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From: Jones, A. <And...@li...> - 2008-10-28 15:06:18
|
Hi all, We have planned a conference call this week on Thurs 30th at the usual time: http://www.timeanddate.com/worldclock/fixedtime.html?day=30&month=10&year=2008&h our=16&min=0&sec=0&p1=136 A couple of people are going to be away this week so we'll hold the call if there is sufficient interest and if there's been any progress since last week - so let me know! Proposed agenda: 1. Review minutes from last week 2. CV / mapping file 3. Any updated examples to review? 4. Review open issues: http://code.google.com/p/psi-pi/issues/list 5. Plan for submission to doc process 6. AOB Dial in details: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 cheers, Andy |
|
From: Matthew C. <mat...@va...> - 2008-10-27 17:42:33
|
Hi all, I thought this is a good venue to ask these questions, it might even have some bearing on standardization. :) It is my understanding that the z ion is not what is produced by ETD, but rather a "z radical" - z plus a proton. Is this correct? Does the same hold true for ECD? If so, then what uses the z ion directly? How will "z radicals" be annotated in AnalysisXML? As a separate ion series in the CV? Thanks, -Matt |
|
From: Martin E. <mar...@ru...> - 2008-10-24 15:19:36
|
Hi Andreas, hi all, I worked on the obo file today; OBOEdit is a silly beast, but in the end it did what I wanted. Changes to the CV: - I restructured it into major branches (see image attached) - considered all current comments of issue 42 (0-5) - added regular expressions for default enzymes as Dbxrefs (will be replaced by 'has_regexp' relations later) - added units, some mascot input parameters, roles, instrument types, ion series (input parameters) - deleted terms now in schema (own branch MOVED_to_schema, later to be destroyed) @Andreas: I browsed existing examples looking for existing cvParam positions and created a new branch/subtree if necessary. Mapping CV to schema via XPath should work for each position. Maybe we have to split some branches further... Best regards Martin |
|
From: Jones, A. <And...@li...> - 2008-10-24 10:34:00
|
Changes to schema: - Included rank as an attribute on SpectrumIdentificationItem - Added cv id attribute in FuGElight_working.xsd - Added KeyRefs for all CvParams - Fixed composite key for SpectrumIdentificationResult Cheers Andy From: Phil Jones @ EBI [mailto:pj...@eb...] Sent: 24 October 2008 10:25 To: psi...@li... Subject: [Psidev-pi-dev] Minutes of telecon, 24 October 16:00 Hi, Please find the minutes of yesterday's teleconference here: http://psidev.info/index.php?q=node/380 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: Phil J. @ E. <pj...@eb...> - 2008-10-24 09:27:35
|
Hi, Please find the minutes of yesterday's teleconference here: http://psidev.info/index.php?q=node/380 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: Matthew C. <mat...@va...> - 2008-10-23 14:55:05
|
I can quickly come up with a straightforward suggestion for representing tags as intermediate results. They aren't identifications, so I'm not sure if they should go in SpectrumIdentificationResult or an element type of their own. But certainly they need a type separate from SpectrumIdentificationItem, i.e. SpectrumSequenceTagItem. So a single SpectrumIdentificationResult for a sequence tagging analysis might look like: > <SpectrumIdentificationResult id="result_ref_178_1"> > <SpectrumSequenceTagItem id="tag_ref_178_1" > NTerminusFlankingMass="123.4" > CTerminusFlankingMass="567.8"> > <SequenceTagEvidence>LKS</SequenceTagEvidence> > <pf:cvParam accession="PI:x" name="directag_total_expect" cvRef="PSI-PI" value="0.00123"/> > <pf:cvParam accession="PI:x" name="directag_intensity_pvalue" cvRef="PSI-PI" value="0.00002"/> > <pf:cvParam accession="PI:x" name="directag_mz_fidelity_pvalue" cvRef="PSI-PI" value="0.0003"/> > <pf:cvParam accession="PI:x" name="directag_rank" cvRef="PSI-PI" value="1"/> > </SpectrumSequenceTagItem> > <SpectrumElement spectrumID="" SpectraData_ref="SD_1"/> > </SpectrumIdentificationResult> > -Matt David Creasy wrote: > Hi everyone, > > There will be an AnalysisXML working group conference call today at: > http://www.timeanddate.com/worldclock/fixedtime.html?day=23&month=10&year=2008&hour=16&min=0&sec=0&p1=136 > > Minutes from last meeting at: > http://psidev.info/index.php?q=node/378 > > Agenda: > > 2. Progress with Sequence Tag example (Matt ) |
|
From: Martin E. <mar...@ru...> - 2008-10-23 14:51:06
|
Oops, is not as easy as adding one row, because the SpecList id is one level up.
Someone please help.
Von: Martin Eisenacher [mailto:mar...@ru...]
Gesendet: Thursday, October 23, 2008 4:46 PM
An: 'Jones, Andy'
Cc: 'psi...@li...'
Betreff: AW: [Psidev-pi-dev] AnalysisXML PMF Example
Yes, that works for our example!
I will add this one row to the schema and commit.
Bye
Martin
Von: Jones, Andy [mailto:And...@li...]
Gesendet: Thursday, October 23, 2008 4:13 PM
An: Martin Eisenacher
Cc: psi...@li...
Betreff: RE: [Psidev-pi-dev] AnalysisXML PMF Example
If we represent different search engines within the same document, we have separate SpectrumIdentificationLists.
So the composite key would work if it is (SpectrumIdentificationList ID, spectrumID, SpectraData_ref) I think?
Cheers
Andy
From: Martin Eisenacher [mailto:mar...@ru...]
Sent: 23 October 2008 15:05
To: Jones, Andy
Cc: psi...@li...
Subject: AW: [Psidev-pi-dev] AnalysisXML PMF Example
Thank you for the changes!
One remark: we run into problems with the composite uniqueness of
(spectrumID,SpectraData_ref), because we assemble proteins with peptides found by different search engines.
Each search engine run is a SpectrumIdentification and has its own SpectrumIdentificationList;
there the same spectrum is (usually) referenced (with the same or another peptide sequences as
SpectrumIdentificationItems, but other scores).
We should drop that composite unique key.
Bye
Martin
Von: Jones, Andy [mailto:And...@li...]
Gesendet: Thursday, October 16, 2008 6:26 PM
An: psi...@li...
Betreff: Re: [Psidev-pi-dev] AnalysisXML PMF Example
New schema uploaded by SVN with changes agreed on the call:
- Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data)
- Altered documentation for SpectrumIdentificationItem to clarify that this is a single peptide-spectrum identification
- Altered documentation for SpectrumIdentificationResult - one SpectrumIdentificationResult for one spectrum
- Moved spectrumID and SpectraData_ref as attributes of SpectrumIdentificationResult, and made these composite unique,
removed SpectrumElement
Andy
From: Pierre-Alain Binz [mailto:pie...@is...]
Sent: 16 October 2008 14:26
To: Jones, Andy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be
attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this,
and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more
molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential
peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in
MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want
to postone for v2, right?
Pierre-Alain
Jones, Andy wrote:
Ah, I was getting confused, I was thinking that there would be one
SpectrumIdentificationItem for one Spectrum, in fact there is one for each
peptide.
The problem with the way it's encoded (probably the only way possible without a
schema change) is that it's not obvious how to tie together all the results from
a single spectrum-protein identification. Even querying for the same spectrumID
will not resolve it, since there may be multiple ranked spectrum-protein
identifications from the same spectrum.
I suggest we look at this in the call, I think we might need an alteration to
the schema to model PMF more intuitively, unless I've misunderstood something.
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 13:54
To: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Hi Andy,
For PMF, with Mascot, (and all other search engines as far as I know),
there is no score assigned to matching a single peak to an individual
peptide. A score for one peak in isolation would have little meaning -
you can only really score the match of the complete spectrum.
David
Jones, Andy wrote:
Hi David,
You may be right that the parameter should be optionally anyway, but in this
particular example is there not some score assigned to the peptide-spectrum
identification?
In the equivalent MS/MS example, we have:
<pf:cvParam accession="PI:00171" name="mascot:score"
cvRef="PSI-PI" value="62.72" />
<pf:cvParam accession="PI:00172" name="mascot:expectation value"
cvRef="PSI-PI" value="0.000863428353297988" />
<pf:cvParam accession="PI:99999" name="mascot_rank"
cvRef="PSI-PI" value="1" />
Are the same sort of scores not valid for PMF as well...?
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 12:29
To: psi...@li...
Subject: [Psidev-pi-dev] AnalysisXML PMF Example
Hi All,
There's an example PMF file here:
http://code.google.com/p/psi-
pi/source/browse/trunk/examples/PMF_example.axml
The only small problem that I can see is that for
<SpectrumIdentificationItem>
the schema has:
<xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0"
maxOccurs="unbounded"/>
<xsd:element ref="pf:Param" maxOccurs="unbounded"/>
and I can't think of any required CV here
To find it, search for
<pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt
to say here here"
I suggest that we have minOccurs=0 for pfParam here unless anyone
disagrees?
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
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--
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: Martin E. <mar...@ru...> - 2008-10-23 14:45:56
|
Yes, that works for our example!
I will add this one row to the schema and commit.
Bye
Martin
Von: Jones, Andy [mailto:And...@li...]
Gesendet: Thursday, October 23, 2008 4:13 PM
An: Martin Eisenacher
Cc: psi...@li...
Betreff: RE: [Psidev-pi-dev] AnalysisXML PMF Example
If we represent different search engines within the same document, we have separate SpectrumIdentificationLists.
So the composite key would work if it is (SpectrumIdentificationList ID, spectrumID, SpectraData_ref) I think?
