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Re: [Psidev-pi-dev] FW: Representing Sequences
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From: Pierre-Alain B. <pie...@is...> - 2008-06-27 15:12:54
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good to me too (a few comments below) David Creasy wrote: > OK by me. > > Jones, Andy wrote: >> >> So how about include length as an attribute and then let all other >> things go in the CV (pI, mass, etc.)? >> >> >> >> >> >> >> >> *From:* Jones, Andy >> *Sent:* 27 June 2008 14:54 >> *To:* 'David Creasy' >> *Subject:* RE: [Psidev-pi-dev] Representing Sequences >> >> >> >> id and name are standard for all elements that inherit from FuGE >> identifiable – this is perhaps a separate discussion as to whether >> the optional name attribute should be there. >> >> >> >> I agree that length may be useful – is this just an integer value >> with no unit? >> >> Yes, I think so. >> >> I’m less sure about pI and mass since mass at least can be calculated >> very simply >> >> Only if you have the sequence... (we have residue masses in the file). >> ... everyone uses the same algorithm for the pI... >> >> >> >> >> >> , and pI values (in my opinion) are pretty inaccurate and fairly >> meaningless >> >> Scandalous! (I happen to agree, but now some people will never speak >> to either of us ever again). >> >> The main problem with mass and pI is that these are 'irrelevant' if >> the sequence is nuleic acid rather than residues. >> Why not just allow CV there? We can share the same CV as the PEFF >> format, which includes, taxonomy, sequence type, gene ID, and lots of >> wonderful other things? >> good. Therefore things like pI, mass, etc should be added in the PEFF CV? (as they might be representing a sequence entry information?) Pierre-Alain >> >> >> >> – unless someone can convince me otherwise? >> >> Cheers >> >> Andy >> >> >> >> >> >> *From:* David Creasy [mailto:dc...@ma...] >> *Sent:* 27 June 2008 14:51 >> *To:* Jones, Andy >> *Cc:* psi...@li... >> <mailto:psi...@li...> >> *Subject:* Re: [Psidev-pi-dev] Representing Sequences >> >> >> >> Hi Andy, >> >> length may be useful, because some people won't want to output the >> actual sequence for space reasons. The other things we wanted to add >> before were pI and mass. >> Why do we want name? Is this for, say, a description line? >> (Also, identifier -> id?) >> >> David >> >> Jones, Andy wrote: >> >> Hi all, >> >> >> >> It was decided on the call that we would like to flag that Sequences >> in the ConceptualMoleculeCollection should have a Boolean attribute >> to capture if they are decoy sequences. At the moment we are using >> the FuGE:Sequence element. I don’t really want to add another >> attribute to this (it’s less problematic cutting down FuGE than >> adding new things), so I’m wondering if we should define our own >> Sequence type in AnalysisXML. This would also allow us to choose >> exactly the relevant attributes. At the moment, Sequence can have all >> of the following: >> >> >> >> <pf:Sequence isCircular="true" >> sequence="String" length="0" isApproximateLength="true" >> SequenceAnnotationSet_ref="String" start="0" end="0" >> identifier="String" name="String"> >> >> >> >> Several of these attributes were created to represent concepts that >> probably will never be required or implemented in AnalysisXML. How >> about the following: >> >> >> >> <DBSequence identifier = “” name = “” isDecoy = “true”> >> >> <seq>MCTMG...</seq> >> >> <pf:DatabaseReference Database_ref="" >> accession="Rev_IPI00013808.1"/> >> >> </DBSequence> >> >> >> >> Are any of the other attributes on Sequence actually required? I’ll >> post a new version of the schema with other changes WRT to >> PeptideEvidence shortly, >> >> Cheers >> >> Andy >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> >> >> >> >> >> >> ------------------------------------------------------------------------- >> Check out the new SourceForge.net Marketplace. >> It's the best place to buy or sell services for >> just about anything Open Source. >> http://sourceforge.net/services/buy/index.php >> >> >> >> >> ------------------------------------------------------------------------ >> >> >> >> >> >> >> >> >> >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... <mailto:Psi...@li...> >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev >> >> >> >> >> -- >> David Creasy >> Matrix Science >> 64 Baker Street >> London W1U 7GB, UK >> Tel: +44 (0)20 7486 1050 >> Fax: +44 (0)20 7224 1344 >> >> dc...@ma... <mailto:dc...@ma...> >> http://www.matrixscience.com >> >> Matrix Science Ltd. is registered in England and Wales >> Company number 3533898 >> >> ------------------------------------------------------------------------ >> >> >> >> >> ------------------------------------------------------------------------- >> Check out the new SourceForge.net Marketplace. >> It's the best place to buy or sell services for >> just about anything Open Source. >> http://sourceforge.net/services/buy/index.php >> >> ------------------------------------------------------------------------ >> >> >> >> >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... <mailto:Psi...@li...> >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev >> >> >> >> >> -- >> David Creasy >> Matrix Science >> 64 Baker Street >> London W1U 7GB, UK >> Tel: +44 (0)20 7486 1050 >> Fax: +44 (0)20 7224 1344 >> >> dc...@ma... <mailto:dc...@ma...> >> http://www.matrixscience.com >> >> Matrix Science Ltd. is registered in England and Wales >> Company number 3533898 >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------- >> Check out the new SourceForge.net Marketplace. >> It's the best place to buy or sell services for >> just about anything Open Source. >> http://sourceforge.net/services/buy/index.php >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev >> > > -- > David Creasy > Matrix Science > 64 Baker Street > London W1U 7GB, UK > Tel: +44 (0)20 7486 1050 > Fax: +44 (0)20 7224 1344 > > dc...@ma... > http://www.matrixscience.com > > Matrix Science Ltd. is registered in England and Wales > Company number 3533898 > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://sourceforge.net/services/buy/index.php > ------------------------------------------------------------------------ > > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > |
