Menu
▾
▴
psidev-pi-dev — General Development List for Proteomics Informatics
You can subscribe to this list here.
| 2006 |
Jan
|
Feb
|
Mar
|
Apr
|
May
|
Jun
(1) |
Jul
(5) |
Aug
(4) |
Sep
(4) |
Oct
(10) |
Nov
(1) |
Dec
(1) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2007 |
Jan
|
Feb
|
Mar
(2) |
Apr
|
May
|
Jun
|
Jul
(4) |
Aug
|
Sep
|
Oct
(1) |
Nov
|
Dec
|
| 2008 |
Jan
|
Feb
(2) |
Mar
(2) |
Apr
(8) |
May
(40) |
Jun
(30) |
Jul
(61) |
Aug
(21) |
Sep
(12) |
Oct
(56) |
Nov
(99) |
Dec
(83) |
| 2009 |
Jan
(3) |
Feb
(9) |
Mar
(1) |
Apr
(5) |
May
(88) |
Jun
(43) |
Jul
(60) |
Aug
(54) |
Sep
(4) |
Oct
(18) |
Nov
(9) |
Dec
(5) |
| 2010 |
Jan
|
Feb
(3) |
Mar
(1) |
Apr
(8) |
May
(10) |
Jun
(8) |
Jul
(10) |
Aug
(18) |
Sep
(11) |
Oct
(19) |
Nov
(14) |
Dec
(26) |
| 2011 |
Jan
(27) |
Feb
(38) |
Mar
(50) |
Apr
(128) |
May
(54) |
Jun
(116) |
Jul
(79) |
Aug
(163) |
Sep
(21) |
Oct
(14) |
Nov
(19) |
Dec
(9) |
| 2012 |
Jan
(7) |
Feb
(34) |
Mar
(34) |
Apr
(50) |
May
(70) |
Jun
(23) |
Jul
(8) |
Aug
(24) |
Sep
(35) |
Oct
(40) |
Nov
(276) |
Dec
(34) |
| 2013 |
Jan
(25) |
Feb
(23) |
Mar
(12) |
Apr
(59) |
May
(31) |
Jun
(11) |
Jul
(21) |
Aug
(7) |
Sep
(18) |
Oct
(11) |
Nov
(12) |
Dec
(18) |
| 2014 |
Jan
(37) |
Feb
(22) |
Mar
(9) |
Apr
(10) |
May
(38) |
Jun
(20) |
Jul
(15) |
Aug
(4) |
Sep
(4) |
Oct
(3) |
Nov
(8) |
Dec
(5) |
| 2015 |
Jan
(13) |
Feb
(34) |
Mar
(27) |
Apr
(5) |
May
(12) |
Jun
(10) |
Jul
(12) |
Aug
(3) |
Sep
(1) |
Oct
(13) |
Nov
|
Dec
(6) |
| 2016 |
Jan
(1) |
Feb
(1) |
Mar
(17) |
Apr
(139) |
May
(120) |
Jun
(90) |
Jul
(10) |
Aug
|
Sep
|
Oct
(11) |
Nov
(6) |
Dec
(2) |
| 2017 |
Jan
(24) |
Feb
(8) |
Mar
(7) |
Apr
(2) |
May
(5) |
Jun
(11) |
Jul
(5) |
Aug
(9) |
Sep
(6) |
Oct
(4) |
Nov
(2) |
Dec
(4) |
| 2018 |
Jan
(7) |
Feb
|
Mar
(4) |
Apr
(6) |
May
(10) |
Jun
(6) |
Jul
(7) |
Aug
|
Sep
(7) |
Oct
(5) |
Nov
(3) |
Dec
(3) |
| 2019 |
Jan
(3) |
Feb
|
Mar
(4) |
Apr
(3) |
May
(2) |
Jun
(6) |
Jul
(3) |
Aug
(2) |
Sep
|
Oct
(2) |
Nov
(12) |
Dec
(1) |
| 2020 |
Jan
(3) |
Feb
(1) |
Mar
(2) |
Apr
|
May
|
Jun
|
Jul
|
Aug
(1) |
Sep
|
Oct
(1) |
Nov
|
Dec
|
| 2021 |
Jan
|
Feb
|
Mar
|
Apr
(3) |
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: <cod...@go...> - 2008-11-27 14:20:22
|
Comment #38 on issue 42 by matthew....@vanderbilt.edu: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 The extra mgf metadata seems like a good reason to go with nativeID instead of ID. In mzML, the ID is totally arbitrary, but the nativeID is not. So if you're working from a non-mzML file, it's perfectly reasonable to use nativeID but not really ID. The basic nativeID for an MGF is the 0-based index into the file. If the title attribute has been written in a way that the reader can parse back to a vendor's nativeID, that's a sensible alternative. The other attributes are pretty messy IMO because they're either not required to be unique or they may encode scans or RTs from multiple acquisitions. I suggest them as userParams. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2008-11-27 13:59:09
|
Comment #37 on issue 42 by dcreasy: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Under <SpectrumIdentificationResult> I would like additional CV to help determine which spectrum in an MGF file the <SpectrumIdentificationResult> came from. As discussed previously, the SpectrumID parameter is sufficient for mzML, but there are several possible indexes for an MGF file (depending on how the file was created). I suggest the following 4 cv terms: mgf title mgf scans mgf rtinseconds mgf rawscans -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: David C. <dc...@ma...> - 2008-11-27 13:35:32
|
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 |
|
From: Martin E. <mar...@ru...> - 2008-11-27 13:18:38
|
Hi!