Cheers
Andy
From: Martin Eisenacher [mailto:mar...@ru...]
Sent: 23 October 2008 15:05
To: Jones, Andy
Cc: psi...@li...
Subject: AW: [Psidev-pi-dev] AnalysisXML PMF Example
Thank you for the changes!
One remark: we run into problems with the composite uniqueness of
(spectrumID,SpectraData_ref), because we assemble proteins with peptides found by different search engines.
Each search engine run is a SpectrumIdentification and has its own SpectrumIdentificationList;
there the same spectrum is (usually) referenced (with the same or another peptide sequences as
SpectrumIdentificationItems, but other scores).
We should drop that composite unique key.
Bye
Martin
Von: Jones, Andy [mailto:And...@li...]
Gesendet: Thursday, October 16, 2008 6:26 PM
An: psi...@li...
Betreff: Re: [Psidev-pi-dev] AnalysisXML PMF Example
New schema uploaded by SVN with changes agreed on the call:
- Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data)
- Altered documentation for SpectrumIdentificationItem to clarify that this is a single peptide-spectrum identification
- Altered documentation for SpectrumIdentificationResult - one SpectrumIdentificationResult for one spectrum
- Moved spectrumID and SpectraData_ref as attributes of SpectrumIdentificationResult, and made these composite unique,
removed SpectrumElement
Andy
From: Pierre-Alain Binz [mailto:pie...@is...]
Sent: 16 October 2008 14:26
To: Jones, Andy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be
attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this,
and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more
molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential
peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in
MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want
to postone for v2, right?
Pierre-Alain
Jones, Andy wrote:
Ah, I was getting confused, I was thinking that there would be one
SpectrumIdentificationItem for one Spectrum, in fact there is one for each
peptide.
The problem with the way it's encoded (probably the only way possible without a
schema change) is that it's not obvious how to tie together all the results from
a single spectrum-protein identification. Even querying for the same spectrumID
will not resolve it, since there may be multiple ranked spectrum-protein
identifications from the same spectrum.
I suggest we look at this in the call, I think we might need an alteration to
the schema to model PMF more intuitively, unless I've misunderstood something.
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 13:54
To: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Hi Andy,
For PMF, with Mascot, (and all other search engines as far as I know),
there is no score assigned to matching a single peak to an individual
peptide. A score for one peak in isolation would have little meaning -
you can only really score the match of the complete spectrum.
David
Jones, Andy wrote:
Hi David,
You may be right that the parameter should be optionally anyway, but in this
particular example is there not some score assigned to the peptide-spectrum
identification?
In the equivalent MS/MS example, we have:
<pf:cvParam accession="PI:00171" name="mascot:score"
cvRef="PSI-PI" value="62.72" />
<pf:cvParam accession="PI:00172" name="mascot:expectation value"
cvRef="PSI-PI" value="0.000863428353297988" />
<pf:cvParam accession="PI:99999" name="mascot_rank"
cvRef="PSI-PI" value="1" />
Are the same sort of scores not valid for PMF as well...?
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 12:29
To: psi...@li...
Subject: [Psidev-pi-dev] AnalysisXML PMF Example
Hi All,
There's an example PMF file here:
http://code.google.com/p/psi-
pi/source/browse/trunk/examples/PMF_example.axml
The only small problem that I can see is that for
<SpectrumIdentificationItem>
the schema has:
<xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0"
maxOccurs="unbounded"/>
<xsd:element ref="pf:Param" maxOccurs="unbounded"/>
and I can't think of any required CV here
To find it, search for
<pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt
to say here here"
I suggest that we have minOccurs=0 for pfParam here unless anyone
disagrees?
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
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Grand prize is a trip for two to an Open Source event anywhere in the world
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--
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
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|
From: Jones, A. <And...@li...> - 2008-10-23 14:13:48
|
If we represent different search engines within the same document, we have separate SpectrumIdentificationLists. So the composite key would work if it is (SpectrumIdentificationList ID, spectrumID, SpectraData_ref) I think? Cheers Andy From: Martin Eisenacher [mailto:mar...@ru...] Sent: 23 October 2008 15:05 To: Jones, Andy Cc: psi...@li... Subject: AW: [Psidev-pi-dev] AnalysisXML PMF Example Thank you for the changes! One remark: we run into problems with the composite uniqueness of (spectrumID,SpectraData_ref), because we assemble proteins with peptides found by different search engines. Each search engine run is a SpectrumIdentification and has its own SpectrumIdentificationList; there the same spectrum is (usually) referenced (with the same or another peptide sequences as SpectrumIdentificationItems, but other scores). We should drop that composite unique key… Bye Martin Von: Jones, Andy [mailto:And...@li...] Gesendet: Thursday, October 16, 2008 6:26 PM An: psi...@li... Betreff: Re: [Psidev-pi-dev] AnalysisXML PMF Example New schema uploaded by SVN with changes agreed on the call: - Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data) - Altered documentation for SpectrumIdentificationItem to clarify that this is a single peptide-spectrum identification - Altered documentation for SpectrumIdentificationResult – one SpectrumIdentificationResult for one spectrum - Moved spectrumID and SpectraData_ref as attributes of SpectrumIdentificationResult, and made these composite unique, removed SpectrumElement Andy From: Pierre-Alain Binz [mailto:pie...@is...] Sent: 16 October 2008 14:26 To: Jones, Andy Cc: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this, and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want to postone for v2, right? Pierre-Alain Jones, Andy wrote: Ah, I was getting confused, I was thinking that there would be one SpectrumIdentificationItem for one Spectrum, in fact there is one for each peptide. The problem with the way it's encoded (probably the only way possible without a schema change) is that it's not obvious how to tie together all the results from a single spectrum-protein identification. Even querying for the same spectrumID will not resolve it, since there may be multiple ranked spectrum-protein identifications from the same spectrum. I suggest we look at this in the call, I think we might need an alteration to the schema to model PMF more intuitively, unless I've misunderstood something. Cheers Andy -----Original Message----- From: David Creasy [mailto:dc...@ma...] Sent: 16 October 2008 13:54 To: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example Hi Andy, For PMF, with Mascot, (and all other search engines as far as I know), there is no score assigned to matching a single peak to an individual peptide. A score for one peak in isolation would have little meaning - you can only really score the match of the complete spectrum. David Jones, Andy wrote: Hi David, You may be right that the parameter should be optionally anyway, but in this particular example is there not some score assigned to the peptide-spectrum identification? In the equivalent MS/MS example, we have: <pf:cvParam accession="PI:00171" name="mascot:score" cvRef="PSI-PI" value="62.72" /> <pf:cvParam accession="PI:00172" name="mascot:expectation value" cvRef="PSI-PI" value="0.000863428353297988" /> <pf:cvParam accession="PI:99999" name="mascot_rank" cvRef="PSI-PI" value="1" /> Are the same sort of scores not valid for PMF as well...? Cheers Andy -----Original Message----- From: David Creasy [mailto:dc...@ma...] Sent: 16 October 2008 12:29 To: psi...@li... Subject: [Psidev-pi-dev] AnalysisXML PMF Example Hi All, There's an example PMF file here: http://code.google.com/p/psi- pi/source/browse/trunk/examples/PMF_example.axml The only small problem that I can see is that for <SpectrumIdentificationItem> the schema has: <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" maxOccurs="unbounded"/> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> and I can't think of any required CV here To find it, search for <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt to say here here" I suggest that we have minOccurs=0 for pfParam here unless anyone disagrees? 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 -- 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: Martin E. <mar...@ru...> - 2008-10-23 14:05:23
|
Thank you for the changes!
One remark: we run into problems with the composite uniqueness of
(spectrumID,SpectraData_ref), because we assemble proteins with peptides found by different search engines.
Each search engine run is a SpectrumIdentification and has its own SpectrumIdentificationList;
there the same spectrum is (usually) referenced (with the same or another peptide sequences as
SpectrumIdentificationItems, but other scores).
We should drop that composite unique key.
Bye
Martin
Von: Jones, Andy [mailto:And...@li...]
Gesendet: Thursday, October 16, 2008 6:26 PM
An: psi...@li...
Betreff: Re: [Psidev-pi-dev] AnalysisXML PMF Example
New schema uploaded by SVN with changes agreed on the call:
- Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data)
- Altered documentation for SpectrumIdentificationItem to clarify that this is a single peptide-spectrum identification
- Altered documentation for SpectrumIdentificationResult - one SpectrumIdentificationResult for one spectrum
- Moved spectrumID and SpectraData_ref as attributes of SpectrumIdentificationResult, and made these composite unique,
removed SpectrumElement
Andy
From: Pierre-Alain Binz [mailto:pie...@is...]
Sent: 16 October 2008 14:26
To: Jones, Andy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be
attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this,
and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more
molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential
peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in
MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want
to postone for v2, right?
Pierre-Alain
Jones, Andy wrote:
Ah, I was getting confused, I was thinking that there would be one
SpectrumIdentificationItem for one Spectrum, in fact there is one for each
peptide.
The problem with the way it's encoded (probably the only way possible without a
schema change) is that it's not obvious how to tie together all the results from
a single spectrum-protein identification. Even querying for the same spectrumID
will not resolve it, since there may be multiple ranked spectrum-protein
identifications from the same spectrum.
I suggest we look at this in the call, I think we might need an alteration to
the schema to model PMF more intuitively, unless I've misunderstood something.
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 13:54
To: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Hi Andy,
For PMF, with Mascot, (and all other search engines as far as I know),
there is no score assigned to matching a single peak to an individual
peptide. A score for one peak in isolation would have little meaning -
you can only really score the match of the complete spectrum.
