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format-version: 1.2
data-version: releases/2016-05-31
date: 10:05:2016 15:33
saved-by: snadendla
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: For more details, see https://github.com/evidenceontology/evidenceontology
ontology: eco
[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 curator inference that links the current annotation to a different evidence-based annotation via background knowledge of the curator." [ECO:go, ECO:MCC]
synonym: "IC" EXACT [GO:IC]
synonym: "inferred by curator" EXACT [GO:IC]
is_a: ECO:0000205 ! curator inference
[Term]
id: ECO:0000002
name: direct assay evidence
def: "Experimental evidence that is based on direct measurement of some aspect of a biological feature." [ECO:MCC, GO:IDA]
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
def: "Used when an annotation is made based on assays that determine the catalytic activity of enzymes." [TAIR:TED]
synonym: "IDA: enzyme assays" RELATED []
xref: PSI-MI:MI\:0415 "enzymatic study"
is_a: ECO:0000039 ! protein assay evidence
[Term]
id: ECO:0000006
name: experimental evidence
def: "An evidence type that is based on the results of a laboratory assay." [ECO:MCC, GOC:ecd]
subset: go_groupings
synonym: "EXP" EXACT [GO:EXP]
synonym: "inferred from experiment" EXACT [GO:EXP]
is_a: ECO:0000000 ! evidence
[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: "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.
synonym: "IEP" EXACT [GO:IEP]
synonym: "inferred from expression pattern" EXACT [GO:IEP]
is_a: ECO:0000006 ! experimental evidence
[Term]
id: ECO:0000009
name: transcript expression evidence
is_a: ECO:0000008 ! expression pattern evidence
[Term]
id: ECO:0000010
name: protein expression evidence
is_a: ECO:0000008 ! expression pattern evidence
is_a: ECO:0000039 ! protein assay evidence
[Term]
id: ECO:0000011
name: genetic interaction evidence
xref: TAIR:TED\:0000006
is_a: ECO:0000059 ! experimental phenotypic evidence
[Term]
id: ECO:0000012
name: functional complementation evidence
def: "Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a mutant background in the organism of the gene's origin or a heterologous organism with a mutation in the homologous gene." [TAIR:TED]
synonym: "IGI: functional complementation" RELATED []
is_a: ECO:0000011 ! genetic interaction evidence
[Term]
id: ECO:0000013
name: transgenic rescue experiment evidence
is_a: ECO:0000012 ! functional complementation evidence
[Term]
id: ECO:0000015
name: mutant phenotype evidence
def: "The IMP evidence code covers those cases when the function, process or cellular localization of a gene product is inferred based on differences in the function, process, or cellular localization between two different alleles of the corresponding gene. The IMP code is used for cases where one allele may be designated 'wild-type' and another as 'mutant'. It is also used in cases where allelic variation occurs naturally and no specific allele is designated as wild-type or mutant. Caution should be used when making annotations from gain-of-function mutations as it may be difficult to infer a gene's normal function from a gain of function mutation, although it is sometimes possible." [GO:IMP]
is_a: ECO:0000059 ! experimental phenotypic evidence
[Term]
id: ECO:0000016
name: loss-of-function mutant phenotype evidence
is_a: ECO:0000015 ! mutant phenotype evidence
[Term]
id: ECO:0000017
name: ectopic expression evidence
def: "Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress or ectopically express the gene product in question." [TAIR:TED]
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: "Used when an annotation is based on a phenotype observed when expressing an anti-sense version of a gene product in a wild-type (for that gene product) background." [TAIR:TED]
synonym: "IMP: anti-sense experiments" RELATED []
is_a: ECO:0000059 ! experimental phenotypic evidence
[Term]
id: ECO:0000019
name: RNAi evidence
def: "Inference based on a phenotype observed when expressing an RNAi construct that includes a fragment of the gene product in a wild-type (for that gene product) background. A double-stranded RNA specifically suppresses the expression of the gene bearing its complementary sequence." [TAIR:TED]
synonym: "IMP: RNAi experiment" RELATED []
is_a: ECO:0000059 ! experimental phenotypic 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
def: "Experimental evidence that is based on characterization of an interaction between a gene product and another molecule." [ECO:MCC]
comment: Molecules interacted with might include protein, nucleic acid, ion, or complex.
