Use cases for evidence codes

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  1. Use IPI to mine protein interaction data (Actually used)
  2. Discriminate between 'experimental' and 'computational' annotations (Actually used)
  3. Filter out IEAs (Actually used)
  4. Use them for an evidence based reasoner/score to either predict or confirm the gene's function/role in a process/localization. For example:
    1. Are there any Arabidopsis genes involved in the biological process 'leaf development' that were evaluated by IGI and IMP.If so give a list of interacting genes (based on IGI code) and info presented in WITH column.
    2. Give a list of rice genes that are orthologous to arabidopsis genes involved in the biological process 'leaf development' and were evaluated by IGI ONLY.
  5. Use in a script or query: the following queries finds potential unsubstantiated or stale ISS assignments:
  6. Evaluate quality by how many distinct types of evidence support an association
  7. IGI and IMP can be used to find predicted phenotypes for genes with common association by a different evidence type
  8. Presence of IDA tells me that a direct assay exists; reference tells me where to find it
  9. To determine what cross-references to GO to add to UniProtKB.