Chain of Evidence (Archived)

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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?