[go] Boundary between IMP and IGI

[Judith Blake]

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

Valerie Wood wrote:
> Benjamin Hitz wrote:
>
>>
>> Do we really need IGI and IMP?   Is the only difference technically  
>> that IGI = double (or 2+?) mutant, IPI = single mutant?
>
>
> 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
>
>
>
>
>>
>> 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
>>
>>
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