format-version: 1.2 data-version: releases/2018-04-06 date: 04:06:2018 22:02 saved-by: rctauber auto-generated-by: OBO-Edit 2.3.1 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/terms/license https://creativecommons.org/publicdomain/zero/1.0/ owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(ObjectProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n\n\n\n############################\n# Classes\n############################\n\n# Class: (entity)\n\nSubClassOf( owl:Thing)\n\n# Class: (transcript expression evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (expression microarray evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (cRNA to DNA expression microarray evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\n\n# Class: (cell growth regulation assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectUnionOf( ))))))\n\n# Class: (cDNA to DNA expression microarray evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\n\n# Class: (DNA to cDNA expression microarray evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\n\n# Class: (northern blot evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (reverse transcription polymerase chain reaction transcription evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (differential hybridization evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))))))\n\n# Class: (subtractive hybridization evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))))))\n\n# Class: (RNA-seq evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (cap analysis of gene expression evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (nano-cap analysis of gene expression evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (competitive growth assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectIntersectionOf(ObjectSomeValuesFrom( ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( )) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) ObjectSomeValuesFrom( )))\n\n# Class: (3D cell culture evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: ([3H]arachidonic acid release assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: ([3H]-thymidine incorporation assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (51Cr release assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (alamarBlue assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (annexin-V staining evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (Boyden chamber assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (caspase assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (cell counting evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (cell permeability assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (cytochrome C release assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (DNA laddering assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (motility wound healing assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (MTS assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (MTT assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (nuclear fragmentation evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (nucleotide analog incorporation assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (WST-1 assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (cell growth assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectUnionOf( )) ObjectSomeValuesFrom( ObjectUnionOf( ))))\n\n# Class: (cell staining evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (cell viability assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (cell proliferation assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (DNA synthesis cell proliferation assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (ATP bioluminescence assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (cytotoxicity assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (chemotaxis assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (apoptotic assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (cross-streak test evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (disk diffusion test evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (tethered cell assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (capillary assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (biofilm formation assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (microtiter plate biofilm assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (air-liquid interface assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (colony biofilm assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (Kadouri drip-fed biofilm assay evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (plaque assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (flow cell biofilm assay evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( )))))\n\n# Class: (zone of inhibition evidence)\n\nEquivalentClasses( ObjectIntersectionOf(ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( ))))))\n\n# Class: (Etest evidence)\n\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ))))\nSubClassOf( ObjectSomeValuesFrom( ObjectIntersectionOf( ObjectSomeValuesFrom( ObjectSomeValuesFrom( )))))\n\n# Class: (cellular_component)\n\nSubClassOf( owl:Thing)\n\n# Class: (biological_process)\n\nSubClassOf( owl:Thing)\n\n# Class: (secondary structure of RNA molecule)\n\nAnnotationAssertion( \"\"^^xsd:string)\n\n\nAnnotationAssertion( \"ECO:0007087\"^^xsd:string)\n) [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 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 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: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 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: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: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 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: 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 [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 [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: ECO:0000000 ! evidence intersection_of: IAO:0000136 GO:0008150 ! biological_process intersection_of: 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 [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 [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 [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 [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 [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] is_a: ECO:0000073 ! experimental genomic evidence [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: traceable author statement def: "A type of author statement that is based on a cited reference." [ECO:MCC, GO:TAS] comment: The traceable author statement (TAS) evidence code covers author statements that are attributed to a cited source. Typically this type of information comes from review articles. Material from the introductions and discussion sections of non-review papers may also be suitable if another reference is cited as the source of experimental work or analysis. When annotating with this code the curator should use caution and be aware that authors often cite papers dealing with experiments that were performed in organisms different from the one being discussed in the paper at hand. Thus a problem with the TAS code is that it may turn out from following up the references in the paper that no experiments were performed on the gene in the organism actually being characterized in the primary paper. For