[go] recombination and toxin in GO

[Midori Harris]

Hi,

Some are in the tracker:

https://sourceforge.net/tracker/index.php?func=detail&aid=1742920&group_id=36855&atid=440764

We've been waiting to hear back from Ariane; I put some questions in the 
tracker item, but she was very busy over the summer.

Much of the rest will probably end up waiting for Jane to come back, 
because she knows this stuff rather better than the rest of the GO 
editors.

m

On Sun, 4 Nov 2007, Suzanna Lewis wrote:

> Hi all,
>
> Just checking in. Did these terms make it into the request queue/tracker. Any 
> progress or change in status to report?
>
> -S
>
> On Jul 10, 2007, at 5:15 AM, Michael Ashburner wrote:
>
>> Ariane
>> 
>> Thanks, I understand that. I think the thing to to do is let Karen and the 
>> GO office work on these terms and then
>> we will see just how much of PhiGO will be covered.
>> 
>> Best - Michael
>> 
>> 
>> On 6 Jul 2007, at 15:37, Ariane Pourbaix wrote:
>> 
>>> Dear Michael,
>>> The reason for assembling that list of phage and recombination terms is 
>>> essentially that we need a robust and structured system to annotate the 
>>> protein families in our ACLAME database. We hope that people using ACLAME 
>>> will then be 'tempted' to use the same ontology. After the meeting we had 
>>> last September in Hinxton I knew just enough to try following the GO 
>>> schema of processes, components and functions. I looked at the virus 
>>> related terms that are in GO and found things like 'capsomer', so I felt 
>>> comfortable introducing the other components of the phage capsid?
>>> I thought it would be good to have as many of these terms in GO as 
>>> possible. If some don' fit we'll just keep them in PhiGO. One point that 
>>> isn't completely clear to me yet is whether we'll better keep PhiGO as it 
>>> is, even if most of it gets integrated in GO.
>>> As Jane mentioned, I think it would be interesting to build a list of 
>>> generic terms for viruses. This I suppose should also be done for mobile 
>>> genetic elements (not easy either).
>>> In my suggestions for some reorganisation of the terms related to 
>>> recombination, I'm afraid some may provoke some discussion if not 
>>> disagreement? in any case I thin it is urgent to get something done there 
>>> because the confusion between the different types of integrases, 
>>> transposases etc. is increasing in recent annotations. Clear and correct 
>>> definitions are obviously required. I'm not sure mine are perfect tough, 
>>> but they are not wrong!
>>> I'm sure we'll progress on this? though on my side it may a bit slow since 
>>> I'm away from the lab and with interrupted internet connection until the 
>>> end of august!
>>> I hope this clarifies things a least a little! Best regards. Ariane.
>>> 
>>> 
>>> Michael Ashburner <ma11 at gen.cam.ac.uk> a écrit :Ariane
>>> 
>>> This looks like very productive work !
>>> 
>>> I am not clear as to the long-term objective, at least wrt to the 
>>> relationship
>>> between this and the GO. I can see that most (if not all) of the terms 
>>> under the
>>> 'phage function' and 'phage process' nodes could well be - and should be - 
>>> incorporated into
>>> the GO. The same goes for the terms under the 3 'recombination' nodes.
>>> 
>>> The 'phage component' terms would be harder. I wonder if what you could 
>>> aim for is
>>> essentially a 'phage anatomy' ontology, analagous to those for cellular 
>>> organisms ?
>>> 
>>> Chris M: Could you have a look at this work ? The obo file is at: 
>>> http://aclame.ulb.ac.be/Classification/PhiGO/PhiGO_live.obo
>>> 
>>> There is a way using OBO-EDIT 1.2 where you can build an ontology for use 
>>> within a domain (e.g. phage)
>>> by picking and choosing from several other ontologies. I am not sure 
>>> exactly how this is done but
>>> I am sure Chris can advise.
>>> 
>>> Best wishes - Michael
>>> 
>>> 
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>> 
>
>