[go] Boundary between IMP and IGI

[Karen Christie]

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.