[go] Boundary between IMP and IGI

Karen Christie kchris at genome.Stanford.EDU
Thu Sep 13 15:04:01 PDT 2007 

While the point you bring up is quite valid, I think this issue is always 
true for IMP and IGI regardless of whether we make the minor change in the 
boundary between IMP and IGI that I am suggesting.


Right now the boundary can be phrased in these sentences:

1. If it's one mutation in the gene you are annotating, it's IMP.

2. If it's one mutation, but in a different gene than the one you are 
annotating, it's IGI.

3. If it's more than one mutation, it's IGI.

4. If it's any kind of cross species expression, it's IGI.


I just think that statements 1 and 2 should be collapsed into 1 statement, 
something like this:

If the annotation is based on a mutation in a single gene, use IMP.

-Karen




On Thu, 13 Sep 2007, Peter D'Eustachio wrote:

> The 1 => IMP, more_than_1 => IGI sounds tidy, but I think it's risky biology. 
> The "foreground" allele that the experimenter intends to study is always 
> being characterized in terms of its properties as expressed in interaction 
> with the background genome, in all its allelic complexity, so the distinction 
> is likely to be artifical in many cases. We're forced back onto the 
> experimenter's judgement as to how many of the alleles in the background 
> matter (and that judgement, in retrospect, is often wrong in the direction of 
> underestimating the number of alleles of other genes making significant 
> contributions).
>
> Peter D'E
>
> ----- Original Message ----- From: "Karen Christie" 
> <kchris at genome.stanford.edu>
> To: "Michael Ashburner" <ma11 at gen.cam.ac.uk>
> Cc: "Judith Blake" <jblake at informatics.jax.org>; "Valerie Wood" 
> <val at sanger.ac.uk>; "Benjamin Hitz" <hitz at genome.stanford.edu>; "Karen 
> Christie" <kchris at genome.stanford.edu>; "GO mailing list" 
> <go at genome.stanford.edu>
> Sent: Thursday, September 13, 2007 12:53 PM
> Subject: Re: [go] Boundary between IMP and IGI
>
>
>> 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
>>>> 
>>>> 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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