Chain of Evidence (Archived)

Chain of Evidence

Background

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.

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:

• Function: TUL1-Ub-ligase activity. ISS + IPI+ IMP allows us to make the assertion that this is a Ub-ligase.