2.01 16:05:2012 13:09 mchibucos evidence_code2.obo evidence_code2.obo This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi evidence A type of information that is used to support an assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence code evidence_code evidence_code2.obo inference from background scientific knowledge A curator inference that links the current annotation to a different evidence-based annotation via background knowledge of the curator. ECO:go http://purl.org/obo/owl/ECO#ECO_go ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC IC GO:IC http://purl.org/obo/owl/GO#GO_IC inferred by curator GO:IC http://purl.org/obo/owl/GO#GO_IC evidence_code2.obo direct assay evidence Experimental evidence that is based on direct measurement of some aspect of a biological feature. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC GO:IDA http://purl.org/obo/owl/GO#GO_IDA evidence_code2.obo reconstitution assay evidence evidence_code2.obo cell fractionation evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IDA: cell fractionation evidence_code2.obo enzyme assay evidence Used when an annotation is made based on assays that determine the catalytic activity of enzymes. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: enzyme assays evidence_code2.obo experimental evidence An evidence type that is based on the results of a laboratory assay. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC GOC:ecd http://purl.org/obo/owl/GOC#GOC_ecd EXP GO:EXP http://purl.org/obo/owl/GO#GO_EXP inferred from experiment GO:EXP http://purl.org/obo/owl/GO#GO_EXP evidence_code2.obo immunofluorescence evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IDA: immunofluorescence evidence_code2.obo expression pattern evidence 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. Experimental evidence that is based on characterization of gene expression. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC GO:IEP http://purl.org/obo/owl/GO#GO_IEP IEP GO:IEP http://purl.org/obo/owl/GO#GO_IEP inferred from expression pattern GO:IEP http://purl.org/obo/owl/GO#GO_IEP evidence_code2.obo transcript expression evidence evidence_code2.obo protein expression evidence evidence_code2.obo genetic interaction evidence evidence_code2.obo TAIR:TED:0000006 http://purl.org/obo/owl/TAIR#TAIR_TED:0000006 functional complementation evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IGI: functional complementation evidence_code2.obo transgenic rescue experiment evidence evidence_code2.obo mutant phenotype evidence 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 http://purl.org/obo/owl/GO#GO_IMP evidence_code2.obo loss-of-function mutant phenotype evidence evidence_code2.obo ectopic expression evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IMP: analysis of overexpression/ectopic expression phenotype evidence_code2.obo anti-sense experiment evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IMP: anti-sense experiments evidence_code2.obo RNAi evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IMP: RNAi experiment evidence_code2.obo specific protein inhibition experiment evidence evidence_code2.obo physical interaction evidence Molecules interacted with might include protein, nucleic acid, ion, or complex. Experimental evidence that is based on characterization of an interaction between a gene product and another molecule. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC inferred from physical interaction GOECO:IPI http://purl.org/obo/owl/GOECO#GOECO_IPI IPI GOECO:IPI http://purl.org/obo/owl/GOECO#GOECO_IPI evidence_code2.obo GOECO:IPI http://purl.org/obo/owl/GOECO#GOECO_IPI co-purification evidence Used in component annotations when a subunit is isolated as part of purification of its larger complex. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IPI: co-purification evidence_code2.obo ligand binding evidence evidence_code2.obo protein binding evidence evidence_code2.obo hybrid interaction evidence evidence_code2.obo nucleic acid hybridization evidence evidence_code2.obo structural similarity evidence Used when an annotation is made based on the structural similarity of the annotated gene or 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 http://purl.org/obo/owl/TAIR#TAIR_TED inferred from sequence or structural similarity GO:ISS http://purl.org/obo/owl/GO#GO_ISS ISS GO:ISS http://purl.org/obo/owl/GO#GO_ISS evidence_code2.obo motif similarity evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED ISS: recognized domains evidence_code2.obo match to InterPro signature evidence evidence_code2.obo BLAST evidence used in manual assertion A type of BLAST evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC curated BLAST analysis evidence_code2.obo protein BLAST evidence used in manual assertion Protein BLAST evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC curated protein BLAST analysis evidence_code2.obo GO_REF:0000012 http://purl.org/obo/owl/GO_REF#GO_REF_0000012 GO_REF:0000018 http://purl.org/obo/owl/GO_REF#GO_REF_0000018 GO_REF:0000027 http://purl.org/obo/owl/GO_REF#GO_REF_0000027 nucleotide BLAST evidence used in manual assertion Nucleotide BLAST evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC curated nucleic acid BLAST analysis evidence_code2.obo traceable author statement 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. An author statement that is based on a cited reference. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC GO:TAS http://purl.org/obo/owl/GO#GO_TAS evidence_code2.obo non-traceable author statement 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. An author statement that is not associated with results presented or a cited reference. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo no biological data found A curator inference that states that a search found no information about a biological feature. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC GO:ND http://purl.org/obo/owl/GO#GO_ND ND GO:ND http://purl.org/obo/owl/GO#GO_ND no biological data available GO:ND http://purl.org/obo/owl/GO#GO_ND evidence_code2.obo not_recorded The evidence not_recorded appears in some legacy annotations; it should not be used for new annotations. An evidence that reflects an annotation was made before curators began tracking evidence types. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC GO:NR http://purl.org/obo/owl/GO#GO_NR not recorded GO:NR http://purl.org/obo/owl/GO#GO_NR NR GO:NR http://purl.org/obo/owl/GO#GO_NR evidence_code2.obo transient rescue experiment evidence evidence_code2.obo protein assay evidence evidence_code2.obo immunological assay evidence evidence_code2.obo similarity evidence An evidence type that is based on comparing likeness of distinct biological entities. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC PhenoScape:IS http://purl.org/obo/owl/PhenoScape#PhenoScape_IS inferred from similarity IS evidence_code2.obo gain-of-function mutant phenotype evidence evidence_code2.obo sequence similarity evidence 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. A type of similarity based on biomolecular sequence. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED inferred from sequence or structural similarity GO:ISS http://purl.org/obo/owl/GO#GO_ISS inferred from sequence similarity ISS GO:ISS http://purl.org/obo/owl/GO#GO_ISS evidence_code2.obo spatial pattern of protein expression evidence evidence_code2.obo protein expression level evidence evidence_code2.obo spatial pattern of transcript expression evidence evidence_code2.obo transcript expression level evidence evidence_code2.obo reporter gene assay evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IEP: expression of a reporter gene evidence_code2.obo voucher specimen analysis evidence 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 http://purl.org/obo/owl/PhenoScape#PhenoScape_DOA IVS evidence_code2.obo genetic similarity evidence 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. A type of similarity based on genotype without respect to expression. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC PhenoScape:IGTS http://purl.org/obo/owl/PhenoScape#PhenoScape_IGTS IGTS inferred from genetic similarity evidence_code2.obo suppressor/enhancer interaction evidence IGI: 'traditional' genetic interactions (e.g. suppressors, synthetic lethals) evidence_code2.obo TAIR:TED:0000063 http://purl.org/obo/owl/TAIR#TAIR_TED:0000063 computational combinatorial evidence 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. A type of combinatorial analysis where data are combined and evaluated by an algorithm. ECO:go http://purl.org/obo/owl/ECO#ECO_go ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo TAIR:TED:0000004 http://purl.org/obo/owl/TAIR#TAIR_TED:0000004 double mutant phenotype evidence 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 http://purl.org/obo/owl/TAIT#TAIT_TED IGI: double mutant analysis evidence_code2.obo array experiment evidence evidence_code2.obo epistatic interaction evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IGI: epistatic interactions evidence_code2.obo phenotypic similarity evidence 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. A type of similarity based on the expression of a genotype in an environment. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC PhenoScape:IPTS http://purl.org/obo/owl/PhenoScape#PhenoScape_IPTS inferred from phenotypic similarity IPTS evidence_code2.obo expression microarray evidence evidence_code2.obo experimental phenotypic evidence Experimental evidence that is based on the expression of a genotype in an environment. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC inferred from phenotype evidence_code2.obo ECO:0000014 positional similarity evidence Used when an annotation is made based on the similarity of the location and or arrangement of structures. PhenoScape:IPS http://purl.org/obo/owl/PhenoScape#PhenoScape_IPS IPS evidence_code2.obo quantitative trait analysis evidence 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 http://purl.org/obo/owl/TAIR#TAIR_tn IGI: quantitative trait analysis evidence_code2.obo genomic microarray evidence evidence_code2.obo compositional similarity evidence Used when an annotation is made based on the similarity of the histological makeup of structures. PhenoScape:ICS http://purl.org/obo/owl/PhenoScape#PhenoScape_ICS ICS evidence_code2.obo functional complementation in heterologous system evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IGI: functional complementation in heterologous system evidence_code2.obo CpG island microarray evidence evidence_code2.obo yeast one-hybrid evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IPI: yeast one-hybrid assay evidence_code2.obo developmental similarity evidence Used when an annotation is made based on the similarity of embryological and/or post-embryonic origin of structures. PhenoScape:IDS http://purl.org/obo/owl/PhenoScape#PhenoScape_IDS IDS evidence_code2.obo yeast 2-hybrid evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IPI: yeast two-hybrid assay evidence_code2.obo differential methylation hybridization evidence evidence_code2.obo co-immunoprecipitation evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IPI: co-immunoprecipitation evidence_code2.obo morphological similarity evidence Used when an annotation is made based on the similarity of the shape, structure or overall configuration of structures. PhenoScape:IMS http://purl.org/obo/owl/PhenoScape#PhenoScape_IMS IMS evidence_code2.obo Sos-recruitment assay evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IPI: Sos-recruitment assay evidence_code2.obo experimental genomic evidence Experimental evidence that characterizes an attribute of the genome underlying a gene product. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC inferred from genomic analysis evidence_code2.obo split-ubiquitin assay evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IPI: split-ubiquitin assay evidence_code2.obo gene expression similarity evidence Used when an annotation is made based on the similarity of expression of genes in structures. PhenoScape:IGES http://purl.org/obo/owl/PhenoScape#PhenoScape_IGES IGES evidence_code2.obo far-Western evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IPI: far-Western analysis evidence_code2.obo methylation-specific polymerase chain reaction evidence methylation-specific PCR evidence evidence_code2.obo Southern hybridization evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED ISS: Southern blotting evidence_code2.obo affinity chromatography evidence "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. A type of ligand binding evidence resulting 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 http://purl.org/obo/owl/ECO#ECO_MCC TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: affinity chromatography evidence_code2.obo phylogenetic evidence A type of similarity that indicates common ancestry. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC PhenoScape:IP http://purl.org/obo/owl/PhenoScape#PhenoScape_IP IP PhenoScape:IP http://purl.org/obo/owl/PhenoScape#PhenoScape_IP evidence_code2.obo targeting sequence prediction evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED ISS: targeting sequence prediction evidence_code2.obo polymerase chain reaction evidence PCR evidence evidence_code2.obo transmembrane domain prediction evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED ISS: transmembrane domain prediction evidence_code2.obo gene neighbors evidence Genomic cluster analyses include synteny and operon structure. Evidence that supports the identity of a gene product on the basis of the identity of neighboring genes. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC GOC:mg http://purl.org/obo/owl/GOC#GOC_mg ICL inferred from genome cluster evidence_code2.obo GO_REF:0000025 http://purl.org/obo/owl/GO_REF#GO_REF_0000025 immunoprecipitation evidence Used when an annotation is made based on a method that precipitates a multivalent antigen by a bivalent antibody. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: immunoprecipitation evidence_code2.obo intermethylated site amplification evidence evidence_code2.obo immunolocalization evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IDA: immunolocalization evidence_code2.obo biological system reconstruction The biological system in question might be a multi-step process or a physical complex comprising several components. A common basis for system reconstruction is orthology, where all of the components of an experimentally characterized complex exist in one organism; if a second organism contains orthologs of all components, then the existence of the complex is inferred. In the case of a genome-wide analysis, a gene product is said to fulfill a necessary function for a pathway or complex when, with all of the other necessary functions or components also present, the pathway or complex is reconstructed. Evidence based on reconstruction of a biological system that is based on an existing experimentally supported model of that biological system. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC GOC:mg http://purl.org/obo/owl/GOC#GOC_mg inferred from system reconstruction ISR evidence_code2.obo restriction landmark genomic scanning evidence RLGS evidence evidence_code2.obo immunogold labelling evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IDA: immunogold labelling evidence_code2.obo epitope-tagged protein immunolocalization evidence Used when an annotation is made based on immunolocalization of recombinant proteins fused with epitopes that are recognized by antibodies. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: immunolocalization of epitope-tagged protein evidence_code2.obo oligonucleotide microarray evidence evidence_code2.obo biological assay evidence Direct assay evidence that is derived by using a living organism to measure the effect of a substance, factor, or condition. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: bioassay evidence_code2.obo electrophoretic mobility shift assay evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IDA: electrophoretic mobility shift assay evidence_code2.obo cDNA microarray evidence evidence_code2.obo in situ hybridization evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IDA: in situ hybridization evidence_code2.obo fractionation evidence evidence_code2.obo Affymetrix array experiment evidence evidence_code2.obo co-fractionation evidence Used when an annotation is made based on fractionation of a protein with other compounds, factors, or macromolecules. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: co-fractionation evidence_code2.obo microarray RNA expression level evidence Used when an annotation is made based on levels of RNA expression determined by microarray experiment. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: transcript levels (e.g. microarray data) evidence_code2.obo Nimblegen array evidence evidence_code2.obo Northern assay evidence Used when an annotation is made based on levels of RNA expression determined by a Northern blot experiment. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: transcript levels (e.g. Northerns) evidence_code2.obo reverse transcription polymerase chain reaction transcription evidence Used when an annotation is made based on levels of RNA expression determined by an RT-PCR experiment (quantitative or otherwise). TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: transcript levels (e.g. RT-PCR) RT-PCR transcription evidence evidence_code2.obo reverse transcription polymerase chain reaction evidence RT-PCR evidence evidence_code2.obo RNA protection assay evidence Used when an annotation is made based on levels of RNA expression determined by an RNA protection assay. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: RNA protection assay evidence_code2.obo Western blot evidence Used when an annotation is made based on levels of protein expression determined by a Western blot assay. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IEP: protein levels (e.g. Western blots) evidence_code2.obo expression library screen evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IEP: expression library screening evidence_code2.obo differential hybridization evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IEP: differential hybridization evidence_code2.obo subtractive hybridization evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IEP: subtractive hybridization evidence_code2.obo over expression analysis evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IMP: analysis of overexpression/ectopic expression phenotype evidence_code2.obo protein localization evidence evidence_code2.obo fusion protein localization evidence evidence_code2.obo green fluorescent protein fusion protein localization evidence GFP fusion protein localization evidence IDA: localization of GFP/YFP fusion protein evidence_code2.obo yellow fluorescent protein fusion protein localization evidence IDA: localization of GFP/YFP fusion protein YFP fusion protein localization evidence evidence_code2.obo beta-glucuronidase fusion protein localization evidence GUS fusion protein localization evidence GUS staining evidence IDA: localization of GUS fusion protein evidence_code2.obo beta-galactosidase fusion protein localization evidence LacZ fusion protein localization evidence evidence_code2.obo transport assay evidence IDA: transport assay evidence_code2.obo nucleic acid binding evidence evidence_code2.obo ribohomopolymer binding assay evidence IDA: ribohomopolymer binding assay evidence_code2.obo thin layer chromatography evidence 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 http://purl.org/obo/owl/ECO#ECO_MCC IDA: thin layer chromatography TLC evidence evidence_code2.obo protein:ion binding evidence evidence_code2.obo Southwestern blot evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IDA: Southwestern analysis evidence_code2.obo Northwestern blot evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IDA: Northwestern analysis evidence_code2.obo in vitro binding evidence IDA: in vitro binding assay evidence_code2.obo in vitro transcription reconstitution assay evidence IDA: in vitro reconstitution assay with recombinant protein evidence_code2.obo in vitro recombinant protein