Davids proposal works well for Sequest and our MPC use case.
I agree with Andy, that we should do it analogously to e.g. the
"residues" attribute of <Modification>.
As I understood the obo type definitions correspond to xsd types;
including more complex types like "psi-pi:listOfChars" looks
unnecessarily complex to me.
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...
Bye
Martin
> -----Ursprüngliche Nachricht-----
> Von: Jones, Andy [mailto:And...@li...]
> Gesendet: Monday, November 24, 2008 4:07 PM
> An: psi...@li...
> Betreff: Re: [Psidev-pi-dev] Ambiguous residues - CV
>
> Looks fine to me, only minor consideration might be the "value" data type for:
> Alternate single letter codes. You could imagine values getting encoded as "DN"
> "D N" "D,N" or "[D/N]" etc.
>
> Elsewhere in the AnalysisXML schema, we have defined an extension data type
> listOfChars, which enforces that values are given as space separated chars: "D N
> M", it would be nice to follow a similar convention although I don't know if it
> would make sense to put this newly defined data type into the CV?
>
> Cheers, Andy
>
>
>
>
> > -----Original Message-----
> > From: David Creasy [mailto:dc...@ma...]
> > Sent: 24 November 2008 14:43
> > To: psi...@li...
> > Subject: [Psidev-pi-dev] Ambiguous residues - CV
> >
> > Hi all,
> >
> > We need CV for the <AmbiguousResidue> element in the analysisXML
> > MassTable. This is when, for example, a search engine sees an 'X' in the
> > fasta file and it tries every other defined residue mass. We decided
> > that we wanted to use CV here in case a search engine implements complex
> > rules for these ambiguous residues.
> >
> > I propose 2 initial CV items to allow either mass or previously defined
> > residue. An example of each type shown in context below:
> >
> > <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>
> >
> > The "Alternate mass" item would be: unitAccession="UO:0000221"
> > unitName="dalton".
> >
> > Does this sound reasonable?
> >
> > Cheers,
> >
> > David
> >
> > --
> > 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
|
|
From: Jones, A. <And...@li...> - 2008-11-27 12:52:34
|
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 |
|
From: David C. <dc...@ma...> - 2008-11-26 17:55:23
|
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 |
|
From: Jones, A. <And...@li...> - 2008-11-26 17:11:42
|
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 |
|
From: <cod...@go...> - 2008-11-26 13:51:37
|
Comment #36 on issue 42 by a.bertsch0815: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Units in terms: We agreed to use the following a structure for units in the CV (stolen from mzML): [Term] id: MS:1000004 name: sample mass def: "Total mass of sample used." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000002 ! mass unit An example in mzML would look like this. <cvParam cvRef="MS" accession="MS:1000016" name="scan time" value="5.8905" unitCvRef="UO" unitAccession="UO:0000031" unitName="minute"/> Which would be straightforward for semantic validation. Any term which has a "has_units" relationship, must have a unit. However, at the moment, cvParam cannot have an unitAccession or unitName or unitCvRef attribute (PropertyValue not included in cvParamType) in the schema. Do I miss something or do we need a schema change if we want to do it similar to mzML, which would be my favorite. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2008-11-26 12:03:26
|
Comment #35 on issue 42 by jensiepen: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Terms need adding for X!Tandem and OMSSA: scoring xtandem: expect xtandem: hyperscore omssa: e_value omssa: p_value source file format omssa csv file xtandem xml file -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: David C. <dc...@ma...> - 2008-11-25 15:52:44
|
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 |
|
From: David C. <dc...@ma...> - 2008-11-25 13:56:55
|
Andy, Martin etc. I've finally written the code to output "real tables" of fragment ions matched for the Mascot examples. I've updated the Mascot_MSMS_example.axml under svn. Look for the first <Fragmentation> and compare with the matches to DAGTISGLNVLR here: http://www.matrixscience.com/cgi/peptide_view.pl?file=../data/20081124/FInAmic.dat&query=1&hit=1 (The AnalysisXML output currently outputs all matches, even to peaks in the noise, so you'll see more matches in xml than in the standard Mascot report). The issues were discussed here; http://code.google.com/p/psi-pi/issues/detail?id=28 There are three issues: a) You'll notice that there are two lots of matches to most series. These correspond to, for example 'b' and 'b++'. I think that we need to add a 'charge' attribute to IonType rather than adding more CV. b) Internals. I want to have the index like 1:3 2:6 to represent DAG and AGTIS in DAGTISGL... However, this doesn't validate c) Immonium ions. Would be nice if the index could be A G I For b and c, is this possible, or are there other suggestions? It was originally suggested by Matt at http://code.google.com/p/psi-pi/issues/detail?id=28#c17 Thanks, David -- 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: Jones, A. <And...@li...> - 2008-11-24 15:07:02
|
