format-version: 1.2
date: 20:12:2007 23:32
saved-by: rhee
auto-generated-by: OBO-Edit 1.101
default-namespace: evidence_code2.obo
namespace-id-rule: * ECO:$sequence(7,0,9999999)$

[Term]
id: ECO:0000000
name: evidence_code

[Term]
id: ECO:0000001
name: inferred by curator
def: "To be used for those cases where an annotation is not supported by any evidence, but can be reasonably inferred by a curator from other GO annotations, for which evidence is available." [ECO:go]
synonym: "IC" RELATED []
is_a: ECO:0000000 ! evidence_code

[Term]
id: ECO:0000002
name: inferred from direct assay
def: "Used to indicate a direct assay was carried out to determine the function, process, or component indicated by the GO term. Curators therefore need to be careful, because an experiment considered as a direct assay for a term from one ontology may be a different kind of evidence for a term from another of the ontologies. In particular, there are more kinds of direct assays for cellular component than for function or process. For example, a fractionation experiment might provide \"direct assay\" evidence that a gene product is in the nucleus, but \"protein interaction\" (IPI) evidence for its function or process." [GO:IDA]
synonym: "IDA" RELATED []
is_a: ECO:0000006 ! inferred from experiment

[Term]
id: ECO:0000003
name: inferred from reconstitution assay
is_a: ECO:0000002 ! inferred from direct assay

[Term]
id: ECO:0000004
name: inferred from cell fractionation
def: "Used when an annotation is made based on separation of subcellular components based on their physical properties, such as density in sucrose density gradients. This evidence is used mostly for annotations to the cellular component ontology." [TAIR:TED]
synonym: "IDA: cell fractionation" RELATED []
is_a: ECO:0000100 ! inferred from fractionation

[Term]
id: ECO:0000005
name: inferred from enzyme assay
def: "Used when an annotation is made based on assays that determine the catalytic activity of enzymes." [TAIR:TED]
synonym: "IDA: enzyme assays" RELATED []
is_a: ECO:0000039 ! inferred from protein assay

[Term]
id: ECO:00000057
name: inferred from sequence alignment
synonym: "<new synonym>" RELATED []
synonym: "ISA" RELATED []
is_a: ECO:0000044 ! inferred from sequence similarity

[Term]
id: ECO:0000006
name: inferred from experiment
is_a: ECO:0000000 ! evidence_code

[Term]
id: ECO:00000060
name: inferred from sequence orthology
synonym: "<new synonym>" RELATED []
synonym: "ISO" RELATED []
is_a: ECO:00000057 ! inferred from sequence alignment

[Term]
id: ECO:00000063
name: inferred from sequence model
synonym: "<new synonym>" RELATED []
synonym: "ISM" RELATED []
is_a: ECO:0000041 ! inferred from similarity

[Term]
id: ECO:00000067
name: inferred from electronic annotation
def: "Used for annotations that depend directly on computation or automated transfer of annotations from a database, particularly when the analysis is performed internally and not published. A key feature that distinguishes this evidence code from others is that it is not made by a curator; use IEA when no curator has checked the specific annotation to verify its accuracy. The actual method used (BLAST search, Swiss-Prot keyword mapping, etc.) doesn't matter." [GO:IEA]
synonym: "<new synonym>" RELATED []
synonym: "IEA" RELATED []
is_a: ECO:0000043 ! inferred from in-silico analysis

[Term]
id: ECO:0000007
name: inferred from immunofluorescence
def: "Used when an annotation is made based on methods that detect the presence of macromolecules, proteins, and compounds by the use of a fluorescent-labeled antibody." [TAIR:TED]
synonym: "IDA: immunofluorescence" RELATED []
is_a: ECO:0000040 ! inferred from immunological assay

[Term]
id: ECO:0000008
name: inferred from expression pattern
def: "The IEP evidence code covers cases where the annotation is inferred from the timing or location of expression of a gene, particularly when comparing a gene that is not yet characterized with the timing or location of expression of genes known to be involved in a particular process. Use this code with caution! It may be difficult to determine whether the expression pattern really indicates that a gene plays a role in a given process, so the IEP evidence code is usually used in conjunction with high level GO terms in the biological process ontology." [GO:IEP]
synonym: "IEP" RELATED []
is_a: ECO:0000006 ! inferred from experiment

