[go] recombination and toxin in GO

[Suzanna Lewis]

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
>>
>>
>> Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers  
>> Yahoo! Mail
>