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From: David C. <dc...@ma...> - 2008-11-20 15:35:37
|
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Hi Martin, (& Sean)<br>
<br>
Yes, you did exactly what we agreed, but maybe we were wrong.... <br>
I don't think that we need to include the specificity in the CV. So,
for the found modifications we have:<br>
<br>
<tt> <Peptide id="peptide_2_4" sequenceMass="1614.774567"
sequenceLength="13"><br>
<Modification location="1" residues="M"
monoisotopicMassDelta="15.994919"><br>
<pf:cvParam accession="Oxidation" name="Oxidation"
cvRef="PSI-MS-MOD" /><br>
</Modification><br>
<Modification location="9" residues="M"
monoisotopicMassDelta="15.994919"><br>
</tt><tt> <pf:cvParam accession="Oxidation" name="Oxidation"
cvRef="PSI-MS-MOD" /><br>
</tt><tt> </Modification><br>
<peptideSequence>MIKTGESGMTVFR</peptideSequence><br>
</Peptide><br>
</tt>Which is fine (and as in the current schema). Having the
specificity in the CV is a duplication here.<br>
<br>
However, for the search modification we currently have:<br>
<tt> <SearchModification fixedMod="false" ><br>
<ModName accession="MOD:TODO" name="Oxidation (M)"
cvRef="UNIMOD" /><br>
<MassDelta value="15.994919" unitAccession="UO:0000221"
unitName="Da" /><br>
<SpecificityRule accession="PI:00188" cvRef="PSI-PI"
name="modification specificity variable" /><br>
</SearchModification><br>
</tt>and we have the following CV:<br>
<br>
id: PI:00187, name: modification specificity fixed<br>
id: PI:00188, name: modification specificity variable<br>
id: PI:00189, name: modification specificity N-term<br>
id: PI:00190, name: modification specificity C-term<br>
<br>
How about we add a residues attribute to SearchModification and then
remove all specificity from the CV? Does this sound reasonable Sean?<br>
Note that the PSI-MS-MOD names don't include any specificities.<br>
(Also, we seem to now have a duplication of CV and attributes for
fixed/variable...). <br>
Can we discuss further on the call?<br>
<br>
David<br>
<br>
Martin Eisenacher wrote:
<blockquote
cite="mid:002b01c94b1b$d9f4f780$8ddee680$@eis...@ru..."
type="cite">
<pre wrap="">Hi!
</pre>
<blockquote type="cite">
<pre wrap="">(btw, I don't think that the .obo file is correct - I don't think that want new ID's)
</pre>
</blockquote>
<pre wrap=""><!---->You mean, we want to use the original unimod.xml-record_id?
But we agreed to have one OBO term for each (modification,specificity) pair.
Bye
Martin
"Martin Eisenacher" <a class="moz-txt-link-rfc2396E" href="mailto:mar...@ru..."><mar...@ru...></a>
11/19/2008 08:55 AM
To
<a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a>
cc
Subject
[Psidev-pi-dev] unimod.obo and XSLT
Hi all!
To report modifications of resulting peptides we want to use unimod.
I assembled a XSLT to transform the XML from
<a class="moz-txt-link-freetext" href="http://www.unimod.org/xml/unimod.xml">http://www.unimod.org/xml/unimod.xml</a>
to a unimod.obo (e.g. with XMLSpy).
For each (modification,specificity) pair an OBO term was created
(technically: a (umod:mod,spec_group) pair was transformed into a term with
a unique accession. For XSLT simplicity the accessions were created as
"PI-UNIMOD:"+record_id+"0"+spec_group, which creates gaps between
accession numbers, but ensures uniqueness).
Only the umod:xref elements PMID, RESID and FindMod are transformed to Dbxrefs in
obo; some of them had an invalid type in the XML, which I corrected
(I will report these to the unimod people).
Other umod:xrefs like "Misc. URL", "Book" or "Other" can be transformed
to property_values later.
I added unimod.obo and unimodXML2OBO.xsl
to <a class="moz-txt-link-freetext" href="http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv">http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv</a>
Hope that helps...