[Term]
id: ECO:0000009
name: inferred from transcript expression
is_a: ECO:0000008 ! inferred from expression pattern

[Term]
id: ECO:0000010
name: inferred from protein expression
is_a: ECO:0000008 ! inferred from expression pattern
is_a: ECO:0000039 ! inferred from protein assay

[Term]
id: ECO:0000011
name: inferred from genetic interaction
synonym: "IGI" RELATED []
xref: TAIR:TED\:0000006
is_a: ECO:0000059 ! inferred from phenotype

[Term]
id: ECO:0000012
name: inferred from functional complementation
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 ! inferred from genetic interaction

[Term]
id: ECO:0000013
name: inferred from transgenic rescue
is_a: ECO:0000012 ! inferred from functional complementation

[Term]
id: ECO:0000015
name: inferred from mutant phenotype
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 ! inferred from phenotype

[Term]
id: ECO:0000016
name: inferred from loss-of-function mutant phenotype
is_a: ECO:0000015 ! inferred from mutant phenotype

[Term]
id: ECO:0000017
name: inferred from ectopic expression
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 ! inferred from phenotype

[Term]
id: ECO:0000018
name: inferred from anti-sense experiment
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 ! inferred from phenotype

[Term]
id: ECO:0000019
name: inferred from RNAi experiment
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 experiments" RELATED []
is_a: ECO:0000059 ! inferred from phenotype

[Term]
id: ECO:0000020
name: inferred from specific protein inhibition
is_a: ECO:0000039 ! inferred from protein assay

[Term]
id: ECO:0000021
name: inferred from physical interaction
def: "Covers physical interactions between the gene product of interest and another molecule (such as a protein, ion or complex). IPI can be thought of as a type of IDA, where the actual binding partner or target can be specified, using \"with\" in the with/from field." [GO:IPI]
synonym: "IPI" RELATED []
is_a: ECO:0000006 ! inferred from experiment

[Term]
id: ECO:0000022
name: inferred from co-purification
def: "Used in component annotations when a subunit is isolated as part of purification of its larger complex." [TAIR:TED]
synonym: "IPI: co-purification" RELATED []
is_a: ECO:0000021 ! inferred from physical interaction

[Term]
id: ECO:0000023
name: inferred from ligand binding
is_a: ECO:0000021 ! inferred from physical interaction

[Term]
id: ECO:0000024
name: inferred from protein binding
is_a: ECO:0000023 ! inferred from ligand binding
is_a: ECO:0000039 ! inferred from protein assay

[Term]
id: ECO:0000025
name: inferred from hybrid interaction
is_a: ECO:0000023 ! inferred from ligand binding

[Term]
id: ECO:0000026
name: inferred from nucleic acid hybridization
is_a: ECO:0000073 ! inferred from genomic analysis

[Term]
id: ECO:0000027
name: inferred from structural similarity
def: "Used when an annotation is made based on the structural similarity of the annotated gene/gene product to a single other gene or group of genes. In the case of a single gene, an accession for the related gene's sequence is entered in the evidence_with field." [TAIR:TED]
synonym: "ISS: structural similarity" RELATED []
is_a: ECO:0000041 ! inferred from similarity

[Term]
id: ECO:0000028
name: inferred from motif similarity
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:0000044 ! inferred from sequence similarity

[Term]
id: ECO:0000029
name: inferred from InterPro motif similarity
is_a: ECO:0000028 ! inferred from motif similarity

[Term]
id: ECO:0000030
name: inferred from curated BLAST match
is_a: ECO:00000057 ! inferred from sequence alignment

[Term]
id: ECO:0000031
name: inferred from curated BLAST match to protein
is_a: ECO:0000030 ! inferred from curated BLAST match

[Term]
id: ECO:0000032
name: inferred from curated BLAST match to nucleic acid
is_a: ECO:0000030 ! inferred from curated BLAST match

