[Go] addition of localization specific process terms ?

Chris Mungall cjm at berkeleybop.org
Tue Mar 24 12:39:36 PDT 2009 

On Mar 24, 2009, at 10:49 AM, Karen Christie wrote:

> 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.

My proposed methodology would be to ask if the location is accidental  
- is the process substantially different from proteolysis elsewhere? A  
quick google suggests that the machinery is different so I would say  
yes, tentatively.

Another clue appears to be that there are labs and people who care  
about "mitochondrial proteolysis" specifically, so we'd be doing them  
an injustice by not pre-composing the term.
Contrast with say "neuron proteolysis"

>
> -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.
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>> 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?
>>>>>> _______________________________________________
>>>>>> 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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>

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