David
Jones, Andy wrote:
Hi David,
You may be right that the parameter should be optionally anyway, but in this
particular example is there not some score assigned to the peptide-spectrum
identification?
In the equivalent MS/MS example, we have:
<pf:cvParam accession="PI:00171" name="mascot:score"
cvRef="PSI-PI" value="62.72" />
<pf:cvParam accession="PI:00172" name="mascot:expectation value"
cvRef="PSI-PI" value="0.000863428353297988" />
<pf:cvParam accession="PI:99999" name="mascot_rank"
cvRef="PSI-PI" value="1" />
Are the same sort of scores not valid for PMF as well...?
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 12:29
To: psi...@li...
Subject: [Psidev-pi-dev] AnalysisXML PMF Example
Hi All,
There's an example PMF file here:
http://code.google.com/p/psi-
pi/source/browse/trunk/examples/PMF_example.axml
The only small problem that I can see is that for
<SpectrumIdentificationItem>
the schema has:
<xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0"
maxOccurs="unbounded"/>
<xsd:element ref="pf:Param" maxOccurs="unbounded"/>
and I can't think of any required CV here
To find it, search for
<pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt
to say here here"
I suggest that we have minOccurs=0 for pfParam here unless anyone
disagrees?
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
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_______________________________________________
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
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_______________________________________________
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
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_______________________________________________
Psidev-pi-dev mailing list
Psi...@li...
https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev
|
|
From: David C. <dc...@ma...> - 2008-10-23 09:38:32
|
Hi everyone, There will be an AnalysisXML working group conference call today at: http://www.timeanddate.com/worldclock/fixedtime.html?day=23&month=10&year=2008&hour=16&min=0&sec=0&p1=136 Minutes from last meeting at: http://psidev.info/index.php?q=node/378 Agenda: 1. Any progress with modifications from the PSI-MOD group (David) [No!] 2. Progress with Sequence Tag example (Matt ) 3. CV - (Andreas and others) 4. Progress with mapping document (Andy) 5. Any issues with moving attributes from <SpectrumElement spectrumID="" SpectraData_ref="" to <SpectrumIdentificationResult. (All) 6. Review of updated PMF search [done] and Combined ETD/CID search [not done] (David) 7. Documentation issues (Andy) 8. AOB 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...> - 2008-10-20 08:54:15
|
Hi Luisa,
Thank you very much indeed.
(I've cc'd the list as I suspect that your reply will be useful for some
time to come)
It's very good to know that the structure makes sense to someone outside
the immediate group.
Hopefully we can agree who's going to do what at the next telecon -
Andreas kindly volunteered to make some proposals as to how to proceed
and this is certainly going to help.
Thanks,
David
Luisa Montecchi wrote:
> Hi David,
>
> Overall the file structure looks good, I aswered for the regular
> expression on the google tracker suggesting to use the following syntax
> xref: value-type:{string,int,xsd} "regular expression"
>
> Some comments:
> 1- save the file in OBO 1.2 you will have less syntax issue with the OBO
> edit (note *less* does not mean *no*). For this in the save has display
> at the bottom you can just change the selection from format 1.0 to 1.2.
> 2- the class 'now_in_SCHEMA', looks like Eric Deutsch 'purgatory' and
> means those terms should be delete but we are not 100% sure. Fine, but
> make sure you delete them before the file go public (do not obsolete
> those terms if nobody ever used them, same for the obsoleted
> palceholders1,2,3,4)
> 3- about the content of 'now_in_SCHEMA' I generally fully agree with it
> I have some doubts for names (peak list software name, modifications
> name, sample name) but maybe you documented in the schema other source
> for those names?
> 4- PI:00043 - input data type: to me given the children this term
> shoulve be input format, if you mean data type I would except children
> like spcetra or peak list or binary data
> 5- Are you using the word 'details' or 'information' or 'parameter' with
> some clear distinctions?
> 6- try to be consistent with upper or lower case, on my opnion the
> easiest for users is to be strictly lower case except for acronyms
> 7- use more synonyms and less parenthensis in the term name
> 8- try to be consistent on singular/plurals on term names
> 9- with time and will try to a bit more verbose on definitions and
> references here is the list of term with no definition
> id: PI:00000 name: protein informatics cv
> id: PI:00054 name: mzML file
> id: PI:00062 name: mgf file
> id: PI:00067 name: dta files
> id: PI:00195 name: reverse
> id: PI:00196 name: randomized
> id: PI:00197 name: forward+reverse
> id: PI:00199 name: Mascot DAT file
> id: PI:00200 name: SEQUEST results
> id: PI:00201 name: mw filter maximum
> id: PI:00202 name: mw filter minimum
> id: PI:00203 name: pi filter maximum
> id: PI:00204 name: pi filter minimum
> id: PI:00207 name: Mascot
> id: PI:00208 name: Sequest
> id: PI:00209 name: Phenyx
> id: PI:00211 name: mass type setting monoisotopic
> id: PI:00212 name: mass type setting average isotopic
>
>
> Most importantly the structure make sense to me, I found terms I expect
> according to their parent names. Remember you are making a CV and you
> providing standardized terminology to support the description of a MS
> search engine results. Try also to ensure that also the mapping with the
> schema is quite intuitive and documented.
>
> I hope this was useful, let me know if I can help,
>
>
> Regards,
>
>
> Luisa
>
>
>
>
>
>
>
>
>
>
>
> David Creasy wrote:
>> Hi Luisa,
>>
>> We've got two issues with the analysisXML CV, and maybe you can point
>> us in the right direction...
>>
>> 1. None of us feel too confident that we've the right skills/time to
>> design a good structure for CV. In fact, in the telecon that we just
>> had, we even discussed (but rejected!) having just a flat CV. Could
>> you be cajoled/bribed into giving us some help, or recommending
>> somebody who has the ability and time...
>>
>> 2. We are slightly confused by what is and what isn't allowed in the
>> obo format. Angel tried to add some terms, and these don't show up in
>> oboedit:
>> http://code.google.com/p/psi-pi/issues/detail?id=30#c33
>> (We assume it's the ! in the regex that causes the problem)
>> If we can't use oboedit, we don't see how we can maintain any
>> structure - using a text editor ends up being too hard. If you've any
>> idea how we can fix this particular issue, that would be great.
>>
>> The current obo file (without the troublesome enzyme) is here:
>>
>> http://code.google.com/p/psi-pi/source/browse/trunk/cv/psi-pi.obo
>> (Maybe it is better than we think - maybe not)
>>
>>
>> Any help or advice that you can give is greatly appreciated.
>>
>>
>> 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: David C. <dc...@ma...> - 2008-10-17 15:10:22
|
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Ah yes... fixed now.<br>
(The examples don't contain real fragment masses yet - I'm just working
on this now).<br>
<br>
David<br>
<br>
Jones, Andy wrote:
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<div class="Section1">
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Another
minor schema update: added Key KeyRef for Measures
within FragmentArray.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">The
FragmentationTable was missing from the Mascot example
(sorry David!). Here is what it should look like:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
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<SpectrumIdentificationList id="SIL_1"
numSequencesSearched="71412"><br>
<FragmentationTable><br>
<Measure id="m_mz"><br>
<pf:cvParam cvRef="PSI-PI" accession="PI:00225"
name="product ion m/z"/><br>
</Measure><br>
<Measure id="m_intensity"><br>
<pf:cvParam cvRef="PSI-PI" accession="PI:00226"
name="product ion intensity"/><br>
</Measure> <br>
</FragmentationTable><o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Also
made a few minor additions to the spec doc.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Cheers<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">
Jones, Andy [<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
<b>Sent:</b> 17 October 2008 13:17<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">A
few more minor schema changes – no changes to instance docs
needed:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Generally
added bits of documentation after reviewing the
autogenerated docs from Eric<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Changed
the data type on MassTable-residue from xsd:string to a
single character A-Z, seem reasonable?<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent: -18pt;"><!--[if !supportLists]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><span
style="">-<span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></span></span><!--[endif]--><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Added
some docs to FuGElight<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">There
is another change I want to make which won’t affect any
current instances but does place an extra restriction.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Currently
AnalysisCollection references pf:ProtocolApplication
and AnalysisProtocolCollection references pf:Protocol, so any
subclasses of
these can be used – including FuGE GenericProtocol and
GenericProtocolApplication (which we don’t want to support in version
1). <o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">We
also have an abstract AnalysisProtocol and
AnalysisProtocolApplication in the schema which we aren’t using. I
would like
to remove all the attributes from AnalysisProtocol and
AnalysisProtocolApplication, just leaving documentation explaining that
this is
an extension point from which new Protocols or ProtocolApplications
will be
added in later versions.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">AnalysisCollection
would then reference
AnalysisProtocolApplication, of which the only available subclasses are
SpectrumIdentification and ProteinDetection (new analyses may be added
in v 2) and
AnalysisProtocolCollection would reference AnalysisProtocol.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">This
won’t affect current instances but is a reasonable
structural change so I wanted to circulate it to the list before I make
this
change – if I don’t hear any dissent I’ll change this.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Cheers<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">
Jones, Andy [<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
<b>Sent:</b> 16 October 2008 17:26<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">New
schema uploaded by SVN with changes agreed on the call:<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">-
Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to
handle PMF data)<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">-
Altered documentation for SpectrumIdentificationItem to
clarify that this is a single peptide-spectrum identification<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">-
Altered documentation for SpectrumIdentificationResult – one
SpectrumIdentificationResult for one spectrum<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">-
Moved spectrumID and SpectraData_ref as attributes of
SpectrumIdentificationResult, and made these composite unique, removed
SpectrumElement<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size: 11pt; font-family: "Calibri","sans-serif"; color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">
Pierre-Alain Binz [<a class="moz-txt-link-freetext" href="mailto:pie...@is...">mailto:pie...@is...</a>] <br>
<b>Sent:</b> 16 October 2008 14:26<br>
<b>To:</b> Jones, Andy<br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Actually, there might be a score associated with
each
peptide - peak couple, similar to "weights" that coulld be attributed
to a specific fragment ion match in a MS/MS spectrum. But at the end,
even if a
software goes through this, and maybe scores the peptides in an
intermediary
process, it will at the end always link a spectrum with one or more
molecule(s)
(in the case of PMF the molecule(s) is(are) proteins). It can annotate
the
spectrum, either with potential peptides of fragments, respectively.