Bye
Martin
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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>
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|
|
From: <cod...@go...> - 2008-11-20 15:10:25
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #26 by dcreasy: Please add [Term] id: PI:0??? name: text file is_a: PI:00043 ! input data type For a simple text file of m/z [intensity] values for a PMF (or single MS-MS?) search -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: <cod...@go...> - 2008-11-20 14:55:25
|
Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #25 by dcreasy: For the mapping file: Error: CV term used in invalid element: 'UO:0000187 - percent' at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance' Error: Value of CVTerm not allowed: 'UO:0000187 - percent, value=0.1' at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance' Error: Value of CVTerm not allowed: 'UO:0000221 - dalton, value=0.5' at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance' -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
|
From: Martin E. <mar...@ru...> - 2008-11-20 14:25:37
|
Hi! >(btw, I don't think that the .obo file is correct - I don't think that want new ID's) You mean, we want to use the original unimod.xml-record_id? But we agreed to have one OBO term for each (modification,specificity) pair. Bye Martin "Martin Eisenacher" <mar...@ru...> 11/19/2008 08:55 AM To psi...@li... cc Subject [Psidev-pi-dev] unimod.obo and XSLT Hi all! To report modifications of resulting peptides we want to use unimod. I assembled a XSLT to transform the XML from http://www.unimod.org/xml/unimod.xml to a unimod.obo (e.g. with XMLSpy). For each (modification,specificity) pair an OBO term was created (technically: a (umod:mod,spec_group) pair was transformed into a term with a unique accession. For XSLT simplicity the accessions were created as "PI-UNIMOD:"+record_id+"0"+spec_group, which creates gaps between accession numbers, but ensures uniqueness). Only the umod:xref elements PMID, RESID and FindMod are transformed to Dbxrefs in obo; some of them had an invalid type in the XML, which I corrected (I will report these to the unimod people). Other umod:xrefs like "Misc. URL", "Book" or "Other" can be transformed to property_values later. I added unimod.obo and unimodXML2OBO.xsl to http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv Hope that helps... Bye Martin ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev ________________________________________ ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ ________________________________________ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
|
From: David C. <dc...@ma...> - 2008-11-20 13:19:42
|
Hi Henning, The original questions put to the mod group in September were: > We need a general solution to three problems: > > 1. A search engine uses unimod and finds a modified residue. It knows > the PSI-MS name is, say 'Oxidation' and the residue is methionine. How > does it (the software, not a human being) determine the PSI-MOD > accession? > 2. A search engine uses their own list of modifications. This might > specify that the delta is 'Oxygen'. The software needs to be able to > look up an accession. > 3. A search engine uses their own list of modifications. This might > specify that the delta is 15.994915 (mono), and 15.9994 (average). The > software needs to be able to look up an accession. > I realise that the second may be tricky and the third impossible! (And > in a sense they aren't your problem), but some advice for the first > one is needed please! An earlier message from John listed the entries for Met oxidation: > Met-O2 is a RESID entry, AA0251, and > all of the Met oxidation states have PSI-MOD entries > MOD:00256 oxidation to L-methionine sulfone > MOD:00719 oxidation to L-methionine sulfoxide > MOD:00720 oxidation to L-methionine (R)-sulfoxide > MOD:00721 oxidation to L-methionine (S)-sulfoxide > The most general oxidation term specifically for Met is > MOD:00709 sulfur oxygenated L-methionine > > The more general oxidation terms available are not specific for > particular amino acids or for number of oxygens. > MOD:00675 oxidized residue > MOD:00676 oxygenated residue > MOD:00679 carbon oxygenated residue > MOD:00680 sulfur oxygenated residue > > If someone needs an oxidation term, specific for original residue, but > not for atom or