[Annotation] process-specific function annotations: a proposal

[David Hill]

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