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Re: [SO-devel] Disulphide and Cross Link (obsolete terms)
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From: Bada, M. <Mik...@uc...> - 2013-02-13 03:33:59
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Yep, no argument here. :) On 2/12/13 8:09 PM, "Suzanna Lewis" <su...@be...> wrote: >Maybe this is obvious, but to be clear the 'di' in disulphide is because >there are 2 sulfide groups. Each sulfide is contributed by the side chain >of one of the 2 cysteine AAs involved. For example, the two peptides in >insulin are connected by disulphide bonds cross-linking across the >cysteines. Seeing a cysteine residue I'd likely look for what other >cysteine residue it will be bound to in the mature protein. I'm sure >Colin or one of the other biochemists can speak to this more accurately. > >>From the SO perspective it's the site of the cysteine AA that is notable >>isn't it. Or even better the pair of them together. > >On Feb 12, 2013, at 6:58 PM, "Bada, Mike" <Mik...@uc...> wrote: > >> Sidestepping the ontology of chemical bonds, I meant that a >> disulfide-bonded amino-acid is an amino-acid residue that's covalently >> connected to a disulfide group, which is commonly referred to as a >> disulfide bond, right? I think terms such as disulfide-bonded residue >> pair and crosslinked residue pair will be tricky to classify (which is >> isn't to say that we shouldn't try if we need them, of course). >> >> Folding in Alan's post, I do agree that at some point we should >>coordinate >> with ChEBI as to which types of entities belong in which ontology. >>There >> are currently residues, DNAs, RNAs, and peptides in both ChEBI & SO, so >> there's already overlap. I don't think non-protein peptide molecules >> should only be in ChEBI, as those are sequences. I'm not theoretically >> against moving SO sequence residues to ChEBI, but we'd first want to >>make >> sure it wouldn't disrupt SO annotation work. Amino-acid and nucleotide >> residue terms are already in the SO, so people may be already annotating >> with them. I'm wondering if applications that rely on parsing the >> annotation files would break if people had to use non-SO terms (e.g., >> ChEBI terms) for annotation. For the annotators out there, would this >>be >> a known issue? >> >> Cheers, >> Mike >> >> >> >> On 2/12/13 3:02 AM, "Colin Batchelor" <Bat...@rs...> wrote: >> >>> Hello, >>> >>> Very wary of "bond" talk, simply because there's a tendency in >>> cheminformatics to think of them as first-class objects on a par with >>> atoms, rather than a mere figure of speech. Perhaps they belong in a >>> history-of-science ontology along with epicycles? >>> >>> To concur, broadly, with Mike, I suppose sequence residues would belong >>> either in the molecular bit of SO or ChEBI, depending on what the >>> ontologies decide between themselves, but I reckon >>> non-sequence-contiguous systems like a disulfide-bonded residue pair >>> ought to live in the molecular bit of SO. Likewise crosslinked residue >>> pair, and then we'd define the terms you wanted as being residues that >>> were part of such a residue pair. Does that make sense? >>> >>> Best wishes, >>> Colin. >>> >>> -----Original Message----- >>> From: Bada, Mike [mailto:Mik...@uc...] >>> Sent: 12 February 2013 00:08 >>> To: ljg...@eb... >>> Cc: SO developers >>> Subject: Re: [SO-devel] Disulphide and Cross Link (obsolete terms) >>> >>> 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 >>>> >>>> >>>> >>>>----------------------------------------------------------------------- >>>> --- >>>> ---- >>>> Master Visual Studio, SharePoint, SQL, ASP.NET, C# 2012, HTML5, CSS, >>>> MVC, Windows 8 Apps, JavaScript and much more. Keep your skills >>>>current >>>> with LearnDevNow - 3,200 step-by-step video tutorials by Microsoft >>>>MVPs >>>> and experts. ON SALE this month only -- learn more at: >>>> http://p.sf.net/sfu/learnnow-d2d >>>> _______________________________________________ >>>> SOng-devel mailing list >>>> SOn...@li... >>>> https://lists.sourceforge.net/lists/listinfo/song-devel >>> >>> >>> >>>------------------------------------------------------------------------ >>>-- >>> ---- >>> Free Next-Gen Firewall Hardware Offer >>> Buy your Sophos next-gen firewall before the end March 2013 and get the >>> hardware for free! 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