number, then we can add them. Just let us know. > > I will look into the other questions in the next two days. So, apologies that my statement below about PSI-MOD not containing the "PSI-MS-label" is not correct in the general sense. However, since there's no PSI-MS-label synonym for Oxidation in PSI-MOD, this (and other) cases require human intervention and knowledge to find the appropriate entry in PSI-MOD. Producing analysisXML instant documents manually is obviously not an option... We really need to be able to use the PSI-MS-label names easily. PSI-MOD may just be overkill for us simple mass spec people, or maybe we are missing something obvious? If you've any ideas, we'd love to hear them. Thanks, David Henning Hermjakob wrote: > Hi, > > David Creasy wrote: >> Hi Sean, >> >> Sean L Seymour wrote: >>> >>> Hi All, >>> >>> I'm rather confused by this decision. (1) Why don't we just use the >>> MS mod synonym names that we already worked hard to establish >>> (already have accessions as part of PSI-Mod), or is this what you >>> mean by Unimod? If so, I don't think they should be called Unimod. >> PSI-MOD doesn't include the MS mod names... and we've not been able to >> get these added, so we just can't use it at the moment. > > I only glance through issues on this list, but I think the above might > not be correct. Please check > http://psidev.sourceforge.net/mod/data/PSI-MOD.obo > and search for "PSI-MS-label". As far as I remember, these have been > manually added explicitly for this purpose. > > -- > > Best regards, > > Henning > > >> We intend to just use the MS mod names, but it's easier to validate it >> if we have a .obo file. >> (btw, I don't think that the .obo file is correct - I don't think that >> want new ID's) >> >>> (2) Are you really going to include the specificity in the accession >>> assigned item? Or is this an issue about how modification search >>> setting are indicated, not how modifications that have been detected >>> are indicated in the results? I'll try to make the meeting tomorrow >>> if it's easier to just set me straight by a short discussion than >>> writing it out. >> Yes, please join us if you can. Still some decisions to be made and it >> would really help to have your input... You might like to read: >> http://code.google.com/p/psi-pi/issues/detail?id=35 >> http://code.google.com/p/psi-pi/issues/detail?id=3 >> >> >> David >>> >>> Sean >>> >>> >>> >>> >>> >>> >>> *"Martin Eisenacher" <mar...@ru...>* >>> >>> 11/19/2008 08:55 AM >>> >>> >>> To >>> psi...@li... >>> cc >>> >>> Subject >>> [Psidev-pi-dev] unimod.obo and XSLT >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> Hi all! >>> >>> To report modifications of resulting peptides we want to use unimod. >>> >>> I assembled a XSLT to transform the XML from >>> http://www.unimod.org/xml/unimod.xml >>> to a unimod.obo (e.g. with XMLSpy). >>> >>> For each (modification,specificity) pair an OBO term was created >>> (technically: a (umod:mod,spec_group) pair was transformed into a >>> term with >>> a unique accession. For XSLT simplicity the accessions were created as >>> "PI-UNIMOD:"+record_id+"0"+spec_group, which creates gaps between >>> accession numbers, but ensures uniqueness). >>> >>> Only the umod:xref elements PMID, RESID and FindMod are transformed >>> to Dbxrefs in >>> obo; some of them had an invalid type in the XML, which I corrected >>> (I will report these to the unimod people). >>> >>> Other umod:xrefs like "Misc. URL", "Book" or "Other" can be transformed >>> to property_values later. >>> >>> I added unimod.obo and unimodXML2OBO.xsl >>> to http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv >>> >>> Hope that helps... >>> >>> Bye >>> Martin >>> >>> >>> ------------------------------------------------------------------------- >>> >>> This SF.Net email is sponsored by the Moblin Your Move Developer's >>> challenge >>> Build the coolest Linux based applications with Moblin SDK & win >>> great prizes >>> Grand prize is a trip for two to an Open Source event anywhere in the >>> world >>> http://moblin-contest.org/redirect.php?banner_id=100&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 -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
|
From: <cod...@go...> - 2008-11-20 12:21:44
|