xref: PSI-MI: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: PSI-MI: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: PSI-MI:MI\:0400 "affinity technology"
is_a: ECO:0000021 ! physical interaction evidence
[Term]
id: ECO:0000024
name: protein binding evidence
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: PSI-MI:MI\:0090 "protein complementation assay"
is_a: ECO:0000023 ! affinity evidence
[Term]
id: ECO:0000026
name: nucleic acid hybridization evidence
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: "Used when an annotation is made based on the presence of a recognized domain or motif in a gene product's (usually protein) primary sequence." [TAIR:TED]
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
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: "Protein BLAST evidence that is used in a manual assertion." [ECO:MCC]
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: "Nucleotide BLAST evidence that is used in a manual assertion." [ECO:MCC]
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: "An 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: "An author statement that is not associated with results presented or a cited reference." [ECO:MCC]
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:MCC, GO:ND]
comment: An assertion of "no biological data found" carries the assumption that a more-or-less exhaustive search has been conducted.
synonym: "ND" EXACT [GO:ND]
synonym: "no biological data available" EXACT [GO:ND]
is_a: ECO:0000205 ! curator inference
[Term]
id: ECO:0000037
name: not_recorded
def: "An evidence that reflects an annotation was made before curators began tracking evidence types." [ECO:MCC, GO:NR]
comment: The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations.
synonym: "not recorded" EXACT [GO:NR]
synonym: "NR" EXACT [GO:NR]
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
is_a: ECO:0000002 ! direct assay evidence
[Term]
id: ECO:0000040
name: immunological assay evidence
is_a: ECO:0000023 ! affinity evidence
[Term]
id: ECO:0000041
name: similarity evidence
def: "An evidence type that is based on comparing likeness of distinct biological entities." [ECO:MCC, PhenoScape:IS]
synonym: "inferred from similarity" RELATED []
synonym: "IS" EXACT []
is_a: ECO:0000000 ! evidence
[Term]
id: ECO:0000042
name: gain-of-function mutant phenotype evidence
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.
synonym: "inferred from sequence or structural similarity" BROAD [GO:ISS]
synonym: "inferred from sequence similarity" EXACT []
synonym: "ISS" BROAD [GO:ISS]
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
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:0000048
name: transcript expression level evidence
is_a: ECO:0000009 ! transcript expression evidence
[Term]
id: ECO:0000049
name: reporter gene assay evidence
def: "Used when an annotation is made on the basis of the expression pattern of a reporter gene. The reporter gene may consist of the native promoter of the gene in question that drives the expression of a readily assayable gene product such as GUS or GFP. The reporter gene may also be a marker of a particular type of physiological response." [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: "Used when an annotation is made on the basis of for a phenotype description for a species or higher level group that given by an author who explicitly references an observation of a voucher specimen(s). Voucher specimens are defined as those specimens with permanent museum catalog numbers. Thus it would be possible for a person to examine this particular specimen and observe the annotated phenotype." [PhenoScape:DOA]
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
synonym: "IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)" RELATED []
xref: TAIR:TED\:0000063
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\:0000004
is_a: ECO:0000212 ! combinatorial evidence
[Term]
id: ECO:0000054
name: double mutant phenotype evidence
def: "Used when an annotation is made based on the phenotype of double mutant organism that contains a mutation in the gene product of interest in addition to a second mutation at an unrelated locus." [TAIT:TED]