[Term]
id: ECO:0000033
name: traceable author statement
def: "The 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." [GO:TAS]
synonym: "TAS" RELATED []
is_a: ECO:0000000 ! evidence_code
is_a: ECO:0000043 ! inferred from in-silico analysis

[Term]
id: ECO:0000034
name: non-traceable author statement
def: "The NAS evidence code should be used in all\ncases where the author makes a statement that a curator wants to capture but\nfor which there are neither results presented nor a specific reference cited\nin the source used to make the annotation. The source of the information may\nbe peer reviewed papers, textbooks, database records or vouchered specimens." [GO:NAS]
synonym: "NAS" RELATED []
is_a: ECO:0000000 ! evidence_code

[Term]
id: ECO:0000035
name: no biological data
def: "Used for annotations when information about the molecular function, biological process, or cellular component of the gene or gene product being annotated is not available. Use of the ND evidence code indicates that the annotator at the contributing database found no information that allowed making an annotation to any term indicating specific knowledge from the ontology in question (molecular function, biological process, or cellular component) as of the date indicated. This code should be used only for annotations to the root terms, molecular function ; GO:0003674, biological process ; GO:0008150, or cellular component ; GO:0005575, which, when used in annotations, indicate that no knowledge is available about a gene product in that aspect of GO." [GO:ND]
synonym: "ND" RELATED []
is_a: ECO:0000000 ! evidence_code

[Term]
id: ECO:0000037
name: not_recorded
def: "Used for annotations done before curators began tracking evidence types (appears in some legacy annotations). It may not be used for new annotations." [GO:NR]
synonym: "NR" RELATED []
is_a: ECO:0000000 ! evidence_code

[Term]
id: ECO:0000038
name: inferred from transient rescue
is_a: ECO:0000012 ! inferred from functional complementation

[Term]
id: ECO:0000039
name: inferred from protein assay
is_a: ECO:0000002 ! inferred from direct assay

[Term]
id: ECO:0000040
name: inferred from immunological assay
is_a: ECO:0000023 ! inferred from ligand binding
is_a: ECO:0000039 ! inferred from protein assay

[Term]
id: ECO:0000041
name: inferred from similarity
synonym: "<new synonym>" RELATED []
synonym: "ISS" RELATED []
is_a: ECO:0000000 ! evidence_code

[Term]
id: ECO:0000042
name: inferred from gain-of-function mutant phenotype
is_a: ECO:0000015 ! inferred from mutant phenotype

[Term]
id: ECO:0000043
name: inferred from in-silico analysis
alt_id: ECO:0000036
xref: TAIR:TED\:0000004
is_a: ECO:0000000 ! evidence_code

[Term]
id: ECO:0000044
name: inferred from sequence similarity
def: "Used when an annotation is made based on the sequence similarity of the annotated gene/gene product to a single other gene or group of genes and this evidence has been examined by a curator." [TAIR:TED]
is_a: ECO:0000041 ! inferred from similarity

[Term]
id: ECO:0000045
name: inferred from spatial pattern of protein expression
is_a: ECO:0000010 ! inferred from protein expression

[Term]
id: ECO:0000046
name: inferred from level of protein expression
is_a: ECO:0000010 ! inferred from protein expression

[Term]
id: ECO:0000047
name: inferred from spatial pattern of transcript expression
is_a: ECO:0000009 ! inferred from transcript expression

[Term]
id: ECO:0000048
name: inferred from level of transcript expression
is_a: ECO:0000009 ! inferred from transcript expression

[Term]
id: ECO:0000049
name: inferred from reporter gene assay
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 ! inferred from phenotype

[Term]
id: ECO:0000050
name: inferred from voucher specimen
def: "Used when an annotation is made on the basis of for a phenotype description\nfor a species or higher level group that given by an author who explicitly\nreferences an observation of a voucher specimen(s). Voucher specimens are\ndefined 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]
is_a: ECO:0000059 ! inferred from phenotype

[Term]
id: ECO:0000052
name: inferred from supressor/enhancer interaction
synonym: "IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals)" RELATED []
xref: TAIR:TED\:0000063
is_a: ECO:0000011 ! inferred from genetic interaction