Issue 44: Issues with all instance docs http://code.google.com/p/psi-pi/issues/detail?id=44 Comment #1 by andrewrobertjones: I don't think we have examples of immonium or other internal ions using the fragmentation ion structure, where the indexes are pairs representing start and end points of ions rather than integer indexes. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: Henning H. <hen...@go...> - 2008-11-20 11:13:44
|
Hi, David Creasy wrote: > Hi Sean, > > Sean L Seymour wrote: >> >> Hi All, >> >> I'm rather confused by this decision. (1) Why don't we just use the MS >> mod synonym names that we already worked hard to establish (already >> have accessions as part of PSI-Mod), or is this what you mean by >> Unimod? If so, I don't think they should be called Unimod. > PSI-MOD doesn't include the MS mod names... and we've not been able to > get these added, so we just can't use it at the moment. I only glance through issues on this list, but I think the above might not be correct. Please check http://psidev.sourceforge.net/mod/data/PSI-MOD.obo and search for "PSI-MS-label". As far as I remember, these have been manually added explicitly for this purpose. -- Best regards, Henning > We intend to just use the MS mod names, but it's easier to validate it > if we have a .obo file. > (btw, I don't think that the .obo file is correct - I don't think that > want new ID's) > >> (2) Are you really going to include the specificity in the accession >> assigned item? Or is this an issue about how modification search >> setting are indicated, not how modifications that have been detected >> are indicated in the results? I'll try to make the meeting tomorrow if >> it's easier to just set me straight by a short discussion than writing >> it out. > Yes, please join us if you can. Still some decisions to be made and it > would really help to have your input... You might like to read: > http://code.google.com/p/psi-pi/issues/detail?id=35 > http://code.google.com/p/psi-pi/issues/detail?id=3 > > > David >> >> Sean >> >> >> >> >> >> >> *"Martin Eisenacher" <mar...@ru...>* >> >> 11/19/2008 08:55 AM >> >> >> To >> psi...@li... >> cc >> >> Subject >> [Psidev-pi-dev] unimod.obo and XSLT >> >> >> >> >> >> >> >> >> >> Hi all! >> >> To report modifications of resulting peptides we want to use unimod. >> >> I assembled a XSLT to transform the XML from >> http://www.unimod.org/xml/unimod.xml >> to a unimod.obo (e.g. with XMLSpy). >> >> For each (modification,specificity) pair an OBO term was created >> (technically: a (umod:mod,spec_group) pair was transformed into a term >> with >> a unique accession. For XSLT simplicity the accessions were created as >> "PI-UNIMOD:"+record_id+"0"+spec_group, which creates gaps between >> accession numbers, but ensures uniqueness). >> >> Only the umod:xref elements PMID, RESID and FindMod are transformed to >> Dbxrefs in >> obo; some of them had an invalid type in the XML, which I corrected >> (I will report these to the unimod people). >> >> Other umod:xrefs like "Misc. URL", "Book" or "Other" can be transformed >> to property_values later. >> >> I added unimod.obo and unimodXML2OBO.xsl >> to http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv >> >> Hope that helps... >> >> Bye >> Martin >> >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's >> challenge >> Build the coolest Linux based applications with Moblin SDK & win great >> prizes >> Grand prize is a trip for two to an Open Source event anywhere in the >> world >> http://moblin-contest.org/redirect.php?banner_id=100&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: <cod...@go...> - 2008-11-20 10:55:22
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Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #24 by andrewrobertjones: The CV needs a version number e.g. added as "remark" at the top of the file, following the convention of PSI-MS. The spec doc (copied from mzML) states: A new psi-pi.obo should then be released by updating the file on the CVS server without changing the name of the file (this would alter the propagation of the file to the OBO website and to other ontology services that rely on file stable URI). For this reason an internal version number with two decimals (x.y.z) should be increased: • x should be increased when a first level term are renamed added deleted or rearranged in the structure. Such rearrangement is suppose to be rare and is very likely to have repercussion on the mapping. • y should be increased when any other term except the first level one is altered. • z should be increased when there is no term addition or deletion but just editing on the definitions or other minor changes. -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2008-11-20 10:43:10
