[Go] addition of localization specific process terms ?
Jennifer Deegan (nee Clark)
jdeegan at ebi.ac.uk
Tue Mar 24 09:18:19 PDT 2009
Hi,
Another route that I would be interested to explore would be the
development of tools to help people find their way around the
pre-composed terms, both for editing and browsing.
For example there could be an OBO-Edit component that displays
pre-composed terms and their ancestors broken into several separate
graphs. The graphs could show the separate implicit ontologies that have
been put together to make the pre-composed terms.
As an example, in the graph:
[i]heart development
---[p]heart valve development
we could right click on heart valve development and choose a menu item
that then opens up two viewer windows showing:
[i]heart
---[p]heart valve
and
[i]development
We could then browse down one implicit ontology or the other. Finding
the anatomical part that we are interested in, we could perhaps click on
'heart valve' to open up a new window. In this window all terms
containing 'heart valve' might be highlighted, or terms not containing
the string (in self or descendent) might be filtered. (Or something
along these lines. I have not figured out how best this could be worked).
I think there is also scope to use this kind of tool to spot where an
implicit ontology is present in GO in two places with differences
between the two structures.
I know we need to work with the pre-composed terms as they are but I
think tools to give us a handle on implicit ontologies could help a lot.
Jennifer
Jim Hu wrote:
> 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 <mailto: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 <mailto: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 <mailto:adiehl at informatics.jax.org>
>> work: +1 (207) 288-6427
>> fax: +1 (207) 288-6131
>>
>> _______________________________________________
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>> Go at geneontology.org <mailto: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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