[Term]
id: ECO:0000053
name: inferred from reviewed computational analysis
def: "Used for: Predictions based on large-scale experiments (e.g. genome-wide two-hybrid, genome-wide synthetic interactions); Predictions based on integration of large-scale datasets of several types; Text-based computation (e.g. text mining). This code is used for annotations based on a non-sequence-based computational method, where the results have been reviewed by an author or a curator. IEA should be used for any computational annotations that are not checked for accuracy by a curator (or by the authors of a paper describing such analysis), and sequence comparisons that have been reviewed use ISS. For microarray results alone, IEP is preferred, but RCA is used when microarray results are combined with results of other types of large-scale experiments." [ECO:go]
synonym: "RCA" RELATED []
is_a: ECO:0000043 ! inferred from in-silico analysis

[Term]
id: ECO:0000054
name: inferred from double mutant analysis
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 ! inferred from genetic interaction

[Term]
id: ECO:0000055
name: inferred from array experiment
is_a: ECO:0000008 ! inferred from expression pattern

[Term]
id: ECO:0000056
name: inferred from epistatic interaction
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 ! inferred from genetic interaction

[Term]
id: ECO:0000058
name: inferred from expression microarray experiment
is_a: ECO:0000055 ! inferred from array experiment

[Term]
id: ECO:0000059
name: inferred from phenotype
alt_id: ECO:0000014
synonym: "IMP" RELATED []
synonym: "inferred from phenotype" EXACT []
is_a: ECO:0000006 ! inferred from experiment

[Term]
id: ECO:0000061
name: inferred from quantitative trait analysis
def: "Used when 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 ! inferred from phenotype

[Term]
id: ECO:0000062
name: inferred from genomic microarray experiment
is_a: ECO:0000055 ! inferred from array experiment

[Term]
id: ECO:0000064
name: inferred from functional complemtation in heterologous system
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 ! inferred from functional complementation

[Term]
id: ECO:0000065
name: inferred from CpG island microarray experiment
is_a: ECO:0000055 ! inferred from array experiment

[Term]
id: ECO:0000066
name: inferred from yeast one-hybrid assay
def: "Used when an annotation is based on the interaction of a protein with a DNA fragment in a yeast one-hybrid assay. 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 []
is_a: ECO:0000025 ! inferred from hybrid interaction

[Term]
id: ECO:0000068
name: inferred from yeast 2-hybrid assay
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 ! inferred from hybrid interaction

[Term]
id: ECO:0000069
name: inferred from differential methylation hybridization
is_a: ECO:0000026 ! inferred from nucleic acid hybridization

[Term]
id: ECO:0000070
name: inferred from co-immunoprecipitation
def: "Used when an annotation is based on the interaction of one gene product with another in a co-immunoprecipitation assay (two or more proteins are precipitated when treated with an antibody specific to a single protein). The interacting protein is referenced in the evidence_with column." [TAIR:TED]
synonym: "IPI: co-immunoprecipitation" RELATED []
is_a: ECO:0000085 ! inferred from immunoprecipitation

[Term]
id: ECO:0000072
name: inferred from Sos-recruitment assay
def: "Used when an annotation is based on the interaction of two proteins in a Sos-recruitment assay. The assay is 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_a: ECO:0000021 ! inferred from physical interaction

[Term]
id: ECO:0000073
name: inferred from genomic analysis
is_a: ECO:0000006 ! inferred from experiment

[Term]
id: ECO:0000074
name: inferred from split-ubiquitin assay
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 []
is_a: ECO:0000021 ! inferred from physical interaction

[Term]
id: ECO:0000076
name: inferred from far-Western assay
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 []
is_a: ECO:0000021 ! inferred from physical interaction

[Term]
id: ECO:0000077
name: inferred from methylation-specific PCR
is_a: ECO:0000082 ! inferred from PCR experiment

[Term]
id: ECO:0000078
name: inferred from Southern blot hybridization
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 []
is_a: ECO:0000026 ! inferred from nucleic acid hybridization