synonym: "IGI: double mutant analysis" RELATED []
is_a: ECO:0000011 ! genetic interaction evidence
[Term]
id: ECO:0000055
name: array experiment evidence
is_a: ECO:0000008 ! expression pattern evidence
[Term]
id: ECO:0000056
name: epistatic interaction evidence
def: "Used when an annotation is based on results of epistatis analysis of an allele of the gene in question and a mutant allele at another locus." [TAIR:TED]
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 []
is_a: ECO:0000041 ! similarity evidence
[Term]
id: ECO:0000058
name: expression microarray evidence
is_a: ECO:0000055 ! array experiment evidence
[Term]
id: ECO:0000059
name: experimental phenotypic evidence
alt_id: ECO:0000014
def: "Experimental evidence that is based on the expression of a genotype in an environment." [ECO:MCC]
synonym: "inferred from phenotype" RELATED []
is_a: ECO:0000006 ! experimental evidence
[Term]
id: ECO:0000060
name: positional similarity evidence
def: "Used when an annotation is made based on the similarity of the location and or arrangement of structures." [PhenoScape:IPS]
synonym: "IPS" EXACT []
is_a: ECO:0000057 ! phenotypic similarity evidence
[Term]
id: ECO:0000061
name: quantitative trait analysis evidence
def: "A type of experimental phenotypic evidence where an annotation is made for a gene product that has not been cloned but is associated with a quantitative trait locus." [TAIR:tn]
synonym: "IGI: quantitative trait analysis" RELATED []
is_a: ECO:0000059 ! experimental phenotypic evidence
[Term]
id: ECO:0000062
name: genomic microarray evidence
is_a: ECO:0000055 ! array experiment evidence
[Term]
id: ECO:0000063
name: compositional similarity evidence
def: "Used when an annotation is made based on the similarity of the histological makeup of structures." [PhenoScape:ICS]
synonym: "ICS" EXACT []
is_a: ECO:0000057 ! phenotypic similarity evidence
[Term]
id: ECO:0000064
name: functional complementation in heterologous system evidence
def: "Used when an annotation is made based on a functional complementation assay in which a wild-type copy of the gene in question is inserted into a heterologous organism with a mutation in the homologous gene." [TAIR:TED]
synonym: "IGI: functional complementation in heterologous system" RELATED []
is_a: ECO:0000012 ! functional complementation evidence
[Term]
id: ECO:0000065
name: CpG island microarray evidence
is_a: ECO:0000055 ! array experiment 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: PSI-MI:MI\:0432 "one hybrid"
is_a: ECO:0000025 ! hybrid interaction evidence
[Term]
id: ECO:0000067
name: developmental similarity evidence
def: "Used when an annotation is made based on the similarity of embryological and/or post-embryonic origin of structures." [PhenoScape:IDS]
synonym: "IDS" EXACT []
is_a: ECO:0000057 ! phenotypic similarity evidence
[Term]
id: ECO:0000068
name: yeast 2-hybrid evidence
def: "Used when an annotation is based on the interaction between two proteins in a yeast two-hybrid assay. The assay involves screening a trap-tagged library with a bait-tagged vector. The library is tagged with a DNA-binding domain (trap) and the bait is tagged with a transcriptional activation domain. Interaction between a library-trap protein and the bait results in activation of a yeast reporter gene whose transcription can be experimentally assayed." [TAIR:TED]
synonym: "IPI: yeast two-hybrid assay" RELATED []
is_a: ECO:0000025 ! hybrid interaction evidence
[Term]
id: ECO:0000069
name: differential methylation hybridization evidence
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: PSI-MI:MI\:0019 "coimmunoprecipitation"
is_a: ECO:0000085 ! immunoprecipitation evidence
[Term]
id: ECO:0000071
name: morphological similarity evidence
def: "Used when an annotation is made based on the similarity of the shape, structure or overall configuration of structures." [PhenoScape:IMS]
synonym: "IMS" EXACT []
is_a: ECO:0000057 ! phenotypic similarity evidence
[Term]
id: ECO:0000072
name: Sos-recruitment assay evidence
def: "A type of physical interaction evidence that is based on a genetic screening system that detects protein-protein interactions and is not based on a transcriptional readout." [TAIR:TED]
