[go] Boundary between IMP and IGI

[Michael Ashburner]

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
>
> 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
>>>
>>>
>>>
>>>
>>
>>
>>
>
>