How do we incorporate evidence codes?
From HAO Wiki
We should think about how we assign and incorporate evidence codes (http://bioportal.bioontology.org/visualize/36625) to homology statements. The evidence code ontology is also available as OBO.
The most relevant ones for us are likely:
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]
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]
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]
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]
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]
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]
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]
id: ECO:0000057 name: inferred from phenotypic similarity def: "Used when comparing organisms, in whole or in part, based on the outcomes of expressions of genotypes in their environments." [PhenoScape:IPTS]
id: ECO:0000060 name: inferred from positional similarity def: "Used when an annotation is made based on the similarity of the location and or arrangement of structures." [PhenoScape:IPS]
id: ECO:0000063 name: inferred from compositional similarity def: "Used when an annotation is made based on the similarity of the histological makeup of structures." [PhenoScape:ICS]
id: ECO:0000071 name: inferred from morphological similarity def: "Used when an annotation is made based on the similarity of the shape, structure or overall configuration of structures." [PhenoScape:IMS]
id: ECO:0000080 name: inferred from phylogeny def: "Used when an annotation is made based on the common ancestry of structures on a particular phylogenetic tree. Typically, other evidence (a type of similarity) supports a prior hypothesis of homology for these structures." [PhenoScape:IP]
Though there may be some instances where these ECOs are appropriate:
id: ECO:0000006 name: inferred from experiment def: "Used in an annotation to indicate that an experimental assay has been located the cited reference, whose results indicate a gene product's function, process involvement, or subcellular location (indicated by the GO term). The IE code is the parent code for the IDA, IMP, IGI, IEP and IPIexperimental codes. The IE evidence code can be used where any of the assays described for the IDA, IMP, IGI, IPI or IEP evidence codes is reported. However it is highly encouraged that groups should annotate to one of the more granular experimental codes (IDA, IMP, IGI, IPI or IEP ) instead of IE, and all curators directly involved in the GO Reference Genome annotation effort are obliged to use these and not IE. The IE code exists for groups who would like to contribute high-quality GO annotations that are produced from directly associating GO terms to gene products by citing experimental published results, but where the group is unable to fit the appropriate specific experimental GO evidence codes to each annotation." [GOC:ecd]
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]
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]
id: ECO:0000067 name: inferred from developmental similarity def: "Used when an annotation is made based on the similarity of embryological and/or post-embryonic origin of structures." [PhenoScape:IDS]
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]
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]
id: ECO:0000179 name: inferred from animal model system
Are any missing? What's the strategy for incorporating these codes. Do we create a homologous_to relationship that's stored elsewhere (i.e., in another database)?
