[go] Boundary between IMP and IGI

Peter D'Eustachio deustp01 at med.nyu.edu
Fri Sep 14 06:04:15 PDT 2007 

Sure. I guess I'm mostly placing a bet on how much this new definition will 
fix. I don't see that it will hurt anything, so there's no objection from 
here about making the change.

Peter

----- Original Message ----- 
From: "Karen Christie" <kchris at genome.stanford.edu>
To: "Peter D'Eustachio" <eustachi at cshl.edu>
Cc: "Karen Christie" <kchris at genome.stanford.edu>; "GO mailing list" 
<go at genome.stanford.edu>
Sent: Thursday, September 13, 2007 6:04 PM
Subject: Re: [go] Boundary between IMP and IGI


> 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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