Looks fine to me, only minor consideration might be the "value" data type for: Alternate single letter codes. You could imagine values getting encoded as "DN" "D N" "D,N" or "[D/N]" etc. Elsewhere in the AnalysisXML schema, we have defined an extension data type listOfChars, which enforces that values are given as space separated chars: "D N M", it would be nice to follow a similar convention although I don't know if it would make sense to put this newly defined data type into the CV? Cheers, Andy > -----Original Message----- > From: David Creasy [mailto:dc...@ma...] > Sent: 24 November 2008 14:43 > To: psi...@li... > Subject: [Psidev-pi-dev] Ambiguous residues - CV > > Hi all, > > We need CV for the <AmbiguousResidue> element in the analysisXML > MassTable. This is when, for example, a search engine sees an 'X' in the > fasta file and it tries every other defined residue mass. We decided > that we wanted to use CV here in case a search engine implements complex > rules for these ambiguous residues. > > I propose 2 initial CV items to allow either mass or previously defined > residue. An example of each type shown in context below: > > <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> > > The "Alternate mass" item would be: unitAccession="UO:0000221" > unitName="dalton". > > Does this sound reasonable? > > Cheers, > > David > > -- > 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...> - 2008-11-24 14:43:14
|
Hi all,
We need CV for the <AmbiguousResidue> element in the analysisXML
MassTable. This is when, for example, a search engine sees an 'X' in the
fasta file and it tries every other defined residue mass. We decided
that we wanted to use CV here in case a search engine implements complex
rules for these ambiguous residues.
I propose 2 initial CV items to allow either mass or previously defined
residue. An example of each type shown in context below:
<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>
The "Alternate mass" item would be: unitAccession="UO:0000221"
unitName="dalton".
Does this sound reasonable?
Cheers,
David
--
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: <cod...@go...> - 2008-11-23 20:06:36
|
Comment #34 on issue 42 by dcreasy: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 [Term] id: PI:00365 name: frag: internal yb ion is_a: PI:00066 ! ions series considered in search is_a: PI:00221 ! fragmentation information At the telecon on 2008-11-20, we agreed to keep ions series found and ions series considered in search separate. The four new ones have been added as single term, but should be separated? -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2008-11-23 20:02:36
|
Comment #33 on issue 42 by dcreasy: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 [Term] id: PI:00146 name: param: a ion-NH3 def: "Ion a - NH3 if a significant and fragment includes RKNQ." [PSI:PI] is_a: PI:00066 ! ions series considered in search Some search engines will only consider a-NH3 ions if the fragment includes RKN or Q residues. Other search engines don't require the RKQN residues. Hence in http://code.google.com/p/psi-pi/issues/detail?id=42#c21 I requested: "TODO: Need CV terms for a-NH3 and also a - NH3 if a significant and fragment includes RKNQ"; Either make an additional term for each of these, or remove the " if a significant and fragment includes RKNQ." etc. from the defline. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2008-11-23 19:58:35
|
Comment #32 on issue 42 by dcreasy: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 [Term] id: PI:00056 name: modification specificity rule def: "The specificity rules for the modifications applied by the search engine (fixed, variable)." [PSI:PI] is_a: PI:00055 ! modification parameters Remove ("fixed, variable)" from the def line Also, remove PI:00187 and PI:00188 as agreed at telecon on 2008-11-20 -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2008-11-21 17:09:58
|
Comment #31 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 more TODOs: - add 2nd parent for Paragon scores -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2008-11-21 15:55:27
|
Comment #30 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 There was an action defined in TeleCon November 12th to look in the schema, where to place search statistics. This is solved because already in the mapping file: terms below search statistics can be CVParams of SpectrumIdentificationList and ProteinDetectionList. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2008-11-21 14:50:18
|
Comment #29 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 more TODOs: - add 2nd parent for Sequest scores (Martin) - add 2nd parent for Paragon scores -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2008-11-21 14:37:53
|
Comment #28 on issue 42 by eisenachM: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Edited OBO to fufill comments 20-27. TODOs: - NEWT.obo (Phil?) - comment 22 (units like in PSI-MS) - comment 25 (problem with values in validation) - comment 27 (terms for matched/unmacthed peaks: we have terms "number of peaks matched", "number of peaks submitted", "number of peaks used"; enough?) -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: Martin E. <mar...@ru...> - 2008-11-20 17:40:34
|
Hi!
I updated the XSLT and unimod.obo in the svn as discussed in the conference.
For an excerpt of the oxidation term (the specificities are property_values) see below.
Of course, the 'property_value: spec_groupX="X"' entries can be dropped.
The names are unique as the UNIMOD ids are.
Bye
Martin
[Term]
id: UNIMOD:35
name: Oxidation
def: "Oxidation or Hydroxylation" [FindMod:HYDR RESID:AA0322 PMID:11212008 PMID:11120890 FindMod:DOPA FindMod:CSEA
PMID:14661084 RESID:AA0026 PMID:15569593 RESID:AA0205 RESID:AA0215 RESID:AA0029 RESID:AA0030 PMID:9004526 RESID:AA0028
PMID:11461766 RESID:AA0027 RESID:AA0235 RESID:AA0146 PMID:14661085 PMID:12781462 PMID:2057999 ]
property_value: record_id="35"
property_value: delta_mono_mass="15.994915"
property_value: delta_avge_mass="15.9994"
property_value: delta_composition="O"
property_value: username_of_poster="unimod"
property_value: group_of_poster="admin"
property_value: date_time_posted="2002-08-19 19:17:11"
property_value: date_time_modified="2008-02-15 05:37:07"
property_value: approved="false"
property_value: spec_group1="1"
property_value: spec_hidden_1="true"
property_value: spec_site_1="D"
property_value: spec_position_1="Anywhere"
property_value: spec_classification_1="Post-translational"
property_value: spec_group2="2"
property_value: spec_hidden_2="true"
property_value: spec_site_2="K"
property_value: spec_position_2="Anywhere"
property_value: spec_classification_2="Post-translational"
.
Von: David Creasy [mailto:dc...@ma...]
Gesendet: Thursday, November 20, 2008 4:36 PM
An: Martin Eisenacher
Cc: 'Sean L Seymour'; psi...@li...
Betreff: Re: AW: [Psidev-pi-dev] unimod.obo and XSLT
Hi Martin, (& Sean)
Yes, you did exactly what we agreed, but maybe we were wrong....
I don't think that we need to include the specificity in the CV. So, for the found modifications we have:
<Peptide id="peptide_2_4" sequenceMass="1614.774567" sequenceLength="13">
<Modification location="1" residues="M" monoisotopicMassDelta="15.994919">
<pf:cvParam accession="Oxidation" name="Oxidation" cvRef="PSI-MS-MOD" />
</Modification>
<Modification location="9" residues="M" monoisotopicMassDelta="15.994919">
<pf:cvParam accession="Oxidation" name="Oxidation" cvRef="PSI-MS-MOD" />
</Modification>
<peptideSequence>MIKTGESGMTVFR</peptideSequence>
</Peptide>
Which is fine (and as in the current schema). Having the specificity in the CV is a duplication here.
However, for the search modification we currently have:
<SearchModification fixedMod="false" >
<ModName accession="MOD:TODO" name="Oxidation (M)" cvRef="UNIMOD" />
<MassDelta value="15.994919" unitAccession="UO:0000221" unitName="Da" />
<SpecificityRule accession="PI:00188" cvRef="PSI-PI" name="modification specificity variable" />
</SearchModification>
and we have the following CV:
id: PI:00187, name: modification specificity fixed
id: PI:00188, name: modification specificity variable
id: PI:00189, name: modification specificity N-term
id: PI:00190, name: modification specificity C-term
How about we add a residues attribute to SearchModification and then remove all specificity from the CV? Does this sound
reasonable Sean?
Note that the PSI-MS-MOD names don't include any specificities.
(Also, we seem to now have a duplication of CV and attributes for fixed/variable...).
Can we discuss further on the call?
David
Martin Eisenacher wrote:
Hi!