Anyway, we
have not encoded any scores to the interpretation of fragment ions in
MS/MS
spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole
point of
discussion, which I think we want to postone for v2, right?<br>
<br>
<br>
Pierre-Alain<br>
<br>
Jones, Andy wrote: <o:p></o:p></p>
<pre>Ah, I was getting confused, I was thinking that there would be one<o:p></o:p></pre>
<pre>SpectrumIdentificationItem for one Spectrum, in fact there is one for each<o:p></o:p></pre>
<pre>peptide.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>The problem with the way it's encoded (probably the only way possible without a<o:p></o:p></pre>
<pre>schema change) is that it's not obvious how to tie together all the results from<o:p></o:p></pre>
<pre>a single spectrum-protein identification. Even querying for the same spectrumID<o:p></o:p></pre>
<pre>will not resolve it, since there may be multiple ranked spectrum-protein<o:p></o:p></pre>
<pre>identifications from the same spectrum.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>I suggest we look at this in the call, I think we might need an alteration to<o:p></o:p></pre>
<pre>the schema to model PMF more intuitively, unless I've misunderstood something.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Cheers<o:p></o:p></pre>
<pre>Andy<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre> <o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>-----Original Message-----<o:p></o:p></pre>
<pre>From: David Creasy [<a moz-do-not-send="true"
href="mailto:dc...@ma...">mailto:dc...@ma...</a>]<o:p></o:p></pre>
<pre>Sent: 16 October 2008 13:54<o:p></o:p></pre>
<pre>To: <a moz-do-not-send="true"
href="mailto:psi...@li...">psi...@li...</a><o:p></o:p></pre>
<pre>Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Hi Andy,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>For PMF, with Mascot, (and all other search engines as far as I know),<o:p></o:p></pre>
<pre>there is no score assigned to matching a single peak to an individual<o:p></o:p></pre>
<pre>peptide. A score for one peak in isolation would have little meaning -<o:p></o:p></pre>
<pre>you can only really score the match of the complete spectrum.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>David<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Jones, Andy wrote:<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>Hi David,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>You may be right that the parameter should be optionally anyway, but in this<o:p></o:p></pre>
<pre>particular example is there not some score assigned to the peptide-spectrum<o:p></o:p></pre>
<pre>identification?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>In the equivalent MS/MS example, we have:<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre> <pf:cvParam accession="PI:00171" name="mascot:score"<o:p></o:p></pre>
<pre>cvRef="PSI-PI" value="62.72" /><o:p></o:p></pre>
<pre> <pf:cvParam accession="PI:00172" name="mascot:expectation value"<o:p></o:p></pre>
<pre>cvRef="PSI-PI" value="0.000863428353297988" /><o:p></o:p></pre>
<pre> <pf:cvParam accession="PI:99999" name="mascot_rank"<o:p></o:p></pre>
<pre>cvRef="PSI-PI" value="1" /><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Are the same sort of scores not valid for PMF as well...?<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Cheers<o:p></o:p></pre>
<pre>Andy<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>-----Original Message-----<o:p></o:p></pre>
<pre>From: David Creasy [<a moz-do-not-send="true"
href="mailto:dc...@ma...">mailto:dc...@ma...</a>]<o:p></o:p></pre>
<pre>Sent: 16 October 2008 12:29<o:p></o:p></pre>
<pre>To: <a moz-do-not-send="true"
href="mailto:psi...@li...">psi...@li...</a><o:p></o:p></pre>
<pre>Subject: [Psidev-pi-dev] AnalysisXML PMF Example<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Hi All,<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>There's an example PMF file here:<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><a moz-do-not-send="true"
href="http://code.google.com/p/psi">http://code.google.com/p/psi</a>-<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
</blockquote>
<pre>pi/source/browse/trunk/examples/PMF_example.axml<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;">
<pre>The only small problem that I can see is that for<o:p></o:p></pre>
<pre> <SpectrumIdentificationItem><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>the schema has:<o:p></o:p></pre>
<pre> <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0"<o:p></o:p></pre>
<pre>maxOccurs="unbounded"/><o:p></o:p></pre>
<pre> <xsd:element ref="pf:Param" maxOccurs="unbounded"/><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>and I can't think of any required CV here<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>To find it, search for<o:p></o:p></pre>
<pre><pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt<o:p></o:p></pre>
<pre>to say here here"<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>I suggest that we have minOccurs=0 for pfParam here unless anyone<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
</blockquote>
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David Creasy
Matrix Science
64 Baker Street
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Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
<a class="moz-txt-link-abbreviated" href="mailto:dc...@ma...">dc...@ma...</a>
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|
From: Jones, A. <And...@li...> - 2008-10-17 14:42:57
|
Another minor schema update: added Key KeyRef for Measures within FragmentArray.
The FragmentationTable was missing from the Mascot example (sorry David!). Here
is what it should look like:
<SpectrumIdentificationList id="SIL_1" numSequencesSearched="71412">
<FragmentationTable>
<Measure id="m_mz">
<pf:cvParam cvRef="PSI-PI" accession="PI:00225" name="product ion
m/z"/>
</Measure>
<Measure id="m_intensity">
<pf:cvParam cvRef="PSI-PI" accession="PI:00226" name="product ion
intensity"/>
</Measure>
</FragmentationTable>
Also made a few minor additions to the spec doc.
Cheers
Andy
From: Jones, Andy [mailto:And...@li...]
Sent: 17 October 2008 13:17
To: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
A few more minor schema changes – no changes to instance docs needed:
- Generally added bits of documentation after reviewing the
autogenerated docs from Eric
- Changed the data type on MassTable-residue from xsd:string to a
single character A-Z, seem reasonable?
- Added some docs to FuGElight
There is another change I want to make which won’t affect any current instances
but does place an extra restriction.
Currently AnalysisCollection references pf:ProtocolApplication and
AnalysisProtocolCollection references pf:Protocol, so any subclasses of these
can be used – including FuGE GenericProtocol and GenericProtocolApplication
(which we don’t want to support in version 1).
We also have an abstract AnalysisProtocol and AnalysisProtocolApplication in the
schema which we aren’t using. I would like to remove all the attributes from
AnalysisProtocol and AnalysisProtocolApplication, just leaving documentation
explaining that this is an extension point from which new Protocols or
ProtocolApplications will be added in later versions.
AnalysisCollection would then reference AnalysisProtocolApplication, of which
the only available subclasses are SpectrumIdentification and ProteinDetection
(new analyses may be added in v 2) and AnalysisProtocolCollection would
reference AnalysisProtocol.
This won’t affect current instances but is a reasonable structural change so I
wanted to circulate it to the list before I make this change – if I don’t hear
any dissent I’ll change this.
Cheers
Andy
From: Jones, Andy [mailto:And...@li...]
Sent: 16 October 2008 17:26
To: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
New schema uploaded by SVN with changes agreed on the call:
- Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data)
- Altered documentation for SpectrumIdentificationItem to clarify that this is a
single peptide-spectrum identification
- Altered documentation for SpectrumIdentificationResult – one
SpectrumIdentificationResult for one spectrum
- Moved spectrumID and SpectraData_ref as attributes of
SpectrumIdentificationResult, and made these composite unique, removed
SpectrumElement
Andy
From: Pierre-Alain Binz [mailto:pie...@is...]
Sent: 16 October 2008 14:26
To: Jones, Andy
Cc: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Actually, there might be a score associated with each peptide - peak couple,
similar to "weights" that coulld be attributed to a specific fragment ion match
in a MS/MS spectrum. But at the end, even if a software goes through this, and
maybe scores the peptides in an intermediary process, it will at the end always
link a spectrum with one or more molecule(s) (in the case of PMF the molecule(s)
is(are) proteins). It can annotate the spectrum, either with potential peptides
of fragments, respectively. Anyway, we have not encoded any scores to the
interpretation of fragment ions in MS/MS spectra. Similarly, we wouldn't do it
for PMF. Annotation is the sole point of discussion, which I think we want to
postone for v2, right?
Pierre-Alain
Jones, Andy wrote:
Ah, I was getting confused, I was thinking that there would be one
SpectrumIdentificationItem for one Spectrum, in fact there is one for each
peptide.
The problem with the way it's encoded (probably the only way possible without a
schema change) is that it's not obvious how to tie together all the results from
a single spectrum-protein identification. Even querying for the same spectrumID
will not resolve it, since there may be multiple ranked spectrum-protein
identifications from the same spectrum.
I suggest we look at this in the call, I think we might need an alteration to
the schema to model PMF more intuitively, unless I've misunderstood something.
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 13:54
To: psi...@li...
Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example
Hi Andy,
For PMF, with Mascot, (and all other search engines as far as I know),
there is no score assigned to matching a single peak to an individual
peptide. A score for one peak in isolation would have little meaning -
you can only really score the match of the complete spectrum.