[Term]
id: ECO:0000079
name: inferred from affinity chromatography
def: "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." [TAIR:TED]
synonym: "IDA: affinity chromatography" RELATED []
is_a: ECO:0000023 ! inferred from ligand binding

[Term]
id: ECO:0000081
name: inferred from targeting sequence prediction
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 ! inferred from motif similarity

[Term]
id: ECO:0000082
name: inferred from PCR experiment
is_a: ECO:0000073 ! inferred from genomic analysis

[Term]
id: ECO:0000083
name: inferred from transmembrane domain prediction
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 ! inferred from motif similarity

[Term]
id: ECO:0000085
name: inferred from immunoprecipitation
def: "Used when an annotation is made based on a method that precipitates a multivalent antigen by a bivalent antibody." [TAIR:TED]
synonym: "IDA: immunoprecipitation" RELATED []
is_a: ECO:0000040 ! inferred from immunological assay

[Term]
id: ECO:0000086
name: inferred from amplification of intermethylated sites
is_a: ECO:0000073 ! inferred from genomic analysis

[Term]
id: ECO:0000087
name: inferred from immunolocalization
def: "Used when an annotation is made based on methods that detect the presence of macromolecules, proteins, and compounds by the use of antibodies." [TAIR:TED]
synonym: "IDA: immunolocalization" RELATED []
is_a: ECO:0000040 ! inferred from immunological assay
is_a: ECO:0000122 ! inferred from protein localization

[Term]
id: ECO:0000089
name: inferred from restriction landmark genomic scanning
is_a: ECO:0000073 ! inferred from genomic analysis

[Term]
id: ECO:0000090
name: inferred from immunogold labelling
def: "Used when an annotation is made based on immunolocalization method that detects an antigen in cytological preparations by using a gold-labeled secondary antibody." [TAIR:TED]
synonym: "IDA: immunogold labelling" RELATED []
is_a: ECO:0000040 ! inferred from immunological assay

[Term]
id: ECO:0000092
name: inferred from immunolocalization of epitope-tagged protein
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 ! inferred from immunolocalization

[Term]
id: ECO:0000093
name: inferred from oligonucleotide microarray
is_a: ECO:0000055 ! inferred from array experiment

[Term]
id: ECO:0000094
name: inferred from bioassay
def: "Used when an annotation is made based on assays using living organisms to measure the effect of a substance, factor, or condition." [TAIR:TED]
synonym: "IDA: bioassay" RELATED []
is_a: ECO:0000002 ! inferred from direct assay

[Term]
id: ECO:0000096
name: inferred from electrophoretic mobility shift assay
def: "Used when an annotation is made based on electrophoretic mobility shift of macromolecules, compounds, and proteins. Most commonly used for detecting the binding of protein to DNA." [TAIR:TED]
synonym: "IDA: electrophoretic mobility shift assay" RELATED []
is_a: ECO:0000002 ! inferred from direct assay

[Term]
id: ECO:0000097
name: inferred from cDNA microarray
is_a: ECO:0000055 ! inferred from array experiment

[Term]
id: ECO:0000098
name: inferred from in situ hybridization
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 ! inferred from nucleic acid hybridization

[Term]
id: ECO:0000100
name: inferred from fractionation
is_a: ECO:0000002 ! inferred from direct assay

[Term]
id: ECO:0000101
name: inferred from Affymetrix array
is_a: ECO:0000055 ! inferred from array experiment

[Term]
id: ECO:0000102
name: inferred from co-fractionation
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 ! inferred from fractionation

[Term]
id: ECO:0000104
name: inferred from level of transcript expression determined by microarray analysis
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 ! inferred from level of transcript expression
is_a: ECO:0000058 ! inferred from expression microarray experiment

[Term]
id: ECO:0000105
name: inferred from Nimblegen array
is_a: ECO:0000055 ! inferred from array experiment

[Term]
id: ECO:0000106
name: inferred from level of transcript expression determined by Northern assay
def: "Used when an annotation is made based on levels of RNA expression determined by a Northern blot experiment." [TAIR:TED]
synonym: "IEP: transcript levels (e.g. Northerns)" RELATED []
is_a: ECO:0000048 ! inferred from level of transcript expression

