Further comment

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Hi,

I'd like to bring the IMP IGI discussion back to the original suggestion, which has been lost in side issue of whether these two codes should be merged. I agree that they should not be merged.

In commenting on the draft of the proposed new evidence codes documentation, Val and Midori brought up some confusion about the use of IGI to annotated genes where a role is inferred based on a mutation in a different gene.

In a lot of ways it seems that it would be a simpler decision between IMP and IGI if the only question is how many genes are mutated?

   1 ==> IMP or
   more than 1 ==> IGI.

Right now, to make the decision, you have to ask a more complicated question that involves which gene is being annotated.

-Karen


On Thu, 13 Sep 2007, Michael Ashburner wrote:

> I also agree with Val, we certainly need both of these, they are very different biologically. > > Michael > > On 11 Sep 2007, at 17:03, Judith Blake wrote: > >> I agree with Val. With multicellular organisms, perhaps even more particularly, it's a long trip between observable heritable phenotypes and understanding the precise genetic interactions that are producing them. > > Judy >


> Benjamin Hitz wrote: > > >>>> Do we really need IGI and IMP? Is the only difference technically that IGI = double (or 2+?) mutant, IPI = single mutant?>> > > Valerie Wood wrote: > We need. > > These are very different types of biological data. The IMP the annotation is derived in some way directly from the *observable phenotype*, but with IGI it is an inference from the the actual *interaction* (the phenotype may be suppressed or the cell may be dead).

> Our current use of IGI includes things which aren't 'truly' genetic interactions but on the whole, it is likely that most databases have recorded non- canonical use and these can be filtered (i.e functional complementation by a heterologous system can be filtered because the 'with' column will contain a entry from another taxon. > > Val