[Ontology-editors] [Chebi-ontology] Notes from today's meeting

[Chris Mungall]

On Jul 10, 2008, at 10:34 AM, Duncan Hull wrote:

> Hi Janna / Colin
>
> Janna Hastings wrote:
>> thanks for this, in fact I believe that Duncan and Barry are  
>> members of the
>> list already :-)
>>
>
> Hello Chebians, yes, I'm on this list.
>> Colin, if you could describe in greater detail the work that you  
>> and Duncan
>> are doing at the moment, perhaps we could find some other way to  
>> assist you
>> with it than lumping all the is-a orphans together at such a high  
>> level?
>>
>
> is-a completeness doesn't bother me too much right now, though I  
> realise
> its importance.
>
> Personally, I'm interested in doing some experimental alignment of  
> ChEBI
> and GO with the help of a reasoner like Pellet and an OWL version  
> of ChEBI.

> My un-tested hunch is, I can probably do useful work with interim
> pre-releases of ChEBI (via Janna), as and when the changes we  
> discussed
> on Wednesday  get incorporated.

Hi Duncan

It would be great if you could work on this! You will want to  
coordinate with Mike Bada (who has done a lot of work on an initial  
alignment from which the logical definitions were generated) and of  
course the GO editors.

You can find some material here:
http://wiki.geneontology.org/index.php/XP:biological_process_xp_chebi

If you find mistakes in GO, use the GO tracker to report them (there  
is a category set up for reporting mistakes discovered via CHEBI)

I'm having some problems running Pellet & the OE reasoner on the  
latest xps. I have suspicions this may to do with is_a overloading,  
haven't had a chance to investigate, or to try Fact++

Some of the things we have been meaning to work on:

- to what extent does is_a-overloading in CHEBI cause erroneous  
inferences about biological processes? (these concern me even more  
than the is_a complete classes)
- can we use abduction / "reverse reasoning" to suggest placement for  
CHEBI orphans based on the implicit chemical entity hierarchy in GO?
- does expanding the much-debated "macro" relations used in the  
current xps into complex OWL expressions (as recommended by Alan  
Ruttenberg) result in useful inferences?
- what kinds of interesting biological questions can be answered by  
the combination of the two resources plus the xps, using either the  
P4 or obo query interfaces?
- can we identify areas of CHEBI in which new relations, necessary  
and sufficient conditions etc will enable inferences of use to GO?

This is in addition to the usual business of maintaining the correct  
classification of biological processes in GO of course.

If you wish to try improving on the current logical definitions you  
can send me the owl or obo, or we can get you an account on obo.sf.net

>
> I can give more details at a later stage if anyone is interested.
>
> Duncan
>
> -- 
> Duncan Hull
> http://duncan.hull.name
> +44 (0) 161 306 5138
>
>
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