[Go] addition of localization specific process terms ?

[Jim Hu]

In general, I like precomposition too.  But for binding, and to a  
lesser extent location, I don't like the idea of having parent terms  
with thousands of children.  The terms like regulation of translation  
of gene X mRNA are terrifying to me.  I noticed that somewhere on  
wiki.geneontology.org, there's a statement that GO will never do those  
kinds of terms by precomposition, but a few terms like that are  
already in GO, and there was recently a sourceforge item about protein  
chaperones for specific gene products.

I usually find terms by searching for a keyword combination,  
navigating to a particular term, and then browsing up and down the  
ontology.  Do others not do the browsing part?  I think that's where  
the massive expansion is most problematic.

I see what you mean about time, but requesting a new term is also a  
time barrier to annotation.

Perhaps a test version of the ontology could be automatically  
generated with ChEBI x binding, and people could see if my intuitions  
or everyone else's are correct.  In general, I suspect that people  
want precomposition for their own annotations and are annoyed at the  
excess terms that they don't see themselves ever using.  E. coli being  
the most distant from everyone else in the phylogeny may be why I'm  
where I am on this! ;)

Jim

On Mar 24, 2009, at 8:38 AM, Alexander Diehl wrote:

> I want to add my agreement to the words of Val and David.  It is  
> much simpler to use a pre-composed existing term in annotation.  One  
> aspect of the annotation process I feel is over looked as we add  
> more complexity to the annotation process is that post-composition  
> adds a significant bit of time to the annotation process, resulting  
> in fewer annotations overall and lower metrics for the database and  
> grant.  While it is important to do detailed and correct annotations  
> whenever possible, anything we can to do to increase throughput,  
> such as precomposing likely terms, is beneficial.  I'm not saying we  
> should add all possible combinations of X and Y, just the  
> appropriate ones.  This is one of the main reasons for having  
> annotators lead ontology development and holding ontology content  
> meetings where expert biologists can discuss processes actually seen  
> in nature, so that the appropriate combinations of X and Y are added.
>
> And knowing which pre-composed terms to use is a matter of training  
> and experience, both in general biology, and in annotation.  There's  
> no way around it.
>
> -- Alex
>
>
> val at sanger.ac.uk wrote:
>> I agree, it is far better to have pre-composed terms if possible,
>> especially for new curators.
>> As we encourage annotation to the most specific term possible it is  
>> hard
>> to overlook the precomposed terms, because we (I hope) always check  
>> the
>> child terms).
>>
>> Val
>>
>>
>>> From someone who has been annotating using a lot of pre- 
>>> composition as
>>> well as post-composition for a reasonably long time;  although  
>>> there is
>>> an initial activation energy to get a pre-composed term into the
>>> ontology, once they are there, they are much easier to use than to  
>>> look
>>> up things in multiple ontologies for post-composition.
>>>
>>> The key to finding pre-composed terms easily is to have a good way  
>>> of
>>> viewing the ontology.
>>>
>>> my 2c
>>>
>>> D
>>>
>>>> I would like to hear the opinion of some of the annotators here. Is
>>>> excessive pre-coordination a concern for curation?
>>>>
>>>>
>>> _______________________________________________
>>> Go mailing list
>>> Go at geneontology.org
>>> http://fafner.stanford.edu/mailman/listinfo/go
>>>
>>>
>>
>>
>>
>>
>>
>
>
> -- 
> Alexander D. Diehl, Ph.D.
> Senior Scientific Curator
> Mouse Genome Informatics
> The Jackson Laboratory
> 600 Main Street
> Bar Harbor, ME  04609
>
> email:  adiehl at informatics.jax.org
> work:  +1 (207) 288-6427
> fax:  +1 (207) 288-6131
>
> _______________________________________________
> Go mailing list
> Go at geneontology.org
> http://fafner.stanford.edu/mailman/listinfo/go

=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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