50 union_of: OBI:0001583 ! half life of binding datum union_of: OBI:0001603 ! binding off rate measurement datum (koff) union_of: OBI:0001605 ! binding on rate measurement datum (kon) property_value: IAO:0000111 "binding constant" xsd:string property_value: IAO:0000112 "The predicted or measured binding affinity of a peptide to a MHC molecule can be captured in the binding constants \"IC50 = 12 nM\" or \"t 1/2 = 30 minutes\". " xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "10/6/11 BP: The distinction between binding datum and binding constant is based on the later being part of an equation. That should be captured in the logical definition here, and used to make it to a defined class. " xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters, Randi Vita, Jason Greenbaum" xsd:string [Term] id: OBI:0001145 name: 3D structure determination of bound complex assay def: "A 3D structure determination assay in which a complex of 2 or more material enties is characterized which provides information on their binding configuration." [] is_a: OBI:0001146 ! binding assay is_a: OBI:0600045 ! 3D structure determination assay property_value: IAO:0000111 "3D structure determination of bound complex assay" xsd:string property_value: IAO:0000112 "Determination of a 3D structure of an antibody binding a protein by X-Ray crystallography, which identifies the specific binding site of the antibody." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 property_value: IAO:0000111 "binding assay" xsd:string property_value: IAO:0000112 "Determination of KD value for an antibody binding a protein using a BIACORE assay. Using plate bound antigen in an ELISA to determine if a mixture of serum antibodies bind the antigen.nnThe following are NOT binding assays, as the desired output is not binding data: RNA microarray experiments to determine levels of gene expression. ChIP experiments to determine where in DNA a transcription factor binds. Using an IL-2 antibody on an ELISA plate to determine presence of IL-2 after stimulating a T cell culture. " xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum" xsd:string property_value: IAO:0000119 "PERSON:Bjoern Peters, Randi Vita, Jason Greenbaum" xsd:string [Term] id: OBI:0001147 name: cell culture expansion def: "a processual entity that results in the increase of cell numbers" [] is_a: OBI:0000094 ! material processing relationship: OBI:0000293 OBI:0100060 ! has_specified_input cultured cell population relationship: OBI:0000299 OBI:0100060 ! has_specified_output cultured cell population relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "cell culture expansion" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "including grow of yeast and bacteria" xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_758 grow" xsd:string property_value: IAO:0000232 "BP:\nadd it as subclass of 'cell culturing'\nJZ:\nNo 'cell culturing' in OBI\nHas term 'cell co-culturing' and 'maintaining cell culture'. Don't think either of it fit. So leave the term under process." xsd:string [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 property_value: IAO:0000111 "gene knock out" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_771 gene_knock_out" xsd:string [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 property_value: IAO:0000111 "gene knock in" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_437 gene_knock_in" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Gene_Knock-in" xsd:string [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 property_value: IAO:0000111 "genetically modified material" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Jie Zheng" xsd:string property_value: IAO:0000119 "GROUP: OBI" xsd:string property_value: IAO:0000232 "term is proposed by BP on Oct 25, 2010 dev call" xsd:string [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 relationship: has_part OBI:0600033 ! cell permeabilization property_value: IAO:0000111 "transfection" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_366 transfection" xsd:string [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 property_value: IAO:0000111 "genetic transformation objective" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Jie Zheng" xsd:string property_value: IAO:0000119 "Person: Jie Zheng" xsd:string property_value: IAO:0000232 "suggested to be added by BP and AR during Oct 25, 2010 dev call" xsd:string [Term] id: OBI:0001154 name: induced mutation def: "a genetic transformation that the modification of the genetic material (either coding or non-coding) of an organism is caused by mutagenic compounds or irradiation." [] is_a: OBI:0600043 ! genetic transformation property_value: IAO:0000111 "induced mutation" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_564 induced_mutation" xsd:string [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 property_value: IAO:0000111 "3D structural organization datum" xsd:string property_value: IAO:0000112 "The atom coordinates found in a PDB (Protein Data Bank) file, generated by X Ray crystallography or NMR. " xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Jason Greenbaum, Randi Vita, Bjoern Peters" xsd:string [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. " [] is_a: IAO:0000416 ! time measurement datum relationship: IAO:0000039 UO:0000003 ! has measurement unit label time unit property_value: IAO:0000111 "half life datum (t 1/2)" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000118 "t 1/2" xsd:string property_value: IAO:0000119 "Bjoern Peters" xsd:string [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 property_value: IAO:0000111 "dose response curve" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Bjoern Peters; Randi Vita" xsd:string [Term] id: OBI:0001177 name: RNA sequencing def: "RNA sequencing is a sequencing process which uses ribonucleic acid as input and results in a the creation of RNA sequence information artifact " [] is_a: OBI:0600047 ! sequencing assay property_value: IAO:0000111 "RNA sequencing" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "BP 12/21:Created based on a request from Melanie" xsd:string property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "Bjoern Peters" xsd:string [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. \n" [] is_a: IAO:0000032 ! scalar measurement datum relationship: IAO:0000039 UO:0000051 ! has measurement unit label concentration unit relationship: IAO:0000136 OBI:0001172 ! is about dose response curve property_value: IAO:0000111 "half maximal effective concentration (EC50)" xsd:string property_value: IAO:0000112 "Determining the potentency of a drug / antibody / toxicant by measuring a graded dose response curve, and determining the concentration of the compound where 50% of its maximal effect is observed. " xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Bjoern Peters; Randi Vita" xsd:string property_value: IAO:0000119 "wikipedia" xsd:string [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 intersection_of: IAO:0000027 ! data item intersection_of: IAO:0000136 OBI:0001588 ! is about binding property_value: IAO:0000111 "binding datum" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Bjoern Peters; Randi Vita" xsd:string [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 relationship: IAO:0000039 UO:0000051 ! has measurement unit label concentration unit relationship: IAO:0000136 OBI:0001172 ! is about dose response curve property_value: IAO:0000111 "half maximal inhibitory concentration (IC50)" xsd:string property_value: IAO:0000112 "Interpolating that at a dose of IC50=12 nM, half of the binding of a comptetitive ligand is inhibited." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Bjoern Peters; Randi Vita" xsd:string property_value: IAO:0000119 "wikipedia" xsd:string [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 property_value: IAO:0000111 "in vivo design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_454 in_vivo_design" xsd:string [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 property_value: IAO:0000111 "genotyping by high throughput sequencing design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_560 genotyping_design" xsd:string [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 property_value: IAO:0000111 "ex vivo design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_808 ex_vivo_design" xsd:string [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 relationship: part_of OBI:0001305 ! genotype information property_value: IAO:0000111 "genetic population background information" xsd:string property_value: IAO:0000112 "genotype information 'C57BL/6J Hnf1a+/-' in this case, C57BL/6J is the genetic population background information" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "proposed and discussed on San Diego OBI workshop, March 2011" xsd:string property_value: IAO:0000117 "Group: OBI group" xsd:string property_value: IAO:0000119 "Group: OBI group" xsd:string [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 property_value: IAO:0000111 "epigenetic modification identification objective" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "Person: Chris Stoeckert" xsd:string [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:0001430 ! transcription profiling design relationship: has_part OBI:0001331 ! transcription profiling identification objective property_value: IAO:0000111 "transcription profiling by high thoughput sequencing design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "Group: ArrayExpress production team" xsd:string [Term] id: OBI:0001247 name: genotyping by high throughput sequencing assay def: "An assay in which high througput sequencer is used to detect polymorphisms in DNA samples" [] is_a: OBI:0000435 ! genotyping assay relationship: RO:0000057 OBI:0400103 ! has participant DNA sequencer property_value: IAO:0000111 "genotyping by high throughput sequencing assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: James Malone" xsd:string property_value: IAO:0000119 "EFO_0002771: genotyping by high throughput sequencing" xsd:string [Term] id: OBI:0001248 name: ChIP-chip assay def: "an assay that aims to investigate the interactions between protein and DNA relying on chromatin immunoprecipitation ('ChIP') combined with microarray technology ('chip'). Specially, it allows the identification of protein binding sites on a genome-wide basis." [] comment: Philippe Rocca-Serra is_a: OBI:0001956 ! assay using chromatin immunoprecipitation relationship: has_part OBI:0000690 ! immunoprecipitation relationship: OBI:0000417 OBI:0001398 ! achieves_planned_objective protein and DNA interaction identification objective relationship: RO:0000057 OBI:0400148 ! has participant DNA microarray property_value: IAO:0000111 "ChIP-chip assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: James Malone" xsd:string property_value: IAO:0000118 "ChIP-on-chip assay" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/ChIP-on-chip" xsd:string [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 relationship: has_part OBI:0001234 ! epigenetic modification identification objective relationship: has_part OBI:0001398 ! protein and DNA interaction identification objective property_value: IAO:0000111 "ChIP-seq design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Chip-Sequencing xsd:string [Term] id: OBI:0001266 name: DNA methylation profiling by high throughput sequencing assay def: "An assay in which the methylation state of DNA is determined and is compared between samples using sequencing based technology" [] comment: Philippe Rocca-Serra is_a: OBI:0000634 ! DNA methylation profiling assay intersection_of: OBI:0000634 ! DNA methylation profiling assay intersection_of: RO:0000057 OBI:0400103 ! has participant DNA sequencer property_value: IAO:0000111 "DNA methylation profiling by high throughput sequencing assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Group: ArrayExpress production team, James Malone, Helen Parkinson" xsd:string property_value: IAO:0000119 "EFO_0002761 methylation profiling by high throughput sequencing" xsd:string [Term] id: OBI:0001271 name: RNA-seq assay def: "An assay 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:0000424 ! transcription profiling assay is_a: OBI:0600047 ! sequencing assay relationship: has_part OBI:0000848 ! polyA RNA extraction relationship: OBI:0000417 OBI:0001331 ! achieves_planned_objective transcription profiling identification objective relationship: RO:0000057 OBI:0400103 ! has participant DNA sequencer property_value: IAO:0000111 "RNA-seq assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: James Malone" xsd:string property_value: IAO:0000118 "transcription profiling by high throughput sequencing" xsd:string property_value: IAO:0000119 "EFO_0002770 transcription profiling by high throughput sequencing" xsd:string property_value: IAO:0000232 "an assay that uses high-throughput sequencing technologies to sequence cDNA in order to get information about a sample's RNA content. RNA-Seq provides researchers with efficient ways to measure transcriptome data experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions.\n\nWEB: http://en.wikipedia.org/wiki/RNA-Seq" xsd:string property_value: IAO:0000232 "JZ: should be inferred as 'DNA sequencing'. Will check in the future." xsd:string [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 relationship: has_part OBI:0001234 ! epigenetic modification identification objective property_value: IAO:0000111 "DNA methylation profiling by array design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "GROUP: ArrayExpress production team" xsd:string [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 property_value: IAO:0000111 "in vitro design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_347 in_vitro_design" xsd:string [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:0001430 ! transcription profiling design relationship: has_part OBI:0001331 ! transcription profiling identification objective property_value: IAO:0000111 "transcription profiling by array design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_533 transcript_identification_design" xsd:string [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 relationship: has_part OBI:0001225 ! genetic population background information relationship: has_part OBI:0001364 ! genetic alteration information property_value: IAO:0000111 "genotype information" xsd:string property_value: IAO:0000112 "Genotype information can be: Mus musculus wild type (in this case the genetic population background information is Mus musculus), C57BL/6J Hnf1a+/- (in this case, C57BL/6J is the genetic population background information and Hnf1a+/- is the allele information" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "discussed on San Diego OBI workshop, March 2011" xsd:string property_value: IAO:0000117 "Group: OBI group" xsd:string property_value: IAO:0000119 "Group: OBI group" xsd:string [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:0001430 ! transcription profiling design relationship: has_part OBI:0001331 ! transcription profiling identification objective property_value: IAO:0000111 "transcription profiling by RT-PCR design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "Group: ArrayExpress production team" xsd:string [Term] id: OBI:0001318 name: proteomic profiling by array assay def: "An assay that proteins in a sample are detected, quantified or otherwise analysed, e.g. antibody profiling using an array based technology" [] is_a: OBI:0000443 ! analyte assay relationship: OBI:0000417 OBI:0000131 ! achieves_planned_objective molecular feature identification objective relationship: RO:0000057 OBI:0400149 ! has participant protein microarray property_value: IAO:0000111 "proteomic profiling by array assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: James Malone" xsd:string property_value: IAO:0000119 "EFO_0002765 proteomic profiling by array" xsd:string [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 property_value: IAO:0000111 "transcription profiling identification objective" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "Group: Penn Group" xsd:string [Term] id: OBI:0001332 name: DNA methylation profiling by array assay def: "An assay in which the methylation state of DNA is determined and is compared between samples using array technology" [] comment: Philippe Rocca-Serra is_a: OBI:0000634 ! DNA methylation profiling assay intersection_of: OBI:0000634 ! DNA methylation profiling assay intersection_of: RO:0000057 OBI:0400148 ! has participant DNA microarray property_value: IAO:0000111 "DNA methylation profiling by array assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: James Malone" xsd:string property_value: IAO:0000119 "EFO_0002759 methylation profiling by array" xsd:string [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." [] comment: post transcription modification design?\nor more clear RNAi design / antibody targeting design?\nneed to check the use cases is_a: OBI:0000115 ! intervention design relationship: has_part OBI:0000015 ! biological feature identification objective property_value: IAO:0000111 "post-transcriptional modification design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_392 cellular_modification_design" xsd:string [Term] id: OBI:0001361 name: transcription profiling by RT-PCR assay def: "An assay in which the transcriptome of a biological sample is analysed by reverse transcription PCR (RT-PCR)" [] is_a: OBI:0000424 ! transcription profiling assay relationship: has_part OBI:0000552 ! reverse transcribed polymerase chain reaction relationship: OBI:0000417 OBI:0001331 ! achieves_planned_objective transcription profiling identification objective relationship: RO:0000057 OBI:0000989 ! has participant PCR instrument property_value: IAO:0000111 "transcription profiling by RT-PCR assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Anna Farne" xsd:string property_value: IAO:0000119 "EFO_0002943: transcription profiling by RT-PCR" xsd:string [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 property_value: IAO:0000111 "genetic alteration information" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "proposed and discussed on San Diego OBI workshop, March 2011" xsd:string property_value: IAO:0000117 "Group: OBI group" xsd:string property_value: IAO:0000119 "Group: OBI group" xsd:string [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 property_value: IAO:0000111 "cellular process design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_810 cellular_process_design" xsd:string [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 property_value: IAO:0000111 "stimulus or stress design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_568 stimulus_or_stress_design" xsd:string [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 property_value: IAO:0000111 "protein and DNA interaction identification objective" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_933 binding_site_identification_design" xsd:string [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." [] is_a: OBI:0001425 ! protein binding site identification design relationship: has_part OBI:0001398 ! protein and DNA interaction identification objective property_value: IAO:0000111 "ChIP-chip design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000118 "ChIP-on-chip design" xsd:string property_value: IAO:0000119 "MO_933 binding_site_identification_design" xsd:string [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 property_value: IAO:0000111 "genetic characteristics information" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_66 IndividualGeneticCharacteristics" xsd:string property_value: IAO:0000232 "MO definition:\nThe genotype of the individual organism from which the biomaterial was derived. Individual genetic characteristics include polymorphisms, disease alleles, and haplotypes.