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Re: [SO-devel] Disulphide and Cross Link (obsolete terms)
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From: Suzanna L. <su...@be...> - 2013-02-13 03:10:04
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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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