(btw, I don't think that the .obo file is correct - I don't think that want new ID's)
You mean, we want to use the original unimod.xml-record_id?
But we agreed to have one OBO term for each (modification,specificity) pair.
Bye
Martin
"Martin Eisenacher" <mailto:mar...@ru...> <mar...@ru...>
11/19/2008 08:55 AM
To
psi...@li...
cc
Subject
[Psidev-pi-dev] unimod.obo and XSLT
Hi all!
To report modifications of resulting peptides we want to use unimod.
I assembled a XSLT to transform the XML from
http://www.unimod.org/xml/unimod.xml
to a unimod.obo (e.g. with XMLSpy).
For each (modification,specificity) pair an OBO term was created
(technically: a (umod:mod,spec_group) pair was transformed into a term with
a unique accession. For XSLT simplicity the accessions were created as
"PI-UNIMOD:"+record_id+"0"+spec_group, which creates gaps between
accession numbers, but ensures uniqueness).
Only the umod:xref elements PMID, RESID and FindMod are transformed to Dbxrefs in
obo; some of them had an invalid type in the XML, which I corrected
(I will report these to the unimod people).
Other umod:xrefs like "Misc. URL", "Book" or "Other" can be transformed
to property_values later.
I added unimod.obo and unimodXML2OBO.xsl
to http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv
Hope that helps...
Bye
Martin
-------------------------------------------------------------------------
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 <http://moblin-contest.org/redirect.php?banner_id=100&url=/> &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 <http://moblin-contest.org/redirect.php?banner_id=100&url=/> &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: Jones, A. <And...@li...> - 2008-11-20 17:17:29
|
Schema updated with agreed changes to SearchModification |
|
From: Phil J. @ E. <pj...@eb...> - 2008-11-20 17:07:12
|
Hi, please find the minutes of the PSI-PI Telecon on the 20 November here: http://psidev.info/index.php?q=node/392 best regards, Phil. -- Phil Jones Senior Software Engineer InterPro Team PANDA Group, EMBL-EBI Wellcome Trust Genome Campus Hinxton, Cambridge, CB10 1SD UK. Work phone: +44 1223 494406 (NEW NUMBER) Skype: philip-jones |
|
From: <cod...@go...> - 2008-11-20 16:55:18
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #27 by delagoya: From phone conf 11/20: Change Quality estimate score "by eye" term to "manual validation" or something like that. Term needed for "number of matched/unmatched peaks"? -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: Martin E. <mar...@ru...> - 2008-11-20 15:50:10
|
Hi Andreas, hi all,
Validating the MPC_example.axml I get the following validation errors (plus suggestion/comment):
Error: CV term used in invalid element: 'BTO:0000255 - brain cell line' at element
'/AnalysisXML/AnalysisSampleCollection/GenericMaterial'
For me, it seems, that the R5 rule cvIdentifierRef is wrong?: BTO instead of PSI-PI?
Error: CV term used in invalid element: 'PI:00194 - quality estimation with decoy database' at element
'/AnalysisXML/AnalysisProtocolCollection/ProteinDetectionProtocol/AnalysisParams'
In my point of view, PI:00194 and its children should be added to R24 with OR.
Error: Value of CVTerm not allowed: 'UO:0000169 - parts per million, value=75.0' at element
'/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance'
Error: Value of CVTerm not allowed: 'UO:0000221 - dalton, value=0.9' at element
'/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance'
Error: Value of CVTerm not allowed: 'UO:0000221 - dalton, value=15.994914622' at element
'/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ModificationParams/SearchModification'
Are these problems with . vs , (english vs. german decimal point?).
Where is the type declared?
Error: Value-type required, but not given (xsd:string): 'PI:00267 - software vendor, value=' at element
'/AnalysisXML/AnalysisSoftwareList/AnalysisSoftware/ContactRole/role'
I think, for software vendor is no value required. In the XML there is an Organization element
containing the name and the CV term describes only the role without value.
Warning: No mapping rule found for element '/AnalysisXML/DataCollection/Inputs/SearchDatabase'
There should be a rule mapping this XPath to PI:00011 (search database details) (allow children).
Warning: Unknown CV term: 'NEWT:9606 - Homo sapiens' at element '/AnalysisXML/AnalysisSampleCollection/GenericMaterial'
Warning: Unknown CV term: 'PI-UNIMOD:3508 - Oxidation' at element '/AnalysisXML/SequenceCollection/Peptide/Modification'
I think these will be obsolete as soon as you link the obo files...
I haven't added these remarks to the issue list, please add those for which you don't agree to
my respective suggestion ;-)
Bye
Martin
|
42 messages has been excluded from this view by a project administrator.