synonym: "IPI: Sos-recruitment assay" RELATED []
is_obsolete: true
[Term]
id: ECO:0000073
name: experimental genomic evidence
def: "Experimental evidence that characterizes 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: "Used when an annotation is based on the interaction of two proteins in a split-ubiquitin assay. 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 ubiquiting (NubG) domain. If bait and prey interact, their interaction brings the NubG and Cub domains close enough together to reconstitute split-ubiquitin, resulting in the release of the reporter protein by the action of the UBPs." [TAIR:TED]
synonym: "IPI: split-ubiquitin assay" RELATED []
xref: PSI-MI:MI\:0112 "ubiquitin reconstruction"
is_a: ECO:0000021 ! physical interaction evidence
[Term]
id: ECO:0000075
name: gene expression similarity evidence
def: "Used when an annotation is made based on the similarity of expression of genes in structures." [PhenoScape:IGES]
synonym: "IGES" EXACT []
is_a: ECO:0000057 ! phenotypic similarity evidence
[Term]
id: ECO:0000076
name: far-Western blotting evidence
def: "Used when an annotation is based on the interaction of protein with another in a far-Western assay. The assay involves separating target proteins on an SDS-PAGE gel, blotting to a membrane, hybridization with a protein probe and visualization using a probe-directed antibody. The interacting protein is referenced in the evidence_with column." [TAIR:TED]
synonym: "IPI: far-Western analysis" RELATED []
xref: PSI-MI:MI\:0047
is_a: ECO:0000021 ! physical interaction evidence
[Term]
id: ECO:0000077
name: methylation-specific polymerase chain reaction evidence
synonym: "methylation-specific PCR evidence" EXACT []
is_a: ECO:0000082 ! polymerase chain reaction evidence
[Term]
id: ECO:0000078
name: southern hybridization evidence
def: "Used when an annotation is based on the hybridization of a probe derived from the gene in question with a gene of known function/process/component. Can also be used when a probe derived from a gene of known function/process/component hybridizes with the gene in question." [TAIR:TED]
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: PSI-MI: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: "Used when a component annotation is made based on the presence of a targeting sequence in a protein's primary sequence. The presence of the targeting sequence may be detected by computational prediction and/or the author's manual examination of the sequence." [TAIR:TED]
synonym: "ISS: targeting sequence prediction" RELATED []
is_a: ECO:0000028 ! motif similarity evidence
[Term]
id: ECO:0000082
name: polymerase chain reaction evidence
synonym: "PCR evidence" EXACT []
is_a: ECO:0000073 ! experimental genomic evidence
[Term]
id: ECO:0000083
name: transmembrane domain prediction evidence
def: "Used when a component annotation is made based on the presence of one or more transmembrane domains in a protein's primary sequence. The presence of the transmembrane domains may be detected by computational prediction and/or the author's manual examination of the sequence." [TAIR:TED]
synonym: "ISS: transmembrane domain prediction" RELATED []
is_a: ECO:0000028 ! motif similarity evidence
[Term]
id: ECO:0000084
name: gene neighbors evidence
def: "Evidence that supports the identity of a gene product 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
[Term]
id: ECO:0000086
name: intermethylated site amplification evidence
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
synonym: "restriction landmark genome scanning evidence" EXACT []
synonym: "RLGS evidence" EXACT []
is_a: ECO:0005519 ! DNA detection assay evidence
[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: "Used when an annotation is made based on immunolocalization of recombinant proteins fused with epitopes that 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: oligonucleotide microarray evidence
is_a: ECO:0000055 ! array experiment evidence
[Term]
id: ECO:0000094
name: biological assay evidence
