[Annotation] process-specific function annotations: a proposal

[jdeegan at ebi.ac.uk]

Hi,

Did you get responses to this?

I am forwarding the mail to the electron transport working group for
comment, as the original proposal at the previous consortium meeting came
from them.

Thanks,

Jen

> I think this is a good idea because the proposal addresses the Evidence
> Code
> Problem (TM) well.
>
>>1) When separate experiments are done in a paper that link a function and
>> a
> process, we capture the individual functional >data and process data by
> annotating the individual experiments. Then, we make an additional
> annotation to a
>>'process- specific function' using the EXP evidence code. In these
> annotations EXP would indicate that there were >several types of
> experimental evidence in the paper that led to the final conclusion.
>
> As long as the individual MF and BP annotations are made with one of the
> experimental codes, it is completely consistent to use the EXP code for
> the
> 'function-specific process' annotation.
>
> IDA + IDA = EXP
> IDA + IMP = EXP
>
> Example:
>
> DNA binding IDA
> regulation of transcription IDA
> DNA binding involved in regulation of transcription (aka transcription
> factor activity) EXP
>
>
>
>>2) When the function of a molecule is very well known and the authors do
>> an
> experiment in a paper that indicates a >process. If it is a
> well-established
> fact that the molecule only performs a certain function and the authors
> clearly indicate >the function-process link, we make a the process
> annotation in the usual way, and then  make the 'process-specific
> >function'
> annotation using the IC evidence code with the molecular function in the
> 'with' field.
>
> Annotations made in this fashion make explicit what is contained in the
> graph.
>
> Example:
>
> protein kinase activity IDA
> protein amino acid phosphorylation IC, evidence_with =GO:0004672 (protein
> kinase activity)
>
> At the meeting, we said that if we made the F-P link between 'protein
> kinase
> activity' and 'protein amino acid phosphorylation' in the graph, then
> anyone
> looking at annotations to the latter term using a browser that took into
> account the graph structure of GO would get any gene products annotated to
> 'protein kinase activity'.  The concern was raised over the annotation not
> being EXPLICIT and not present in the gene association file if the BP
> annotation was not made.
>
> David's proposal addresses this concern and makes use of the IC evidence
> code in a manner consistent with the current guidelines for using that
> code.
>
> My two cents,
>
> Tanya
>
> On Fri, Apr 10, 2009 at 4:25 PM, David Hill <dph at informatics.jax.org>
> wrote:
>
>> Hi Everyone,
>>
>> At the GOC meeting in Eugene, Tanya presented a proposal to create new
>> 'process-specific' function terms so that we can create part_of links
>> between the MF and BP ontologies. We decided to go ahead with this
>> proposal,
>> but in the discussion afterwards, there was some concern about how
>> annotators would use these terms. Specifically, it was brought up that
>> often
>> a single experiment does not give evidence that a gene product has a
>> specific molecular function AND a role in a specific biological process.
>> Another case was brought up that the molecular function of some gene
>> products are very well characterized and in most cases when a researcher
>> studies the process that the gene product is involved in, it is a given
>> that
>> the product is performing its well-known function.
>>
>> It seems to me that in these cases and from the discussion in Eugene, we
>> are not able to represent the conclusions from these papers not because
>> the
>> authors don't make strong cases for function-process information, but
>> because we are limited to making separate annotations for each
>> experiment
>> and are not able to represent the collective data and keep with our
>> evidence
>> code paradigm. I think it's unfortunate that we can't capture these
>> types of
>> data, when they often represent the detail of knowledge that is a
>> 'given' in
>> the field. I propose that we begin to capture these data in the
>> following
>> way:
>>
>> 1) When separate experiments are done in a paper that link a function
>> and a
>> process, we capture the individual functional data and process data by
>> annotating the individual experiments. Then, we make an additional
>> annotation to a 'process-specific function' using the EXP evidence code.
>> In
>> these annotations EXP would indicate that there were several types of
>> experimental evidence in the paper that led to the final conclusion.
>>
>> 2) When the function of a molecule is very well known and the authors do
>> an
>> experiment in a paper that indicates a process. If it is a
>> well-established
>> fact that the molecule only performs a certain function and the authors
>> clearly indicate the function-process link, we make a the process
>> annotation
>> in the usual way, and then  make the 'process-specific function'
>> annotation
>> using the IC evidence code with the molecular function in the 'with'
>> field.
>>
>> I think that this might get around some of the frustration that
>> annotators
>> were feeling at the meeting.
>>
>> Fire away!
>>
>> David
>>
>> --
>> David P. Hill, Ph.D.
>> Bioinformatics Scientist: Ontology Development
>> Gene Ontology Consortium
>> The Jackson Laboratory
>> www.geneontology.org
>> www.informatics.jax.org
>> tel:207-288-6430
>>
>> _______________________________________________
>> Annotation mailing list
>> Annotation at geneontology.org
>> http://fafner.stanford.edu/mailman/listinfo/annotation
>>
>
>
>
> --
> Tanya Berardini
> TAIR Curator
> www.arabidopsis.org
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