Email synopsis: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
(New page: Boundary between IMP and IGI ------------------------------------------------------- In response to the new draft of the evidence code documentation, some discussion came up between Midor...)
 
No edit summary
Line 1: Line 1:
Boundary between IMP and IGI
-------------------------------------------------------


In response to the new draft of the evidence code documentation, some
Hi,
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
A couple comments on this thread.
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
First, I agree with numerous comments that IMP and IGI should remain separate codes.
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
All I'd like to do is simplify the boundary between these two codes. Particularly in trying to come up with a decision tree/flow chart for making evidence code decisions, and in thinking about experiences in trying to teach people how to make GO annotations and select evidence codes, it would be really nice if the boundary were something simple like "Is one gene mutated? or more than one?" versus something where you also have to include a question about which gene are you annotating.
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.
Below, I have inserted specific responses to a couple of Val's comments.


-Karen
-Karen




**IMP:
On Tue, 11 Sep 2007, Valerie Wood wrote:


> mutation in gene B provides information about gene A being
> 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.
> 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):
Hmmm, yes, probably somewhat unfortunate that we have been so reluctant to add evidence codes that we kludged cross-species expression into IGI...
  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):
On Tue, 11 Sep 2007, Valerie Wood wrote:
  This is still a bit is unclear to me
>
> The pombe community are very fond of 'localization dependency' experiments to dissect the
> pathways involved in the function and formation of large proteinaceous complexes such as the spindle pole body, or the polarisome, or signaling networks like the SIN. For example:
> PMID:12034771
> PMID:11676915
> PMID: 16775007
> PMID: 10864871
>
> I've curated these as IGI (in accordance with current documentation), but I'd be happy to move them to IMP as only a single gene is mutated. It has never bothered me too much that they are IGI because one could predict that if there is a 'localization dependency', and because the experiments are targeted at gene products known to exist in the same complex or pathway, and have the same phenotype when mutated, then the pair of genes would also display a genetic interaction (although these experiments don't show one).
>
> If I did move these to IMP I would like to be able to continue to capture the 'gene product' which didn't localize properly in the 'with' column. But would be confusing because this is usually the allele for IMP. Alternatively I could just filter out this from the GO submission file (although it is biologically useful information).


  "We also use this code for situations where a mutation in gene A
If these go to IMP, I don't think the with column would be the place to record the mislocalized gene product. The with column should remain the place to record the allele, or at least the gene, which is mutated.
  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
To record the mislocalized gene product, I think you might need to use the proposed structured note column that David and Chris are working on a proposal for.
  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):
> 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
> Karen Christie wrote:
   > seems they are OK as IGI, so I just wanted to double check.........
>
 
>> Boundary between IMP and IGI
   Your annotations are consistent with the existing documentation. What
>> -------------------------------------------------------
   I'm saying is that I think the documentation should recommend IMP for
>>
   these.
>> 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
   I think I still wouldn't put B is 'with' with IMP, because a few
>> versus the IMP evidence codes. As this issue was not a specific gripe
   groups would put the allele of A used in the experiment, and others
>> of anyone on the Evidence Code Committee, it was not discussed.
   would leave 'with' blank.
>>
 
>> However, one of the goals of this revision was to have guidelines that
   >  The original documentation says: # Inference about one gene drawn
>> make sense and I completely see the point that it doesn't really make
   > from the phenotype of a mutation in a different gene I don't have an
>> sense to say that making an inference from a strain with one mutation
   > example of this though. I forgot what it is used for, although I
>> is a genetic interaction, even when you are annotating a gene other
   > used to know......
>> than the one that is mutant.
 
>>
   I would also prefer to recommend IMP for these.
>> 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.
>>
>>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

Revision as of 12:32, 20 September 2007

Hi,

A couple comments on this thread.

First, I agree with numerous comments that IMP and IGI should remain separate codes.

All I'd like to do is simplify the boundary between these two codes. Particularly in trying to come up with a decision tree/flow chart for making evidence code decisions, and in thinking about experiences in trying to teach people how to make GO annotations and select evidence codes, it would be really nice if the boundary were something simple like "Is one gene mutated? or more than one?" versus something where you also have to include a question about which gene are you annotating.

Below, I have inserted specific responses to a couple of Val's comments.

-Karen


On Tue, 11 Sep 2007, Valerie Wood wrote:

> 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.

Hmmm, yes, probably somewhat unfortunate that we have been so reluctant to add evidence codes that we kludged cross-species expression into IGI...

On Tue, 11 Sep 2007, Valerie Wood wrote: > > The pombe community are very fond of 'localization dependency' experiments to dissect the > pathways involved in the function and formation of large proteinaceous complexes such as the spindle pole body, or the polarisome, or signaling networks like the SIN. For example: > PMID:12034771 > PMID:11676915 > PMID: 16775007 > PMID: 10864871 > > I've curated these as IGI (in accordance with current documentation), but I'd be happy to move them to IMP as only a single gene is mutated. It has never bothered me too much that they are IGI because one could predict that if there is a 'localization dependency', and because the experiments are targeted at gene products known to exist in the same complex or pathway, and have the same phenotype when mutated, then the pair of genes would also display a genetic interaction (although these experiments don't show one). > > If I did move these to IMP I would like to be able to continue to capture the 'gene product' which didn't localize properly in the 'with' column. But would be confusing because this is usually the allele for IMP. Alternatively I could just filter out this from the GO submission file (although it is biologically useful information).

If these go to IMP, I don't think the with column would be the place to record the mislocalized gene product. The with column should remain the place to record the allele, or at least the gene, which is mutated.

To record the mislocalized gene product, I think you might need to use the proposed structured note column that David and Chris are working on a proposal for.


> Val > > > > > > > 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. >> >> > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.