2010 GO camp downstream effect

From GO Wiki
Jump to navigation Jump to search

1. Background

2. Review of current GO annotation practices

  • Annotating signaling biological processes to transcription factors
  • when not to capture phenotypes : from 22nd Feb Jamboree call [1], Tanya: It's not uncommon for the initial publications to describe a mutant phenotype, with a developmental defect, and then later publications to describe much more explicit functions or processes. You should always annotate based on whatever evidence is available. Once you've done that, the question becomes, "When do we keep or remove the phenotype-based annotations?" At TAIR, their policy is to keep the developmental terms if they think that their users would expect to see them. Some participants suggested that one would expect all orthologs to have the same development-type annotations, across organisms. Others disagreed with this expectation.


3. Proposed annotation policy

4. Examples (papers) and discussion of GO annotation issues

  • Val: Sc nat5 is missing downstream annotations, such as sporulation. See NAT5


  • (Submitted by Pascale): There are several SF items about growth/cell growth/cell proliferation. I know some of the terms were done to accommodate experiments done in Dicty - often people look at the rate of cell proliferation as a general phenotype, and we have been capturing this. It's very high level and usually IMP, but in the absence of other information it seems relevant (otherwise people would not bother testing it).

What do people think about this? To me it's similar to the issue of annotating from IEP or to high level developmental terms by IMP. The question is, what data are too general to be useful to capture?

  • Organismal behaviors are always quite controversial. For example, lonp gene of rat is annotated to aging.

5. Suggestions for Quality Control procedures


Back to 2010_GO_camp_Meeting_Agenda