Updated November 9, 2007
- Enzyme assays
- In vitro reconstitution (e.g. transcription)
- Immunofluorescence (for cellular component)
- Cell fractionation (for cellular component)
- Physical interaction/binding assay (sometimes appropriate for cellular component or molecular function)
The IDA evidence code is 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.
For transfection experiments or other experiments where a gene from one organism or tissue is put into a system that is not its normal environment, the annotator should use the author's intent and interpretation of the experiment as a guide as to whether IMP or IDA is appropriate. When the author is comparing differences between alleles, regardless of the simplicity or complexity of the assay, IMP is appropriate. When the author is using an expression system as a way to investigate the normal function of a gene product, IDA is appropriate.
Examples where the IDA evidence code should be used:
- Binding assays can provide direct assay evidence for annotating to the xxx binding molecular function terms. (Use IDA only when no identifier can be placed in the with/from column; when there is an appropriate ID for the with/from column, use IPI).
- Assays describing the isolation of a complex by immunoprecipitation of a tagged subunit should use IDA, not IPI. Thus this type of assay can provide IDA for annotation to a component term for the specific complex because it is a direct assay for a complex.
- Transfections into a cell line, overexpression, or ectopic expression of a gene when the expression system used is considered to be an assay system to address basic, normal functions of gene product even if it would not normally be expressed in that cell type or location. If the experiments were conducted to assess the normal function of the gene and the assay system is believed to reproduce this function, i.e., the authors would consider their experiment to be a direct assay, and not a comparison between various alleles of a gene, then the IDA code should be used. This is in contrast with a situation where overexpression affects the function or expression of the gene and that difference from normal is used to make an inference about the normal function; in this case use the IMP evidence code.
Examples where the IDA evidence code should not be used:
- Binding assays where it is possible to put an ID corresponding to the specific binding partner that was shown to interact directly the gene product being annotated should be annotated with the IPI code, not with IDA.
- Transfection into a cell line, overexpression, or ectopic expression of a gene where the effects of various alleles of a gene are compared to each other or to wild-type. For this type of experiment, annotate using IMP.