[transport] Re: Transporter activity overhaul

[Midori Harris]

Hi,

It's great to see how much this group has done in just a few weeks. I'm 
nowhere near expert level myself, but the upper level organization looks 
fine as far as I can tell. I've taken the liberty of fixing a couple of 
typos, and I have some comments, mostly pretty small.

Looks like a missing relationship:
substrate-specific transmembrane transporter activity GO:0022891 is_a 
substrate-specific transporter activity GO:0022892

For these term names, make singular and correct case, and shouldn't they 
have 'activity' at the end?
transmembrane electron transfer carriers GO:0022865
Transmembrane 1-Electron Transfer Carriers GO:0022866
transmembrane 2-Electron Transfer Carriers GO:0022867

The def of large uncharged polar molecule transporter activity GO:0022815 
should be worded more like the others.

The def wording for cation transmembrane transporter activity GO:0008324 
should be  more like that of anion transmembrane transporter activity 
GO:0008509.

Amine transporter activity GO:0005275 is under transmembrane transporter 
activity, but its def doesn't have the across-a-membrane bit, nor do those 
of at least some of the children.

The def of mobile ion carrier activity GO:0022809 doesn't seem to 
emphasize the activity quite enough. Maybe something like "Enables the 
movement of an ion by enclosing the ion and traveling across the membrane; 
does not form a fully open pore in the membrane."?

I guess this is historical, but it seems odd that the def of voltage-gated 
ion channel activity GO:0005244 has an explanation of what an ion is, when 
the parent terms don't. In a similar vein, cation channel activity 
GO:0005261 has a "reaction" whereas most other defs don't.

That said, I know it would be a huge task to get all of the definitions 
fully consistently worded, and as long as the glaring problems are fixed, 
it's probably not a high priority.

Cheers, and thanks again for all the effort,
midori

On Wed, 9 May 2007, J Clark wrote:

> 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.)
>
>
>