\n\nexamples in ArrayExpress\nwild_type\nMutaMouse (CD2F1 mice with lambda-gt10LacZ integration)\nAlfpCre; SNF5 flox/knockout\np53 knock out\nC57Bl/6 gp130lox/lox MLC2vCRE/+\nfer-15; fem-1\ndf/df\npat1-114/pat1-114 ade6-M210/ade6-M216 h+/h+ (cells are diploid)\n" xsd:string [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 property_value: IAO:0000111 "protein binding site identification design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_933 binding_site_identification_design" xsd:string [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 property_value: IAO:0000111 "transcription profiling design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_533 transcript_identification_design" xsd:string [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 relationship: has_part OBI:0000131 ! molecular feature identification objective property_value: IAO:0000111 "proteomic profiling by array design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng, Dan Berrios" xsd:string property_value: IAO:0000119 "Group: ArrayExpress production team" xsd:string property_value: IAO:0000233 https://github.com/obi-ontology/obi/issues/854 xsd:string [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 relationship: has_part OBI:0000113 ! sequence feature identification objective property_value: IAO:0000111 "genotyping design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_560 genotyping_design" xsd:string [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 relationship: has_part OBI:0000015 ! biological feature identification objective property_value: IAO:0000111 "genetic modification design" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_447 genetic_modification_design" xsd:string [Term] id: OBI:0001463 name: transcription profiling by array assay def: "An assay in which the transcriptome of a biological sample is analysed using array technology." [] is_a: OBI:0000424 ! transcription profiling assay relationship: OBI:0000417 OBI:0001331 ! achieves_planned_objective transcription profiling identification objective relationship: RO:0000057 OBI:0400148 ! has participant DNA microarray property_value: IAO:0000111 "transcription profiling by array assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "JZ: add alternative term: 'RNA profiling by array assay' requested by ENCODE developer.\nSee tracker: https://sourceforge.net/p/obi/obi-terms/757/" xsd:string property_value: IAO:0000117 "Person: James Malone" xsd:string property_value: IAO:0000118 "RNA profiling by array assay" xsd:string property_value: IAO:0000119 "EFO_0002768: transcription profiling by array" xsd:string [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)." [] is_a: OBI:0100051 ! specimen property_value: IAO:0000111 "specimen from organism" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000118 "tissue specimen" xsd:string property_value: IAO:0000119 "MO_954 organism_part" xsd:string [Term] id: OBI:0001491 name: radioactivity detection binding assay def: "binding assay that uses radioactivity detection as an indicator of binding" [] is_a: OBI:0001146 ! binding assay intersection_of: OBI:0001146 ! binding assay intersection_of: has_part OBI:0000201 ! radioactivity detection property_value: IAO:0000111 "radioactivity detection binding assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Bjoern Peters, Randi Vita" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:0001499 name: fluorescence detection binding assay def: "binding assay that uses fluorescence detection as an indicator of binding" [] is_a: OBI:0001146 ! binding assay intersection_of: OBI:0001146 ! binding assay intersection_of: has_part OBI:0001501 ! fluorescence detection assay property_value: IAO:0000111 "fluorescence detection binding assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Bjoern Peters, Randi Vita" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:0001501 name: fluorescence detection assay def: "An assay in which a material's fluorescence is determined." [] is_a: OBI:0000070 ! assay property_value: IAO:0000111 "fluorescence detection assay" xsd:string property_value: IAO:0000112 "Using a laser to stimulate a cell culture that was previously labeled with fluorescent antibodies to detect light emmission at a different wavelength in order to determine the presence of surface markers the antibodies are specific for." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 property_value: IAO:0000111 "purification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_406 purify" xsd:string [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 property_value: IAO:0000111 "specimen with pre- or post-mortem status" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "organizational term, used in description of specimen that is created from known pre- or post-mortem status" xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "MO_84 OrganismStatus" xsd:string [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 relationship: IAO:0000039 UO:0000051 ! has measurement unit label concentration unit property_value: IAO:0000111 "equilibrium dissociation constant (KD)" xsd:string property_value: IAO:0000112 "KD = 32 nM is the equilibrium dissociation rate found for peptide SIINFEKL binding to H-2 Kb" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Bjoern Peters, Randi Vita" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 property_value: IAO:0000111 "equilibrium association constant (KA)" xsd:string property_value: IAO:0000112 "KA = 10^-12 M^-1 is the equilibirum association constant maximally found for antibody binding to haptens. " xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Bjoern Peters, Randi Vita" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 property_value: IAO:0000111 "rate measurement datum" xsd:string property_value: IAO:0000112 "The rate of disassociation of a peptide from a complex with an MHC molecule measured by the ratio of bound and unbound peptide per unit of time." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Bjoern Peters, Randi Vita" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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:0001144 ! binding constant is_a: OBI:0001191 ! half maximal inhibitory concentration (IC50) property_value: IAO:0000111 "equilibrium dissociation constant (KD) approximated by IC50" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Bjoern Peters, Randi Vita" xsd:string property_value: IAO:0000119 http://dx.doi.org/10.1016/0006-2952(73)90196-2\n xsd:string [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 relationship: IAO:0000136 OBI:0000811 ! is about primary structure of DNA macromolecule property_value: IAO:0000111 "DNA sequence data" xsd:string property_value: IAO:0000112 "The part of a FASTA file that contains the letters ACTGGGAA " xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "OBI call; Bjoern Peters" xsd:string property_value: IAO:0000119 "OBI call; Melanie Courtout" xsd:string property_value: IAO:0000232 "8/29/11 call: This is added after a request from Melanie and Yu. They should review it further. This should be a child of 'sequence data', and as of the current definition will infer there. " xsd:string [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:0001144 ! binding constant is_a: OBI:0001180 ! half maximal effective concentration (EC50) property_value: IAO:0000111 "equilibrium dissociation constant (KD) approximated by EC50" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Bjoern Peters, Randi Vita" xsd:string property_value: IAO:0000119 "Assay Development: Fundamentals and Practices, By Ge Wu, page 74" xsd:string [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) property_value: IAO:0000111 "half life of binding datum" xsd:string property_value: IAO:0000112 "The 45 minute period in which one half of the complexes formed by peptide ligand bound to a HLA-A*0201molecule disassociate." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Bjoern Peters, Randi Vita" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:0001588 name: binding def: "The process of material entities forming complexes. " [] is_a: GO:0008150 ! biological_process property_value: IAO:0000111 "binding" xsd:string property_value: IAO:0000112 "A peptide binding to an MHC molecule to form a complex. " xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "9/28/11 BP: The disposition referenced is the one of the ligand to bind the molecule. This along with binding as a function / process needs to be figured out with GO which is inconsistent at this point. " xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters, Randi Vita" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 property_value: IAO:0000111 "binding off rate measurement datum (koff)" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Bjoern Peters, Randi Vita" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 property_value: IAO:0000111 "binding on rate measurement datum (kon)" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Bjoern Peters, Randi Vita" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 intersection_of: OBI:0000443 ! analyte assay intersection_of: OBI:0000293 OBI:0000038 {all_some="true"} ! has_specified_input chromatography column intersection_of: OBI:0000293 OBI:0000601 {all_some="true"} ! has_specified_input chromatography consumable property_value: IAO:0000111 "analytical chromatography" xsd:string property_value: IAO:0000112 "Detection of the presence of blood group A specific antibodies by passing a serum sample through an affinity column containing blood group A carbohydrate, and quantifying the protein content eluted from the column." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 intersection_of: OBI:0000185 ! imaging assay intersection_of: OBI:0000293 OBI:0000990 {all_some="true"} ! has_specified_input electron microscope property_value: IAO:0000111 "electron microscopy imaging assay" xsd:string property_value: IAO:0000112 "Using gold labeled antibodies to stain a mouse brain slice and use electron microscopy to generate an image that shows the location of the antibodies within the tissue structure." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:0001632 name: immuno staining assay def: "A detection of 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 ! detection of molecular label property_value: IAO:0000111 "immuno staining assay" xsd:string property_value: IAO:0000112 "Detection of the presence of VCAM molecules on the surface of cells in a histology slide using an enzyme-linked antibody followed by enzyme activation to release a dye." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 intersection_of: BFO:0000040 ! material entity intersection_of: OBI:0000312 OBI:0001505 ! is_specified_output_of purification property_value: IAO:0000111 "purified material" xsd:string property_value: IAO:0000112 "A mixture of peptide molecules that has been run through an HPLC column to remove 65" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "GROUP: OBI call " xsd:string property_value: IAO:0000119 "OBI conference call" xsd:string [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 intersection_of: OBI:0001146 ! binding assay intersection_of: OBI:0000293 OBI:0000930 {all_some="true"} ! has_specified_input calorimeter property_value: IAO:0000111 "calorimetric binding assay" xsd:string property_value: IAO:0000112 "A solution of a proteins is titrated into a solution containing a specific antibody. The heat released upon their interaction (delta H) is monitored over time where each peak represents a heat change associated with the injection of a small volume of sample into the reaction cell. As successive amounts of the ligand are titrated into the cell, the quantity of heat absorbed or released is in direct proportion to the amount of binding. As the system reaches saturation, the heat signal diminishes until only heats of dilution are observed. A binding curve is then obtained from a plot of the heats from each injection against the ratio of protein and antibody in the cell . " xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 relationship: has_part OBI:0001501 ! fluorescence detection assay property_value: IAO:0000111 "antibody binding detection by fluorescence quenching" xsd:string property_value: IAO:0000112 "The binding affinity of Fab 4-4-20 for the fluorescein molecule was determined using the fluorescence quenching assay, by placing the Fab and the fluorescein together in a well and measuring the fluorescence after each addition of increasing concentrations of the Fab (PMID: 8637844). " xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:0001670 name: RNA protection assay def: "RPA is a technique to assess the presence and estimate 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." [] is_a: OBI:0000070 ! assay property_value: IAO:0000111 "RNA protection assay" xsd:string property_value: IAO:0000112 "Absolute concentrations of mRNA for type I and type VI collagen in the canine meniscus in normal and ACL-deficient knee joints obtained by RNase protection assay.\nWildey GM, Billetz AC, Matyas JR, Adams ME, McDevitt CA.\nJ Orthop Res. 2001 Jul;19(4):650-8.\nPMID: 11518275" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra; Marcus Chibucos" xsd:string property_value: IAO:0000118 "RPA; RNAse protection assay" xsd:string property_value: IAO:0000119 "adapted from wikipedia + PMID:16491611" xsd:string [Term] id: OBI:0001671 name: electrophoretic mobility shift assay def: "is an assay which aims to provide information about Protein-DNA or Protein-RNA interaction and which used gel electrophoresis and relies 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." [] is_a: OBI:0001146 ! binding assay property_value: IAO:0000111 "electrophoretic mobility shift assay " xsd:string property_value: IAO:0000112 "Electrophoretic mobility shift assay reveals a novel recognition sequence for Setaria italica NAC protein.\nPuranik S, Kumar K, Srivastava PS, Prasad M.\nPlant Signal Behav. 2011 Oct;6(10):1588-90. Epub 2011 Oct 1.\nPMID: 21918373" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra; Marcus Chibucos" xsd:string property_value: IAO:0000118 "EMSA,gel shift assay, gel mobility shift assay, band shift assay, gel retardation assay" xsd:string property_value: IAO:0000119 PMID:6269071 xsd:string [Term] id: OBI:0001672 name: gene knock-down assay def: "is an assay which transiently disrupts gene transcripts by expressing antisense RNA constructs or delivering RNA interfering molecules in cells." [] is_a: OBI:0000070 ! assay property_value: IAO:0000111 "gene knock-down assay" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra; Marcus Chibucos" xsd:string property_value: IAO:0000119 PMID:17430206 xsd:string [Term] id: OBI:0001673 name: nano-cap analysis of gene expression def: "nano-CAGE is a type of CAGE developed to work from very low amount (nanogram scale) of mRNA samples" [] is_a: OBI:0000424 ! transcription profiling assay property_value: IAO:0000111 "nano-cap analysis of gene expression " xsd:string property_value: IAO:0000112 "Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. \nPMID:20543846\n" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra; Marcus Chibucos" xsd:string property_value: IAO:0000118 "nano-CAGE" xsd:string property_value: IAO:0000119 "PMID: 20543846" xsd:string [Term] id: OBI:0001674 name: cap analysis of gene expression def: "An assay which aims at monitoring 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 " [] is_a: OBI:0000424 ! transcription profiling assay is_a: OBI:0600047 ! sequencing assay relationship: has_part OBI:0000552 ! reverse transcribed polymerase chain reaction relationship: has_part OBI:0000626 ! DNA sequencing relationship: OBI:0000293 OBI:0000880 ! has_specified_input RNA extract relationship: OBI:0000417 OBI:0001331 ! achieves_planned_objective transcription profiling identification objective relationship: RO:0000057 OBI:0400103 ! has participant DNA sequencer property_value: IAO:0000111 "cap analysis of gene expression " xsd:string property_value: IAO:0000112 "5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing.\nTakahashi H, Lassmann T, Murata M, Carninci P.\nNat Protoc. 2012 Feb 23;7(3):542-61. doi: 10.1038/nprot.2012.005.\nPMID: 22362160" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra; Marcus Chibucos" xsd:string property_value: IAO:0000118 "CAGE" xsd:string property_value: IAO:0000119 PMID:14663149 xsd:string [Term] id: OBI:0001681 name: yeast one-hybrid def: "The one-hybrid variation of this technique is designed to investigate protein–DNA interactions and uses a single fusion protein in which the AD is linked directly to the binding domain. " [] is_a: OBI:0001146 ! binding assay property_value: IAO:0000111 "yeast one-hybrid " xsd:string property_value: IAO:0000112 "Yeast one-hybrid assays for gene-centered human gene regulatory network mapping. Nat Methods. 2011 Oct 30;8(12):1050-2. doi: 10.1038/nmeth.1764.\nPMID: 22037702 " xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra; Marcus Chibucos" xsd:string property_value: IAO:0000118 "Y1H" xsd:string property_value: IAO:0000119 "PMID: 22218861" xsd:string property_value: IAO:0000232 "add regulatory region DNA binding;obo:GO:0000975;" xsd:string [Term] id: OBI:0001682 name: bacterial one-hybrid def: " is a method for identifying 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" [] is_a: OBI:0001681 ! yeast one-hybrid property_value: IAO:0000111 "bacterial one-hybrid " xsd:string property_value: IAO:0000112 "A systematic characterization of factors that regulate Drosophila segmentation via a bacterial one-hybrid system.\nNoyes MB, Meng X, Wakabayashi A, Sinha S, Brodsky MH, Wolfe SA.\nNucleic Acids Res. 2008 May;36(8):2547-60. Epub 2008 Mar 10.\nPMID: 18332042" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra; Marcus Chibucos" xsd:string property_value: IAO:0000118 "B1H" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Bacterial_one-hybrid_system xsd:string property_value: IAO:0000232 "add regulatory region DNA binding;obo:GO:0000975;" xsd:string [Term] id: OBI:0001683 name: chromosome organization assay by fluorescence in situ hybridization def: "is an in situ hybridization assay that uses fluorescence as means of detection chromosomal integrity" [] is_a: OBI:0001686 ! in situ hybridization property_value: IAO:0000111 "chromosome organization assay by fluorescence in situ hybridization" xsd:string property_value: IAO:0000112 "Duplication of intrachromosomal insertion segments 4q32→q35 confirmed by comparative genomic hybridization and fluorescent in situ hybridization.PMID:22384449" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "Changed label from fluorescence in situ hybridization as per tracker item #788" xsd:string property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra; Marcus Chibucos" xsd:string property_value: IAO:0000118 "FISH" xsd:string [Term] id: OBI:0001684 name: methylation-specific polymerase chain reaction def: "is an assay which 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." [] is_a: OBI:0000070 ! assay property_value: IAO:0000111 "methylation-specific polymerase chain reaction " xsd:string property_value: IAO:0000112 "Methylation status of breast cancer resistance protein detected by methylation-specific polymerase chain reaction analysis is correlated inversely with its expression in drug-resistant lung cancer cells. PMID: 18219662" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "2015-03-30 OBI dev call:\nThe assay was defined as equvivalent to\n(assay and (has_specified_input some 'binding complex 3D structure determination assay') and (has_specified_output some \n('data item' and ('is about' some 'regulation of DNA methylation')))) and (achieves_planned_objective some 'epigenetic modification identification objective')\n 'binding complex 3D structure determination assay' is a process and cannot be the input of another process which cause inconsistent.\nIn the call, we decided to remove axiom and will discuss it in the assay harmonization discussion.\nsee tracker:\nhttps://sourceforge.net/p/obi/obi-terms/747/\n\n" xsd:string property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra; Marcus Chibucos" xsd:string property_value: IAO:0000118 "MSP" xsd:string property_value: IAO:0000119 PMID:8790415 xsd:string [Term] id: OBI:0001685 name: amplification of intermethylated sites (AIMS) assay def: " amplification of intermethylated sites (AIMS) is an assay appropriate for genome-wide estimates of DNA methylation and the discovery of specific methylated 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." [] is_a: OBI:0000634 ! DNA methylation profiling assay property_value: IAO:0000111 "amplification of intermethylated sites (AIMS) assay " xsd:string property_value: IAO:0000112 "Analysis of DNA methylation by amplification of intermethylated sites (AIMS).PMID:18987810" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra; Marcus Chibucos" xsd:string property_value: IAO:0000118 "AIMS assay,intermethylated site amplification " xsd:string property_value: IAO:0000119 "PMID: 18987810" xsd:string [Term] id: OBI:0001686 name: in situ hybridization def: "is an assay using artificially induced nucleic hybridization to localize a specific DNA or RNA sequence in a portion or section of tissue " [] is_a: OBI:0000070 ! assay property_value: IAO:0000111 "in situ hybridization" xsd:string property_value: IAO:0000112 "Use of in situ hybridization to examine gene expression in the embryonic, neonatal, and adult urogenital system.\nPMID:22639265\n" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra; Marcus Chibucos" xsd:string property_value: IAO:0000118 "ISH" xsd:string property_value: IAO:0000119 PMID:9021518 xsd:string [Term] id: OBI:0001689 name: cytochalasin-induced inhibition of actin polymerization assay def: "is 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 property_value: IAO:0000111 "cytochalasin-induced inhibition of actin polymerization assay" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra; Marcus Chibucos" xsd:string property_value: IAO:0000232 "add ;actin filament polymerization obo:GO:0070358;" xsd:string [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 property_value: IAO:0000111 "cellular structure feature identification objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "OBI group" xsd:string [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 intersection_of: OBI:0000443 ! analyte assay intersection_of: has_part OBI:0000690 ! immunoprecipitation intersection_of: OBI:0000293 GO:0042571 {all_some="true"} ! has_specified_input immunoglobulin complex, circulating property_value: IAO:0000111 "immunoprecipitation assay" xsd:string property_value: IAO:0000112 "Determining if a cell is producing a protein using a protein specific antibody to immunoprecipitate the cell lysate. Determining if the serum of a patient contains antibodies against HBV core protein by immunoprecipitating purified HBV core protein with the patients serum." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 intersection_of: OBI:0000711 ! library preparation intersection_of: OBI:0000299 OBI:0000722 ! has_specified_output paired-end library property_value: http://purl.org/dc/elements/1.1/source "ENCODE project" xsd:string property_value: IAO:0000111 "paired-end library preparation" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Venkat Malladi, Jie Zheng" xsd:string property_value: IAO:0000119 "Venkat Malladi, Jie Zheng" xsd:string [Term] id: OBI:0001861 name: methylation-sensitive restriction enzyme sequencing assay def: "An assay that identifies unmethylated CpGs by use of methylation sensitive restriction enzymes to fragment DNA." [] is_a: OBI:0000626 ! DNA sequencing is_a: OBI:0001266 ! DNA methylation profiling by high throughput sequencing assay relationship: has_part OBI:0000626 ! DNA sequencing relationship: has_part OBI:0000711 ! library preparation relationship: has_part OBI:0600050 ! specific enzymatic cleavage relationship: OBI:0000417 OBI:0001234 ! achieves_planned_objective epigenetic modification identification objective relationship: RO:0000057 OBI:0400103 ! has participant DNA sequencer property_value: http://purl.org/dc/elements/1.1/source "ENCODE project" xsd:string property_value: IAO:0000111 "methylation-sensitive restriction enzyme sequencing assay" xsd:string property_value: IAO:0000112 "Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842]" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Venkat Malladi, Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000118 "MRE-seq" xsd:string property_value: IAO:0000118 "MRE-seq assay" xsd:string property_value: IAO:0000119 "Maunakea et al. Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature. 2010 Jul 8;466(7303):253-7. [PMID:20613842]" xsd:string [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 relationship: RO:0000085 OBI:0000399 ! has function solid support function property_value: IAO:0000111 "assay array" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Chris Stoeckert, Jie Zheng, Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Penn Group" xsd:string [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 intersection_of: BFO:0000040 ! material entity intersection_of: RO:0000087 OBI:0000086 ! has role reagent role relationship: OBI:0000312 OBI:0000094 ! is_specified_output_of material processing property_value: IAO:0000111 "reagent" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2013-6-5 MHB: Clarifications regarding the distinction between reagetns and devices were made at the May 2013 Philly Workshop. Reagents are distinguished from devices that also participate in scientific techniques by the fact that reagents are chemical or biological in nature and necessarily participate in some chemical interaction or reaction during the realization of their experimental role. By contrast, devices do not participate in such chemical reactions/interactions. Note that there are cases where devices use reagent components during their operation, where the reagent-device distinction is less clear. For examples, see editor note on OBI:device." xsd:string property_value: IAO:0000117 "PERSON:Matthew Brush" xsd:string property_value: IAO:0000119 "PERSON:Matthew Brush" xsd:string [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 property_value: IAO:0000111 "cell freezing medium" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Matthew Brush" xsd:string [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." [] is_a: OBI:0000415 ! polymerase chain reaction relationship: has_part OBI:0302892 ! enzymatic ligation property_value: IAO:0000111 "multiplex ligation-mediated amplification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000118 "LMA" xsd:string property_value: IAO:0000118 "MLPA" xsd:string property_value: IAO:0000118 "Multiplex ligation-dependent probe amplification" xsd:string property_value: IAO:0000119 "web: http://en.wikipedia.org/wiki/Multiplex_Ligation-dependent_Probe_Amplification\nPubmed: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1867615/" xsd:string [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 property_value: IAO:0000111 "chromosome conformation identification objective" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "Group: Penn Group" xsd:string [Term] id: OBI:0001919 name: Carbon-copy chromosome conformation capture assay def: "An assay that is used to analyze the organization of chromosomes at the genome-wide scale." [] is_a: OBI:0600047 ! sequencing assay relationship: has_part OBI:0000626 ! DNA sequencing relationship: has_part OBI:0000711 ! library preparation relationship: has_part OBI:0000800 ! cross linking relationship: has_part OBI:0001914 ! multiplex ligation-mediated amplification relationship: has_part OBI:0600050 ! specific enzymatic cleavage relationship: OBI:0000299 OBI:0001573 ! has_specified_output DNA sequence data relationship: OBI:0000417 OBI:0001917 ! achieves_planned_objective chromosome conformation identification objective relationship: RO:0000057 OBI:0400103 ! has participant DNA sequencer property_value: http://purl.org/dc/elements/1.1/source "ENCODE project" xsd:string property_value: IAO:0000111 "Carbon-copy chromosome conformation capture assay" xsd:string property_value: IAO:0000112 "van Berkum et al. Determining spatial chromatin organization of large genomic regions using 5C technology. Methods Mol Biol (2009) vol. 567 pp. 189-213 [PMID:19588094]" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Venkat Malladi, Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000118 "5C" xsd:string property_value: IAO:0000118 "5C assay" xsd:string property_value: IAO:0000119 "\"Dostie et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006 October; 16(10):1299-309.[PMID:16954542]\"" xsd:string [Term] id: OBI:0001925 name: chromatin immunoprecipitation with exonuclease sequencing assay def: "A ChIP-seq assay to identify protein binding sites using an exonuclease to provide greater binding resolution of immunoprecipitation assay by genome wide sequencing." [] is_a: OBI:0000716 ! ChIP-seq assay relationship: has_part OBI:0000800 ! cross linking relationship: has_part OBI:0600050 ! specific enzymatic cleavage relationship: OBI:0000299 OBI:0001573 ! has_specified_output DNA sequence data relationship: RO:0000057 OBI:0400114 ! has participant sonicator property_value: http://purl.org/dc/elements/1.1/source "ENCODE project" xsd:string property_value: IAO:0000111 "chromatin immunoprecipitation with exonuclease sequencing assay" xsd:string property_value: IAO:0000112 "Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082]" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Venkat Malladi, Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000118 "ChIP-exo assay" xsd:string property_value: IAO:0000119 "Rhee et al. Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution. Cell. 2011 Dec;147(6):1408-19. [PMID:22153082]" xsd:string [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 property_value: IAO:0000111 "categorical value specification" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string [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 property_value: IAO:0000111 "scalar value specification" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string [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 property_value: IAO:0000111 "value specification" xsd:string property_value: IAO:0000112 "The value of 'positive' in a classification scheme of \"positive or negative\"; the value of '20g' on the quantitative scale of mass." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "This term is currently a descendant of 'information content entity', which requires that it 'is about' something. A value specification of '20g' for a measurement data item of the mass of a particular mouse 'is about' the mass of that mouse. However there are cases where a value specification is not clearly about any particular. In the future we may change 'value specification' to remove the 'is about' requirement." xsd:string property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string [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 intersection_of: BFO:0000040 ! material entity intersection_of: has_part REO:0000280 ! molecular label intersection_of: OBI:0000312 OBI:0600038 ! is_specified_output_of addition of molecular label property_value: IAO:0000111 "molecular-labeled material" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Matthew Brush" xsd:string property_value: IAO:0000119 "OBI developer call, 3-12-12" xsd:string [Term] id: OBI:0001954 name: ChIP assay def: "An assay in which protein-DNA complexes are extracted from short regions of chromatin and are reversibly cross linked, immunoprecipitated with antibodies or tags, purified, and amplified with the aim of analysis gene- and promoter-specific known targets" [] is_a: OBI:0001956 ! assay using chromatin immunoprecipitation is_a: OBI:0002020 ! epigenetic modification assay relationship: has_part OBI:0000690 ! immunoprecipitation relationship: OBI:0000417 OBI:0001234 ! achieves_planned_objective epigenetic modification identification objective relationship: OBI:0000417 OBI:0001398 ! achieves_planned_objective protein and DNA interaction identification objective property_value: IAO:0000111 "ChIP assay" xsd:string property_value: IAO:0000112 "PMID: 6379641\nGilmour & Lis. Proc Natl Acad Sci U S A. 1984 Jul;81(14):4275-9.\nand can be found linked from here:\n" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "chromatin immunoprecipitation assay" xsd:string property_value: IAO:0000119 "adapted from CHS protocols, wikipedia, life tech, ChIP-seq term definition" xsd:string property_value: IAO:0000232 "as per user (pployd) request and proposal by Alan Ruttenberg\nhttp://sourceforge.net/p/obi/obi-terms/707/" xsd:string [Term] id: OBI:0001956 name: assay using chromatin immunoprecipitation def: "an assay which uses immunoprecipitation and which produces data about protein-DNA interaction or DNA epigenetic modification" [] is_a: OBI:0001700 ! immunoprecipitation assay property_value: IAO:0000111 "assay using chromatin immunoprecipitation" xsd:string property_value: IAO:0000112 http://www.lifetechnologies.com/uk/en/home/life-science/epigenetics-noncoding-rna-research/chromatin-remodeling/chromatin-immunoprecipitation-chip.html xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "as per user (pployd) request and proposal by Alan Ruttenberg\nhttp://sourceforge.net/p/obi/obi-terms/707/" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string [Term] id: OBI:0001977 name: cytometry assay def: "An assay that measures properties of cells." [] is_a: OBI:0000070 ! assay property_value: IAO:0000111 "cytometry assay" xsd:string property_value: IAO:0000112 "An intracellular material detection by flow cytometry assay measuring peforin inside a culture of T cells." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 ! fluorescence detection binding assay relationship: has_part OBI:0001501 ! fluorescence detection assay property_value: IAO:0000111 "fluorescence quenching binding assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 intersection_of: OBI:0000443 ! analyte assay intersection_of: OBI:0000293 OBI:0400147 {all_some="true"} ! has_specified_input microarray property_value: IAO:0000111 "microarray assay" xsd:string property_value: IAO:0000112 "Measuring if sera from an influenza A virus immunizedmouse binds to Hemagglutinin protein that is immobilized on a microarray." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 property_value: IAO:0000111 "immunohistochemistry" xsd:string property_value: IAO:0000112 "Staining a brain tissue sample from an Alzheimer's disease patient with antibodies to amyloid beta to identify amyloid plaques." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:0002020 name: epigenetic modification assay def: "An assay that identifies epigenetic modification including histone modifications, open chromatin, and DNA methylation." [] is_a: OBI:0000070 ! assay intersection_of: OBI:0000070 ! assay intersection_of: OBI:0000417 OBI:0001234 ! achieves_planned_objective epigenetic modification identification objective property_value: http://purl.org/dc/elements/1.1/source "Beta Cell Biology Consoritum" xsd:string property_value: IAO:0000111 "epigenetic modification assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "Penn group" xsd:string [Term] id: OBI:0002035 name: peptide mass fingerprinting def: "A mass spectrometry assay in which an unknown protein of interest is cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass spectrometer. These masses are then compared to values in a database containing known protein sequences." [] is_a: OBI:0000470 ! mass spectrometry assay property_value: http://purl.org/dc/elements/1.1/source "Saccharomyces Genome Database (SGD)" xsd:string property_value: IAO:0000111 "peptide mass fingerprinting" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "Details see tracker: https://sourceforge.net/p/obi/obi-terms/725/" xsd:string property_value: IAO:0000117 "Janos Demeter, Chris Stoeckert" xsd:string property_value: IAO:0000118 "PMF" xsd:string property_value: IAO:0000118 "protein fingerprinting" xsd:string property_value: IAO:0000119 "ERO:0001668 (http://en.wikipedia.org/wiki/Peptide_mass_fingerprinting)" xsd:string [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 intersection_of: BFO:0000040 ! material entity intersection_of: RO:0002351 OBI:0100051 {all_only="true"} ! has member specimen property_value: http://purl.org/dc/elements/1.1/source "Biobank" xsd:string property_value: IAO:0000111 "collection of specimens" xsd:string property_value: IAO:0000112 "Blood cells collected from multiple donors over the course of a study." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "Details see tracker: https://sourceforge.net/p/obi/obi-terms/778/" xsd:string property_value: IAO:0000117 "Person: Chris Stoeckert, Jie Zheng" xsd:string property_value: IAO:0000119 "OBIB, OBI" xsd:string [Term] id: OBI:0002082 name: reporter gene assay def: "An assay in which expression of a reporter gene is detected that was inserted under the control of a regulatory sequence of interest." [] is_a: OBI:0000070 ! assay property_value: IAO:0000111 "reporter gene assay" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "tracker item: 781" xsd:string property_value: IAO:0000117 "Chris Stoeckert, Paul D. Thomas" xsd:string property_value: IAO:0000118 "reporter gene detection assay" xsd:string property_value: IAO:0000119 "Paul D. Thomas, Yang Chai; FaceBase" xsd:string [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 property_value: http://purl.org/dc/elements/1.1/source "Biobank" xsd:string property_value: IAO:0000111 "physical store" xsd:string property_value: IAO:0000112 "a freezer. a humidity controlled box." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "For details see tracker item: http://sourceforge.net/p/obi/obi-terms/793/" xsd:string property_value: IAO:0000117 "Chris Stoeckert" xsd:string property_value: IAO:0000119 "Duke Biobank, OBIB" xsd:string [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." [] is_a: OBI:0000552 ! reverse transcribed polymerase chain reaction property_value: http://purl.org/dc/elements/1.1/source "ENCODE" xsd:string property_value: IAO:0000111 "rapid amplification of cDNA ends" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "For details see tracker item: https://sourceforge.net/p/obi/obi-terms/790/" xsd:string property_value: IAO:0000117 "Jason Hilton, Chris Stoeckert" xsd:string property_value: IAO:0000118 "RACE" xsd:string property_value: IAO:0000119 http://www.clontech.com/US/Products/cDNA_Synthesis_and_Library_Construction/RACE_Rapid_Amplification_of_cDNA_Ends/5_Prime_RACE_and_3_Prime_RACE xsd:string [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." [] is_a: OBI:0001630 ! analytical chromatography intersection_of: OBI:0001630 ! analytical chromatography intersection_of: OBI:0000293 OBI:0001057 {all_some="true"} ! has_specified_input high performance liquid chromatography instrument property_value: IAO:0000111 "high performance liquid chromotography assay" xsd:string property_value: IAO:0000112 "On-line coupled immunoaffinity chromatography-reversed-phase high-performance liquid chromatography (IAC-HPLC) with detection by quadrupole ion trap mass spectrometry using a particle beam interface has been developed for the determination of the steroids, dexamethasone and flumethasone. HEMA (polyhydroxyethylmethacrylate) was evaluated as a support material for the anti-dexamethasone antibodies used in IAC. Antibody cross-reactivity and non-specific binding have been investigated for the HEMA bound anti-dexamethasone IAC column. The on-line IAC-HPLC-MS determination of dexamethasone and flumethasone in post-administration equine urine samples showed precisions (R.S.D.) of 8.0 and 7.1%, respectively, with limits of detection in the range 3-4 ng/ml." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "ImmPort" xsd:string property_value: IAO:0000118 "HPLC" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/9491555 xsd:string [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 intersection_of: OBI:0000185 ! imaging assay intersection_of: OBI:0000293 OBI:0400169 {all_some="true"} ! has_specified_input microscope property_value: IAO:0000111 "microscopy assay" xsd:string property_value: IAO:0000112 "Lung, liver, and spleen tissue samples were collected from female BALB/c mice and fixed in 100% formalin solution, embedded in paraffin, sectioned, and stained with hematoxylin and eosin. The stained samples were examined for signs of pathological changes under light microscopy." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "ImmPort" xsd:string property_value: IAO:0000119 http://www.ncbi.nlm.nih.gov/pubmed/21685355 xsd:string [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 property_value: IAO:0000111 "protein localization assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Rebecca Tauber" xsd:string property_value: IAO:0000119 "OBI development call" xsd:string [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 property_value: IAO:0000111 "subcellular protein localization assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Rebecca Tauber" xsd:string property_value: IAO:0000119 "ECO" xsd:string [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 relationship: has_part OBI:0000893 ! real time polymerase chain reaction assay property_value: IAO:0000111 "ChIP-qPCR assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert" xsd:string property_value: IAO:0000119 PMID:18388953 xsd:string [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." [] is_a: OBI:0000443 ! analyte assay property_value: IAO:0000111 "dot blot assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000118 "dot blot analysis" xsd:string property_value: IAO:0000119 PMID:10473518 xsd:string [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." [] is_a: OBI:0000443 ! analyte assay property_value: IAO:0000111 "ATP bioluminescence assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Rebecca Tauber" xsd:string property_value: IAO:0000118 "ATP quantitation assay" xsd:string property_value: IAO:0000118 "cell viability ATP quantitation assay" xsd:string property_value: IAO:0000119 "ECO" xsd:string [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 property_value: IAO:0000111 "electrophysiology assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "Note that electrophysiological manipulations also exist which involve processes that alter the electrophysiological properties of cells and tissues." xsd:string property_value: IAO:0000117 "Gully Burns" xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Electrophysiology xsd:string [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 ! intra cellular electrophysiology recording property_value: IAO:0000111 "patch clamp assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Gully Burns" xsd:string property_value: IAO:0000119 ECO:0006012 xsd:string property_value: IAO:0000119 http://www.annualreviews.org/doi/pdf/10.1146/annurev.ph.46.030184.002323 xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Patch_clamp xsd:string [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 property_value: IAO:0000111 "whole-cell patch clamp assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Gully Burns" xsd:string property_value: IAO:0000119 ECO:0006015 xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Patch_clamp#Whole-cell_recording_or_whole-cell_patch xsd:string [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 property_value: IAO:0000111 "cell-attached patch clamp assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Gully Burns" xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Patch_clamp#Cell-attached_patch xsd:string [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 property_value: IAO:0000111 "inside-out patch clamp assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Gully Burns" xsd:string property_value: IAO:0000119 http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Patch_clamp#Inside-out_patch xsd:string [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 property_value: IAO:0000111 "outside-out patch clamp assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Gully Burns" xsd:string property_value: IAO:0000119 http://www.leica-microsystems.com/science-lab/the-patch-clamp-technique/ xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Patch_clamp#Outside-out_patch xsd:string [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." [] is_a: OBI:0000454 ! extracellular electrophysiology recording property_value: IAO:0000111 "electroencephalography" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Gully Burns" xsd:string property_value: IAO:0000118 "EEG" xsd:string [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 is_a: OBI:0001977 ! cytometry assay property_value: IAO:0000111 "single-unit recording" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "Can be used on any cell, not just neurons." xsd:string property_value: IAO:0000117 "Gully Burns" xsd:string property_value: IAO:0000119 http://www.thieme.com/media/samples/pubid-80418214.pdf xsd:string [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 property_value: IAO:0000111 "local field potential recording" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Gully Burns" xsd:string property_value: IAO:0000119 doi:10.1007/978-1-4614-7320-6_723-1 xsd:string [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 property_value: IAO:0000111 "histologic grade according to AJCC 7th edition" xsd:string property_value: IAO:0000112 " G4: Undifferentiated" xsd:string property_value: IAO:0000112 "G1:Well differentiated " xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "histologic grade according to the Fuhrman Nuclear Grading System" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "Histologic Grade (Fuhrman Nuclear Grading System)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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 property_value: IAO:0000111 "histologic grade for ovarian tumor" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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 property_value: IAO:0000111 "histologic grade for ovarian tumor according to a two-tier grading system" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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 property_value: IAO:0000111 "histologic grade for ovarian tumor according to the World Health Organization" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic primary tumor stage for colon and rectum according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pT: Pathologic spread colorectal primary tumor (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic primary tumor stage for lung according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pT: Pathologic spread lung primary tumor (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic primary tumor stage for kidney according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pT: Pathologic spread kidney primary tumor (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic primary tumor stage for ovary according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pT: Pathologic spread ovarian primary tumor (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic lymph node stage for colon and rectum according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic lymph node stage for lung according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pN: Pathologic spread colon lymph nodes (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic lymph node stage for kidney according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pN: Pathologic spread kidney lymph nodes (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic lymph node stage for ovary according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "pN: Pathologic spread ovarian lymph nodes (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic distant metastases stage for colon according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "M: colon distant metastases (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic distant metastases stage for lung according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "M: lung distant metastases (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic distant metastases stage for kidney according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "M: kidney distant Metastases (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "pathologic distant metastases stage for ovary according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "M: ovarian distant metastases (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "clinical tumor stage group according to AJCC 7th edition" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "Clinical tumor stage group (AJCC 7th Edition)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "International Federation of Gynecology and Obstetrics cervical cancer stage value specification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "Clinical FIGO stage" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "International Federation of Gynecology and Obstetrics ovarian cancer stage value specification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "Pathologic Tumor Stage Grouping for ovarian cancer (FIGO)" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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)." [] is_a: OBI:0001930 ! categorical value specification property_value: IAO:0000111 "performance status value specification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "Performance Status Scale" xsd:string property_value: IAO:0000119 https://en.wikipedia.org/wiki/Performance_status xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0002356 ! performance status value specification property_value: IAO:0000111 "Eastern Cooperative Oncology Group score value specification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "ECOG score" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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." [] is_a: OBI:0002356 ! performance status value specification property_value: IAO:0000111 "Karnofsky score vaue specification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris Stoeckert, Helena Ellis" xsd:string property_value: IAO:0000118 "Karnofsky Score" xsd:string property_value: IAO:0000119 "NCI BBRB, OBI" xsd:string property_value: IAO:0000234 "NCI BBRB" xsd:string [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 relationship: OBI:0000293 PR:000023089 ! has_specified_input DNA ligase relationship: OBI:0000417 OBI:0001398 ! achieves_planned_objective protein and DNA interaction identification objective property_value: IAO:0000111 "nuclear ligation assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris S" xsd:string property_value: IAO:0000119 "PMID: 8327891" xsd:string [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." [] is_a: OBI:0002438 ! nuclear ligation assay relationship: OBI:0000417 OBI:0001917 ! achieves_planned_objective chromosome conformation identification objective property_value: IAO:0000111 "chromosome conformation capture assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris S" xsd:string property_value: IAO:0000118 "3C assay" xsd:string property_value: IAO:0000119 http://www.nature.com/nprot/journal/v2/n7/full/nprot.2007.243.html xsd:string property_value: IAO:0000119 PMID:11847345 xsd:string [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 property_value: IAO:0000111 "Hi-C assay" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Chris S" xsd:string property_value: IAO:0000119 PMID:20461051 xsd:string [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 relationship: RO:0000081 BFO:0000040 ! role of material entity property_value: IAO:0000111 "measurand role" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Alan Ruttenberg, Jie Zheng" xsd:string property_value: IAO:0000119 https://en.wiktionary.org/wiki/measurand xsd:string property_value: IAO:0000233 https://github.com/obi-ontology/obi/issues/778 xsd:string [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." [] is_a: OBI:0000253 ! artificially induced nucleic acid hybridization property_value: IAO:0000111 "suppression subtractive hybridization" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Rebecca Tauber" xsd:string property_value: IAO:0000118 "SSH" xsd:string property_value: IAO:0000118 "subtractive hybridization" xsd:string property_value: IAO:0000119 PMID:14970460 xsd:string [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." [] is_a: OBI:0000253 ! artificially induced nucleic acid hybridization property_value: IAO:0000111 "differential screening hybridization" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Rebecca Tauber" xsd:string property_value: IAO:0000118 "differential screening" xsd:string property_value: IAO:0000118 "DSH" xsd:string property_value: IAO:0000119 PMID:25472628 xsd:string [Term] id: OBI:0002516 name: brain specimen def: "A specimen that is derived from brain." [] is_a: OBI:0001479 ! specimen from organism property_value: IAO:0000111 "brain specimen" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Chris Stoeckert" xsd:string property_value: IAO:0000119 "Chris Stoeckert, NCI BBRB " xsd:string [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 property_value: IAO:0000111 "Epstein Barr virus transformed B cell" xsd:string property_value: IAO:0000112 "PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Susanna Sansone" xsd:string property_value: IAO:0000119 "GROUP: OBI Biomaterial Branch" xsd:string [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 union_of: NCBITaxon:10239 ! Viruses union_of: NCBITaxon:2 ! Bacteria union_of: NCBITaxon:2157 ! Archaea union_of: NCBITaxon:2759 ! Eukaryota property_value: IAO:0000111 "organism" xsd:string property_value: IAO:0000112 "animal" xsd:string property_value: IAO:0000112 "fungus" xsd:string property_value: IAO:0000112 "plant" xsd:string property_value: IAO:0000112 "virus" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms')" xsd:string property_value: IAO:0000116 "13-02-2009:\nOBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus.\nThis issue is outside the scope of OBI." xsd:string property_value: IAO:0000117 "GROUP: OBI Biomaterial Branch" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Organism" xsd:string [Term] id: OBI:0100051 name: specimen def: "A material entity that has the specimen role." [] is_a: BFO:0000040 ! material entity intersection_of: BFO:0000040 ! material entity intersection_of: RO:0000087 OBI:0000112 ! has role specimen role property_value: IAO:0000111 "specimen" xsd:string property_value: IAO:0000112 "Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation." xsd:string property_value: IAO:0000117 "PERSON: James Malone" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "GROUP: OBI Biomaterial Branch" xsd:string [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. is_a: OBI:0000047 ! processed material relationship: OBI:0000312 OBI:0600024 ! is_specified_output_of maintaining cell culture relationship: OBI:0000643 CL:0000010 ! has grain cultured cell relationship: OBI:0000643 CL:0000010 ! has grain cultured cell property_value: IAO:0000111 "cultured cell population" xsd:string property_value: IAO:0000112 "A cultured cell population applied in an experiment: \"293 cells expressing TrkA were serum-starved for 18 hours and then neurotrophins were added for 10 min before cell harvest.\" (Lee, Ramee, et al. \"Regulation of cell survival by secreted proneurotrophins.\" Science 294.5548 (2001): 1945-1948).\n\nA cultured cell population maintained in vitro: \"Rat cortical neurons from 15 day embryos are grown in dissociated cell culture and maintained in vitro for 8–12 weeks\" (Dichter, Marc A. \"Rat cortical neurons in cell culture: culture methods, cell morphology, electrophysiology, and synapse formation.\" Brain Research 149.2 (1978): 279-293)." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "2013-6-5 MHB: This OBI class was formerly called 'cell culture', but label changed and definition updated following CLO alignment efforts in spring 2013, during which the intent of this class was clarified to refer to portions of a culture or line rather than a complete cell culture or line." xsd:string property_value: IAO:0000117 "PERSON:Matthew Brush" xsd:string property_value: IAO:0000118 "cell culture sample" xsd:string property_value: IAO:0000119 "PERSON:Matthew Brush" xsd:string [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 relationship: RO:0001000 UBERON:0000465 ! derives from material anatomical entity property_value: IAO:0000111 "organ section" xsd:string property_value: IAO:0000112 "A liver slice used in a perfusion experiment.\nThyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Helen Parkinson" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "GROUP: CEBS" xsd:string property_value: IAO:0000119 "GROUP: OBI Biomaterial Branch" xsd:string [Term] id: OBI:0200000 name: data transformation def: "A planned process that produces output data from input data." [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 IAO:0000027 ! has_specified_input data item relationship: OBI:0000293 IAO:0000027 ! has_specified_input data item relationship: OBI:0000299 IAO:0000027 ! has_specified_output data item relationship: OBI:0000299 IAO:0000027 ! has_specified_output data item property_value: IAO:0000111 "data transformation" xsd:string property_value: IAO:0000112 "The application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "Helen Parkinson" xsd:string property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000117 "Richard Scheuermann" xsd:string property_value: IAO:0000117 "Ryan Brinkman" xsd:string property_value: IAO:0000117 "Tina Hernandez-Boussard" xsd:string property_value: IAO:0000118 "data analysis" xsd:string property_value: IAO:0000118 "data processing" xsd:string property_value: IAO:0000119 "Branch editors" xsd:string [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 property_value: IAO:0000111 "differential expression analysis objective" xsd:string property_value: IAO:0000112 "Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string [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 relationship: OBI:0000417 OBI:0200188 ! achieves_planned_objective cross validation objective property_value: IAO:0000111 "leave one out cross validation method" xsd:string property_value: IAO:0000112 "The authors conducted leave-one-out cross validation to estimate the strength and accuracy of the differentially expressed filtered genes. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/3/368" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893049&group_id=177891&atid=886178" xsd:string property_value: IAO:0000117 "Person:Helen Parkinson" xsd:string [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: OBI:0200171 ! partitioning data transformation is_a: OBI:0200175 ! class discovery data transformation relationship: OBI:0000299 OBI:0000648 ! has_specified_output clustered data set relationship: OBI:0000417 OBI:0200172 ! achieves_planned_objective partitioning objective relationship: OBI:0000417 OBI:0200178 ! achieves_planned_objective class discovery objective property_value: IAO:0000111 "k-means clustering" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/K-means" xsd:string [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: OBI:0200175 ! class discovery data transformation relationship: OBI:0000299 OBI:0000648 ! has_specified_output clustered data set relationship: OBI:0000417 OBI:0200178 ! achieves_planned_objective class discovery objective property_value: IAO:0000111 "hierarchical clustering" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering" xsd:string [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." [] is_a: OBI:0200175 ! class discovery data transformation relationship: OBI:0000299 OBI:0000648 ! has_specified_output clustered data set relationship: OBI:0000417 OBI:0200178 ! achieves_planned_objective class discovery objective property_value: IAO:0000111 "dimensionality reduction" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "data projection" xsd:string property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string property_value: IAO:0000119 "PERSON: Melanie Courtot" xsd:string [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." [] is_a: OBI:0200050 ! dimensionality reduction property_value: IAO:0000111 "principal components analysis dimensionality reduction" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "pca data reduction" xsd:string property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string property_value: IAO:0000119 "PERSON: Melanie Courtot" xsd:string [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 property_value: IAO:0000111 "mass spectrometry analysis" xsd:string property_value: IAO:0000114 IAO:0000123 [Term] id: OBI:0200111 name: data visualization def: "An planned process that creates images, diagrams or animations from the input data." [] is_a: OBI:0000011 ! planned process relationship: OBI:0000293 IAO:0000027 ! has_specified_input data item relationship: OBI:0000293 IAO:0000027 ! has_specified_input data item property_value: IAO:0000111 "data visualization" xsd:string property_value: IAO:0000112 "Generation of a heatmap from a microarray dataset" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000117 "Tina Boussard" xsd:string property_value: IAO:0000118 "data encoding as image" xsd:string property_value: IAO:0000118 "visualization" xsd:string property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string property_value: IAO:0000119 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000119 "PERSON: Tina Boussard" xsd:string property_value: IAO:0000232 "Possible future hierarchy might include this:\ninformation_encoding\n>data_encoding\n>>image_encoding" xsd:string [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 property_value: IAO:0000111 "data transformation objective" xsd:string property_value: IAO:0000112 "normalize objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "Modified definition in 2013 Philly OBI workshop" xsd:string property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [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 property_value: IAO:0000111 "partitioning data transformation" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [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 property_value: IAO:0000111 "partitioning objective" xsd:string property_value: IAO:0000112 "A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Elisabetta Manduchi" xsd:string property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string [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." [] is_a: OBI:0200000 ! data transformation property_value: IAO:0000111 "class discovery data transformation" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "clustering data transformation" xsd:string property_value: IAO:0000118 "unsupervised classification data transformation" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [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." [] is_a: OBI:0200166 ! data transformation objective property_value: IAO:0000111 "class discovery objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "clustering objective" xsd:string property_value: IAO:0000118 "discriminant analysis objective" xsd:string property_value: IAO:0000118 "unsupervised classification objective" xsd:string property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [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." [] is_a: OBI:0200166 ! data transformation objective property_value: IAO:0000111 "class prediction objective" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "classification objective" xsd:string property_value: IAO:0000118 "supervised classification objective" xsd:string property_value: IAO:0000119 "PERSON: Elisabetta Manduchi" xsd:string property_value: IAO:0000119 "PERSON: James Malone" xsd:string [Term] id: OBI:0200188 name: cross validation objective def: "A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis." [] is_a: OBI:0200172 ! partitioning objective property_value: IAO:0000111 "cross validation objective" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "James Malone" xsd:string property_value: IAO:0000118 "rotation estimation objective" xsd:string property_value: IAO:0000119 "WEB: http://en.wikipedia.org/wiki/Cross_validation" xsd:string [Term] id: OBI:0200190 name: clustered data visualization def: "A data visualization which has input of a clustered data set and produces an output of a report graph which is capable of rendering data of this type." [] is_a: OBI:0200111 ! data visualization relationship: OBI:0000293 OBI:0000648 ! has_specified_input clustered data set property_value: IAO:0000111 "clustered data visualization" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "James Malone" xsd:string [Term] id: OBI:0200197 name: spectrum analysis objective def: "is a data transformation objective where the aim is to analyse some aspect of spectral data by some data transformation process. " [] is_a: OBI:0200166 ! data transformation objective property_value: IAO:0000111 "spectrum analysis objective" xsd:string property_value: IAO:0000112 "Calculation of characteristic path length in mass spectrometry" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Tina Boussard" xsd:string property_value: IAO:0000117 "Person:Helen Parkinson" xsd:string [Term] id: OBI:0302716 name: pool of specimens def: "A pool of specimens is a mixture of a population of samples which have been gathered from one or more sample populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish." [] is_a: OBI:0000953 ! processed specimen property_value: IAO:0000111 "pool of specimens" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish" xsd:string property_value: IAO:0000117 "PERSON: Jennifer Fostel" xsd:string property_value: IAO:0000119 "GROUP: CEBS" xsd:string [Term] id: OBI:0302729 name: chemical solution def: "A material entity that is made up of at least 2 scattered molecular aggregates, one playing the role of solvent and the other one playing the role of solute." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000111 "chemical solution" xsd:string property_value: IAO:0000112 "PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "liquid chemical solution" xsd:string property_value: IAO:0000119 "GROUP: OBI Biomaterial Branch" xsd:string [Term] id: OBI:0302732 name: solvent role def: "solvent role is a role which inheres in a molecular entity capable of ensuring the dissolution of another chemical entity and realized by the process of solvation" [] is_a: BFO:0000023 ! role relationship: BFO:0000054 OBI:0000685 ! realized in creating a mixture of molecules in solution relationship: RO:0000052 CHEBI:23367 ! inheres in molecular entity property_value: IAO:0000111 "solvent role" xsd:string property_value: IAO:0000112 "PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation)" xsd:string [Term] id: OBI:0302733 name: solute role def: "solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution" [] is_a: BFO:0000023 ! role relationship: BFO:0000054 OBI:0000685 ! realized in creating a mixture of molecules in solution relationship: RO:0000052 CHEBI:23367 ! inheres in molecular entity property_value: IAO:0000111 "solute role" xsd:string property_value: IAO:0000112 "PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "adapted from wikipedia (http://en.wikipedia.org/wiki/Solute)" xsd:string [Term] id: OBI:0302736 name: comet assay def: "a comet assay is an assay which utilizes gel electrophoresis on cell exposed to a challenge with the objective to assess DNA damage (DNA breakage) by determining the size and shape of DNA migration in cell placed in an electric field in specific conditions." [] is_a: OBI:0000070 ! assay relationship: OBI:0000293 CL:0000000 ! has_specified_input cell relationship: OBI:0000293 OBI:0000439 ! has_specified_input agarose gel relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective relationship: RO:0000057 OBI:0400140 ! has participant gel tank relationship: RO:0000057 OBI:0400142 ! has participant power supply property_value: IAO:0000111 "comet assay" xsd:string property_value: IAO:0000112 "PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "SCGE assay" xsd:string property_value: IAO:0000118 "single cell gel electrophoresis assay" xsd:string property_value: IAO:0000119 "PMID:7686265 .Mutat Res. 1993 Jul;288(1):47-63.The single cell gel electrophoresis assay (comet assay): a European review." xsd:string [Term] id: OBI:0302859 name: genetically modified organism def: "an organism that is the output of a genetic transformation process" [] is_a: OBI:0001151 ! genetically modified material is_a: OBI:0100026 ! organism intersection_of: OBI:0100026 ! organism intersection_of: OBI:0000312 OBI:0600043 ! is_specified_output_of genetic transformation property_value: IAO:0000111 "genetically modified organism" xsd:string property_value: IAO:0000112 "A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis.\nNat Protoc. 2008;3(10):1550-8. PMID: 18802436" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "OBI Biomaterial" xsd:string [Term] id: OBI:0302876 name: dissolved material entity def: "A material entity that has been going through a process of being put into solution" [] is_a: OBI:0000576 ! scattered molecular aggregate property_value: IAO:0000111 "dissolved material entity" xsd:string property_value: IAO:0000112 "Salt molecules that have been mixed into water" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Person:Bjoern Peters" xsd:string property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string [Term] id: OBI:0302884 name: extraction def: "A material separation in which a desired component of an input material is separated from the remainder" [] is_a: OBI:0600014 ! material component separation relationship: OBI:0000417 OBI:0000681 ! achieves_planned_objective separation into different composition objective property_value: IAO:0000111 "extraction" xsd:string property_value: IAO:0000112 "nucleic acid extraction using phenol chloroform" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000116 "Current the output of material processing defined as the molecular entity, main component in the output material entity, rather than the material entity that have grain molecular entity. \n'nucleic acid extract' is the output of 'nucleic acid extraction' and has grain 'nucleic acid'. However, the output of 'nucleic acid extraction' is 'nucleic acid' rather than 'nucleic acid extract'. We are aware of this issue and will work it out in the future." xsd:string property_value: IAO:0000117 "Person:Bjoern Peters" xsd:string property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string [Term] id: OBI:0302887 name: staining def: "Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound." [] is_a: OBI:0000094 ! material processing relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "staining" xsd:string property_value: IAO:0000112 "PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining" xsd:string [Term] id: OBI:0302890 name: polymerization def: "polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. polymerization results in molecular entity of high molecular weight" [] is_a: OBI:0000094 ! material processing relationship: OBI:0000293 CHEBI:23367 ! has_specified_input molecular entity relationship: OBI:0000299 CHEBI:33839 ! has_specified_output macromolecule relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "polymerization" xsd:string property_value: IAO:0000112 "PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "PRS:22102008: need to import catalyst from CHEBI 35223" xsd:string property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "OBI-Branch" xsd:string [Term] id: OBI:0302892 name: enzymatic ligation def: "An enzymatic ligation is a planned process in which molecules are joined by covalent bonds through the action of an material entity with a ligase activity" [] is_a: OBI:0000094 ! material processing relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "enzymatic ligation" xsd:string property_value: IAO:0000112 "PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "OBI-Branch" xsd:string [Term] id: OBI:0302903 name: nucleic acid hybridization def: "a planned process by which totally or partially complementary, single-stranded nucleic acids are combined into a single molecule called heteroduplex or homoduplex to an extent depending on the amount of complementarity." [] is_a: OBI:0000094 ! material processing property_value: IAO:0000111 "nucleic acid hybridization" xsd:string property_value: IAO:0000112 "PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]" xsd:string property_value: OBI:0001847 "hybridization assay" xsd:string [Term] id: OBI:0302905 name: elution def: "the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions)" [] is_a: OBI:0000094 ! material processing relationship: OBI:0000299 OBI:0000318 ! has_specified_output eluate relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective relationship: RO:0000057 OBI:0000038 ! has participant chromatography column property_value: IAO:0000111 "elution" xsd:string property_value: IAO:0000112 "PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "wordnet.princeton.edu/perl/webwn" xsd:string [Term] id: OBI:0400008 name: flow cytometer analyzer def: "An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for analysis." [] is_a: OBI:0400044 ! flow cytometer relationship: has_part OBI:0400043 ! flow cell relationship: has_part OBI:0400065 ! light source relationship: has_part OBI:0400079 ! optical filter relationship: has_part OBI:0400082 ! photodetector relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "flow cytometer analyzer" xsd:string property_value: IAO:0000112 "FACS Calibur, Luminex 100" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "John Quinn" xsd:string property_value: IAO:0000119 http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm xsd:string [Term] id: OBI:0400043 name: flow cell def: "Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell." [] is_a: OBI:0000967 ! container relationship: RO:0000085 OBI:0000370 ! has function contain function property_value: IAO:0000111 "flow cell" xsd:string property_value: IAO:0000112 "Biofilm Flow Cell" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Person:John Quinn" xsd:string property_value: IAO:0000118 "flow_cell" xsd:string property_value: IAO:0000119 http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm xsd:string [Term] id: OBI:0400044 name: flow cytometer def: "A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium." [] is_a: OBI:0400137 ! cytometer relationship: has_part OBI:0400043 ! flow cell relationship: has_part OBI:0400065 ! light source relationship: has_part OBI:0400078 ! obscuration bar relationship: has_part OBI:0400079 ! optical filter relationship: has_part OBI:0400082 ! photodetector relationship: has_part OBI:0400153 ! droplet sorter property_value: IAO:0000111 "flow cytometer" xsd:string property_value: IAO:0000112 "FACS Calibur" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "John Quinn" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Flow_cytometer xsd:string [Term] id: OBI:0400065 name: light source def: "A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiber optics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interrogation point. The light source in a flow cytometer is usually a laser." [] is_a: OBI:0001032 ! light emission device relationship: RO:0000085 OBI:0000367 ! has function light emission function property_value: IAO:0000111 "light source" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Elizabeth M. Goralczyk" xsd:string property_value: IAO:0000117 "John Quinn" xsd:string property_value: IAO:0000117 "Olga Tchuvatkina" xsd:string property_value: IAO:0000119 "Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253" xsd:string [Term] id: OBI:0400078 name: obscuration bar def: "An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device." [] is_a: OBI:0000932 ! material separation device relationship: RO:0000085 OBI:0000378 ! has function filter function property_value: IAO:0000111 "obscuration bar" xsd:string property_value: IAO:0000112 "obscuration bar in a flow cytometer" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000119 "Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249" xsd:string property_value: IAO:0000119 "John Quinn" xsd:string [Term] id: OBI:0400079 name: optical filter def: "An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length." [] is_a: OBI:0000932 ! material separation device relationship: RO:0000085 OBI:0000378 ! has function filter function property_value: IAO:0000111 "optical filter" xsd:string property_value: IAO:0000112 "720 LP filter, 580/30 BP filter" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "John Quinn" xsd:string property_value: IAO:0000119 http://en.wikipedia.org/wiki/Optical_filter xsd:string [Term] id: OBI:0400082 name: photodetector def: "A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on impact with a cell (for example), or the flourescence emitted by excitation of a fluorescent dye." [] is_a: OBI:0000832 ! measurement device relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "photodetector" xsd:string property_value: IAO:0000112 "A photomultiplier tube, a photo diode" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "John Quinn" xsd:string property_value: IAO:0000119 http://einstein.stanford.edu/content/glossary/glossary.html xsd:string [Term] id: OBI:0400103 name: DNA sequencer def: "A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences." [] is_a: OBI:0000832 ! measurement device relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "DNA sequencer" xsd:string property_value: IAO:0000112 "ABI 377 DNA Sequencer, ABI 310 DNA Sequencer" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Trish Whetzel" xsd:string property_value: IAO:0000119 "MO" xsd:string [Term] id: OBI:0400104 name: array scanner def: "An processed material which acquires images of fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip" [] is_a: OBI:0000398 ! image creation device relationship: RO:0000085 OBI:0000397 ! has function image acquisition function relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "array scanner" xsd:string property_value: IAO:0000112 "GenePix 4200A, GenePix4000B" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Trish Whetzel" xsd:string property_value: IAO:0000119 "GROUP: MGED Ontology" xsd:string [Term] id: OBI:0400110 name: hybridization chamber def: "A device which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide." [] is_a: OBI:0002089 ! physical store relationship: RO:0000085 OBI:0000370 ! has function contain function relationship: RO:0000085 OBI:0000401 ! has function environment control function property_value: IAO:0000111 "hybridization chamber" xsd:string property_value: IAO:0000112 "Glass Array Hybridization Cassette" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Trish Whetzel" xsd:string property_value: IAO:0000119 "MO_563 hybridization_chamber" xsd:string [Term] id: OBI:0400111 name: hybridization station def: "A device which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature." [] is_a: OBI:0002089 ! physical store intersection_of: OBI:0000968 ! device intersection_of: has_part OBI:0400110 ! hybridization chamber intersection_of: RO:0000085 OBI:0000401 ! has function environment control function property_value: IAO:0000111 "hybridization station" xsd:string property_value: IAO:0000112 "Labnet Problot12" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Trish Whetzel" xsd:string property_value: IAO:0000119 "MO_497 hybridization station" xsd:string [Term] id: OBI:0400114 name: sonicator def: "A device that converts a variable electrical current to mechanical vibration of a metallic probe. The device is used for the lysis of cells, the mixing of compounds or solutions, to framgent molecules of DNA, or to create emulsions." [] is_a: OBI:0001033 ! perturbation device relationship: RO:0000085 OBI:0000377 ! has function perturb function property_value: IAO:0000111 "sonicator" xsd:string property_value: IAO:0000112 "Sonicator 3000" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Trish