this reason we recommend (when time and resources allow) that curators track down the cited paper and annotate directly from the experimental paper using the appropriate experimental evidence code. When this is not possible and it is necessary to annotate from reviews, the TAS code is the appropriate code to use for statements that are associated with a cited reference. Once an annotation has been made to a given term using an experimental evidence code, we recommend removing any annotations made to the same term using the TAS evidence code. is_a: ECO:0000204 ! author statement disjoint_from: ECO:0000034 ! non-traceable author statement [Term] id: ECO:0000034 name: non-traceable author statement def: "A type of author statement that is not associated with results presented or a cited reference." [ECO:SN] comment: The non-traceable author statement evidence code should be used in all cases where the author makes a statement that a curator wants to capture but for which there are neither results presented nor a specific reference cited in the source used to make the annotation. The source of the information may be peer reviewed papers, textbooks, database records or vouchered specimens. 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 [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 [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 [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 ! 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 nucleic acid hybridization evidence where methylation-sensitive restriction enzymes are utilized to analyze methylated DNA fragments by hybridizing them to a CpG island microarray." [PMID:18987809] synonym: "CpG island microarray evidence" EXACT [] is_a: ECO:0000026 ! nucleic acid hybridization evidence [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] synonym: "inferred from genomic analysis" EXACT [] is_a: ECO:0000006 ! experimental evidence [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 polymerase chain reaction 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] synonym: "methylation-specific PCR evidence" EXACT [] is_a: ECO:0000082 ! polymerase chain reaction evidence [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 [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 [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] synonym: "PCR evidence" EXACT [] is_a: ECO:0000073 ! experimental genomic evidence [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: intermethylated site amplification evidence def: "A type of experimental genomic 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 methylated sequences." [PMID:18987810, url:https\://www.ncbi.nlm.nih.gov/probe/docs/techpcr/] is_a: ECO:0000073 ! experimental genomic evidence [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 [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 experimental genomic 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:0000073 ! experimental genomic 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_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 ! 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 ! 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/] synonym: "IDA: in situ hybridization" RELATED [] is_a: ECO:0000026 ! nucleic acid hybridization evidence [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 ! 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 property_value: IAO:0000234 "CollecTF" xsd:string [Term] id: ECO:0000108 name: reverse transcription polymerase chain reaction transcription evidence def: "A type of transcript expression evidence in which expression levels are determined through RT-PCR (quantitative or otherwise)." [TAIR:TED] synonym: "IEP: transcript levels (e.g. RT-PCR)" RELATED [] synonym: "RT-PCR transcription evidence" EXACT [] is_a: ECO:0000009 ! transcript expression evidence is_a: ECO:0000109 ! reverse transcription polymerase chain reaction evidence [Term] id: ECO:0000109 name: reverse transcription polymerase chain reaction evidence def: "A type of polymerase chain reaction evidence where RNA is reverse transcribed into cDNA and amplified for product measurement in real time for transcription analysis i.e. qPCR." [ECO:SW, PMID:11013345, PMID:12901609] comment: The starting product for PCR, and therefore amplification volume, is directly correlated to the transcription rate. synonym: "qRT-PCR" EXACT [PMID:12901609] synonym: "RT-PCR evidence" EXACT [] is_a: ECO:0000082 ! polymerase chain reaction evidence 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 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 [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 [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 protein assay evidence where sub-cellular localization of a protein within a cell is determined." [GO:0008104, url:http\://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019937] is_a: ECO:0000039 ! protein assay 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 [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 [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 [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 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 [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 [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 [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 [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 [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 [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 [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 ! traceable author statement union_of: ECO:0000034 ! non-traceable author statement 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 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 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 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 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 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 polymerase chain reaction evidence where the reaction product is quantified in real-time across cycles by means of fluorescent dyes 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.\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). synonym: "Q-PCR evidence" EXACT [] synonym: "qRT-PCR evidence" RELATED [] synonym: "quantitative PCR evidence" EXACT [] synonym: "real-time PCR evidence" EXACT [] synonym: "real-time polymerase chain reaction evidence" EXACT [] is_a: ECO:0000082 ! polymerase chain reaction evidence property_value: IAO:0000234 "CollecTF" xsd:string created_by: mchibucos creation_date: 2010-11-16T05:57:20Z [Term] id: ECO:0000232 name: chromosome conformation capture-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, and DNA processing and quantitation." [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 [] is_a: ECO:0000073 ! experimental genomic evidence created_by: mchibucos creation_date: 2010-11-17T12:27:14Z [Term] id: ECO:0000233 name: chromosome conformation capture evidence def: "A type of chromosome conformation capture-based evidence that is derived by performing a type of 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 [] is_a: ECO:0000232 ! chromosome conformation capture-based evidence created_by: mchibucos creation_date: 2010-11-17T12:46:15Z [Term] id: ECO:0000234 name: circularized chromosome conformation capture evidence def: "A type of chromosome conformation capture-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] 