transcription reconstitution assay evidence IDA: in vitro reconstitution assay with recombinant protein evidence_code2.obo heterologous protein expression evidence IDA: protein expression in heterologous system evidence_code2.obo protein separation evidence evidence_code2.obo protein separation followed by direct sequencing evidence IDA: protein separation and direct sequencing evidence_code2.obo protein separation followed by fragment identification evidence IDA: protein separation and fragment identification evidence_code2.obo heterologous system uptake evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IDA: uptake assay in heterologous system evidence_code2.obo electrophysiology assay evidence evidence_code2.obo two-electrode voltage clamp experiment evidence IDA: two-electrode voltage clamp technique evidence_code2.obo transcription assay evidence_code2.obo transcriptional activation assay Used when an annotation is made based on assays that show transcriptional activation of a specific target reporter gene. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IDA: transcriptional activation assay evidence_code2.obo biochemical trait analysis evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IMP: analysis of biochemical trait evidence_code2.obo mutant physiological response evidence 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 http://purl.org/obo/owl/TAIR#TAIR_TED IMP: analysis of physiological response evidence_code2.obo mutant visible phenotype evidence Used when an annotation is made based on the visual examination of a mutant phenotype; for example, abnormalities in organism morphology. TAIR:TED http://purl.org/obo/owl/TAIR#TAIR_TED IMP: analysis of visible trait evidence_code2.obo genomic context evidence This type of evidence might include identity of neighboring genes, operon structure, synteny, phylogenetic analysis, or other whole-genome analysis. An evidence type that is based on the location of a gene, which gives rise to a gene product, within the genome. ECO:go http://purl.org/obo/owl/ECO#ECO_go ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo in vivo assay evidence evidence_code2.obo animal model system study evidence A type of experimental evidence arising from the investigation of an animal model system. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo clinical study evidence A type of experimental evidence arising from a controlled investigation that uses human subjects. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo in vitro assay evidence evidence_code2.obo in vitro culture assay evidence ex vivo assay evidence_code2.obo cell-free assay evidence in vitro assay evidence_code2.obo enzyme inhibition experiment evidence evidence_code2.obo sequence alignment evidence Used when a sequence alignment is the basis for making an annotation, but only when the alignment has been manually reviewed; or if the information is in a published paper, the authors have manually reviewed the evidence. Such alignments may be pairwise alignments or multiple alignments. BLAST produces pairwise alignments and any annotations based solely on the evaluation of BLAST results should use this code. url:http://www.geneontology.org/GO.evidence.shtml http://purl.org/obo/owl/url#url_http://www.geneontology.org/GO.evidence.shtml inferred from sequence alignment GO:ISA http://purl.org/obo/owl/GO#GO_ISA ISA GO:ISA http://purl.org/obo/owl/GO#GO_ISA evidence_code2.obo ECO:00000057 sequence orthology evidence Orthology is a relationship between genes in different species indicating that the genes derive from a common ancestor. Orthology is established by multiple criteria generally 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 http://purl.org/obo/owl/url#url_http://www.geneontology.org/GO.evidence.shtml inferred from sequence orthology GO:ISO http://purl.org/obo/owl/GO#GO_ISO ISO GO:ISO http://purl.org/obo/owl/GO#GO_ISO ortholog evidence evidence_code2.obo ECO:00000060 match to sequence model evidence 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. Sequence similarity evidence that is based on a sequence-based statistical model that predicts the function of a gene product. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC url:http://www.geneontology.org/GO.evidence.shtml http://purl.org/obo/owl/url#url_http://www.geneontology.org/GO.evidence.shtml inferred from sequence model GO:ISM http://purl.org/obo/owl/GO#GO_ISM ISM GO:ISM http://purl.org/obo/owl/GO#GO_ISM evidence_code2.obo ECO:00000063 automatic assertion 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. An assertion method that does not involve human review. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC IEA GOECO:IEA http://purl.org/obo/owl/GOECO#GOECO_IEA inferred from electronic annotation GOECO:IEA http://purl.org/obo/owl/GOECO#GOECO_IEA evidence_code2.obo ECO:00000067 GO_REF:0000004 http://purl.org/obo/owl/GO_REF#GO_REF_0000004 GO_REF:0000023 http://purl.org/obo/owl/GO_REF#GO_REF_0000023 GOECO:IEA http://purl.org/obo/owl/GOECO#GOECO_IEA author statement An evidence type that is based on an assertion by the author of a paper, which is read by a curator. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo curator inference An evidence type that is based on conclusions drawn by a curator. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo BLAST evidence A type of sequence alignment evidence obtained with basic local alignment search tool (BLAST). ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo nucleotide BLAST evidence BLAST evidence from aligning nucleotide sequence with nucleotide sequence. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo protein BLAST evidence BLAST evidence from aligning amino acid or translated nucleotide sequence with amino acid or translated nucleotide sequence. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo BLAST evidence used in automatic assertion A type of BLAST evidence that is used in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo nucleotide BLAST evidence used in automatic assertion Nucleotide BLAST evidence that is used in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo protein BLAST evidence used in automatic assertion Protein BLAST evidence that is used in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo combinatorial evidence 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. A type of evidence that arises out of the integration of more than one line of evidence. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC inferred from in-silico analysis evidence_code2.obo ECO:0000036 ECO:0000043 combinatorial evidence used in automatic assertion 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. A type of combinatorial analysis that is used in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo biological aspect of descendant evidence 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. 