[Annotation] process-specific function annotations: a proposal

[Tanya Berardini]

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
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>



-- 
Tanya Berardini
TAIR Curator
www.arabidopsis.org
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