def: "Direct assay evidence that is derived by using a living organism to measure the effect of a substance, factor, or condition." [ECO:MCC, TAIR:TED]
synonym: "IDA: bioassay" RELATED []
is_a: ECO:0000002 ! direct assay evidence
[Term]
id: ECO:0000095
name: cell growth assay evidence
def: "A type of in vivo 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:0000178 ! in vivo assay evidence
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: PSI-MI:MI\:0413 "electrophoretic mobility shift assay"
is_a: ECO:0000002 ! direct assay evidence
[Term]
id: ECO:0000097
name: cDNA microarray evidence
is_a: ECO:0000055 ! array experiment evidence
[Term]
id: ECO:0000098
name: in situ hybridization evidence
def: "Used when an annotation is made based on a method that hybridizes a labeled nucleic acid probe to a tissue or cell specimen in which the cellular structures are still intact. Depending on the label and protocol used, the probe may detect complementary DNA or RNA by hybridizing specifically to that gene or sequence." [TAIR:TED]
synonym: "IDA: in situ hybridization" RELATED []
is_a: ECO:0000026 ! nucleic acid hybridization evidence
[Term]
id: ECO:0000100
name: fractionation evidence
is_a: ECO:0000002 ! direct assay evidence
[Term]
id: ECO:0000101
name: Affymetrix array experiment evidence
is_a: ECO:0000055 ! array experiment evidence
[Term]
id: ECO:0000102
name: co-fractionation evidence
def: "Used when an annotation is made based on fractionation of a protein with other compounds, factors, or macromolecules." [TAIR:TED]
synonym: "IDA: co-fractionation" RELATED []
is_a: ECO:0000100 ! fractionation evidence
[Term]
id: ECO:0000104
name: microarray RNA expression level evidence
def: "Used when an annotation is made based on levels of RNA expression determined by microarray experiment." [TAIR:TED]
synonym: "IEP: transcript levels (e.g. microarray data)" RELATED []
is_a: ECO:0000048 ! transcript expression level evidence
is_a: ECO:0000058 ! expression microarray evidence
[Term]
id: ECO:0000105
name: Nimblegen array evidence
is_a: ECO:0000055 ! array experiment evidence
[Term]
id: ECO:0000106
name: northern assay evidence
def: "A type of transcript expression level 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 blot" EXACT []
is_a: ECO:0000048 ! transcript expression level evidence
[Term]
id: ECO:0000108
name: reverse transcription polymerase chain reaction transcription evidence
def: "Used when an annotation is made based on levels of RNA expression determined by an RT-PCR experiment (quantitative or otherwise)." [TAIR:TED]
synonym: "IEP: transcript levels (e.g. RT-PCR)" RELATED []
synonym: "RT-PCR transcription evidence" EXACT []
is_a: ECO:0000048 ! transcript expression level 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
[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
[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
[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: "Used when an annotation is made based on results of a differential hybridization experiment that demonstrates expression of an RNA under one condition and not another." [TAIR:TED]
synonym: "IEP: differential hybridization" RELATED []
is_a: ECO:0000009 ! transcript expression evidence
is_a: ECO:0000026 ! nucleic acid hybridization evidence
[Term]
id: ECO:0000118
name: subtractive hybridization evidence
def: "Used when an annotation is made based on results of a subtractive hybridization experiment that demonstrates expression of an RNA under one condition and not another." [TAIR:TED]
synonym: "IEP: subtractive hybridization" RELATED []
is_a: ECO:0000009 ! transcript expression evidence
is_a: ECO:0000026 ! nucleic acid hybridization evidence
[Term]
id: ECO:0000120
name: over expression analysis evidence
def: "Used when an annotation is made based on the analysis of the phenotype of a wild-type or mutant transgenic organism that has been engineered to overexpress the gene product in question." [TAIR:TED]
synonym: "IMP: analysis of overexpression/ectopic expression phenotype" RELATED []
is_a: ECO:0000059 ! experimental phenotypic evidence
[Term]
id: ECO:0000122
name: protein localization evidence
is_a: ECO:0000039 ! protein assay evidence