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: "4C" EXACT [] synonym: "chromosome conformation capture on chip" EXACT [] synonym: "circularized 3C" EXACT [] is_a: ECO:0000232 ! chromosome conformation capture-based evidence created_by: mchibucos creation_date: 2010-11-19T01:20:28Z [Term] id: ECO:0000235 name: carbon-copy chromosome conformation capture evidence def: "A type of chromosome conformation capture-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 [] is_a: ECO:0000232 ! chromosome conformation capture-based evidence 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] synonym: "3C" BROAD [] synonym: "3C-PCR" EXACT [] is_a: ECO:0000233 ! chromosome conformation capture evidence created_by: mchibucos creation_date: 2010-11-19T03:00:47Z [Term] id: ECO:0000237 name: chromosome conformation capture-qPCR evidence def: "A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step." [ECO:MCC] synonym: "3C-qPCR" EXACT [] synonym: "3C-quantitative PCR" EXACT [] synonym: "3C-real-time PCR" EXACT [] is_a: ECO:0000233 ! chromosome conformation capture 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 capture-based evidence that is derived by performing immunoprecipitation enrichment of ligated fragments events prior to product quantitation." [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 capture-based evidence created_by: mchibucos creation_date: 2010-11-19T04:24:03Z [Term] id: ECO:0000239 name: chromosome conformation capture sequencing evidence def: "A type of chromosome conformation capture-based evidence that is derived by inverse polymerase chain reaction (inverse PCR) on a circularized 3C library prior to product quantitation with high-throughput (HT) sequencing." [ECO:MCC] 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: "3C-seq" EXACT [] synonym: "4C sequencing" EXACT [] synonym: "4C-seq" EXACT [] synonym: "circularized 3C sequencing" EXACT [] synonym: "circularized 3C-seq" EXACT [] is_a: ECO:0000232 ! chromosome conformation capture-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 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 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:0000269 {is_inferred="true"} ! experimental 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 created_by: mchibucos creation_date: 2011-01-11T12:54:50Z [Term] id: ECO:0000296 name: green fluorescent protein transcript localization evidence def: "A type of transcriptional activation assay evidence that is based on transcriptional activation of a green fluorescent protein (GFP) reporter gene." [ECO:MCC, ECO:RCT] comment: This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of green fluorescent protein". synonym: "localization of GFP transcript" EXACT [] is_a: ECO:0000170 ! transcriptional activation assay created_by: mchibucos creation_date: 2011-01-11T02:31:19Z [Term] id: ECO:0000297 name: LacZ transcript localization evidence def: "A type of transcriptional activation assay evidence that is based on transcriptional activation of a LacZ reporter gene." [ECO:MCC] comment: This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of LacZ protein". is_a: ECO:0000170 ! transcriptional activation assay created_by: mchibucos creation_date: 2011-01-11T02:53:19Z [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 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: non-traceable author statement used in manual assertion def: "A type of non-traceable author statement that is used in a manual assertion." [ECO:MCC] synonym: "NAS" EXACT [GOECO:NAS] synonym: "non-traceable author statement" EXACT [GOECO:NAS] xref: GOECO:NAS "non-traceable author statement" is_a: ECO:0000034 ! non-traceable author statement is_a: ECO:0000302 {is_inferred="true"} ! author statement used in manual assertion intersection_of: ECO:0000034 ! non-traceable author statement 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: traceable author statement used in manual assertion def: "A type of traceable author statement that is used in a manual assertion." [ECO:MCC] synonym: "TAS" EXACT [GOECO:TAS] synonym: "traceable author statement" EXACT [GOECO:TAS] xref: GOECO:TAS "traceable author statement" is_a: ECO:0000033 ! traceable author statement is_a: ECO:0000302 {is_inferred="true"} ! author statement used in manual assertion intersection_of: ECO:0000033 ! traceable author statement 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 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 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:0000269 {is_inferred="true"} ! experimental 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:0000269 {is_inferred="true"} ! experimental 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 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 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 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 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 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 ! 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: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 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 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 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 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: IAO:0000136 GO:0008283 ! 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: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 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 ! 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 ! 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 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 ! 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 ! 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 ! 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 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 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 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 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 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 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 ! 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: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 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 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 expression pattern 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:0000098 ! in situ hybridization evidence 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 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 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 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 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 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 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 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 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 ! cell proliferation relationship: OBI:0000312 OBI:0000892 ! is_specified_output_of Southern blot analysis 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 ! cell proliferation relationship: OBI:0000312 OBI:0000893 ! is_specified_output_of real time polymerase chain reaction 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 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 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 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 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 ! DNA synthesis involved in DNA