Chain of Evidence

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Evidence Summation

Background

  • We have 2 types of evidence summation:
    • A leads to B, B leads to C (chain of evidence)
    • Combination of 2 types of experiments is used (summation)

Chain of evidence

  • A leads to B, B leads to C

An example of this is when a curator makes an ISS annotation to a gene product A which is similar to geneproduct B and gene product B is annotated to termX with IC evidence code. This was discussed in great detail during couple of annotation calls. ISS from IC Proposal, Annotation Call Minutes

Summation of evidence

  • Annotation to a term is supported by 2 evidence codes

Often curators are faced with a situation where they review the entire body of literature for a gene product and use the comprehensive knowledge to make an annotation or use multiple lines of evidence from a single paper to support an annotation and one piece of evidence alone cannot support the annotation on its own. Although the individual groups have ways to display the evidence in a nested manner to imply that multiple pieces of evidence contributed to that annotation, the GAF file lists one annotation in a row and this situation is less than satisfactory. Can we come up with a system to encode the chain of evidence in an annotation so that it is machine readable and makes sense to a bench biologist.

We also want to be able to say that IMP is from PubMed-A and ISS is from PubMed-B. Can we say something like IMP from PMID:12345, ISS from PMID:54321?

Examples
  • Component ontology- Authors show ISS type evidence (hydropathy plot/sequence analysis) to show a protein is integral membrane protein, then in another experiment (fractionation) show that the gp localizes with a organelle marker and infer with the combined evidence that the protein is an integral membrane protein of that organelle. Examples in yeast: SHR3, SAC1, PHO84
  • Biological process: Papers picked for annotation jamboree (11/8/2010)
  • Function: TUL1-Ub-ligase activity. ISS + IPI+ IMP allows us to make the assertion that this is a Ub-ligase.
  • Paper A reports gpA is involved in wnt signaling. Paper B from IMP concludes that the gpA is involved in heart development. Combining these 2, one can infer that this gp is involved in wnt signaling during heart development.

Questions

  • What happens when you have 2 IDA experiments to support the result?