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From: David C. <dc...@ma...> - 2008-11-25 15:52:44
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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=2008&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_SpecificationDraft.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 |
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From: Jones, A. <And...@li...> - 2008-11-26 17:11:42
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New schema uploaded: Added attribute charge on IonType Added documentation for Immonium and internal ions. Added UnitCVRef to FuGElight_working.xsd - example documents need to be updated since the presence of this attribute is not checked by XSD (should be present whenever unitName is) > -----Original Message----- > From: David Creasy [mailto:dc...@ma...] > Sent: 25 November 2008 15:53 > To: psi...@li... > Subject: [Psidev-pi-dev] PSI-PI Working group conference call on Wednesday > 26th November at 4:00pm UK time > > 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 |
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From: David C. <dc...@ma...> - 2008-11-26 17:55:23
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Jones, Andy wrote: > New schema uploaded: > > > Added attribute charge on IonType Done for the Mascot examples > > Added documentation for Immonium and internal ions. Internals now have start and end in the Mascot examples > > Added UnitCVRef to FuGElight_working.xsd - example documents need to be updated > since the presence of this attribute is not checked by XSD (should be present > whenever unitName is) Done in the Mascot examples for the CV. However, do we also want to add the unitCvRef to: <FragmentTolerance> <PlusValue unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton" value="0.5" /> <MinusValue unitCvRef="UO" unitAccession="UO:0000221" unitName="dalton" value="0.5" /> </FragmentTolerance> David > > >> -----Original Message----- >> From: David Creasy [mailto:dc...@ma...] >> Sent: 25 November 2008 15:53 >> To: psi...@li... >> Subject: [Psidev-pi-dev] PSI-PI Working group conference call on Wednesday >> 26th November at 4:00pm UK time >> >> 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 > > ------------------------------------------------------------------------- > 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 |
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From: Jones, A. <And...@li...> - 2008-11-27 12:52:34
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New schema uploaded: Added UnitCVRef to PropertyValue in FuGElight_working.xsd Cheers, Andy > -----Original Message----- > From: David Creasy [mailto:dc...@ma...] > Sent: 26 November 2008 17:55 > 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 > > > Jones, Andy wrote: > > New schema uploaded: > > > > > > Added attribute charge on IonType > Done for the Mascot examples > > > > Added documentation for Immonium and internal ions. > Internals now have start and end in the Mascot examples > > > > > Added UnitCVRef to FuGElight_working.xsd - example documents need to be > updated > > since the presence of this attribute is not checked by XSD (should be present > > whenever unitName is) > Done in the Mascot examples for the CV. > > However, do we also want to add the unitCvRef to: > <FragmentTolerance> > <PlusValue unitCvRef="UO" unitAccession="UO:0000221" > unitName="dalton" value="0.5" /> > <MinusValue unitCvRef="UO" unitAccession="UO:0000221" > unitName="dalton" value="0.5" /> > </FragmentTolerance> > > > David > > > > > > >> -----Original Message----- > >> From: David Creasy [mailto:dc...@ma...] > >> Sent: 25 November 2008 15:53 > >> To: psi...@li... > >> Subject: [Psidev-pi-dev] PSI-PI Working group conference call on Wednesday > >> 26th November at 4:00pm UK time > >> > >> 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 > > > > ------------------------------------------------------------------------- > > 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 |
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From: David C. <dc...@ma...> - 2008-11-27 13:35:32
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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=2008&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_SpecificationDraft.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 |
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From: Jones, A. <And...@li...> - 2008-11-27 15:33:19
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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? 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). 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 |
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Re: [Psidev-pi-dev] PSI-PI Working group conference call
onWednesday 26th November at 4:00pm UK time
From: Jones, A. <And...@li...> - 2008-11-27 15:51:03
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Minor schema update: Changed datatype on "code" attribute of AmbiguityGroup to psi-pi:chars (only single letter code allowed now), previously was xsd:string. Should not require any changes to instance docs > -----Original Message----- > From: Jones, Andy [mailto:And...@li...] > Sent: 27 November 2008 15:33 > To: David Creasy; psi...@li... > Subject: Re: [Psidev-pi-dev] PSI-PI Working group conference call onWednesday > 26th November at 4:00pm UK time > > 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? > > 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). > > 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 > > ------------------------------------------------------------------------- > 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 |
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From: David C. <dc...@ma...> - 2008-11-27 15:57:59
|
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
|
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From: Jones, A. <And...@li...> - 2008-11-27 16:18:46
|
Ah I missed this proposal. Are these are the only two mechanisms we need/want?
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,
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
|
|
From: David C. <dc...@ma...> - 2008-11-27 16:38:00
|
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
|
|
From: David C. <dc...@ma...> - 2008-11-28 19:01:12
|
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 |
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