Whetzel" xsd:string property_value: IAO:0000119 "MO" xsd:string [Term] id: OBI:0400115 name: spectrophotometer def: "A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance." [] is_a: OBI:0000832 ! measurement device relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "spectrophotometer" xsd:string property_value: IAO:0000112 "Helios Gamma Spectrophotometer" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000117 "Trish Whetzel" xsd:string property_value: IAO:0000119 "MO" xsd:string [Term] id: OBI:0400116 name: thermal cycler def: "An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time." [] is_a: OBI:0002089 ! physical store relationship: RO:0000085 OBI:0000370 ! has function contain function relationship: RO:0000085 OBI:0000401 ! has function environment control function property_value: IAO:0000111 "thermal cycler" xsd:string property_value: IAO:0000112 "Piko(tm) 96-well Thermal Cycler" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000117 "Trish Whetzel" xsd:string property_value: IAO:0000118 "DNA_amplifier" xsd:string property_value: IAO:0000118 "PCR_machine" xsd:string property_value: IAO:0000118 "Polymerase_Chain_Reaction_ machine" xsd:string property_value: IAO:0000118 "thermocycler" xsd:string property_value: IAO:0000119 "MO" xsd:string [Term] id: OBI:0400137 name: cytometer def: "A cytometer is an instrument for counting and measuring cells." [] is_a: OBI:0000832 ! measurement device relationship: has_part OBI:0400065 ! light source relationship: has_part OBI:0400079 ! optical filter relationship: has_part OBI:0400082 ! photodetector relationship: RO:0000085 OBI:0000453 ! has function measure function property_value: IAO:0000111 "cytometer" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Melanie Courtot" xsd:string property_value: IAO:0000119 http://medical.merriam-webster.com/medical/cytometer xsd:string [Term] id: OBI:0400140 name: gel tank def: "a device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules." [] is_a: OBI:0002089 ! physical store relationship: RO:0000085 OBI:0000370 ! has function contain function relationship: RO:0000085 OBI:0000401 ! has function environment control function property_value: IAO:0000111 "gel tank" xsd:string property_value: IAO:0000112 "CHEF gel box, slab gel box, capillary electrophoresis" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Person:Frank Gibson" xsd:string property_value: IAO:0000117 "Person:Kevin Clancy" xsd:string property_value: IAO:0000118 "electrophoresis box" xsd:string property_value: IAO:0000118 "electrophoresis unit" xsd:string property_value: IAO:0000119 sep:00095 xsd:string [Term] id: OBI:0400142 name: power supply def: "A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time." [] is_a: OBI:0000968 ! device relationship: RO:0000085 OBI:0000384 ! has function electricity supply function property_value: IAO:0000111 "power supply" xsd:string property_value: IAO:0000112 "A AC/DC transformer that generates the reqired power for an electrophoresis apparatus" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000117 "Frank Gibson" xsd:string property_value: IAO:0000118 "electrical power supply" xsd:string property_value: IAO:0000118 "power pack" xsd:string property_value: IAO:0000118 "power supply unit" xsd:string property_value: IAO:0000118 "PSU" xsd:string property_value: IAO:0000119 "PERSON: Daniel Schober" xsd:string property_value: IAO:0000119 sep:00093 xsd:string property_value: IAO:0000232 "was power_pack, maps to SEP electrical_power_supply" xsd:string [Term] id: OBI:0400147 name: microarray def: "A processed material that is made to be used in an analyte assay. It consists of a physical immobilisation matrix in which substances that bind the analyte are placed in regular spatial position." [] is_a: OBI:0001865 ! assay array property_value: IAO:0000111 "microarray" xsd:string property_value: IAO:0000112 "An affymetrix U133 array is a microarray. Microarrays include 1 and 2-color arrays, custom and commercial arrays (e.g, Affymetrix, Agilent, Nimblegen, Illumina, etc.) for expression profiling, DNA variant detection, protein binding, and other genomic and functional genomic assays." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000119 "PERSON: Chris Stoeckert" xsd:string [Term] id: OBI:0400148 name: DNA microarray def: "A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample." [] is_a: OBI:0400147 ! microarray property_value: IAO:0000111 "DNA microarray" xsd:string property_value: IAO:0000112 "Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). \"Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis\". Microbiology 150: 3363-3382. doi:10.1099/mic.0.27221-0. PMID 15470115" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Daniel Schober" xsd:string property_value: IAO:0000117 "PERSON: Frank Gibson" xsd:string property_value: IAO:0000118 "DNA Chip" xsd:string property_value: IAO:0000118 "DNA-array" xsd:string property_value: IAO:0000119 Web:@2008/03/03 xsd:string [Term] id: OBI:0400149 name: protein microarray def: "A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions." [] is_a: OBI:0400147 ! microarray property_value: IAO:0000111 "protein microarray" xsd:string property_value: IAO:0000112 "The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Daniel Schober" xsd:string property_value: IAO:0000119 "PERSON: Daniel Schober" xsd:string [Term] id: OBI:0400153 name: droplet sorter def: "A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original\nsample for particles of interest based on qualities determined by gating) or disposal." [] is_a: OBI:0000932 ! material separation device relationship: RO:0000085 OBI:0000403 ! has function sort function property_value: IAO:0000111 "droplet sorter" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "OBI Instrument branch" xsd:string property_value: IAO:0000119 "OBI Instrument branch" xsd:string [Term] id: OBI:0400168 name: microtome def: "A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand." [] is_a: OBI:0000932 ! material separation device relationship: RO:0000085 OBI:0000372 ! has function material separation function relationship: RO:0000085 OBI:0000379 ! has function mechanical function property_value: IAO:0000111 "microtome" xsd:string property_value: IAO:0000112 "PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON: Phillippe Rocca-Serra" xsd:string property_value: IAO:0000119 "PERSON: Daniel Schober" xsd:string [Term] id: OBI:0400169 name: microscope def: "A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)" [] is_a: OBI:0000398 ! image creation device relationship: RO:0000085 OBI:0000369 ! has function magnify function relationship: RO:0000085 OBI:0000397 ! has function image acquisition function property_value: IAO:0000111 "microscope" xsd:string property_value: IAO:0000112 "PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "PERSON: Phillippe Rocca-Serra" xsd:string property_value: IAO:0000119 "wikipedia" xsd:string [Term] id: OBI:0500000 name: study design def: "A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution." [] is_a: IAO:0000104 ! plan specification relationship: has_part OBI:0000272 ! protocol property_value: IAO:0000111 "study design" xsd:string property_value: IAO:0000112 "a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available." xsd:string property_value: IAO:0000117 "PERSON: Chris Stoeckert" xsd:string property_value: IAO:0000118 "experimental design" xsd:string property_value: IAO:0000232 "rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol." xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl [Term] id: OBI:0500001 name: clinical study design def: "Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach]" [] is_a: OBI:0500000 ! study design property_value: IAO:0000111 "clinical study design" xsd:string property_value: IAO:0000112 "PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "The definition needs to be extended to other things than simply patients" xsd:string property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "Clinical Research Glossary Version 4.0 CDICS glossary group" xsd:string [Term] id: OBI:0500010 name: reference design def: "A reference experiment design type is where all samples are compared to a common reference." [] is_a: OBI:0500000 ! study design property_value: IAO:0000111 "reference design" xsd:string property_value: IAO:0000112 "PMID: 12933549" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "Philippe Rocca-Serra on behalf of MO" xsd:string property_value: IAO:0000119 "MO_699" xsd:string [Term] id: OBI:0600000 name: adding substance to cell culture def: "is process in which a material substance is added to a cell culture" [] is_a: OBI:0000274 ! adding a material entity into a target relationship: OBI:0000293 OBI:0100060 ! has_specified_input cultured cell population relationship: OBI:0000299 OBI:0100060 ! has_specified_output cultured cell population relationship: OBI:0000417 OBI:0000434 ! achieves_planned_objective adding material objective property_value: IAO:0000111 "adding substance to cell culture" xsd:string property_value: IAO:0000112 "adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "renamed from 'administering substance to cell culture', to reflect that administration is commonly used only for organisms" xsd:string property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:0600005 name: collecting specimen from organism def: "a process with the objective to obtain a material entity that was part of an organism for potential future use in an investigation" [] is_a: OBI:0000659 ! specimen collection process relationship: OBI:0000293 OBI:0100026 ! has_specified_input organism relationship: OBI:0000299 OBI:0100051 ! has_specified_output specimen relationship: OBI:0000417 OBI:0000684 ! achieves_planned_objective specimen collection objective property_value: IAO:0000111 "collecting specimen from organism" xsd:string property_value: IAO:0000112 "taking a sputum sample from a cancer patient, taking the spleen from a killed mouse, collecting a urine sample from a patient" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:0600007 name: administering substance in vivo def: "A process by which a substance is intentionally given to an organism resulting in exposure of the organism to that substance." [] is_a: OBI:0000274 ! adding a material entity into a target relationship: OBI:0000293 OBI:0100026 ! has_specified_input organism relationship: OBI:0000299 OBI:0100026 ! has_specified_output organism relationship: OBI:0000417 OBI:0000434 ! achieves_planned_objective adding material objective property_value: IAO:0000111 "administering substance in vivo" xsd:string property_value: IAO:0000112 "Balb/c mice received an intracameral or subconjunctival injection of trinitrophenylated spleen cells" xsd:string property_value: IAO:0000112 "injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "2009-11-10. Tracker: https://sourceforge.net/tracker/?func=detail&aid=2893050&group_id=177891&atid=886178" xsd:string property_value: IAO:0000116 "Different routes and means of administration should go as children underneath this" xsd:string property_value: IAO:0000116 "needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor." xsd:string property_value: IAO:0000116 "Update the definition based on the discussion. Details see the tracker:\nhttps://sourceforge.net/p/obi/obi-terms/738/" xsd:string property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000117 "Person:Bjoern Peters" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:0600014 name: material component separation def: "a material processing in which components of an input material become segregated in space" [] is_a: OBI:0000094 ! material processing relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 BFO:0000040 ! has_specified_output material entity property_value: IAO:0000111 "material component separation" xsd:string property_value: IAO:0000112 "Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor, or purification" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Bjoern Peters" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:0600017 name: detection of molecular label def: "an assay that detects the presence or a quality of a molecular label which is a proxy for the detection of the molecular target to which the label is attached" [] is_a: OBI:0000070 ! assay relationship: BFO:0000055 REO:0000171 ! realizes molecular label role relationship: OBI:0000293 OBI:0001936 ! has_specified_input molecular-labeled material relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective property_value: IAO:0000111 "detection of molecular label" xsd:string property_value: IAO:0000112 "Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Matthew Brush" xsd:string property_value: IAO:0000119 "OBI developer call, 3-12-12" xsd:string [Term] id: OBI:0600020 name: histology assay def: "the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement" [] is_a: OBI:0000070 ! assay relationship: has_part OBI:0000185 ! imaging assay relationship: has_part OBI:0000341 ! histological sample preparation relationship: has_part OBI:0302887 ! staining relationship: has_part OBI:0600005 ! collecting specimen from organism relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective property_value: IAO:0000111 "histology" xsd:string property_value: IAO:0000112 "the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney" xsd:string property_value: IAO:0000118 "histopathology" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: IAO:0000232 "need to incorporate parts\\n---\\nThis is a very vague term, it should be in the same place as transcriptomics, proteomics metaboloimcs. It is the 'study' of tissues, not the process of studying tissues\\n" xsd:string property_value: IAO:0000232 "PRS:20090901: addition of alternative term = histopathology" xsd:string [Term] id: OBI:0600024 name: maintaining cell culture def: "a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing" [] is_a: OBI:0000838 ! material maintenance relationship: OBI:0000293 OBI:0100060 ! has_specified_input cultured cell population relationship: OBI:0000299 OBI:0100060 ! has_specified_output cultured cell population relationship: OBI:0000417 OBI:0000806 ! achieves_planned_objective material maintenance objective property_value: IAO:0000111 "maintaining cell culture" xsd:string property_value: IAO:0000112 "When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [Term] id: OBI:0600025 name: substance detection def: "any protocol which results in the detection of a specified substance" [] is_a: OBI:0000070 ! assay relationship: OBI:0000293 BFO:0000040 ! has_specified_input material entity relationship: OBI:0000299 IAO:0000109 ! has_specified_output measurement datum relationship: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective property_value: IAO:0000111 "substance detection" xsd:string property_value: IAO:0000112 "the detection of phycoerytherin by means of flow cytometry" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Kevin Clancy" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 relationship: OBI:0000293 CHEBI:33697 ! has_specified_input ribonucleic acid relationship: OBI:0000293 OBI:0000419 ! has_specified_input reverse transcriptase relationship: OBI:0000299 CHEBI:16991 ! has_specified_output deoxyribonucleic acid relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "artificially induced reverse transcription" xsd:string property_value: IAO:0000112 "The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "It could also be added that the reverse transcriptase is bearer of a GO:0003964 RNA-directed DNA polymerase activity, which is realized in this process." xsd:string property_value: IAO:0000116 "We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope" xsd:string property_value: IAO:0000117 "PERSON:Kevin Clancy" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 relationship: OBI:0000293 CL:0000000 ! has_specified_input cell relationship: OBI:0000299 CL:0000000 ! has_specified_output cell relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "cell permeabilization" xsd:string property_value: IAO:0000112 "Electroporation of HeLa cells to allow transfection with pUC19." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "need to add output cell has_quality permeable" xsd:string property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: IAO:0000232 "definition blessed by Jay, Alan, Randi" xsd:string [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 relationship: OBI:0000293 CL:0000000 ! has_specified_input cell relationship: OBI:0000293 OBI:0000079 ! has_specified_input culture medium relationship: OBI:0000299 OBI:0100060 ! has_specified_output cultured cell population relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "'establishing cell culture'" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Matthew Brush" xsd:string property_value: IAO:0000119 "PERSON:Matthew Brush" xsd:string [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" [] is_a: OBI:0000094 ! material processing relationship: OBI:0000293 OBI:1110109 ! has_specified_input target of material addition relationship: OBI:0000293 REO:0000280 ! has_specified_input molecular label relationship: OBI:0000299 OBI:0001936 ! has_specified_output molecular-labeled material relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "addition of molecular label" xsd:string property_value: IAO:0000112 "The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Matthew Brush" xsd:string property_value: IAO:0000118 "labeling" xsd:string property_value: IAO:0000119 "OBI developer call, 3-12-12" xsd:string [Term] id: OBI:0600043 name: genetic transformation def: "the introduction. alteration or integration of genetic material into a cell or organism" [] is_a: OBI:0000094 ! material processing relationship: OBI:0000299 OBI:0001151 ! has_specified_output genetically modified material relationship: OBI:0000417 OBI:0001153 ! achieves_planned_objective genetic transformation objective property_value: IAO:0000111 "genetic transformation" xsd:string property_value: IAO:0000112 "The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON:Kevin Clancy" xsd:string property_value: IAO:0000118 "genetic modification" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 intersection_of: OBI:0000070 ! assay intersection_of: OBI:0000299 OBI:0001155 ! has_specified_output 3D structural organization datum property_value: IAO:0000111 "3D structure determination assay" xsd:string property_value: IAO:0000112 "The use of X-ray crystallography to determine the 3D coordinates of atoms in a protein." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 relationship: OBI:0000299 OBI:0000318 ! has_specified_output eluate relationship: OBI:0000417 OBI:0000681 ! achieves_planned_objective separation into different composition objective relationship: RO:0000057 OBI:0000038 ! has participant chromatography column relationship: RO:0000057 OBI:0000048 ! has participant chromatography device property_value: IAO:0000111 "preparative chromatography" xsd:string property_value: IAO:0000112 "The use of gas chromatography in order separate out from an input sample of eggs a fraction that would be enriched for pesticides." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Kevin Clancy; Bjoern Peters" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [Term] id: OBI:0600047 name: sequencing assay def: "the use of a chemical or biochemical means to infer the sequence of a biomaterial" [] is_a: OBI:0000070 ! assay intersection_of: OBI:0000299 OBI:0000973 ! has_specified_output sequence data intersection_of: OBI:0000417 OBI:0000441 ! achieves_planned_objective assay objective property_value: IAO:0000111 "sequencing assay" xsd:string property_value: IAO:0000112 "The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "has_output should be sequence of input; we don't have sequence well defined yet" xsd:string property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [Term] id: OBI:0600050 name: specific enzymatic cleavage def: "a protocol application to digest the fraction of input material that is susceptible to that enzyme" [] is_a: OBI:0000231 ! enzymatic cleavage property_value: IAO:0000111 "specific enzymatic cleavage" xsd:string property_value: IAO:0000112 "The use of a protease to digest a protein into peptides" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Kevin Clancy" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 relationship: OBI:0000417 OBI:0000681 ! achieves_planned_objective separation into different composition objective property_value: IAO:0000111 "gradient separation" xsd:string property_value: IAO:0000112 "the use of a sucrose gradient to isolate mitochondria" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Kevin Clancy" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 relationship: OBI:0000417 OBI:0000681 ! achieves_planned_objective separation into different composition objective relationship: RO:0000057 OBI:0400140 ! has participant gel tank relationship: RO:0000057 OBI:0400142 ! has participant power supply property_value: IAO:0000111 "electrophoresis" xsd:string property_value: IAO:0000112 "Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Kevin Clancy" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: IAO:0000232 "Need to define more terms like gel_separation, matrix,centrifugation, and the connection between the force used to separate materials and the medium or barriers." xsd:string [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 relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "selection by survival" xsd:string property_value: IAO:0000112 "The insertion of a gene for antibiotic resistance into a cell population and subsequent growth in the presence of the antibiotic to select for those cells which were successfully transfected" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Kevin Clancy" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [Term] id: OBI:0600055 name: DNA cleavage, restriction analysis def: "the use of enzymes to cut DNA molecules, the study of DNA through cleavage, mapping, and analysis of the fragments" [] is_a: OBI:0000231 ! enzymatic cleavage relationship: OBI:0000293 CHEBI:33697 ! has_specified_input ribonucleic acid property_value: IAO:0000111 "DNA cleavage, restriction analysis" xsd:string property_value: IAO:0000112 "the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON:Kevin Clancy" xsd:string property_value: IAO:0000118 "restriction enzyme assay" xsd:string property_value: IAO:0000119 "the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components" xsd:string [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 relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "enzymatic amplification" xsd:string property_value: IAO:0000112 "the use of a polymerase chain reaction to amplify a fragment of DNA" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PERSON:Kevin Clancy" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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" [] is_a: OBI:0000094 ! material processing relationship: BFO:0000055 OBI:0000411 ! realizes cloning vector role relationship: OBI:0000293 OBI:0000737 ! has_specified_input cloning vector relationship: OBI:0000299 OBI:0000731 ! has_specified_output recombinant vector relationship: OBI:0000417 OBI:0000456 ! achieves_planned_objective material transformation objective property_value: IAO:0000111 "recombinant vector cloning" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "pa_branch (Alan, Randi, Kevin, Jay, Bjoern)" xsd:string property_value: IAO:0000118 "molecular cloning" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string [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 relationship: OBI:0000299 CHEBI:33697 ! has_specified_output ribonucleic acid property_value: IAO:0000111 "RNA extraction" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: IAO:0000232 "requested by Helen Parkinson for MO" xsd:string [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 relationship: OBI:0000299 CHEBI:33696 ! has_specified_output nucleic acid property_value: IAO:0000111 "nucleic acid extraction" xsd:string property_value: IAO:0000112 "Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet." xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000117 "PlanAndPlannedProcess Branch" xsd:string property_value: IAO:0000119 "OBI branch derived" xsd:string property_value: IAO:0000232 "requested by Helen Parkinson for MO. Could be defined class" xsd:string [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." [] is_a: OBI:0000731 ! recombinant vector relationship: OBI:0000312 OBI:0600064 ! is_specified_output_of recombinant vector cloning relationship: OBI:0000643 OBI:0000731 ! has grain recombinant vector property_value: IAO:0000111 "phage display library" xsd:string property_value: IAO:0000112 "PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000118 "display library" xsd:string property_value: IAO:0000119 "WEB: http://www.immuneepitope.org/home.do" xsd:string property_value: IAO:0000232 "PRS: 22022008. class moved under population,\nmodification of definition and replacement of biomaterials in previous definition with 'material'\naddition of has_role restriction" xsd:string [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 relationship: OBI:0000312 OBI:0600043 ! is_specified_output_of genetic transformation property_value: IAO:0000111 "transgenic organism" xsd:string property_value: IAO:0000112 "HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein\nPossible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "PRS:22-02-2008: is a organism which has output_role during genetic modification of type (KO) protocol-application" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 GROUP:IEDB xsd:string [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 relationship: BFO:0000055 OBI:1110093 ! realizes disposition to infect an organism relationship: RO:0000057 IDO:0000586 ! has participant infection property_value: IAO:0000111 "infection process" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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:0043234 ! protein complex union_of: GO:0019815 ! B cell receptor complex union_of: GO:0042101 ! T cell receptor complex union_of: GO:0042571 ! immunoglobulin complex, circulating property_value: IAO:0000111 "adaptive immune receptor" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 property_value: IAO:0000111 "experimental infection of cell culture" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:1110034 name: antigen def: "is a material entity that has the antigen role" [] is_a: BFO:0000040 ! material entity property_value: IAO:0000111 "antigen" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 relationship: BFO:0000054 OBI:1110021 ! realized in infection process property_value: IAO:0000111 "disposition to infect an organism" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:1110108 name: material to be added def: "a material that is added to another one in a material combination process" [] is_a: BFO:0000040 ! material entity property_value: IAO:0000111 "material to be added" xsd:string property_value: IAO:0000112 "A mixture of peptides that is being added into a cell culture." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "10/26/09: This defined class is used as a 'macro expression' to reduce the size of the IEDB export" xsd:string property_value: IAO:0000116 "2010/02/24 Alan Ruttenberg: I think this might generate confusion as the common use of the term would consider something to be a specimen during the realization of the role, not only if it bears it. However having this class as a probe, or for display, or as a macro might be useful. Ideally we would mark or segregate such classes" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:1110109 name: target of material addition def: "A material entity into which another is being added in a material combinatino process" [] is_a: BFO:0000040 ! material entity property_value: IAO:0000111 "target of material addition" xsd:string property_value: IAO:0000112 "A cell culture into which a mixture of peptides is being added." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "10/26/09: This defined class is used as a 'macro' to reduce the size of the IEDB export." xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:1110120 name: assay antigen role def: "Any molecule recognized by the adaptive immune receptors? Recognized means bound with a certain affinity? From GO ag binding:Interacting selectively with 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. see OBI_1110120 below" [] is_a: BFO:0000023 ! role relationship: BFO:0000054 OBI:0000070 ! realized in assay property_value: IAO:0000111 "assay antigen role" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [Term] id: OBI:1110122 name: pathologic process def: "abnormal, harmful processes caused by or associated with a disease" [] is_a: GO:0008150 ! biological_process property_value: IAO:0000111 "pathologic process" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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 relationship: has_part OBI:0000201 ! radioactivity detection property_value: IAO:0000111 "chromium release assay" xsd:string property_value: IAO:0000112 "Autologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1. After a 4-h incubation of the effector cells with the target cells, supernatants were collected following brief centrifugation and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac). Percent specific killing was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PlanAndPlannedProcess Branch, IEDB" xsd:string property_value: IAO:0000119 "IEDB" xsd:string [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: BFO:0000016 ! disposition property_value: IAO:0000111 "fluorescence" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [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:0001237 ! quality of a single physical entity property_value: IAO:0000111 "behavioral quality" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [Term] id: PATO:0001237 name: quality of a single physical entity def: "A physical object quality which inheres in a single-bearer." [] is_a: BFO:0000019 ! quality property_value: IAO:0000111 "quality of a single physical entity" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [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:0001237 ! quality of a single physical entity property_value: IAO:0000111 "alive" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [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:0001237 ! quality of a single physical entity property_value: IAO:0000111 "dead" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [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: BFO:0000016 ! disposition property_value: IAO:0000111 "radioactive" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [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 property_value: IAO:0000111 "handedness" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [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 property_value: IAO:0000111 "left handedness" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [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 property_value: IAO:0000111 "right handedness" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [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 property_value: IAO:0000111 "ambidextrous handedness" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pato.owl [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." [] is_a: CHEBI:16670 ! peptide property_value: IAO:0000111 "protein" xsd:string property_value: IAO:0000112 "antithrombin III is a protein" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [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." [] is_a: OBI:0000427 ! enzyme is_a: PR:000000001 ! protein property_value: IAO:0000111 "DNA ligase" xsd:string property_value: IAO:0000116 "Definition defined by OBI developers: an enzyme that covalently joins two compatible pieces of DNA through the cleavage of an ATP molecule" xsd:string property_value: IAO:0000118 "ligase" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: PR:000025471 name: nuclease S1 def: "A protein that is a translation product of the Aspergillus oryzae nucS gene or a 1:1 ortholog thereof." [] is_a: PR:000000001 ! protein property_value: IAO:0000111 "nuclease S1" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/pr.owl [Term] id: REO:0000171 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." [] is_a: BFO:0000023 ! role property_value: IAO:0000111 "molecular label role" xsd:string property_value: IAO:0000116 "MHB (9-29-13): 'molecular label role' imported from the Reagent Ontology and replaced OBI:OBI_0000140 (label role)" xsd:string property_value: IAO:0000118 "molecular tracer role" xsd:string property_value: IAO:0000119 "OBI developer call, 3-12-12" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/reo.owl [Term] id: REO:0000280 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" [] is_a: CHEBI:23367 ! molecular entity intersection_of: CHEBI:23367 ! molecular entity intersection_of: RO:0000087 REO:0000171 ! has role molecular label role property_value: IAO:0000111 "molecular label" xsd:string property_value: IAO:0000118 "molecular tracer" xsd:string property_value: IAO:0000119 "OBI developer call, 3-12-12" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/reo.owl [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." [] is_a: BFO:0000031 ! generically dependent continuant property_value: IAO:0000111 "region" xsd:string property_value: IAO:0000118 "primary structure of sequence macromolecule" xsd:string property_value: IAO:0000118 "sequence" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/so.owl [Term] id: Subset is_a: IAO:0000102 ! data about an ontology part [Term] id: UBERON:0000178 name: blood def: "A fluid that is composed of blood plasma and erythrocytes." [] is_a: UBERON:0000463 ! organism substance property_value: IAO:0000111 "blood" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [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 property_value: IAO:0000111 "organism substance" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000465 name: material anatomical entity def: "Anatomical entity that has mass." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000111 "material anatomical entity" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0000477 name: anatomical cluster def: "Anatomical group that has its parts adjacent to one another." [] is_a: BFO:0000040 ! material entity property_value: IAO:0000111 "anatomical cluster" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [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 property_value: IAO:0000111 "tissue" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [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 property_value: IAO:0000111 "brain" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [Term] id: UBERON:0001088 name: urine def: "Excretion that is the output of a kidney" [] is_a: UBERON:0000463 ! organism substance property_value: IAO:0000111 "urine" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl [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 property_value: IAO:0000111 "length unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [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 property_value: IAO:0000111 "mass unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [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 property_value: IAO:0000111 "time unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000005 name: temperature unit def: "A unit which is a standard measure of the average kinetic energy of the particles in a sample of matter." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "temperature unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000006 name: substance unit def: "A unit which is a standardised quantity of an element or compound with uniform composition." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "substance unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000051 name: concentration unit def: "A unit which represents a standard measurement of how much of a given substance there is mixed with another substance." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "concentration unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000095 name: volume unit def: "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "volume unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000105 name: frequency unit def: "A unit which is a standard measure of the number of repetitive actions in a particular time." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "frequency unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000270 name: volumetric flow rate unit def: "A unit which is a standard measure of the volume of fluid which passes through a given surface per unit time ." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "volumetric flow rate unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: UO:0000280 name: rate unit def: "A unit which represents a standard measurement occurrence of a process per unit time." [] is_a: IAO:0000003 ! measurement unit label property_value: IAO:0000111 "rate unit" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/uo.owl [Term] id: http://purl.obolibrary.org/obo/ECO:000156 name: quantitative reverse transcription polymerase chain reaction evidence used in automatic assertion. def: "A type of quantitative reverse transcription polymerase chain reaction evidence used in automatic assertion." [] is_a: ECO:0007475 {is_inferred="true"} ! reverse transcription polymerase chain reaction evidence used in automatic assertion is_a: http://purl.obolibrary.org/obo/ECO:0001566 ! quantitative reverse transcription polymerase chain reaction evidence intersection_of: http://purl.obolibrary.org/obo/ECO:0001566 ! quantitative reverse transcription polymerase chain reaction evidence intersection_of: used_in ECO:0000203 ! automatic assertion created_by: jbmunro creation_date: 2018-07-07T12:00:00Z [Term] id: http://purl.obolibrary.org/obo/ECO:0001566 name: quantitative reverse transcription polymerase chain reaction evidence def: "A type of reverse transcription polymerase chain reaction evidence that combines reverse transcription polymerase chain reaction and real time polymerase chain reaction to quantitatively assay for the detection of RNA levels." [] synonym: "qRT-PCR evidence" EXACT [] synonym: "quantitative real-time RT-PCR evidence" EXACT [] synonym: "quantitative RT-PCR evidence" EXACT [] synonym: "real-time qRT-PCR evidence" EXACT [] synonym: "real-time quantitative reverse transcription PCR evidence" EXACT [] synonym: "real-time reverse transcription polymerase chain reaction evidence" EXACT [] synonym: "real-time RT-PCR evidence" EXACT [] synonym: "RRT-PCR evidence" EXACT [] synonym: "rRT-PCR evidence" EXACT [] synonym: "RT-qPCR evidence" EXACT [] is_a: ECO:0000109 ! reverse transcription polymerase chain reaction evidence created_by: jbmunro creation_date: 2018-07-07T12:00:00Z [Term] id: http://purl.obolibrary.org/obo/ECO:0001567 name: quantitative reverse transcription polymerase chain reaction evidence used in manual assertion def: "A type of quantitative reverse transcription polymerase chain reaction evidence used in manual assertion." [] is_a: ECO:0001808 {is_inferred="true"} ! reverse transcription polymerase chain reaction evidence used in manual assertion is_a: http://purl.obolibrary.org/obo/ECO:0001566 ! quantitative reverse transcription polymerase chain reaction evidence intersection_of: http://purl.obolibrary.org/obo/ECO:0001566 ! quantitative reverse transcription polymerase chain reaction evidence intersection_of: used_in ECO:0000218 ! manual assertion created_by: jbmunro creation_date: 2018-07-07T12:00:00Z [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 property_value: IAO:0000111 "realized in" xsd:string property_value: IAO:0000112 "this disease is realized in this disease course" xsd:string property_value: IAO:0000112 "this fragility is realized in this shattering" xsd:string property_value: IAO:0000112 "this investigator role is realized in this investigation" xsd:string property_value: IAO:0000118 "is realized by" xsd:string property_value: IAO:0000118 "realized_in" xsd:string property_value: IAO:0000600 "[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/bfo.owl 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 property_value: IAO:0000111 "realizes" xsd:string property_value: IAO:0000112 "this disease course realizes this disease" xsd:string property_value: IAO:0000112 "this investigation realizes this investigator role" xsd:string property_value: IAO:0000112 "this shattering realizes this fragility" xsd:string property_value: IAO:0000600 "to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])" xsd:string property_value: isDefinedBy http://purl.obolibrary.org/obo/iao.owl domain: BFO:0000015 ! process range: BFO:0000017 ! realizable entity [Typedef] id: BFO:0000062 name: preceded by property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:preceded_by xsd:string property_value: IAO:0000111 "preceded by" xsd:string property_value: IAO:0000116 "An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other." xsd:string property_value: IAO:0000118 "is preceded by" xsd:string property_value: IAO:0000118 "preceded_by" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_transitive: true inverse_of: BFO:0000063 ! precedes [Typedef] id: BFO:0000063 name: precedes property_value: IAO:0000111 "precedes" xsd:string domain: BFO:0000003 ! occurrent range: BFO:0000003 ! occurrent is_transitive: true is_a: RO:0002222 ! temporal relation [Typedef] id: IAO:0000039 name: has measurement unit label range: IAO:0000003 ! measurement unit label is_functional: true is_a: has_part ! has_part [Typedef] id: IAO:0000136 name: is about def: "is_about is a (currently) primitive relation that relates an information artifact to an entity." [] property_value: IAO:0000112 "This document is about information artifacts and their representations" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of \"mentions\" relation. Weaken the is_about relationship to be primitive. \n\nWe will try to build it back up by elaborating the various subproperties that are more precisely defined.