David
Jones, Andy wrote:
Hi David,
You may be right that the parameter should be optionally anyway,
but in this
particular example is there not some score assigned to the
peptide-spectrum
identification?
In the equivalent MS/MS example, we have:
<pf:cvParam accession="PI:00171" name="mascot:score"
cvRef="PSI-PI" value="62.72" />
<pf:cvParam accession="PI:00172"
name="mascot:expectation value"
cvRef="PSI-PI" value="0.000863428353297988" />
<pf:cvParam accession="PI:99999" name="mascot_rank"
cvRef="PSI-PI" value="1" />
Are the same sort of scores not valid for PMF as well...?
Cheers
Andy
-----Original Message-----
From: David Creasy [mailto:dc...@ma...]
Sent: 16 October 2008 12:29
To: psi...@li...
Subject: [Psidev-pi-dev] AnalysisXML PMF Example
Hi All,
There's an example PMF file here:
http://code.google.com/p/psi-
pi/source/browse/trunk/examples/PMF_example.axml
The only small problem that I can see is that for
<SpectrumIdentificationItem>
the schema has:
<xsd:element ref="psi-pi:PeptideEvidence"
minOccurs="0"
maxOccurs="unbounded"/>
<xsd:element ref="pf:Param" maxOccurs="unbounded"/>
and I can't think of any required CV here
To find it, search for
<pf:cvParam accession="PI:xxxxx" name="TODO: Required
content, but nowt
to say here here"
I suggest that we have minOccurs=0 for pfParam here
unless anyone
disagrees?
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
-------------------------------------------------------------------------
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Developer's
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--
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...> - 2008-10-17 12:40:38
|
I've updated the four Mascot MSMS examples and the PMF example as discussed in the call. Is the PMF example any clearer now? http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml Corresponding Mascot report can be seen here: http://www.matrixscience.com/cgi/master_results.pl?file=../data/F981122.dat For the MS-MS, I wonder if we should have 'rank' as an attribute for <SpectrumIdentificationItem> rather than using CV since I think it will be common across all search engines? (This is http://code.google.com/p/psi-pi/issues/detail?id=42, 1st comment). David Jones, Andy wrote: > New schema uploaded by SVN with changes agreed on the call: > > > > > > - Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle > PMF data) > > - Altered documentation for SpectrumIdentificationItem to clarify that > this is a single peptide-spectrum identification > > - Altered documentation for SpectrumIdentificationResult – one > SpectrumIdentificationResult for one spectrum > > - Moved spectrumID and SpectraData_ref as attributes of > SpectrumIdentificationResult, and made these composite unique, removed > SpectrumElement > > > > > > Andy > > > > > > *From:* Pierre-Alain Binz [mailto:pie...@is...] > *Sent:* 16 October 2008 14:26 > *To:* Jones, Andy > *Cc:* psi...@li... > *Subject:* Re: [Psidev-pi-dev] AnalysisXML PMF Example > > > > Actually, there might be a score associated with each peptide - peak > couple, similar to "weights" that coulld be attributed to a specific > fragment ion match in a MS/MS spectrum. But at the end, even if a > software goes through this, and maybe scores the peptides in an > intermediary process, it will at the end always link a spectrum with one > or more molecule(s) (in the case of PMF the molecule(s) is(are) > proteins). It can annotate the spectrum, either with potential peptides > of fragments, respectively. Anyway, we have not encoded any scores to > the interpretation of fragment ions in MS/MS spectra. Similarly, we > wouldn't do it for PMF. Annotation is the sole point of discussion, > which I think we want to postone for v2, right? > > > Pierre-Alain > > Jones, Andy wrote: > > Ah, I was getting confused, I was thinking that there would be one > > SpectrumIdentificationItem for one Spectrum, in fact there is one for each > > peptide. > > > > The problem with the way it's encoded (probably the only way possible without a > > schema change) is that it's not obvious how to tie together all the results from > > a single spectrum-protein identification. Even querying for the same spectrumID > > will not resolve it, since there may be multiple ranked spectrum-protein > > identifications from the same spectrum. > > > > I suggest we look at this in the call, I think we might need an alteration to > > the schema to model PMF more intuitively, unless I've misunderstood something. > > > > Cheers > > Andy > > > > > > > > > > > > > > -----Original Message----- > > From: David Creasy [mailto:dc...@ma...] > > Sent: 16 October 2008 13:54 > > To: psi...@li... <mailto:psi...@li...> > > Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example > > > > Hi Andy, > > > > For PMF, with Mascot, (and all other search engines as far as I know), > > there is no score assigned to matching a single peak to an individual > > peptide. A score for one peak in isolation would have little meaning - > > you can only really score the match of the complete spectrum. > > > > David > > > > Jones, Andy wrote: > > > > Hi David, > > > > You may be right that the parameter should be optionally anyway, but in this > > particular example is there not some score assigned to the peptide-spectrum > > identification? > > > > In the equivalent MS/MS example, we have: > > > > <pf:cvParam accession="PI:00171" name="mascot:score" > > cvRef="PSI-PI" value="62.72" /> > > <pf:cvParam accession="PI:00172" name="mascot:expectation value" > > cvRef="PSI-PI" value="0.000863428353297988" /> > > <pf:cvParam accession="PI:99999" name="mascot_rank" > > cvRef="PSI-PI" value="1" /> > > > > Are the same sort of scores not valid for PMF as well...? > > > > Cheers > > Andy > > > > > > > > -----Original Message----- > > From: David Creasy [mailto:dc...@ma...] > > Sent: 16 October 2008 12:29 > > To: psi...@li... <mailto:psi...@li...> > > Subject: [Psidev-pi-dev] AnalysisXML PMF Example > > > > Hi All, > > > > There's an example PMF file here: > > > > http://code.google.com/p/psi- > > > > pi/source/browse/trunk/examples/PMF_example.axml > > > > The only small problem that I can see is that for > > <SpectrumIdentificationItem> > > > > the schema has: > > <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" > > maxOccurs="unbounded"/> > > <xsd:element ref="pf:Param" maxOccurs="unbounded"/> > > > > and I can't think of any required CV here > > > > To find it, search for > > <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt > > to say here here" > > > > I suggest that we have minOccurs=0 for pfParam here unless anyone > > > > disagrees? > > > > 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... <mailto: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=/ <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... <mailto: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=/ <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... <mailto:Psi...@li...> > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > -- > > David Creasy > > Matrix Science > > 64 Baker Street > > London W1U 7GB, UK > > Tel: +44 (0)20 7486 1050 > > Fax: +44 (0)20 7224 1344 > > > > dc...@ma... <mailto:dc...@ma...> > > http://www.matrixscience.com > > > > Matrix Science Ltd. is registered in England and Wales > > Company number 3533898 > > > > ------------------------------------------------------------------------- > > 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=/ <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... <mailto: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=/ <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > _______________________________________________ > > Psidev-pi-dev mailing list > > Psi...@li... <mailto: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...> - 2008-10-17 12:30:51
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> Is the PMF example any clearer now? > http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml Looks good to me now. I think there's a chance that people may find the way results are separated into SpectrumIdentificationItems and ProteinHypotheses slightly confusing since the separation makes less sense for PMF than MS/MS but we probably have to live with this if we want to re-use the same general model structures. > For the MS-MS, I wonder if we should have 'rank' as an attribute for > <SpectrumIdentificationItem> rather than using CV since I think it will > be common across all search engines? > (This is http://code.google.com/p/psi-pi/issues/detail?id=42, 1st comment). I'm in favour of this change, although it would have to be an optional attribute (and well documented) since it makes no sense for PMF data. Cheers Andy > -----Original Message----- > From: David Creasy [mailto:dc...@ma...] > Sent: 17 October 2008 12:53 > To: Jones, Andy > Cc: psi...@li... > Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example > > I've updated the four Mascot MSMS examples and the PMF example as > discussed in the call. > > Is the PMF example any clearer now? > http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml > > Corresponding Mascot report can be seen here: > http://www.matrixscience.com/cgi/master_results.pl?file=../data/F981122.dat > > For the MS-MS, I wonder if we should have 'rank' as an attribute for > <SpectrumIdentificationItem> rather than using CV since I think it will > be common across all search engines? > (This is http://code.google.com/p/psi-pi/issues/detail?id=42, 1st comment). > > David > > Jones, Andy wrote: > > New schema uploaded by SVN with changes agreed on the call: > > > > > > > > > > > > - Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle > > PMF data) > > > > - Altered documentation for SpectrumIdentificationItem to clarify that > > this is a single peptide-spectrum identification > > > > - Altered documentation for SpectrumIdentificationResult – one > > SpectrumIdentificationResult for one spectrum > > > > - Moved spectrumID and SpectraData_ref as attributes of > > SpectrumIdentificationResult, and made these composite unique, removed > > SpectrumElement > > > > > > > > > > > > Andy > > > > > > > > > > > > *From:* Pierre-Alain Binz [mailto:pie...@is...] > > *Sent:* 16 October 2008 14:26 > > *To:* Jones, Andy > > *Cc:* psi...@li... > > *Subject:* Re: [Psidev-pi-dev] AnalysisXML PMF Example > > > > > > > > Actually, there might be a score associated with each peptide - peak > > couple, similar to "weights" that coulld be attributed to a specific > > fragment ion match in a MS/MS spectrum. But at the end, even if a > > software goes through this, and maybe scores the peptides in an > > intermediary process, it will at the end always link a spectrum with one > > or more molecule(s) (in the case of PMF the molecule(s) is(are) > > proteins). It can annotate the spectrum, either with potential peptides > > of fragments, respectively. Anyway, we have not encoded any scores to > > the interpretation of fragment ions in MS/MS spectra. Similarly, we > > wouldn't do it for PMF. Annotation is the sole point of discussion, > > which I think we want to postone for v2, right? > > > > > > Pierre-Alain > > > > Jones, Andy wrote: > > > > Ah, I was getting confused, I was thinking that there would be one > > > > SpectrumIdentificationItem for one Spectrum, in fact there is one for each > > > > peptide. > > > > > > > > The problem with the way it's encoded (probably the only way possible without a > > > > schema change) is that it's not obvious how to tie together all the results from > > > > a single spectrum-protein identification. Even querying for the same spectrumID > > > > will not resolve it, since there may be multiple ranked spectrum-protein > > > > identifications from the same spectrum. > > > > > > > > I suggest we look at this in the call, I think we might need an alteration to > > > > the schema to model PMF more intuitively, unless I've misunderstood > something. > > > > > > > > Cheers > > > > Andy > > > > > > > > > > > > > > > > > > > > > > > > > > > > -----Original Message----- > > > > From: David Creasy [mailto:dc...