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 http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo rapid divergence from ancestral sequence evidence Long branch lengths indicate that descendant sequences may have acquired different or additional functions than the ancestral sequence. A type of phylogenetic evidence characterized by long phylogenetic tree branch lengths following a duplication event. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo phylogenetic determination of loss of key residues evidence The loss of certain residues important for function can indicate that a sequence lacks a particular function. A type of phylogenetic evidence characterized by the absence of key sequence residues. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo assertion method A means by which a statement is made about an entity. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo manual assertion 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. An assertion method that involves human review. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo nucleotide sequencing assay evidence A sequencing assay result for a biopolymer that comprises nucleotides. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC DNA sequencing OBI:0000626 http://purl.org/obo/owl/OBI#OBI_0000626 evidence_code2.obo sequencing assay evidence A type of experimental evidence where the order of molecules that constitute a biopolymer is determined. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC OBI:0600047 http://purl.org/obo/owl/OBI#OBI_0600047 evidence_code2.obo high throughput nucleotide sequencing assay evidence Typically thousands to millions of reads are produced in parallel. A nucleotide sequencing assay result that is derived from a parallelized sequencing technique. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo Illumina sequencing evidence 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. A high throughput nucleotide sequencing result derived by Illumina (Solexa) sequencing technology. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC Solexa sequencing result OBI:0000724 http://purl.org/obo/owl/OBI#OBI_0000724 evidence_code2.obo 454 pyrosequencing evidence 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. A high throughput nucleotide sequencing result derived by 454 pyrosequencing technology. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC pyrosequencing OBI:0000730 http://purl.org/obo/owl/OBI#OBI_0000730 evidence_code2.obo SOLiD sequencing evidence 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. A high throughput nucleotide sequencing result derived by SOLiD sequencing technology. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC OBI:0000706 http://purl.org/obo/owl/OBI#OBI_0000706 evidence_code2.obo chain termination sequencing evidence 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. A nucleotide sequencing assay result derived by the chain termination sequencing method. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC OBI:0000695 http://purl.org/obo/owl/OBI#OBI_0000695 dye terminator sequencing Sanger sequencing evidence_code2.obo chromatin immunoprecipitation evidence 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). An immunoprecipitation experiment that is used to identify a protein binding site on a genomic DNA sequence. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC ChIP evidence evidence_code2.obo chromatin immunoprecipitation-PCR evidence A chromatin immunoprecipitation (ChIP) experiment that uses polymerase chain reaction (PCR) for DNA detection. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC ChIP-PCR evidence evidence_code2.obo chromatin immunoprecipitation-qPCR evidence A chromatin immunoprecipitation (ChIP) experiment that uses quantitative polymerase chain reaction (qPCR) for DNA detection. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC ChIP-qPCR evidence evidence_code2.obo chromatin immunoprecipitation-seq evidence A chromatin immunoprecipitation (ChIP) experiment that uses high-throughput sequencing for DNA detection. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC OBI:0000716 http://purl.org/obo/owl/OBI#OBI_0000716 ChIP-seq evidence ChIP-SEQ evidence OBI:0000716 http://purl.org/obo/owl/OBI#OBI_0000716 evidence_code2.obo chromatin immunoprecipitation-chip evidence A chromatin immunoprecipitation (ChIP) experiment that uses a tiling microarray for DNA detection. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC ChIP-chip evidence ChIP-on-chip evidence evidence_code2.obo quantitative polymerase chain reaction evidence 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. A polymerase chain reaction experiment where the reaction product is quantified in real-time across cycles by means of fluorescent dyes. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC Q-PCR evidence qRT-PCR evidence quantitative PCR evidence real-time PCR evidence real-time polymerase chain reaction evidence evidence_code2.obo chromosome conformation capture-based evidence 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. 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 http://purl.org/obo/owl/ECO#ECO_MCC 3C chromosome conformation capture evidence_code2.obo chromosome conformation capture evidence 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. 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 http://purl.org/obo/owl/ECO#ECO_MCC 3C evidence_code2.obo circularized chromosome conformation capture evidence 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. 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 http://purl.org/obo/owl/ECO#ECO_MCC 4C chromosome conformation capture on chip circularized 3C evidence_code2.obo carbon-copy chromosome conformation capture evidence 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. A type of chromosome conformation capture-based evidence that is derived by performing ligation-mediated amplification (LMA) prior to product quantitation. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC 5C carbon-copy 3C evidence_code2.obo chromosome conformation capture-PCR evidence A type of chromosome conformation capture evidence that is derived by performing polymerase chain reaction (PCR) in the quantitation step. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC 3C 3C-PCR evidence_code2.obo chromosome conformation capture-qPCR evidence A type of chromosome conformation capture evidence that is derived by performing quantitative polymerase chain reaction (qPCR) in the quantitation step. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC 3C-qPCR 3C-quantitative PCR 3C-real-time PCR evidence_code2.obo Hi-C evidence 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. 