\n\nSome currently missing phenomena that should be considered \"about\" are predications - \"The only person who knows the answer is sitting beside me\" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic." xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Smith, Ceusters, Ruttenberg, 2000 years of philosophy" xsd:string domain: IAO:0000030 ! information content entity [Typedef] id: IAO:0000219 name: denotes def: "denotes is 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" [] property_value: IAO:0000112 "A person's name denotes the person. A variable name in a computer program denotes some piece of memory. Lexically equivalent strings can denote different things, for instance \"Alan\" can denote different people. In each case of use, there is a case of the denotation relation obtaining, between \"Alan\" and the person that is being named." xsd:string property_value: IAO:0000116 "2009-11-10 Alan Ruttenberg. Old definition said the following to emphasize the generic nature of this relation. We no longer have 'specifically denotes', which would have been primitive, so make this relation primitive.\ng denotes r =def \nr is a portion of reality\nthere is some c that is a concretization of g \nevery c that is a concretization of g specifically denotes r" xsd:string property_value: IAO:0000117 "person:Alan Ruttenberg" xsd:string property_value: IAO:0000119 "Conversations with Barry Smith, Werner Ceusters, Bjoern Peters, Michel Dumontier, Melanie Courtot, James Malone, Bill Hogan" xsd:string is_a: IAO:0000136 ! is about [Typedef] id: IAO:0000413 name: is duration of def: "relates a process to a time-measurement-datum that represents the duration of the process" [] property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person:Alan Ruttenberg" xsd:string domain: IAO:0000416 ! time measurement datum range: BFO:0000015 ! process is_a: IAO:0000136 ! is about [Typedef] id: OBI:0000293 name: has_specified_input 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." [] property_value: IAO:0000111 "has_specified_input" xsd:string property_value: IAO:0000111 "has_specified_input" xsd:string property_value: IAO:0000112 "see is_input_of example_of_usage" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000116 "8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works." xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string property_value: IAO:0000117 "PERSON: Melanie Coutot" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant inverse_of: OBI:0000295 ! is_specified_input_of [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." [] property_value: IAO:0000111 "is_specified_input_of" xsd:string property_value: IAO:0000112 "some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [Typedef] id: OBI:0000299 name: has_specified_output 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." [] property_value: IAO:0000111 "has_specified_output" xsd:string property_value: IAO:0000111 "has_specified_output" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON: Bjoern Peters" xsd:string property_value: IAO:0000117 "PERSON: Larry Hunter" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl domain: OBI:0000011 ! planned process is_a: RO:0000057 ! has participant inverse_of: OBI:0000312 ! is_specified_output_of [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." [] property_value: IAO:0000111 "is_manufactured_by" xsd:string property_value: IAO:0000112 "http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000117 "Liju Fan" xsd:string property_value: IAO:0000118 "has_make" xsd:string property_value: IAO:0000118 "has_manufacturer" xsd:string domain: BFO:0000040 ! material entity [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." [] property_value: IAO:0000111 "is_specified_output_of" xsd:string property_value: IAO:0000111 "is_specified_output_of" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Alan Ruttenberg" xsd:string property_value: IAO:0000117 "PERSON:Bjoern Peters" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl range: OBI:0000011 ! planned process is_a: RO:0000056 ! participates in [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." [] property_value: IAO:0000111 "achieves_planned_objective" xsd:string property_value: IAO:0000112 "A cell sorting process achieves the objective specification 'material separation objective'" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "BP, AR, PPPB branch" xsd:string property_value: IAO:0000119 "PPPB branch derived" xsd:string property_value: IAO:0000232 "modified according to email thread from 1/23/09 in accordince with DT and PPPB branch" xsd:string domain: OBI:0000011 ! planned process range: IAO:0000005 ! objective specification inverse_of: OBI:0000833 ! objective_achieved_by [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." [] property_value: IAO:0000111 "has grain" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000116 "Discussion in Karslruhe with, among others, Alan Rector, Stefan Schulz, Marijke Keet, Melanie Courtot, and Alan Ruttenberg. Definition take from the definition of granular parthood in the cited paper. Needs work to put into standard form" xsd:string property_value: IAO:0000117 "PERSON: Alan Ruttenberg" xsd:string property_value: IAO:0000119 "PAPER: Granularity, scale and collectivity: When size does and does not matter, Alan Rector, Jeremy Rogers, Thomas Bittner, Journal of Biomedical Informatics 39 (2006) 333-349" xsd:string is_a: has_part ! has_part [Typedef] id: OBI:0000646 name: supplies def: "A relation between an organisation or person and a material entity 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." [] property_value: IAO:0000111 "supplies" xsd:string property_value: IAO:0000114 IAO:0000123 property_value: IAO:0000117 "GROUP: Relations branch" xsd:string 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." [] property_value: IAO:0000111 "has_supplier" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: Alan Rutternberg" xsd:string property_value: IAO:0000117 "PERSON: Cristian Cocos" xsd:string property_value: IAO:0000117 "PERSON: Frank Gibson" xsd:string property_value: IAO:0000117 "PERSON: Melanie Courtot" xsd:string domain: BFO:0000040 ! material entity [Typedef] id: OBI:0000833 name: objective_achieved_by def: "This relation obtains between a a objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process." [] property_value: IAO:0000111 "objective_achieved_by" xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "OBI" xsd:string property_value: IAO:0000119 "OBI" xsd:string domain: IAO:0000005 ! objective specification range: OBI:0000011 ! planned process [Typedef] id: OBI:0001938 name: has value specification def: "A relation between an information content entity and a value specification that specifies its value." [] property_value: IAO:0000111 "has value specification" xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "PERSON: James A. Overton" xsd:string property_value: IAO:0000119 "OBI" xsd:string domain: IAO:0000030 ! information content entity range: OBI:0001933 ! value specification is_a: has_part ! has_part [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" [] property_value: IAO:0000111 "inheres in" xsd:string property_value: IAO:0000112 "this fragility inheres in this vase" xsd:string property_value: IAO:0000112 "this red color inheres in this apple" xsd:string property_value: IAO:0000116 "A dependent inheres in its bearer at all times for which the dependent exists." xsd:string property_value: IAO:0000118 "inheres_in" xsd:string property_value: RO:0001900 RO:0001901 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" [] property_value: IAO:0000111 "bearer of" xsd:string property_value: IAO:0000112 "this apple is bearer of this red color" xsd:string property_value: IAO:0000112 "this vase is bearer of this fragility" xsd:string property_value: IAO:0000116 "A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist." xsd:string property_value: IAO:0000118 "bearer_of" xsd:string property_value: IAO:0000118 "is bearer of" xsd:string property_value: RO:0001900 RO:0001901 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" [] property_value: IAO:0000111 "participates in" xsd:string property_value: IAO:0000112 "this blood clot participates in this blood coagulation" xsd:string property_value: IAO:0000112 "this input material (or this output material) participates in this process" xsd:string property_value: IAO:0000112 "this investigator participates in this investigation" xsd:string property_value: IAO:0000118 "participates_in" xsd:string 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" [] property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:has_participant xsd:string property_value: IAO:0000111 "has participant" xsd:string property_value: IAO:0000112 "this blood coagulation has participant this blood clot" xsd:string property_value: IAO:0000112 "this investigation has participant this investigator" xsd:string property_value: IAO:0000112 "this process has participant this input material (or this output material)" xsd:string property_value: IAO:0000116 "Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time." xsd:string property_value: IAO:0000118 "has_participant" xsd:string 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." [] property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string 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." [] property_value: IAO:0000112 "A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant)." xsd:string property_value: IAO:0000112 "An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process)." xsd:string 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" [] property_value: IAO:0000112 "this catalysis function is a function of this enzyme" xsd:string property_value: IAO:0000116 "A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "function_of" xsd:string property_value: IAO:0000118 "is function of" xsd:string 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" [] property_value: IAO:0000112 "this red color is a quality of this apple" xsd:string property_value: IAO:0000116 "A quality inheres in its bearer at all times for which the quality exists." xsd:string property_value: IAO:0000118 "is quality of" xsd:string property_value: IAO:0000118 "quality_of" xsd:string 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" [] property_value: IAO:0000112 "this investigator role is a role of this person" xsd:string property_value: IAO:0000116 "A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "is role of" xsd:string property_value: IAO:0000118 "role_of" xsd:string 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" [] property_value: IAO:0000112 "this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)" xsd:string property_value: IAO:0000116 "A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists." xsd:string property_value: IAO:0000118 "has_function" xsd:string 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" [] property_value: IAO:0000112 "this apple has quality this red color" xsd:string property_value: IAO:0000116 "A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist." xsd:string property_value: IAO:0000118 "has_quality" xsd:string 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" [] property_value: IAO:0000112 "this person has role this investigator role (more colloquially: this person has this role of investigator)" xsd:string property_value: IAO:0000116 "A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists." xsd:string property_value: IAO:0000118 "has_role" xsd:string domain: BFO:0000004 ! independent continuant range: BFO:0000023 ! role is_a: RO:0000053 ! bearer of [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" [] property_value: IAO:0000111 "derives from" xsd:string property_value: IAO:0000112 "this cell derives from this parent cell (cell division)" xsd:string property_value: IAO:0000112 "this nucleus derives from this parent nucleus (nuclear division)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'." xsd:string property_value: IAO:0000118 "derives_from" xsd:string property_value: IAO:0000412 http://purl.obolibrary.org/obo/ro.owl 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" [] property_value: IAO:0000112 "this parent cell derives into this cell (cell division)" xsd:string property_value: IAO:0000112 "this parent nucleus derives into this nucleus (nuclear division)" xsd:string property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops into'. To avoid making statements about a future that may not come to pass, it is often better to use the backward-looking 'derives from' rather than the forward-looking 'derives into'." xsd:string property_value: IAO:0000118 "derives_into" xsd:string [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" [] property_value: IAO:0000111 "is location of" xsd:string property_value: IAO:0000112 "my head is the location of my brain" xsd:string property_value: IAO:0000112 "this cage is the location of this rat" xsd:string property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000118 "location_of" xsd:string property_value: RO:0001900 RO:0001901 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" [] property_value: http://purl.org/dc/elements/1.1/source http://www.obofoundry.org/ro/#OBO_REL:located_in xsd:string property_value: IAO:0000111 "located in" xsd:string property_value: IAO:0000112 "my brain is located in my head" xsd:string property_value: IAO:0000112 "this rat is located in this cage" xsd:string property_value: IAO:0000116 "Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus" xsd:string property_value: IAO:0000116 "Most location relations will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000118 "located_in" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true [Typedef] id: RO:0002087 name: immediately preceded by comment: X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "starts_at_end_of" xsd:string 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) property_value: IAO:0000117 "David Osumi-Sutherland" xsd:string property_value: IAO:0000118 "ends_at_start_of" xsd:string property_value: IAO:0000118 "meets" xsd:string is_a: BFO:0000063 ! precedes [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. property_value: IAO:0000114 IAO:0000125 property_value: IAO:0000116 "move to BFO?" xsd:string property_value: IAO:0000119 "Allen" xsd:string range: BFO:0000003 ! occurrent [Typedef] id: RO:0002350 name: member of def: "is member of is a mereological relation between a item and a collection." [] property_value: IAO:0000112 "An organism that is a member of a population of organisms" xsd:string property_value: IAO:0000118 "is member of" xsd:string property_value: IAO:0000118 "member part of" xsd:string property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 is_a: part_of ! 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." [] property_value: IAO:0000119 "SIO" xsd:string property_value: RO:0001900 RO:0001901 is_a: has_part ! has_part [Typedef] id: has_part name: has part name: has_part namespace: external def: "a core relation that holds between a whole and its part" [] xref: BFO:0000051 property_value: IAO:0000111 "has part" xsd:string property_value: IAO:0000112 "my body has part my brain (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)" xsd:string property_value: IAO:0000112 "this year has part this day (occurrent parthood)" xsd:string property_value: IAO:0000116 "Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part." xsd:string property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.)\n\nA continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'." xsd:string property_value: IAO:0000118 "has_part" xsd:string property_value: RO:0001900 RO:0001901 is_transitive: true [Typedef] id: negatively_regulates name: negatively regulates namespace: external xref: RO:0002212 is_a: regulates ! regulates transitive_over: part_of ! part of [Typedef] id: part_of name: part of namespace: external def: "a core relation that holds between a part and its whole" [] xref: BFO:0000050 property_value: IAO:0000111 "is part of" xsd:string property_value: IAO:0000112 "my brain is part of my body (continuant parthood, two material entities)" xsd:string property_value: IAO:0000112 "my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)" xsd:string property_value: IAO:0000112 "this day is part of this year (occurrent parthood)" xsd:string property_value: IAO:0000116 "Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other." xsd:string property_value: IAO:0000116 "Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime" xsd:string property_value: IAO:0000116 "Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.)\n\nA continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'." xsd:string property_value: IAO:0000118 "part_of" xsd:string property_value: RO:0001900 RO:0001901 property_value: seeAlso http://www.obofoundry.org/ro/#OBO_REL:part_of xsd:string is_transitive: true inverse_of: has_part ! has_part [Typedef] id: positively_regulates name: positively regulates namespace: external xref: RO:0002213 holds_over_chain: negatively_regulates negatively_regulates is_a: regulates ! regulates transitive_over: part_of ! part of [Typedef] id: regulates name: regulates namespace: external xref: RO:0002211 is_transitive: true transitive_over: part_of ! part of [Typedef] id: used_in name: used_in def: "A relation connecting a piece of evidence to an assertion method, where that assertion method is supported by the evidence." [GOC:cjm] comment: In the future we may use a more generic relation with weaker domain and range constraints taken from IAO, RO or OBI. xref: ECO:9000000 domain: ECO:0000000 ! evidence range: ECO:0000217 ! assertion method inverse_of: uses ! uses created_by: mchibucos creation_date: 2010-12-09T05:00:20Z [Typedef] id: uses name: uses xref: ECO:9000001