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

[Bada, M. <Mik...@uc...>]

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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