[transport] Transporter activity overhaul

[J Clark]

Hi,

I'm sure many of you will know that we have been doing a lot of work on 
the transporter activity section of the function ontology. Well it's 
been going on for quite a while now and we have revamped a lot of the 
top level terms, though the work is by no means over.

Anyway, two of the four people on the working group are away on holiday 
for the next couple of weeks so I thought this might be a good time for 
you all to have a quick look at what we've done if you're interested. 
The file can be downloaded from:

http://cvsweb.geneontology.org/cgi-bin/cvsweb.cgi/go/scratch/transport.obo

and you can vew it by loading it into OBO-Edit.

You can see the part we've changed by using the term search facility and 
searching on 'ancestor' 'name' 'equals' 'transporter activity'.
I have attached a couple of pictures of how to set up the search in case 
that's useful.

If any of you can see anything that's still glaringly wrong and easy to 
fix could you possibly send me a list? As far I can see it's mostly the 
more granular terms that need moved around or redefined and the more 
difficult undefined terms that still need fixed. Also there are 
questions over chaperone activities, things to do with drug, xenobiotic 
and so on, and a stricter application of standard definitions to the 
graph. We have plans to get on to these, but it would be nice to have 
some feedback on what we've done at this half way point.

If you would like to know what we have done then the notes are here:
http://wiki.geneontology.org/index.php?title=Transporters

In general the changes that you will notice are that 'permease' 'porter' 
and 'carrier' no longer appear in term names and that the structure and 
definitions are along the lines shown here:

http://wiki.geneontology.org/index.php/Docs

Hope you like it.

Thanks,

Jen

(on behalf of the transporter activity working group
Jennifer Clark, Michelle Gwinn-Giglio, Val Wood and IanPaulsen.)


-- 
Gene Ontology Consortium
EMBL-European Bioinformatics Institute
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