Re: [SO-devel] Disulphide and Cross Link (obsolete terms)

[Colin B. <Bat...@rs...>]

Hello,

I would strongly recommend, from a point of view of clarity, using ChEBI instead of MOD. MOD is terribly unclear about whether something is a process or part of a molecule and there is very little in it that wouldn't be better covered in ChEBI (if it's part of a molecule) or GO (if it's a process).

Best wishes,
Colin.

-----Original Message-----
From: Leyla Garcia [mailto:ljg...@eb...] 
Sent: 13 February 2013 11:45
To: Bada, Mike
Cc: SO developers
Subject: Re: [SO-devel] Disulphide and Cross Link (obsolete terms)

Hi Mike,

Thanks for your reply.

Indeed, we treat them as sequence residues. That is why we have moved from SO to MOD for those two terms, we are using MOD:00689 for disulfide bonds and MOD:00033 for cross links.

>I think that the chemical links themselves, i.e., disulphide bonds and 
>crosslinks, are outside the scope of the SO.  However, sequence 
>residues aren't (at least for now--we've been wondering about that), so 
>I think terms like disulphide-bonded amino-acid residue and crosslinked 
>residue could be created as sequence residue subclasses.  Since you're 
>annotating sequences, I'm guessing that would work for you?

As you have wondering about having sequence residues in SO, maybe see what is cover in MOD would be worth. I am not sure whether these two ontologies should/could overlap or if they are definitely meant to represent similar concepts from different perspectives.

Cheers,

Leyla

On 12/02/2013 00:08, Bada, Mike wrote:
> Hi Leyla,
>
> I've been working with Karen on a refactored version of the SO that 
> we'd like to put out for public comment hopefully relatively soon.  I 
> haven't seen a response to your question (sent a while ago, sorry), so 
> I'll chime in.
>
> I think that the chemical links themselves, i.e., disulphide bonds and 
> crosslinks, are outside the scope of the SO.  However, sequence 
> residues aren't (at least for now--we've been wondering about that), 
> so I think terms like disulphide-bonded amino-acid residue and 
> crosslinked residue could be created as sequence residue subclasses.  
> Since you're annotating sequences, I'm guessing that would work for you?
>
> The representation of binding sites is being cleaned up, as there are 
> currently terms for those in several different places right now.  
> We'll likely keep binding_site (SO:0000409), so you could use that for now.
> (SO:0100018 is for polypeptide_binding_motif.)
>
> Cheers,
> Mike
>
>
>
> On 1/18/13 9:40 AM, "ljg...@eb..." <ljg...@eb...> wrote:
>
>> Dear all,
>>
>> I am looking for the replacement terms for SO:0001088 (disulphide 
>> bond) and SO:0001087 (cross link). Both are currently obsolete, I am 
>> wondering what are the terms that replace them in SO? At UniProt we 
>> currently use them as protein sequence annotations but as they are 
>> deprecated, we would to update the ontological term. Something 
>> similar also happens with
>> SO:0001091 (binding site); for that one we also use SO:0100018 which 
>> is still a valid term. Should we only use the last one for bindings sites?
>>
>> Regards,
>>
>> Leyla García
>> UniProt Developer
>>
>>
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