[Term]
id: ECO:0000108
name: inferred from level of transcript expression determined by RT-PCR
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 []
is_a: ECO:0000048 ! inferred from level of transcript expression
is_a: ECO:0000109 ! inferred from RT-PCR experiment

[Term]
id: ECO:0000109
name: inferred from RT-PCR experiment
is_a: ECO:0000082 ! inferred from PCR experiment

[Term]
id: ECO:0000110
name: inferred from RNA protection assay
def: "Used when an annotation is made based on levels of RNA expression determined by an RNA protection assay." [TAIR:TED]
synonym: "IEP: RNA protection assay" RELATED []
is_a: ECO:0000009 ! inferred from transcript expression

[Term]
id: ECO:0000112
name: inferred from Western blot assay
def: "Used when an annotation is made based on levels of protein expression determined by a Western blot assay." [TAIR:TED]
synonym: "IEP: protein levels (e.g. Western blots)" RELATED []
is_a: ECO:0000046 ! inferred from level of protein expression

[Term]
id: ECO:0000114
name: inferred from expression library screening
def: "Used when an annotation is made on the basis of a protein expression library screen where a protein of interest is isolated on the basis of its hybridization to an antibody raised to a homologous protein." [TAIR:TED]
synonym: "IEP: expression library screening" RELATED []
is_a: ECO:0000010 ! inferred from protein expression
is_a: ECO:0000040 ! inferred from immunological assay

[Term]
id: ECO:0000116
name: inferred from differential hybridization
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 ! inferred from transcript expression
is_a: ECO:0000026 ! inferred from nucleic acid hybridization

[Term]
id: ECO:0000118
name: inferred from subtractive hybridization
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 ! inferred from transcript expression
is_a: ECO:0000026 ! inferred from nucleic acid hybridization

[Term]
id: ECO:0000120
name: inferred from over expression
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 ! inferred from phenotype

[Term]
id: ECO:0000122
name: inferred from protein localization
is_a: ECO:0000039 ! inferred from protein assay

[Term]
id: ECO:0000124
name: inferred from localization of fusion protein
is_a: ECO:0000122 ! inferred from protein localization

[Term]
id: ECO:0000126
name: inferred from localization of GFP fusion protein
synonym: "IDA: localization of GFP/YFP fusion protein" RELATED []
is_a: ECO:0000124 ! inferred from localization of fusion protein

[Term]
id: ECO:0000128
name: inferred from localization of YFP fusion protein
synonym: "IDA: localization of GFP/YFP fusion protein" RELATED []
is_a: ECO:0000124 ! inferred from localization of fusion protein

[Term]
id: ECO:0000130
name: inferred from localiztion of GUS fusion protein
synonym: "IDA: localization of GUS fusion protein" RELATED []
is_a: ECO:0000124 ! inferred from localization of fusion protein

[Term]
id: ECO:0000132
name: inferred from localization of lacZ fusion protein
is_a: ECO:0000124 ! inferred from localization of fusion protein

[Term]
id: ECO:0000134
name: inferred from transport assay
synonym: "IDA: transport assay" RELATED []
is_a: ECO:0000002 ! inferred from direct assay

[Term]
id: ECO:0000136
name: inferred from nucleic acid binding assay
is_a: ECO:0000023 ! inferred from ligand binding

[Term]
id: ECO:0000138
name: inferred from ribohomopolymer binding assay
synonym: "IDA: ribohomopolymer binding assay" RELATED []
is_a: ECO:0000136 ! inferred from nucleic acid binding assay

[Term]
id: ECO:0000140
name: inferred from thin layer chromatographic assay
synonym: "IDA: thin layer chromatography" RELATED []
is_a: ECO:0000002 ! inferred from direct assay

[Term]
id: ECO:0000142
name: inferred from protein:ion binding assay
is_a: ECO:0000024 ! inferred from protein binding

[Term]
id: ECO:0000144
name: inferred from Southwestern analysis
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 ! inferred from nucleic acid binding assay

