[Go] addition of localization specific process terms ?

[Karen Christie]

So, what are the existing guidelines for precomposition? I started this 
thread, and I still don't know whether the existing guidelines suggest 
that it would, or would not, be appropriate to request a term for 
"mitochondrial proteolysis", which was the starting point of this 
discussion.

-Karen

On Tue, 24 Mar 2009, Chris Mungall wrote:

[snip]

> True. I am wondering if sometimes annotators simply do not make a request and 
> annotate to the most specific currently pre-composed term, even if the new 
> term they want falls within the precomposition guidelines. I hope not.








> On Mar 24, 2009, at 9:00 AM, Jim Hu wrote:
>
>> 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.
>
> I think this experiment would be biased to confirm your intuitions!
>
> If we materialized the full binding x CHEBI xp then we would end up 
> propagating all the unusual CHEBI distinctions and naming issues in GO.
>
> Anyway, I don't think anyone has ever argued in favour of materializing the 
> full cross-product. The GO pre-composition rules would state that we would 
> create a new "X binding" as child of "Y binding", if the process of binding 
> to X was significantly different form binding to Y. Whilst the application of 
> this rule will be fuzzy in places, it would still be premature to do the full 
> pre-composition.
>
>> 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! ;)
>
> maybe..
>
> of course it's possible to use the taxon constraints Jen created to 
> automatically filter GO such that you (E coli) never see a term like 
> mitochondrial translation. I can show folks how to set up this filter in OE, 
> and work with the software groups who make annotation tools to recapitulate 
> the logic there.
>
>> 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?
>>>>>> 
>>>>>> 
>>>>> _______________________________________________
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>>>>> Go at geneontology.org
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>>>>> 
>>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>> 
>>> 
>>> -- 
>>> 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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