[go] Boundary between IMP and IGI

[Benjamin Hitz]

Do we really need IGI and IMP?   Is the only difference technically  
that IGI = double (or 2+?) mutant, IPI = single mutant?

Ben

On Sep 10, 2007, at 4:18 PM, Karen Christie wrote:

> Boundary between IMP and IGI
> -------------------------------------------------------
>
> In response to the new draft of the evidence code documentation, some
> discussion came up between Midori and Val about the usage of the IGI
> versus the IMP evidence codes. As this issue was not a specific gripe
> of anyone on the Evidence Code Committee, it was not discussed.
>
> However, one of the goals of this revision was to have guidelines that
> make sense and I completely see the point that it doesn't really make
> sense to say that making an inference from a strain with one mutation
> is a genetic interaction, even when you are annotating a gene other
> than the one that is mutant.
>
> We were also asked to make a decision tree/flow chart for evidence
> code decisions (I have a draft I'll send out later), and I think it
> would be a much simpler decision if there was a clear line between 1
> mutant gene and multiple mutant genes.
>
> I think it would make a lot more sense if any annotations made on the
> basis of mutation, or comparison between alleles, of a single gene
> should use IMP.  Since we already allow use of the with field for IMP
> to record the mutant allele, it might make more sense to use IMP for
> any annotation based on a phenotype of a single gene and just record
> the mutant allele in the with field. Since not all groups track
> alleles, perhaps we should also allow with for IMP to contain the name
> of the gene without specifically designating an allele.
>
> Below is transcript of the discussion that occurred on this issue.
>
> -Karen
>
>
> **IMP:
>
>> mutation in gene B provides information about gene A being
>> annotated. For this type of experiment, use the IGI code.  and IGI:
>> Inference about one gene drawn from the phenotype of a mutation in a
>> different gene
>
> Midori (15 Jun 2007):
>   I have always disagreed with this usage: I've argued that IMP  
> would be
>   more appropriate, because in the examples given, only one gene is
>   mutated, so the "combination of alterations" criterion for IGI is  
> not
>   met. But it's an argument that I lost years ago. Oh well.
>
> Val (22 Jun 2007):
>   This is still a bit is unclear to me
>
>   "We also use this code for situations where a mutation in gene A
>   provides information about the function, process, or component of  
> gene
>   B. If a mutation in gene A causes a mislocalization of gene B,  
> gene A
>   is annotated to protein localization with gene B in the with/from
>   column using IGI."
>
>   In the protein localization example above a mutation in gene A is
>   providing information about gene A (protein localization) not about
>   gene B (the protein localized).
>
>   I have made a number of these type of annotations to 'protein
>   localization, (the fission yeast community are very keen on
>   localization dependency experiments for functionally connected gene
>   products). However, I thought I had used the wrong evidence code
>   (using the existing documentation) and that they should be IMP (I
>   wanted to capture the protein localized and at the time I had no  
> other
>   way to do it). These were on my todo list to fix.  It now seems they
>   are OK as IGI, so I just wanted to double check.........
>
>   The original documentation says:
>   # Inference about one gene drawn from the phenotype of a mutation  
> in a
>   different gene I don't have an example of this though. I forgot what
>   it is used for, although I used to know......
>
> Midori (22 Jun 2007, in response to Val):
>   > I have made a number of these type of annotations to 'protein
>   > localization, (the fission yeast community are very keen on
>   > localization dependency experiments for functionally connected  
> gene
>   > products). However, I thought I had used the wrong evidence code
>   > (using the existing documentation) and that they should be IMP (I
>   > wanted to capture the protein localized and at the time I had no
>   > other way to do it). These were on my todo list to fix.  It now
>   > seems they are OK as IGI, so I just wanted to double  
> check.........
>
>   Your annotations are consistent with the existing documentation.  
> What
>   I'm saying is that I think the documentation should recommend IMP  
> for
>   these.
>
>   I think I still wouldn't put B is 'with' with IMP, because a few
>   groups would put the allele of A used in the experiment, and others
>   would leave 'with' blank.
>
>   >  The original documentation says: # Inference about one gene drawn
>   > from the phenotype of a mutation in a different gene I don't  
> have an
>   > example of this though. I forgot what it is used for, although I
>   > used to know......
>
>   I would also prefer to recommend IMP for these.

--
Ben Hitz
Senior Scientific Programmer ** Saccharomyces Genome Database ** GO  
Consortium
Stanford University ** hitz at genome.stanford.edu