@ma...] > > > > Sent: 16 October 2008 13:54 > > > > To: psi...@li... <mailto:psidev-pi- > de...@li...> > > > > Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example > > > > > > > > Hi Andy, > > > > > > > > For PMF, with Mascot, (and all other search engines as far as I know), > > > > there is no score assigned to matching a single peak to an individual > > > > peptide. A score for one peak in isolation would have little meaning - > > > > you can only really score the match of the complete spectrum. > > > > > > > > David > > > > > > > > Jones, Andy wrote: > > > > > > > > Hi David, > > > > > > > > You may be right that the parameter should be optionally anyway, but in this > > > > particular example is there not some score assigned to the peptide- > spectrum > > > > identification? > > > > > > > > In the equivalent MS/MS example, we have: > > > > > > > > <pf:cvParam accession="PI:00171" name="mascot:score" > > > > cvRef="PSI-PI" value="62.72" /> > > > > <pf:cvParam accession="PI:00172" name="mascot:expectation > value" > > > > cvRef="PSI-PI" value="0.000863428353297988" /> > > > > <pf:cvParam accession="PI:99999" name="mascot_rank" > > > > cvRef="PSI-PI" value="1" /> > > > > > > > > Are the same sort of scores not valid for PMF as well...? > > > > > > > > Cheers > > > > Andy > > > > > > > > > > > > > > > > -----Original Message----- > > > > From: David Creasy [mailto:dc...@ma...] > > > > Sent: 16 October 2008 12:29 > > > > To: psi...@li... <mailto:psidev-pi- > de...@li...> > > > > Subject: [Psidev-pi-dev] AnalysisXML PMF Example > > > > > > > > Hi All, > > > > > > > > There's an example PMF file here: > > > > > > > > http://code.google.com/p/psi- > > > > > > > > pi/source/browse/trunk/examples/PMF_example.axml > > > > > > > > The only small problem that I can see is that for > > > > <SpectrumIdentificationItem> > > > > > > > > the schema has: > > > > <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" > > > > maxOccurs="unbounded"/> > > > > <xsd:element ref="pf:Param" maxOccurs="unbounded"/> > > > > > > > > and I can't think of any required CV here > > > > > > > > To find it, search for > > > > <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but > nowt > > > > to say here here" > > > > > > > > I suggest that we have minOccurs=0 for pfParam here unless anyone > > > > > > > > disagrees? > > > > > > > > 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... <mailto: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=/ > <http://moblin-contest.org/redirect.php?banner_id=100&url=/> > > > > _______________________________________________ > > > > Psidev-pi-dev mailing list > > > > Psi...@li... <mailto:Psidev-pi- > de...@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=/ <http://moblin- > contest.org/redirect.php?banner_id=100&url=/> > > > > _______________________________________________ > > > > Psidev-pi-dev mailing list > > > > Psi...@li... <mailto:Psidev-pi- > de...@li...> > > > > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > > > > > > > -- > > > > David Creasy > > > > Matrix Science > > > > 64 Baker Street > > > > London W1U 7GB, UK > > > > Tel: +44 (0)20 7486 1050 > > > > Fax: +44 (0)20 7224 1344 > > > > > > > > dc...@ma... <mailto:dc...@ma...> > > > > http://www.matrixscience.com > > > > > > > > Matrix Science Ltd. is registered in England and Wales > > > > Company number 3533898 > > > > > > > > ------------------------------------------------------------------------- > > > > 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=/ <http://moblin- > contest.org/redirect.php?banner_id=100&url=/> > > > > _______________________________________________ > > > > Psidev-pi-dev mailing list > > > > Psi...@li... <mailto:Psidev-pi- > de...@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=/ <http://moblin- > contest.org/redirect.php?banner_id=100&url=/> > > > > _______________________________________________ > > > > Psidev-pi-dev mailing list > > > > Psi...@li... <mailto:Psidev-pi- > de...@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...> - 2008-10-17 12:17:16
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A few more minor schema changes – no changes to instance docs needed: - Generally added bits of documentation after reviewing the autogenerated docs from Eric - Changed the data type on MassTable-residue from xsd:string to a single character A-Z, seem reasonable? - Added some docs to FuGElight There is another change I want to make which won’t affect any current instances but does place an extra restriction. Currently AnalysisCollection references pf:ProtocolApplication and AnalysisProtocolCollection references pf:Protocol, so any subclasses of these can be used – including FuGE GenericProtocol and GenericProtocolApplication (which we don’t want to support in version 1). We also have an abstract AnalysisProtocol and AnalysisProtocolApplication in the schema which we aren’t using. I would like to remove all the attributes from AnalysisProtocol and AnalysisProtocolApplication, just leaving documentation explaining that this is an extension point from which new Protocols or ProtocolApplications will be added in later versions. AnalysisCollection would then reference AnalysisProtocolApplication, of which the only available subclasses are SpectrumIdentification and ProteinDetection (new analyses may be added in v 2) and AnalysisProtocolCollection would reference AnalysisProtocol. This won’t affect current instances but is a reasonable structural change so I wanted to circulate it to the list before I make this change – if I don’t hear any dissent I’ll change this. Cheers Andy From: Jones, Andy [mailto:And...@li...] Sent: 16 October 2008 17:26 To: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example New schema uploaded by SVN with changes agreed on the call: - Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data) - Altered documentation for SpectrumIdentificationItem to clarify that this is a single peptide-spectrum identification - Altered documentation for SpectrumIdentificationResult – one SpectrumIdentificationResult for one spectrum - Moved spectrumID and SpectraData_ref as attributes of SpectrumIdentificationResult, and made these composite unique, removed SpectrumElement Andy From: Pierre-Alain Binz [mailto:pie...@is...] Sent: 16 October 2008 14:26 To: Jones, Andy Cc: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this, and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want to postone for v2, right? Pierre-Alain Jones, Andy wrote: Ah, I was getting confused, I was thinking that there would be one SpectrumIdentificationItem for one Spectrum, in fact there is one for each peptide. The problem with the way it's encoded (probably the only way possible without a schema change) is that it's not obvious how to tie together all the results from a single spectrum-protein identification. Even querying for the same spectrumID will not resolve it, since there may be multiple ranked spectrum-protein identifications from the same spectrum. I suggest we look at this in the call, I think we might need an alteration to the schema to model PMF more intuitively, unless I've misunderstood something. Cheers Andy -----Original Message----- From: David Creasy [mailto:dc...@ma...] Sent: 16 October 2008 13:54 To: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example Hi Andy, For PMF, with Mascot, (and all other search engines as far as I know), there is no score assigned to matching a single peak to an individual peptide. A score for one peak in isolation would have little meaning - you can only really score the match of the complete spectrum. David Jones, Andy wrote: Hi David, You may be right that the parameter should be optionally anyway, but in this particular example is there not some score assigned to the peptide-spectrum identification? In the equivalent MS/MS example, we have: <pf:cvParam accession="PI:00171" name="mascot:score" cvRef="PSI-PI" value="62.72" /> <pf:cvParam accession="PI:00172" name="mascot:expectation value" cvRef="PSI-PI" value="0.000863428353297988" /> <pf:cvParam accession="PI:99999" name="mascot_rank" cvRef="PSI-PI" value="1" /> Are the same sort of scores not valid for PMF as well...? Cheers Andy -----Original Message----- From: David Creasy [mailto:dc...@ma...] Sent: 16 October 2008 12:29 To: psi...@li... Subject: [Psidev-pi-dev] AnalysisXML PMF Example Hi All, There's an example PMF file here: http://code.google.com/p/psi- pi/source/browse/trunk/examples/PMF_example.axml The only small problem that I can see is that for <SpectrumIdentificationItem> the schema has: <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" maxOccurs="unbounded"/> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> and I can't think of any required CV here To find it, search for <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt to say here here" I suggest that we have minOccurs=0 for pfParam here unless anyone disagrees? 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 -- 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: Jones, A. <And...@li...> - 2008-10-17 10:33:57