[Term]
id: ECO:0000124
name: fusion protein localization evidence
is_a: ECO:0000122 ! protein localization evidence
[Term]
id: ECO:0000126
name: green fluorescent protein fusion protein localization evidence
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
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
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
synonym: "LacZ fusion protein localization evidence" EXACT []
is_a: ECO:0000124 ! fusion protein localization evidence
[Term]
id: ECO:0000134
name: transport assay evidence
synonym: "IDA: transport assay" RELATED []
is_a: ECO:0000002 ! direct assay evidence
[Term]
id: ECO:0000136
name: nucleic acid binding evidence
is_a: ECO:0000023 ! affinity evidence
[Term]
id: ECO:0000138
name: ribohomopolymer binding assay evidence
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
is_a: ECO:0000024 ! protein binding evidence
[Term]
id: ECO:0000144
name: Southwestern blot evidence
def: "Used when an annotation is made based on a Southwestern blot analysis, which detects DNA binding of proteins using labeled DNA as probe hybridizing to electrophoretically separated proteins." [TAIR:TED]
synonym: "IDA: Southwestern analysis" RELATED []
is_a: ECO:0000136 ! nucleic acid binding evidence
[Term]
id: ECO:0000146
name: Northwestern blot evidence
def: "Used when an annotation is made based on a Northwestern blot analysis, which detects RNA binding of proteins using labeled RNA as probe hybridizing to electrophoretically separated proteins." [TAIR:TED]
synonym: "IDA: Northwestern analysis" RELATED []
is_a: ECO:0000136 ! nucleic acid binding evidence
[Term]
id: ECO:0000148
name: in vitro binding evidence
synonym: "IDA: in vitro binding assay" RELATED []
is_obsolete: true
[Term]
id: ECO:0000150
name: in vitro transcription reconstitution assay evidence
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
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
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: "Used when an annotation is made based on small molecule update assays carried out in a heterologous system that contains a recombinant protein." [TAIR:TED]
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 experiment evidence
def: "A type of electrophysiology assay 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:0000164 ! electrophysiology assay evidence
[Term]
id: ECO:0000168
name: transcription assay
is_a: ECO:0000002 ! direct assay evidence
[Term]
id: ECO:0000170
name: transcriptional activation assay
def: "Used when an annotation is made based on assays that show transcriptional activation of a specific target reporter gene." [TAIR:TED]
synonym: "IDA: transcriptional activation assay" RELATED []
is_a: ECO:0000168 ! transcription assay
[Term]
id: ECO:0000172
name: biochemical trait analysis evidence
def: "Used when an annotation is made based on the analysis of a biochemical aspect of a mutant phenotype; for example, the accumulation of a biosynthetic intermediate." [TAIR:TED]
synonym: "IMP: analysis of biochemical trait" RELATED []
is_a: ECO:0000059 ! experimental phenotypic evidence
[Term]
id: ECO:0000174
name: mutant physiological response evidence
def: "Used when an annotation is made based on the physiological response of a mutant to an external stimulus; for example, abnormal growth of the root in response to gravity, delay in flowering in response to varying light conditions." [TAIR:TED]
synonym: "IMP: analysis of physiological response" RELATED []
is_a: ECO:0000015 ! mutant phenotype evidence
[Term]
id: ECO:0000176
name: mutant visible phenotype evidence
def: "Used when an annotation is made based on the visual examination of a mutant phenotype; for example, abnormalities in organism morphology." [TAIR:TED]
synonym: "IMP: analysis of visible trait" RELATED []
is_a: ECO:0000015 ! mutant phenotype evidence
[Term]
id: ECO:0000177
name: genomic context evidence
def: "An evidence type that is based on the location of a gene, which gives rise to a gene product, within the genome." [ECO:go, ECO:MCC]
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
is_a: ECO:0000094 ! biological assay evidence
[Term]
id: ECO:0000179