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Re: [Psidev-pi-dev] PSI-PI Working group conference call on Wednesday 26th November at 4:00pm UK time
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From: David C. <dc...@ma...> - 2008-11-28 19:01:12
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Hi, Nobody has disagreed with: > Maybe safest to stick with the original proposal of just CV... We already have the CV (PI:00360 and PI:00361) and the validator accepts these so I've updated and committed the Mascot examples under svn. David David Creasy wrote: > Hi, > > Jones, Andy wrote: >> Ah I missed this proposal. Are these are the only two mechanisms we >> need/want? > One day, someone may well want to do something more involved... > >> If so, we could just build the whole thing into the schema: >> >> <AmbiguousResidue Code="B" SubstituteResidues="D N"/> >> >> <AmbiguousResidue Code="Z"> >> <AlternateResidue Mass="129.042593"/> >> <AlternateResidue Mass="128.058578"/> >> </AmbiguousResidue> >> >> The downsides are if someone decides another mechanism is needed we >> cannot >> extend this. Also, I'm not sure we can validate that only one >> mechanism or the >> other is used (but this issue is the same whichever way we solve the >> problem). >> >> In fact, do we need to allow it to be done both ways... Couldn't we >> just enforce >> that it is done in the latter way, > Could do, but not so nice because: > - It would be quite verbose - most search engines will use 'X' to mean > all other residues. > - It's a little harder to understand with just numbers. > <SequenceCollection> > <DBSequence id="A"> > <seq>MAXXPAVK... > <Peptide > <peptideSequence>MAKAPAVK > ... > <PeptideEvidence start="1" end="8" DBSequence_Ref="A" ..... > > Maybe safest to stick with the original proposal of just CV and accept > that the list of chars is not properly validated? > > David >> >> Cheers >> Andy >> >> >> >> >> >> >>> -----Original Message----- >>> From: David Creasy [mailto:dc...@ma...] >>> Sent: 27 November 2008 15:58 >>> To: Jones, Andy >>> Cc: psi...@li... >>> Subject: Re: [Psidev-pi-dev] PSI-PI Working group conference call on >>> Wednesday >>> 26th November at 4:00pm UK time >>> >>> Hi Andy >>> >>> Jones, Andy wrote: >>>> I have a query about something in the minutes: >>>> >>>> <MassTable is="MT1"> >>>> <Residue Code="A" Mass="71.037114"/> >>>> ... >>>> <Residue Code="Y" Mass="163.063329"/> >>>> >>>> <AmbiguousResidue Code="B"> >>>> <pf:cvParam accession="PI:xxxx" name="Alternate single letter codes" >>>> cvRef="PSI-PI" value="DN"/> >>>> </AmbiguousResidue> >>>> <AmbiguousResidue Code="Z"> >>>> <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI" >>>> value="129.042593"/> >>>> <pf:cvParam accession="PI:yyyy" name="Alternate mass" cvRef="PSI-PI" >>>> value="128.058578"/> >>>> </AmbiguousResidue> >>>> . . . >>>> </MassTable> >>>> >>>> >>>> I think we agreed that the value attribute above for "Alternate single >> letter >>>> codes" should be "D N" i.e. space separated chars, is this correct? >>> Yes, this is what we agreed. >>> >>>> If so, I'm not sure if I was supposed to add this as documentation >>>> to the >> XSD or >>>> if we want to add this documentation to the CV term (the latter >>>> seems better >> to >>>> me). >>> Adding it to the CV term seems better. However, Martin proposed a >>> different approach in an email a little earlier today: >>> >>> >>> > What do you think about:? >>> ... >>> <AmbiguousResidue Code="B" ResidueRef="D N"/> >>> <AmbiguousResidue Code="Z"> >>> <pf:cvParam accession="PI:yyyy" name="Alternate mass" >>> cvRef="PSI-PI" >>> value="129.042593"/> >>> <pf:cvParam accession="PI:yyyy" name="Alternate mass" >>> cvRef="PSI-PI" >>> value="128.058578"/> >>> </AmbiguousResidue> >>> >>> ResidueRef can be type listOfChar. >>> >>> Disadvantage is the mix of schema and CVParam mechanisms... >>> ------------------ >>> >>> I don't have a preference either way. Any thoughts Andy? >>> >>> David >>> >>>> Cheers, Andy >>>> >>>> >>>> >>>>> -----Original Message----- >>>>> From: David Creasy [mailto:dc...@ma...] >>>>> Sent: 27 November 2008 13:35 >>>>> To: psi...@li... >>>>> Subject: Re: [Psidev-pi-dev] PSI-PI Working group conference call on >>> Wednesday >>>>> 26th November at 4:00pm UK time >>>>> >>>>> Minutes are here: >>>>> >>>>> http://psidev.info/index.php?q=node/395 >>>>> >>>>> Most action items already done... >>>>> >>>>> >>>>> >>>>> David Creasy wrote: >>>>>> Hi everyone, >>>>>> >>>>>> There will be an AnalysisXML working group conference call on >>>>>> WEDNESDAY >>>>>> (instead of Thursday, because it is Thanksgiving in the US) at: >>>>>> >>> http://www.timeanddate.com/worldclock/fixedtime.html?day=26&month=11&year=2 >>> >>>>> 008&hour=16&min=0&sec=0&p1=136 >>>>>> Minutes, including action items ;) from last meeting at: >>>>>> http://psidev.info/index.php?q=node/392 >>>>>> >>>>>> Agenda: >>>>>> 1. Review of minutes of last meeting >>>>>> >>>>>> 2. Internal fragment ions >>>>>> >>>>>> 3. Ambiguous residues >>>>>> >>>>>> 4. Status of mapping document, CV and examples. >>>>>> >>>>>> 5. Please review the latest documentation: >>>>>> >>>>>> http://psi- >>> pi.googlecode.com/svn/trunk/specification_document/analysisXML_SpecificationDr >>> >>>>> aft.doc >>>>>> >>>>>> Dial in details: >>>>>> >>>>>> + Germany: 08001012079 >>>>>> + Switzerland: 0800000860 >>>>>> + UK: 08081095644 >>>>>> + USA: 1-866-314-3683 >>>>>> + Generic international: +44 2083222500 (UK number) >>>>>> >>>>>> access code: 297427 >>>>>> >>>>> -- >>>>> 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 >>>>> >>>>> ------------------------------------------------------------------------- >>>>> >>>>> This SF.Net email is sponsored by the Moblin Your Move Developer's >>> challenge >>>>> Build the coolest Linux based applications with Moblin SDK & win great >> prizes >>>>> Grand prize is a trip for two to an Open Source event anywhere in >>>>> the world >>>>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>>>> _______________________________________________ >>>>> 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 >>> >>> ------------------------------------------------------------------------- >>> >>> This SF.Net email is sponsored by the Moblin Your Move Developer's >>> challenge >>> Build the coolest Linux based applications with Moblin SDK & win >>> great prizes >>> Grand prize is a trip for two to an Open Source event anywhere in the >>> world >>> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >>> _______________________________________________ >>> 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 |