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Hi Eric, This looks really good, thanks v much! Not wanting to give you more work... but there’s a few minor things to fix if you get a chance, should be fairly simple I think: - Attributes – if required/optional is unspecified, currently “-“ is shown. XSD default is optional – so replace “-“ with “optional”. - The attributes and documentation for FuGE elements is not being extracted e.g. Organization. If this is a big headache you could always generate a separate document for FuGElight and I’ll manually compile them? - Documentation missing where elements have been referenced as sub-elements e.g. AnalysisSoftwareList à AnalysisSoftware and all references to FuGE elements of this type say “?!?” Cheers Andy From: Eric Deutsch [mailto:ede...@sy...] Sent: 17 October 2008 07:43 To: psi...@li... Subject: Re: [Psidev-pi-dev] Spec doc Hi everyone, I updated the current draft of the on-line autogenerated schema docs to the latest svn. The result is at: http://www.peptideatlas.org/tmp/AnalysisXML_working.html It looks like the current mapping file is just a template without any term mappings themselves. Just as a test, I wrote into the axml-mapping.xml file the mapping information for SearchType and it seemed to pull it out of the CV nicely: http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType The autogeneration pulls examples out of one file. I randomly chose Mascot_MSMS_example.axml. Is there a better instance document to automatically pull examples out of? Regards, Eric ________________________________ From: Jones, Andy [mailto:And...@li...] Sent: Monday, October 13, 2008 7:07 AM To: psi...@li... Subject: [Psidev-pi-dev] Spec doc Hi all, A new version of the spec document has been uploaded by SVN (in the specification_document directory), and previous versions have been put in a subfolder. I think the document is getting there... Main tasks still to do: - Finish section on use cases when we have finally agreed the list online and made all the example files. - Import some parts of the example files to demonstrate a few specific points - Import the autogenerated documentation Before we can submit, the main outstanding issues are: - CV - looking through the CV there is still a fair bit of work to do, there’s quite a few terms with missing or incorrect documentation - Mapping file - Finish example files. Prior to the call on Thurs, can we have a think about how we plan to get the CV into shape and discuss it as a main agenda item... Also new schema uploaded with a few bits of improved documentation. Cheers Andy |
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From: David C. <dc...@ma...> - 2008-10-17 08:43:30
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Hi Eric, <br>
<br>
Eric Deutsch wrote:
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<div class="Section1">
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">Hi everyone,
I updated the current draft
of the on-line autogenerated schema docs to the latest svn. The result
is at:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><a moz-do-not-send="true"
href="http://www.peptideatlas.org/tmp/AnalysisXML_working.html">http://www.peptideatlas.org/tmp/AnalysisXML_working.html</a></span></font></p>
</div>
</blockquote>
That's looking great, thanks. I'll be starting to use it rather than
trawling through the schema...<br>
<br>
<blockquote cite="mid:1FA6C1F2633447F4BED00987D6AF412E@fozzie"
type="cite">
<div class="Section1">
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">It looks like the current
mapping file is just a template
without any term mappings themselves. Just as a test, I wrote into the
axml-mapping.xml file the mapping information for SearchType and it
seemed to
pull it out of the CV nicely:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><a moz-do-not-send="true"
href="http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType">http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType</a></span></font></p>
</div>
</blockquote>
Looks like it's going to be a very useful tool once the mapping file is
more complete.<br>
<blockquote cite="mid:1FA6C1F2633447F4BED00987D6AF412E@fozzie"
type="cite">
<div class="Section1">
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">The autogeneration pulls
examples out of one file. I
randomly chose Mascot_MSMS_example.axml. Is there a better instance
document to
automatically pull examples out of?</span></font></p>
</div>
</blockquote>
The X Tandem and Omssa examples will be rather similar to the Mascot
ones Since a simple ms-ms search result probably demonstrates the most
common 'use case' it may be the best example for the time being.
Presumably it takes the first occurrence of each element that it sees.
Maybe we should also try and make a 'search engine neutral' example.<br>
<br>
Cheers,<br>
<br>
David<br>
<br>
<blockquote cite="mid:1FA6C1F2633447F4BED00987D6AF412E@fozzie"
type="cite">
<div class="Section1">
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Regards,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Eric<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0in 0in 0in 4pt;">
<div>
<div class="MsoNormal" style="text-align: center;" align="center"><font
face="Times New Roman" size="3"><span
style="font-size: 12pt; font-family: "Times New Roman";">
<hr tabindex="-1" align="center" size="2" width="100%"></span></font></div>
<p class="MsoNormal"><b><font face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma; font-weight: bold;">From:</span></font></b><font
face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma;"> Jones, Andy
[<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
<b><span style="font-weight: bold;">Sent:</span></b> Monday, October
13, 2008
7:07 AM<br>
<b><span style="font-weight: bold;">To:</span></b>
<a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b><span style="font-weight: bold;">Subject:</span></b>
[Psidev-pi-dev] Spec doc</span></font><font face="Times New Roman"
size="3"><span style="font-size: 12pt; font-family: "Times New Roman";"><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Hi all,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">A new version of the spec
document has been uploaded by SVN (in the
specification_document directory), and previous versions have been put
in a
subfolder. I think the document is getting there... <o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Main tasks still to do:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Finish
section on use cases when we have finally agreed the list
online and made all the example files.<o:p></o:p></span></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Import
some parts of the example files to demonstrate a few specific
points<o:p></o:p></span></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Import
the autogenerated documentation<o:p></o:p></span></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Before we can submit, the main
outstanding issues are:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">CV
- looking through the CV there is still a fair bit of work to do,
there’s quite a few terms with missing or incorrect documentation<o:p></o:p></span></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Mapping
file<o:p></o:p></span></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Finish
example files.<o:p></o:p></span></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Prior to the call on Thurs, can
we have a think about how we plan to
get the CV into shape and discuss it as a main agenda item...<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Also new schema uploaded with a
few bits of improved documentation.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Cheers<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Andy<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="margin-left: 0.25in;"><font face="Calibri"
size="2"><span style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
</div>
</div>
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_______________________________________________
Psidev-pi-dev mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Psi...@li...">Psi...@li...</a>
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</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
David Creasy
Matrix Science
64 Baker Street
London W1U 7GB, UK
Tel: +44 (0)20 7486 1050
Fax: +44 (0)20 7224 1344
<a class="moz-txt-link-abbreviated" href="mailto:dc...@ma...">dc...@ma...</a>
<a class="moz-txt-link-freetext" href="http://www.matrixscience.com">http://www.matrixscience.com</a>
Matrix Science Ltd. is registered in England and Wales
Company number 3533898</pre>
</body>
</html>
|
|
From: Eric D. <ede...@sy...> - 2008-10-17 06:44:06
|
Hi everyone, I updated the current draft of the on-line autogenerated schema docs to the latest svn. The result is at: http://www.peptideatlas.org/tmp/AnalysisXML_working.html It looks like the current mapping file is just a template without any term mappings themselves. Just as a test, I wrote into the axml-mapping.xml file the mapping information for SearchType and it seemed to pull it out of the CV nicely: http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType The autogeneration pulls examples out of one file. I randomly chose Mascot_MSMS_example.axml. Is there a better instance document to automatically pull examples out of? Regards, Eric _____ From: Jones, Andy [mailto:And...@li...] Sent: Monday, October 13, 2008 7:07 AM To: psi...@li... Subject: [Psidev-pi-dev] Spec doc Hi all, A new version of the spec document has been uploaded by SVN (in the specification_document directory), and previous versions have been put in a subfolder. I think the document is getting there... Main tasks still to do: - Finish section on use cases when we have finally agreed the list online and made all the example files. - Import some parts of the example files to demonstrate a few specific points - Import the autogenerated documentation Before we can submit, the main outstanding issues are: - CV - looking through the CV there is still a fair bit of work to do, there's quite a few terms with missing or incorrect documentation - Mapping file - Finish example files. Prior to the call on Thurs, can we have a think about how we plan to get the CV into shape and discuss it as a main agenda item... Also new schema uploaded with a few bits of improved documentation. Cheers Andy |
|
From: David C. <dc...@ma...> - 2008-10-16 17:18:25
|
Minutes are here: http://psidev.info/index.php?q=node/378 Next telecon, same time next week. Preliminary agenda here: http://psidev.info/index.php?q=node/379 David David Creasy wrote: > Hi everyone, > > There will be an AnalysisXML working group conference call on Thursday at: > http://www.timeanddate.com/worldclock/fixedtime.html?day=16&month=10&year=2008&hour=16&min=0&sec=0&p1=136 > > > Minutes from last meeting at: > http://psidev.info/index.php?q=node/376 > > Agenda: > > 1. Review of minutes from last week. Looks as though many things have > been done! > > 2. Review of the list of example files - what others are required? See: > http://psidev.info/index.php?q=node/319#deliverablequicklinks > for the current list. > > 3. Progress with mapping file. Current file at: > http://code.google.com/p/psi-pi/source/browse/trunk/cv/axml-mapping.xml > > 4. The CV. What still needs doing and who is going to do it. > Current obo file at: > http://code.google.com/p/psi-pi/source/browse/trunk/cv/psi-pi.obo > > 5. AOB > > 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: Jones, A. <And...@li...> - 2008-10-16 16:26:43
|
