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substrates

J Clark jclark at ebi.ac.uk
Tue Apr 24 05:42:41 PDT 2007


It's on mondays at 2.30 BST on skype.

That would be great if you could join.

Thanks,

Jen


Peter D'Eustachio wrote:

> This all makes sense - the transport vs binding vs trafficking 
> distinction is good.
> 
> I'd like to join the conference call - when is it?
> 
> Peter
> 
> ----- Original Message ----- From: "Valerie Wood" <val at sanger.ac.uk>
> To: "Peter D'Eustachio" <eustachi at cshl.edu>
> Cc: "J Clark" <jclark at ebi.ac.uk>; <transport at genome.stanford.edu>
> Sent: Tuesday, April 24, 2007 8:07 AM
> Subject: Re: substrates
> 
> 
>>
>> I wonder if anyone has used any of the substrate terms to annotate 
>> these gene products to 'transporter activity' or its children though?. 
>> If so, we may not be able to move them directly under "transmembrane 
>> transporter activity"
>>
>> We had an idea that we would create some sort of 'transport chaperone' 
>> under the binding terms which could have the relevent synonyms for 
>> searching.
>>
>> I think we were possible even going to have
>>
>> transporter activity
>> --transmembrane transorter acrtivity
>> --transport chaperone (wording and def to be discussed)
>>
>> protein binding
>> --transport chaperone
>>
>> But, as there is no functional relationship between these it probably 
>> isn't necessary (or correct) to have the
>> 'transporter activity' parentage at all?
>>
>> One of the probelms we have is that the def of 'transporter activity' 
>> is quite vague and it doesn't restrict annotations to 'transmembrane 
>> transport':
>>
>> Enables the directed movement of substances (such as macromolecules, 
>> small molecules, ions) into, out of, within or between cells.
>>
>> It has been used to annotate various other things like  trafficking 
>> molecules (SNAP receptors, SNAREs),  and various other things. If 
>> people are agreed that it should never be used for these we could 
>> approach this slightly differently.
>>
>> Peter, perhaps you could join the conf call when we deal with this 
>> high level part?
>>
>> Val
>>
>>
>>
>> Peter D'Eustachio wrote:
>>
>>> Hi Jen
>>>
>>> Yes - that's how we use them. When we want to talk about the behavior 
>>> of albumin, we would use a "binding" term.
>>>
>>> Peter
>>>
>>> ----- Original Message ----- From: "J Clark" <jclark at ebi.ac.uk>
>>> To: "Peter D'Eustachio" <deustp01 at med.nyu.edu>
>>> Cc: <transport at genome.stanford.edu>
>>> Sent: Tuesday, April 24, 2007 6:40 AM
>>> Subject: Re: substrates
>>>
>>>
>>>> Hi Peter,
>>>>
>>>> Thanks, I see what you mean. If I move these terms under the term 
>>>> 'transmembrane transporter activity' would you be happy with that?
>>>>
>>>> Thanks,
>>>>
>>>> Jen
>>>>
>>>> Peter D'Eustachio wrote:
>>>>
>>>>> Narrow answer: No.
>>>>>
>>>>> Broad, somewhat tangential answer: yes, maybe. Biologists certainly 
>>>>> talk about serum albumin and cortisol binding globulin as 
>>>>> "transporters" of the hydrophobic small molecules that bind to them 
>>>>> in the blood and thus move from tissue to tissue, but this clearly 
>>>>> amounts to overloading of the word "transport" as far as we are 
>>>>> concerned.
>>>>>
>>>>> Peter D'Etc
>>>>>
>>>>> ----- Original Message ----- From: "J Clark" <jclark at ebi.ac.uk>
>>>>> To: <transport at genome.stanford.edu>
>>>>> Sent: Monday, April 23, 2007 10:44 AM
>>>>> Subject: substrates
>>>>>
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Can anybody think of any example of transport of the following
>>>>>> substrates (belonging in the function ontology) that is not
>>>>>> straightforward transport from one side of a membrane to another?
>>>>>>
>>>>>> organic acid transporter activity
>>>>>> tricarboxylic acid transporter activity
>>>>>> carbohydrate transporter activity
>>>>>> alcohol transporter activity
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> Jen
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>> -- 
>>>> Gene Ontology Consortium
>>>> EMBL-European Bioinformatics Institute
>>>
>>>
>>>
>>>
>>
>>
>> -- 
>> --------------------------------------------------------------------------- 
>>
>> Valerie Wood Tel: 01223 496909
>> S. pombe Genome Project Fax: 01223 494919        Wellcome Trust Sanger 
>> Institute email: val at sanger.ac.uk
>> Wellcome Trust Genome Campus http://www.genedb.org/genedb/pombe 
>> Hinxton, Cambridge, CB10 1HH http://www.sanger.ac.uk/Projects/S_pombe
>>

-- 
Gene Ontology Consortium
EMBL-European Bioinformatics Institute



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