replication relationship: OBI:0000312 OBI:0000895 ! is_specified_output_of total RNA extract 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 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 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 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 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 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 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 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 ! cell proliferation relationship: OBI:0000312 OBI:0000894 ! is_specified_output_of protein extract 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 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001009 ! allograft transplantation experiment evidence 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001012 ! behavioral assay evidence 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001032 ! constitutively active mutant evidence 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001038 ! deletion mutation evidence 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001042 ! dominant-negative mutant evidence 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: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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001103 ! natural variation mutant evidence 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001113 ! point mutation evidence 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001128 ! syngeneic transplantation experiment evidence 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001137 ! xenotransplantation experiment evidence 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:0000269 {is_inferred="true"} ! experimental 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: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 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 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 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 [] 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 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] synonym: "qRT-PCR evidence" BROAD [] synonym: "RT-PCR evidence" BROAD [] 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 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 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 [] 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 polymerase chain reaction evidence where a mRNA primer is used for RT-PCR and terminal deoxynucleotidyl transferase (TdT) is used to add identical nucleotides to the 3' end of the cDNA after which PCR with a different primer and TdT-oligomer are performed in the other sense to obtain the full length sequence of a RNA transcript." [ECO:SW, PMID:17498297] comment: RACE PCR is frequently used to verify transcription start sites relevant to the function of transcription factor binding sites such as repression. synonym: "RACE PCR" EXACT [PMI:17498297] is_a: ECO:0000082 ! polymerase chain reaction 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 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 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 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 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: premethylation 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" RELATED [] 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 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 ! 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 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 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 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 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 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 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 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 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 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 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 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 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0005529 ! random mutagenesis evidence 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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:0006935 ! 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 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:0006935 ! 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001801 ! alkaline phosphatase reporter gene assay evidence 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 [] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001802 ! beta-galactosidase reporter gene assay evidence 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001803 ! chloramphenicol acetyltransferase reporter gene assay evidence 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:0000501 {is_inferred="true"} ! 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:0000501 {is_inferred="true"} ! evidence used in automatic assertion is_a: ECO:0001806 ! chromatin immunoprecipitation- exonuclease evidence 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:0000501 {is_inferred="true"} ! 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:0000501 {is_inferred="true"} ! evidence used in automatic assertion is_a: ECO:0001824 ! DNA adenine methyltransferase identification evidence 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:0000501 {is_inferred="true"} ! 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001829 ! ferric uptake regulator titration assay evidence 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:0000501 {is_inferred="true"} ! evidence used in automatic assertion is_a: ECO:0001812 ! genomic systematic evolution of ligands by exponential amplification evidence 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 [] is_a: ECO:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001816 ! green fluorescent protein reporter gene assay evidence 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 [] is_a: ECO:0000501 {is_inferred="true"} ! evidence used in automatic assertion is_a: ECO:0001816 ! green fluorescent protein reporter gene assay evidence 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:0000501 {is_inferred="true"} ! 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001804 ! beta-glucuronidase reporter gene assay evidence 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:0000501 {is_inferred="true"} ! evidence used in automatic assertion is_a: ECO:0005520 ! interferometric reflectance imaging sensor evidence 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0001805 ! luciferase reporter gene assay evidence 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:0000501 {is_inferred="true"} ! evidence used in automatic 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: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: premethylation interference footprinting evidence used in manual assertion def: "A type of premethylation interference footprinting evidence that is used in a manual assertion." [ECO:SN] synonym: "methylation interference footprinting" RELATED [] is_a: ECO:0001827 ! premethylation interference footprinting evidence is_a: ECO:0006083 {is_inferred="true"} ! nucleic acid binding evidence used in manual assertion intersection_of: ECO:0001827 ! premethylation 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] synonym: "Q-PCR evidence" BROAD [] synonym: "quantitative PCR evidence" BROAD [] synonym: "real-time PCR evidence" BROAD [] synonym: "real-time polymerase chain reaction evidence" BROAD [] 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0005528 ! site-directed mutagenesis evidence 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:0000501 {is_inferred="true"} ! evidence used in automatic assertion is_a: ECO:0001823 ! x-ray crystallography evidence 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0005537 ! xylE reporter gene assay evidence 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0005673 ! ad-hoc qualitative phenotype observation evidence 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0005675 ! ad-hoc quantitative phenotype observation evidence 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 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 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: traceable 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 [] is_a: ECO:0000033 ! traceable author statement created_by: rctauber creation_date: 2016-11-30T09:44:47Z [Term] id: ECO:0006017 name: traceable author statement from published clinical study used in manual assertion def: "A type of traceable 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:0000304 {is_inferred="true"} ! traceable author statement used in manual assertion is_a: ECO:0006016 ! traceable author statement from published clinical study intersection_of: ECO:0006016 ! traceable 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 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 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 ! 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 ! 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 ! 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0006032 ! optogenetic evidence 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 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 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 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 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0006053 ! pharmacological assay evidence 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:0000269 {is_inferred="true"} ! experimental 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 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:0000501 {is_inferred="true"} ! 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 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: "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 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 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0007075 ! phenomic profiling assay evidence 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:0000269 {is_inferred="true"} ! experimental evidence used in manual assertion is_a: ECO:0007077 ! colony morphology evidence 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 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:0005605 {is_inferred="true"} ! disk diffusion test evidence relationship: IAO:0000136 GO:0046677 ! 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: 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] subset: gosubset_prok 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 [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 subset: gosubset_prok synonym: "necrosis" RELATED [] is_a: GO:0008150 ! biological_process [Term] id: GO:0005575 name: cellular_component namespace: cellular_component alt_id: GO:0008372 def: "The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together." [GOC:go_curators, 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. Note that 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 ND, no data, 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 subset: gosubset_prok 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 [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 subset: gosubset_prok 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 subset: gosubset_prok 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 subset: gosubset_prok 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: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] subset: gosubset_prok 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 [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 [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 subset: gosubset_prok 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 subset: gosubset_prok 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 subset: gosubset_prok 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 subset: gosubset_prok 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] subset: gosubset_prok 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 subset: gosubset_prok is_a: GO:0071702 ! organic substance transport [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 [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 subset: gosubset_prok 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] subset: gosubset_prok synonym: "taxis in response to chemical stimulus" EXACT [] xref: Wikipedia:Chemotaxis is_a: GO:0042330 ! taxis [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 subset: gosubset_prok synonym: "response to abiotic stress" RELATED [] synonym: "response to biotic stress" RELATED [] is_a: GO:0050896 ! response to stimulus [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 subset: gosubset_prok 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: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 [Term] id: GO:0008150 name: biological_process namespace: biological_process alt_id: GO:0000004 alt_id: GO:0007582 alt_id: GO:0044699 def: "Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end." [GOC:go_curators, GOC:isa_complete] 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. Note that 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 ND, no data, 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 subset: gosubset_prok synonym: "biological process" EXACT [] synonym: "physiological process" EXACT [] synonym: "single organism process" RELATED [] synonym: "single-organism process" RELATED [] xref: Wikipedia:Biological_process created_by: janelomax creation_date: 2012-09-19T15:05:24Z [Term] id: GO:0008152 name: metabolic process namespace: biological_process 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 subset: gosubset_prok synonym: "metabolic process resulting in cell growth" NARROW [] synonym: "metabolism" EXACT [] synonym: "metabolism resulting in cell growth" 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: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 subset: gosubset_prok 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 subset: gosubset_prok is_a: GO:0008150 ! biological_process [Term] id: GO:0009056 name: catabolic process namespace: biological_process 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 subset: gosubset_prok synonym: "breakdown" EXACT [] synonym: "catabolism" EXACT [] synonym: "degradation" EXACT [] 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 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: gosubset_prok synonym: "biopolymer catabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "macromolecule breakdown" EXACT [] synonym: "macromolecule catabolism" EXACT [] synonym: "macromolecule degradation" EXACT [] 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: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 subset: gosubset_prok synonym: "anabolism" EXACT [] synonym: "biosynthesis" EXACT [] synonym: "formation" RELATED [] 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: gosubset_prok 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: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 subset: gosubset_prok 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 subset: gosubset_prok synonym: "detoxification response" NARROW [] synonym: "toxin resistance" RELATED [] synonym: "toxin susceptibility/resistance" RELATED [] is_a: GO:0042221 ! response to chemical [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_pir subset: goslim_plant subset: gosubset_prok 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 created_by: janelomax creation_date: 2012-12-11T16:56:55Z [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] subset: gosubset_prok 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 [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 [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] subset: gosubset_prok 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] subset: gosubset_prok is_a: GO:0046942 ! carboxylic acid 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 subset: gosubset_prok 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] subset: gosubset_prok 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] subset: gosubset_prok 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 subset: gosubset_prok 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: goslim_pir subset: goslim_plant subset: gosubset_prok 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: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: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] subset: gosubset_prok 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: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] subset: gosubset_prok 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] subset: gosubset_prok 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: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: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 subset: gosubset_prok 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] subset: gosubset_prok 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 subset: gosubset_prok 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: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: goslim_chembl subset: goslim_generic subset: goslim_pir subset: goslim_plant subset: gosubset_prok synonym: "growth pattern" RELATED [] synonym: "non-developmental growth" RELATED [GOC:mah] is_a: GO:0008150 ! biological_process [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 subset: gosubset_prok is_a: GO:0008150 ! biological_process [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: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 subset: gosubset_prok 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] subset: gosubset_prok synonym: "directed movement in response to stimulus" EXACT [] xref: Wikipedia:Taxis is_a: GO:0040011 ! locomotion [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 subset: gosubset_prok is_a: GO:0044764 ! multi-organism cellular process [Term] id: GO:0043170 name: macromolecule metabolic process namespace: biological_process alt_id: GO:0043283 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 subset: gosubset_prok synonym: "biopolymer metabolic process" EXACT [GOC:mtg_chebi_dec09] synonym: "macromolecule metabolism" EXACT [] is_a: GO:0071704 ! organic substance metabolic process [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] subset: goslim_pir subset: gosubset_prok 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 subset: gosubset_prok 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] subset: gosubset_prok 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] subset: gosubset_prok 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] subset: gosubset_prok 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] subset: gosubset_prok 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: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] subset: gosubset_prok 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] subset: gosubset_prok 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: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: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 subset: gosubset_prok 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 subset: gosubset_prok synonym: "antibiotic susceptibility/resistance" RELATED [] is_a: GO:0009636 ! response to toxic substance [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] subset: gosubset_prok 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 subset: gosubset_prok 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] subset: gosubset_prok is_a: GO:0015711 ! organic anion transport is_a: GO:0015849 ! organic acid transport [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 subset: gosubset_prok 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 [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: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 subset: gosubset_prok synonym: "physiological response to stimulus" EXACT [] is_a: GO:0008150 ! biological_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 subset: gosubset_prok 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: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 subset: gosubset_prok synonym: "establishment of localisation" 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 subset: gosubset_prok 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: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 [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: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: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] subset: gosubset_prok 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: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: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 created_by: tanyaberardini creation_date: 2014-06-06T13:54:36Z [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: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: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: 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:0000030 name: information content entity def: "A generically dependent continuant that is about some thing." [] is_a: BFO:0000031 ! generically dependent continuant 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: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 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: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 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: 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:0000047 name: processed material def: "Is a material entity that is created or changed during material processing." [] is_a: BFO:0000040 ! material entity 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: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 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:0000094 name: material processing def: "A planned process which results in physical changes in a specified input material" [] is_a: OBI:0000011 ! planned process 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: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: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 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 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: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 