New schema uploaded by SVN with changes agreed on the call: - Made cvParam minOccurs = 0 on SpectrumIdentificationItem (to handle PMF data) - Altered documentation for SpectrumIdentificationItem to clarify that this is a single peptide-spectrum identification - Altered documentation for SpectrumIdentificationResult – one SpectrumIdentificationResult for one spectrum - Moved spectrumID and SpectraData_ref as attributes of SpectrumIdentificationResult, and made these composite unique, removed SpectrumElement Andy From: Pierre-Alain Binz [mailto:pie...@is...] Sent: 16 October 2008 14:26 To: Jones, Andy Cc: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this, and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want to postone for v2, right? Pierre-Alain Jones, Andy wrote: Ah, I was getting confused, I was thinking that there would be one SpectrumIdentificationItem for one Spectrum, in fact there is one for each peptide. The problem with the way it's encoded (probably the only way possible without a schema change) is that it's not obvious how to tie together all the results from a single spectrum-protein identification. Even querying for the same spectrumID will not resolve it, since there may be multiple ranked spectrum-protein identifications from the same spectrum. I suggest we look at this in the call, I think we might need an alteration to the schema to model PMF more intuitively, unless I've misunderstood something. Cheers Andy -----Original Message----- From: David Creasy [mailto:dc...@ma...] Sent: 16 October 2008 13:54 To: psi...@li... Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example Hi Andy, For PMF, with Mascot, (and all other search engines as far as I know), there is no score assigned to matching a single peak to an individual peptide. A score for one peak in isolation would have little meaning - you can only really score the match of the complete spectrum. David Jones, Andy wrote: Hi David, You may be right that the parameter should be optionally anyway, but in this particular example is there not some score assigned to the peptide-spectrum identification? In the equivalent MS/MS example, we have: <pf:cvParam accession="PI:00171" name="mascot:score" cvRef="PSI-PI" value="62.72" /> <pf:cvParam accession="PI:00172" name="mascot:expectation value" cvRef="PSI-PI" value="0.000863428353297988" /> <pf:cvParam accession="PI:99999" name="mascot_rank" cvRef="PSI-PI" value="1" /> Are the same sort of scores not valid for PMF as well...? Cheers Andy -----Original Message----- From: David Creasy [mailto:dc...@ma...] Sent: 16 October 2008 12:29 To: psi...@li... Subject: [Psidev-pi-dev] AnalysisXML PMF Example Hi All, There's an example PMF file here: http://code.google.com/p/psi- pi/source/browse/trunk/examples/PMF_example.axml The only small problem that I can see is that for <SpectrumIdentificationItem> the schema has: <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" maxOccurs="unbounded"/> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> and I can't think of any required CV here To find it, search for <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt to say here here" I suggest that we have minOccurs=0 for pfParam here unless anyone disagrees? 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 -- 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: Pierre-Alain B. <pie...@is...> - 2008-10-16 13:24:27
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Actually, there might be a score associated with each peptide - peak couple, similar to "weights" that coulld be attributed to a specific fragment ion match in a MS/MS spectrum. But at the end, even if a software goes through this, and maybe scores the peptides in an intermediary process, it will at the end always link a spectrum with one or more molecule(s) (in the case of PMF the molecule(s) is(are) proteins). It can annotate the spectrum, either with potential peptides of fragments, respectively. Anyway, we have not encoded any scores to the interpretation of fragment ions in MS/MS spectra. Similarly, we wouldn't do it for PMF. Annotation is the sole point of discussion, which I think we want to postone for v2, right? Pierre-Alain Jones, Andy wrote: > Ah, I was getting confused, I was thinking that there would be one > SpectrumIdentificationItem for one Spectrum, in fact there is one for each > peptide. > > The problem with the way it's encoded (probably the only way possible without a > schema change) is that it's not obvious how to tie together all the results from > a single spectrum-protein identification. Even querying for the same spectrumID > will not resolve it, since there may be multiple ranked spectrum-protein > identifications from the same spectrum. > > I suggest we look at this in the call, I think we might need an alteration to > the schema to model PMF more intuitively, unless I've misunderstood something. > > Cheers > Andy > > > > > > >> -----Original Message----- >> From: David Creasy [mailto:dc...@ma...] >> Sent: 16 October 2008 13:54 >> To: psi...@li... >> Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example >> >> Hi Andy, >> >> For PMF, with Mascot, (and all other search engines as far as I know), >> there is no score assigned to matching a single peak to an individual >> peptide. A score for one peak in isolation would have little meaning - >> you can only really score the match of the complete spectrum. >> >> David >> >> Jones, Andy wrote: >> >>> Hi David, >>> >>> You may be right that the parameter should be optionally anyway, but in this >>> particular example is there not some score assigned to the peptide-spectrum >>> identification? >>> >>> In the equivalent MS/MS example, we have: >>> >>> <pf:cvParam accession="PI:00171" name="mascot:score" >>> cvRef="PSI-PI" value="62.72" /> >>> <pf:cvParam accession="PI:00172" name="mascot:expectation value" >>> cvRef="PSI-PI" value="0.000863428353297988" /> >>> <pf:cvParam accession="PI:99999" name="mascot_rank" >>> cvRef="PSI-PI" value="1" /> >>> >>> Are the same sort of scores not valid for PMF as well...? >>> >>> Cheers >>> Andy >>> >>> >>> >>>> -----Original Message----- >>>> From: David Creasy [mailto:dc...@ma...] >>>> Sent: 16 October 2008 12:29 >>>> To: psi...@li... >>>> Subject: [Psidev-pi-dev] AnalysisXML PMF Example >>>> >>>> Hi All, >>>> >>>> There's an example PMF file here: >>>> >>>> http://code.google.com/p/psi- >>>> >> pi/source/browse/trunk/examples/PMF_example.axml >> >>>> The only small problem that I can see is that for >>>> <SpectrumIdentificationItem> >>>> >>>> the schema has: >>>> <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" >>>> maxOccurs="unbounded"/> >>>> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> >>>> >>>> and I can't think of any required CV here >>>> >>>> To find it, search for >>>> <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt >>>> to say here here" >>>> >>>> I suggest that we have minOccurs=0 for pfParam here unless anyone >>>> >> disagrees? >> >>>> 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 >>> >> -- >> 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: Jones, A. <And...@li...> - 2008-10-16 13:05:45
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Ah, I was getting confused, I was thinking that there would be one SpectrumIdentificationItem for one Spectrum, in fact there is one for each peptide. The problem with the way it's encoded (probably the only way possible without a schema change) is that it's not obvious how to tie together all the results from a single spectrum-protein identification. Even querying for the same spectrumID will not resolve it, since there may be multiple ranked spectrum-protein identifications from the same spectrum. I suggest we look at this in the call, I think we might need an alteration to the schema to model PMF more intuitively, unless I've misunderstood something. Cheers Andy > -----Original Message----- > From: David Creasy [mailto:dc...@ma...] > Sent: 16 October 2008 13:54 > To: psi...@li... > Subject: Re: [Psidev-pi-dev] AnalysisXML PMF Example > > Hi Andy, > > For PMF, with Mascot, (and all other search engines as far as I know), > there is no score assigned to matching a single peak to an individual > peptide. A score for one peak in isolation would have little meaning - > you can only really score the match of the complete spectrum. > > David > > Jones, Andy wrote: > > Hi David, > > > > You may be right that the parameter should be optionally anyway, but in this > > particular example is there not some score assigned to the peptide-spectrum > > identification? > > > > In the equivalent MS/MS example, we have: > > > > <pf:cvParam accession="PI:00171" name="mascot:score" > > cvRef="PSI-PI" value="62.72" /> > > <pf:cvParam accession="PI:00172" name="mascot:expectation value" > > cvRef="PSI-PI" value="0.000863428353297988" /> > > <pf:cvParam accession="PI:99999" name="mascot_rank" > > cvRef="PSI-PI" value="1" /> > > > > Are the same sort of scores not valid for PMF as well...? > > > > Cheers > > Andy > > > > > >> -----Original Message----- > >> From: David Creasy [mailto:dc...@ma...] > >> Sent: 16 October 2008 12:29 > >> To: psi...@li... > >> Subject: [Psidev-pi-dev] AnalysisXML PMF Example > >> > >> Hi All, > >> > >> There's an example PMF file here: > >> > >> http://code.google.com/p/psi- > pi/source/browse/trunk/examples/PMF_example.axml > >> > >> The only small problem that I can see is that for > >> <SpectrumIdentificationItem> > >> > >> the schema has: > >> <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" > >> maxOccurs="unbounded"/> > >> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> > >> > >> and I can't think of any required CV here > >> > >> To find it, search for > >> <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt > >> to say here here" > >> > >> I suggest that we have minOccurs=0 for pfParam here unless anyone > disagrees? > >> > >> 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 > > -- > 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...> - 2008-10-16 12:53:46
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Hi Andy, For PMF, with Mascot, (and all other search engines as far as I know), there is no score assigned to matching a single peak to an individual peptide. A score for one peak in isolation would have little meaning - you can only really score the match of the complete spectrum. David Jones, Andy wrote: > Hi David, > > You may be right that the parameter should be optionally anyway, but in this > particular example is there not some score assigned to the peptide-spectrum > identification? > > In the equivalent MS/MS example, we have: > > <pf:cvParam accession="PI:00171" name="mascot:score" > cvRef="PSI-PI" value="62.72" /> > <pf:cvParam accession="PI:00172" name="mascot:expectation value" > cvRef="PSI-PI" value="0.000863428353297988" /> > <pf:cvParam accession="PI:99999" name="mascot_rank" > cvRef="PSI-PI" value="1" /> > > Are the same sort of scores not valid for PMF as well...? > > Cheers > Andy > > >> -----Original Message----- >> From: David Creasy [mailto:dc...@ma...] >> Sent: 16 October 2008 12:29 >> To: psi...@li... >> Subject: [Psidev-pi-dev] AnalysisXML PMF Example >> >> Hi All, >> >> There's an example PMF file here: >> >> http://code.google.com/p/psi-pi/source/browse/trunk/examples/PMF_example.axml >> >> The only small problem that I can see is that for >> <SpectrumIdentificationItem> >> >> the schema has: >> <xsd:element ref="psi-pi:PeptideEvidence" minOccurs="0" >> maxOccurs="unbounded"/> >> <xsd:element ref="pf:Param" maxOccurs="unbounded"/> >> >> and I can't think of any required CV here >> >> To find it, search for >> <pf:cvParam accession="PI:xxxxx" name="TODO: Required content, but nowt >> to say here here" >> >> I suggest that we have minOccurs=0 for pfParam here unless anyone disagrees? >> >> 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 -- 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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