[Term]
id: ECO:0000146
name: inferred from Northwestern analysis
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 ! inferred from nucleic acid binding assay

[Term]
id: ECO:0000148
name: inferred from in vitro binding assay
synonym: "IDA: in vitro binding assay" RELATED []
is_a: ECO:0000021 ! inferred from physical interaction

[Term]
id: ECO:0000150
name: inferred from in vitro transcription reconstitution assay
synonym: "IDA: in vitro reconstitution assay with recombinant protein" RELATED []
is_a: ECO:0000003 ! inferred from reconstitution assay

[Term]
id: ECO:0000152
name: inferred from in vitro transcription reconstitution assay with recombinant protein
synonym: "IDA: in vitro reconstitution assay with recombinant protein" RELATED []
is_a: ECO:0000150 ! inferred from in vitro transcription reconstitution assay

[Term]
id: ECO:0000154
name: inferred from protein expression in heterologous system
synonym: "IDA: protein expression in heterologous system" RELATED []
is_a: ECO:0000010 ! inferred from protein expression

[Term]
id: ECO:0000156
name: inferred from protein separation
is_a: ECO:0000100 ! inferred from fractionation

[Term]
id: ECO:0000158
name: inferred from protein separation followed by direct sequencing
synonym: "IDA: protein separation and direct sequencing" RELATED []
is_a: ECO:0000156 ! inferred from protein separation

[Term]
id: ECO:0000160
name: inferred from protein separation followed by fragment identification
synonym: "IDA: protein separation and fragment identification" RELATED []
is_a: ECO:0000156 ! inferred from protein separation

[Term]
id: ECO:0000162
name: inferred from uptake assay in a heterologous system
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 ! inferred from transport assay

[Term]
id: ECO:0000164
name: inferred from electrophysiological experiment
is_a: ECO:0000002 ! inferred from direct assay

[Term]
id: ECO:0000166
name: inferred from two-electrode voltage clamp technique
synonym: "IDA: two-electrode voltage clamp technique" RELATED []
is_a: ECO:0000164 ! inferred from electrophysiological experiment

[Term]
id: ECO:0000168
name: inferred from transcription assay
is_a: ECO:0000002 ! inferred from direct assay

[Term]
id: ECO:0000170
name: inferred from 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 ! inferred from transcription assay

[Term]
id: ECO:0000172
name: inferred from biochemical trait
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 ! inferred from phenotype

[Term]
id: ECO:0000174
name: inferred from physiological response
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:0000059 ! inferred from phenotype

[Term]
id: ECO:0000176
name: inferred from visible phenotype
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:0000059 ! inferred from phenotype

[Term]
id: ECO:0000177
name: inferred from genomic context
def: "Used whenever information about the genomic context of a gene product forms part of the evidence for a particular annotation. Genomic context includes, but is not limited to, such things as identity of the genes neighboring the gene product in question (i.e. synteny), operon structure, and phylogenetic or other whole genome analysis." [ECO:go]
synonym: "IGC" RELATED []
is_a: ECO:0000000 ! evidence_code

[Term]
id: ECO:0000178
name: Inferred from in vivo assay
is_a: ECO:0000094 ! inferred from bioassay

[Term]
id: ECO:0000179
name: inferred from animal model system
is_a: ECO:0000178 ! Inferred from in vivo assay

[Term]
id: ECO:0000180
name: inferred from clinical study
is_a: ECO:0000178 ! Inferred from in vivo assay

[Term]
id: ECO:0000181
name: inferred from in vitro assay
is_a: ECO:0000094 ! inferred from bioassay

[Term]
id: ECO:0000182
name: inferred from in vitro culture assay
synonym: "ex vivo assay" RELATED []
is_a: ECO:0000181 ! inferred from in vitro assay

[Term]
id: ECO:0000183
name: inferred from cell-free assay
synonym: "in vitro assay" RELATED []
is_a: ECO:0000181 ! inferred from in vitro assay

[Term]
id: ECO:0000184
name: inferred from enzyme inhibition
is_a: ECO:0000005 ! inferred from enzyme assay
is_a: ECO:0000020 ! inferred from specific protein inhibition