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: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 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: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 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: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 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:0000423 name: extract def: "an extract is a material entity which results from an extraction process" [] is_a: OBI:0000047 ! processed material 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 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: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 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: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 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: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 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: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 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: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 property_value: IAO:0000111 "recombinant vector" xsd:string property_value: IAO:0000114 IAO:0000123 [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: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 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: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: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 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: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 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 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:0000894 name: protein extract def: "a protein extract is the output of an extraction process from tissues or cell cultures resulting in a solution of cellular and/or organellar proteins in buffer solution used to prevent degradation," [] is_a: OBI:0000423 ! extract property_value: IAO:0000111 "protein extract" xsd:string property_value: IAO:0000112 "PMID: 20032479. A bovine whey protein extract stimulates human neutrophils to generate bioactive IL-1Ra through a NF-kappaB- and MAPK-dependent mechanism. Rusu D, Drouin R, Pouliot Y, Gauthier S, Poubelle PE.\nJ Nutr. 2010 Feb;140(2):382-91. Epub 2009 Dec 23." xsd:string property_value: IAO:0000114 IAO:0000120 property_value: IAO:0000117 "Person: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "OBI & wikipedia" xsd:string [Term] id: OBI:0000895 name: total RNA extract def: "A RNA extract that is the output of an extraction process in which total celluar and organelle RNA molecules are isolated from a specimen." [] is_a: OBI:0000880 ! RNA extract property_value: IAO:0000111 "total RNA extract" xsd:string property_value: IAO:0000112 "Extraction of total RNA from cells with Qiagen mini RNeasy kit." 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:0000896 name: secondary structure of RNA molecule is_a: OBI:0000885 ! secondary structure of sequence macromolecule property_value: IAO:0000111 "secondary structure of RNA molecule" xsd:string property_value: IAO:0000112 "PMID: 15630685: Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA." xsd:string property_value: IAO:0000114 IAO:0000123 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 [Term] id: OBI:0000897 name: DEPC structure mapping assay def: "is a single-nucleotide-resolution nucleic acid structure mapping assay which uses DEPC as reagent and chemical probe to generate data and information at nucleotide resolution scale contributing to the determination of nucleic acid secondary structure" [] is_a: OBI:0001017 ! single-nucleotide-resolution nucleic acid structure mapping assay using chemical probing property_value: IAO:0000111 "DEPC structure mapping assay" xsd:string property_value: IAO:0000112 "PMID:2446263. Probing the structure of RNAs in solution. Nucleic Acids Res. 1987 Nov 25;15(22):9109-28." xsd:string property_value: IAO:0000114 IAO:0000122 property_value: IAO:0000117 "Person: Philippe Rocca-Serra" xsd:string property_value: IAO:0000119 "RNA ontology" 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: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 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: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 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: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: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 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: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:0001147 name: cell culture expansion def: "a processual entity that results in the increase of cell numbers" [] is_a: OBI:0000094 ! material processing 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: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: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: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 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: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 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: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 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: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 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: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 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: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: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: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 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: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 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: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: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: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: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 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 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: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: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: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 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: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 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: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 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: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 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:0600043 name: genetic transformation def: "the introduction. alteration or integration of genetic material into a cell or organism" [] is_a: OBI:0000094 ! material processing 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: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 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: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: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 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: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 [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 is_a: RO:0000057 ! has participant [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 is_a: RO:0000056 ! participates in [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 [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 [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