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 http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo chromosome conformation capture sequencing evidence 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. 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 http://purl.org/obo/owl/ECO#ECO_MCC 3C sequencing 3C-seq 4C sequencing 4C-seq circularized 3C sequencing circularized 3C-seq evidence_code2.obo anatomical perturbation evidence Experimental phenotypic evidence where a structural feature of an organism is disrupted. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo environmental perturbation evidence Many environmental factors are subject to modification, such as temperature, pressure, humidity, radiation, and so forth. Experimental phenotypic evidence where the extra-organismal context of an organism is modified. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC mechanical constraint evidence evidence_code2.obo tissue ablation evidence 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. A type of anatomical perturbation that is based on disruption of tissue. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC ablated tissue evidence evidence_code2.obo tissue grafting evidence A type of anatomical perturbation that is based on adding tissue to an organism through a graft procedure. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo combinatorial evidence used in manual assertion 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. A type of combinatorial analysis that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo computational combinatorial evidence used in manual assertion A type of computational combinatorial analysis that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC inferred from reviewed computational analysis GOECO:RCA http://purl.org/obo/owl/GOECO#GOECO_RCA RCA GOECO:RCA http://purl.org/obo/owl/GOECO#GOECO_RCA evidence_code2.obo GOECO:RCA http://purl.org/obo/owl/GOECO#GOECO_RCA computational combinatorial evidence used in automatic assertion A type of computational combinatorial analysis that is used in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo sequence alignment evidence used in manual assertion Sequence alignment evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC inferred from sequence alignment GOECO:ISA http://purl.org/obo/owl/GOECO#GOECO_ISA ISA GOECO:ISA http://purl.org/obo/owl/GOECO#GOECO_ISA evidence_code2.obo GOECO:ISA http://purl.org/obo/owl/GOECO#GOECO_ISA sequence alignment evidence used in automatic assertion Sequence alignment evidence that is used in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo sequence similarity evidence used in automatic assertion Sequence similarity evidence that is used in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo sequence similarity evidence used in manual assertion Sequence similarity evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo GOECO:ISS http://purl.org/obo/owl/GOECO#GOECO_ISS similarity evidence used in automatic assertion Similarity evidence that is used in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo similarity evidence used in manual assertion Similarity evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo genetic similarity evidence used in manual assertion Genetic similarity evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo genetic similarity evidence used in automatic assertion Genetic similarity evidence that is used in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo match to sequence model evidence used in manual assertion A match to sequence model evidence that is employed in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo GO_REF:0000011 http://purl.org/obo/owl/GO_REF#GO_REF_0000011 GOECO:ISM http://purl.org/obo/owl/GOECO#GOECO_ISM match to sequence model evidence used in automatic assertion A match to sequence model evidence that is employed in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo GO_REF:0000002 http://purl.org/obo/owl/GO_REF#GO_REF_0000002 GO_REF:0000019 http://purl.org/obo/owl/GO_REF#GO_REF_0000019 motif similarity evidence used in manual assertion Motif similarity evidence that is employed in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo motif similarity evidence used in automatic assertion Motif similarity evidence that is employed in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo match to InterPro signature evidence used in automatic assertion A match to InterPro signature evidence that is employed in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo match to InterPro signature evidence used in manual assertion A match to InterPro signature evidence that is employed in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo targeting sequence prediction evidence used in automatic assertion A targeting sequence prediction that is employed in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo targeting sequence prediction evidence used in manual assertion A targeting sequence prediction that is employed in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo transmembrane domain prediction evidence used in automatic assertion Transmembrane domain prediction that is employed in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo transmembrane domain prediction evidence used in manual assertion Transmembrane domain prediction that is employed in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo sequence orthology evidence used in automatic assertion Sequence orthology evidence that is employed in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC Ortholog evidence evidence_code2.obo GO_REF:0000003 http://purl.org/obo/owl/GO_REF#GO_REF_0000003 GO_REF:0000019 http://purl.org/obo/owl/GO_REF#GO_REF_0000019 GO_REF:0000035 http://purl.org/obo/owl/GO_REF#GO_REF_0000035 sequence orthology evidence used in manual assertion Sequence orthology evidence that is employed in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC Ortholog evidence evidence_code2.obo GOECO:ISO http://purl.org/obo/owl/GOECO#GOECO_ISO enzyme-linked immunoabsorbent assay evidence An immunological assay that binds an antigen to a substrate and utilizes an antibody directly or indirectly linked to an enzyme to determine the amount of bound antigen. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC ELISA enzyme-linked immunosorbent assay evidence_code2.obo flow cytometry evidence A direct assay that passes a stream of cells or particles past a light source, followed by using a detector to monitor light scatter or fluorochrome excitation to characterize the cells or particles. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC FCM evidence_code2.obo experimental evidence used in manual assertion A type of experimental evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo GOECO:EXP http://purl.org/obo/owl/GOECO#GOECO_EXP expression evidence used in manual assertion A type of expression pattern evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo GOECO:IEP http://purl.org/obo/owl/GOECO#GOECO_IEP array experiment evidence used in manual assertion A type of array experiment evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo Affymetrix array experiment evidence used in manual assertion A type of Affymetrix array experiment evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo cDNA microarray evidence used in manual assertion A type of evidence arising from a cDNA microarray experiment that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo CpG island microarray evidence used in manual assertion A type of evidence arising from a CpG island microarray experiment that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo expression microarray evidence used in manual assertion A type of expression microarray evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo genomic microarray evidence used in manual assertion A type of evidence arising from a genomic microarray experiment that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo Nimblegen array evidence used in manual assertion A type of evidence arising from a Nimblegen array experiment that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo oligonucleotide microarray evidence used in manual assertion A type of evidence arising from an oligonucleotide microarray experiment that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo Western blot evidence used in manual assertion A type of Western blot assay that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo protein expression level evidence used in manual assertion A type of protein expression level analysis that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo expression library screen evidence used in manual assertion A type of expression library screen data that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo heterologous protein expression evidence used in manual assertion A type of heterologous protein expression analysis that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo spatial pattern of protein expression evidence used in manual assertion A type of protein expression spatial pattern analysis that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo protein expression evidence used in manual assertion A type of protein expression analysis that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo microarray RNA expression level evidence used in manual assertion A type of microarray RNA expression level data that is used in manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo transcript expression level used in manual assertion A type of transcript expression level data that is used in manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo differential hybridization evidence used in manual assertion A type of differential hybridization experiment that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo RNA protection assay evidence used in manual assertion A type of RNA protection assay that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo spatial pattern of transcript expression evidence used in manual assertion A type of spatial pattern of transcript expression analysis that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo subtractive hybridization evidence used in manual assertion A type of subtractive hybridization experiment that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo transcript expression evidence used in manual assertion A type of transcript expression evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo morpholino experiment evidence 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. A type of experimental phenotypic evidence that uses anti-sense by introducing morpholino oligonucleotides into the cytosol of a cell. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC anti-sense evidence_code2.obo systematic evolution of ligands by exponential amplification evidence 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. 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 http://purl.org/obo/owl/ECO#ECO_MCC url:http://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment http://purl.org/obo/owl/url#url_http://en.wikipedia.org/wiki/Systematic_Evolution_of_Ligands_by_Exponential_Enrichment in vitro evolution evidence in vitro selection evidence SELEX evidence evidence_code2.obo bacterial one-hybrid evidence 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. A type of evidence arising from a hybrid interaction experiment 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 http://purl.org/obo/owl/ECO#ECO_MCC B1H evidence evidence_code2.obo RNA-seq evidence 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. A type of transcript expression evidence based on high-throughput (HT) sequencing of fragmented cDNA molecules. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC RNA sequencing whole transcriptome shotgun sequencing PMID:18611170 http://purl.org/obo/owl/PMID#PMID_18611170 WTSS evidence_code2.obo green fluorescent protein transcript localization evidence This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of green fluorescent protein". A transcriptional activation assay that uses a green fluorescent protein (GFP) reporter gene. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC localization of GFP transcript evidence_code2.obo LacZ transcript localization evidence This term describes transcriptional activation; to describe immunolocalization of the protein, use the term "immunolocalization of LacZ protein". A transcriptional activation assay that uses a LacZ reporter gene. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo cleavage arrested development evidence 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. A type of experimental phenotypic evidence where embryonic development proceeds although cytokinesis is blocked. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo cytochalasin experiment evidence Cytochalasin inhibits cytokinesis by blocking the formation of contractile microfilaments. A type of cleavage arrested development that arises after treatment with cytochalasin. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo green fluorescent protein immunolocalization evidence This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of green fluorescent protein transcript". A type of immunolocalization experiment data that was generated using green fluorescent protein (GFP) as a marker. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC GFP immunolocalization evidence evidence_code2.obo beta-galactosidase protein immunolocalization evidence This term describes immunolocalization of the protein; to describe transcriptional activation, use the term "localization of LacZ transcript". A type of immunolocalization experiment data that was generated using LacZ protein as a marker. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC LacZ protein immunolocalization evidence evidence_code2.obo author statement used in manual assertion A type of author statement that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo non-traceable author statement used in manual assertion A type of non-traceable author statement that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC NAS GOECO:NAS http://purl.org/obo/owl/GOECO#GOECO_NAS non-traceable author statement GOECO:NAS http://purl.org/obo/owl/GOECO#GOECO_NAS evidence_code2.obo GOECO:NAS http://purl.org/obo/owl/GOECO#GOECO_NAS traceable author statement used in manual assertion A type of traceable author statement that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC TAS GOECO:TAS http://purl.org/obo/owl/GOECO#GOECO_TAS traceable author statement GOECO:TAS http://purl.org/obo/owl/GOECO#GOECO_TAS evidence_code2.obo GOECO:TAS http://purl.org/obo/owl/GOECO#GOECO_TAS curator inference used in manual assertion A type of curator inference that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo GOECO:IC http://purl.org/obo/owl/GOECO#GOECO_IC inference from background scientific knowledge used in manual assertion A type of inference from background scientific knowledge that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo no biological data found used in manual assertion A type of no biological data found that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo GOECO:ND http://purl.org/obo/owl/GOECO#GOECO_ND biological aspect of ancestor evidence 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. 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 http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo cap analysis of gene expression evidence 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. 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 http://purl.org/obo/owl/ECO#ECO_MCC CAGE PMID:16489339 http://purl.org/obo/owl/PMID#PMID_16489339 evidence_code2.obo nano-cap analysis of gene expression evidence 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. 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 http://purl.org/obo/owl/ECO#ECO_MCC nanoCAGE PMID:20543846 http://purl.org/obo/owl/PMID#PMID_20543846 evidence_code2.obo imported information An evidence type that is based on work performed by a person or group prior to a use by different person or group. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo imported information used in manual assertion A type of imported information that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo imported information used in automatic assertion A type of imported information that is used in an automatic assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo direct assay evidence used in manual assertion A type of direct assay evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC IDA GOECO:IDA http://purl.org/obo/owl/GOECO#GOECO_IDA inferred from direct assay GOECO:IDA http://purl.org/obo/owl/GOECO#GOECO_IDA evidence_code2.obo GOECO:IDA http://purl.org/obo/owl/GOECO#GOECO_IDA mutant phenotype evidence used in manual assertion A type of mutant phenotype evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC IMP GOECO:IMP http://purl.org/obo/owl/GOECO#GOECO_IMP inferred from mutant phenotype GOECO:IMP http://purl.org/obo/owl/GOECO#GOECO_IMP evidence_code2.obo GOECO:IMP http://purl.org/obo/owl/GOECO#GOECO_IMP genetic interaction evidence used in manual assertion A type of genetic interaction experiment evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC IGI GOECO:IGI http://purl.org/obo/owl/GOECO#GOECO_IGI inferred from genetic interaction GOECO:IGI http://purl.org/obo/owl/GOECO#GOECO_IGI evidence_code2.obo GOECO:IGI http://purl.org/obo/owl/GOECO#GOECO_IGI genomic context evidence used in manual assertion A type of genomic context evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC IGC GOECO:IGC http://purl.org/obo/owl/GOECO#GOECO_IGC inferred from genomic context GOECO:IGC http://purl.org/obo/owl/GOECO#GOECO_IGC evidence_code2.obo GOECO:IGC http://purl.org/obo/owl/GOECO#GOECO_IGC biological aspect of ancestor evidence used in manual assertion A type of biological aspect of ancestor evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC IBA GOECO:IBA http://purl.org/obo/owl/GOECO#GOECO_IBA inferred from biological aspect of ancestor GOECO:IBA http://purl.org/obo/owl/GOECO#GOECO_IBA evidence_code2.obo GOECO:IBA http://purl.org/obo/owl/GOECO#GOECO_IBA biological aspect of descendant evidence used in manual assertion A type of biological aspect of descendant evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC IBD GOECO:IBD http://purl.org/obo/owl/GOECO#GOECO_IBD inferred from biological aspect of descendant GOECO:IBD http://purl.org/obo/owl/GOECO#GOECO_IBD evidence_code2.obo GOECO:IBD http://purl.org/obo/owl/GOECO#GOECO_IBD phylogenetic determination of loss of key residues evidence used in manual assertion A type of phylogenetic determination of loss of key residues evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC IKR GOECO:IKR http://purl.org/obo/owl/GOECO#GOECO_IKR IMR GOECO:IKR http://purl.org/obo/owl/GOECO#GOECO_IKR inferred from key residues GOECO:IKR http://purl.org/obo/owl/GOECO#GOECO_IKR inferred from missing residues GOECO:IKR http://purl.org/obo/owl/GOECO#GOECO_IKR evidence_code2.obo GOECO:IKR http://purl.org/obo/owl/GOECO#GOECO_IKR GOECO:IMR http://purl.org/obo/owl/GOECO#GOECO_IMR rapid divergence from ancestral sequence evidence used in manual assertion A type of rapid divergence from ancestral sequence evidence that is used in a manual assertion. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC inferred from rapid divergence GOECO:IRD http://purl.org/obo/owl/GOECO#GOECO_IRD IRD GOECO:IRD http://purl.org/obo/owl/GOECO#GOECO_IRD evidence_code2.obo GOECO:IRD http://purl.org/obo/owl/GOECO#GOECO_IRD imported manually asserted information used in automatic assertion 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 http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo imported automatically asserted information used in automatic assertion Evidence 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 http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo imaging assay evidence Direct assay evidence derived from analysis of an image. ECO:MCC http://purl.org/obo/owl/ECO#ECO_MCC evidence_code2.obo chromatography evidence 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 http://purl.org/obo/owl/ECO#ECO_MCC chromatographic evidence evidence_code2.obo used_in evidence_code2.obo