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

[Leyla G. <ljg...@eb...>]

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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