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Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #23 by andrewrobertjones: Some of the XSD data types look to be incorrect (e.g. see below), several instances of xsd:decimal should be xsd:float or xsd:double [Term] id: PI:00154 name: sequest:probability def: "The SEQUEST result 'Probability'." [PSI:PI] xref: value-type:xsd\:decimal "The allowed value-type for this CV term." is_a: PI:00153 ! search engine specific score -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2008-11-20 10:01:05
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Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #22 by andrewrobertjones: For parameters that require units, we should follow the PSI-MS structure as follows, linking explicitly to the Unit CV [Term] id: MS:1000004 name: sample mass def: "Total mass of sample used." [PSI:MS] xref: value-type:xsd\:float "The allowed value-type for this CV term." is_a: MS:1000548 ! sample attribute relationship: has_units UO:0000002 ! mass unit -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: David C. <dc...@ma...> - 2008-11-19 19:54:00
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<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> <html> <head> <meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type"> </head> <body bgcolor="#ffffff" text="#000000"> Hi Sean,<br> <br> Sean L Seymour wrote: <blockquote cite="mid:OFB...@ap..." type="cite"><br> <font face="sans-serif" size="2">Hi All,</font> <br> <br> <font face="sans-serif" size="2">I'm rather confused by this decision. (1) Why don't we just use the MS mod synonym names that we already worked hard to establish (already have accessions as part of PSI-Mod), or is this what you mean by Unimod? If so, I don't think they should be called Unimod. </font></blockquote> PSI-MOD doesn't include the MS mod names... and we've not been able to get these added, so we just can't use it at the moment.<br> We intend to just use the MS mod names, but it's easier to validate it if we have a .obo file.<br> (btw, I don't think that the .obo file is correct - I don't think that want new ID's)<br> <br> <blockquote cite="mid:OFB...@ap..." type="cite"><font face="sans-serif" size="2">(2) Are you really going to include the specificity in the accession assigned item? Or is this an issue about how modification search setting are indicated, not how modifications that have been detected are indicated in the results? I'll try to make the meeting tomorrow if it's easier to just set me straight by a short discussion than writing it out.</font> <br> </blockquote> Yes, please join us if you can. Still some decisions to be made and it would really help to have your input... You might like to read:<br> <a class="moz-txt-link-freetext" href="http://code.google.com/p/psi-pi/issues/detail?id=35">http://code.google.com/p/psi-pi/issues/detail?id=35</a><br> <a class="moz-txt-link-freetext" href="http://code.google.com/p/psi-pi/issues/detail?id=3">http://code.google.com/p/psi-pi/issues/detail?id=3</a><br> <br> <br> David<br> <blockquote cite="mid:OFB...@ap..." type="cite"><br> <font face="sans-serif" size="2">Sean</font> <br> <br> <br> <br> <br> <br> <br> <table width="100%"> <tbody> <tr valign="top"> <td width="40%"><font face="sans-serif" size="1"><b>"Martin Eisenacher" <a class="moz-txt-link-rfc2396E" href="mailto:mar...@ru..."><mar...@ru...></a></b> </font> <p><font face="sans-serif" size="1">11/19/2008 08:55 AM</font> </p> </td> <td width="59%"> <table width="100%"> <tbody> <tr valign="top"> <td> <div align="right"><font face="sans-serif" size="1">To</font></div> </td> <td><font face="sans-serif" size="1"><a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a></font> </td> </tr> <tr valign="top"> <td> <div align="right"><font face="sans-serif" size="1">cc</font></div> </td> <td><br> </td> </tr> <tr valign="top"> <td> <div align="right"><font face="sans-serif" size="1">Subject</font></div> </td> <td><font face="sans-serif" size="1">[Psidev-pi-dev] unimod.obo and XSLT</font></td> </tr> </tbody> </table> <br> <table> <tbody> <tr valign="top"> <td> <br> </td> <td><br> </td> </tr> </tbody> </table> <br> </td> </tr> </tbody> </table> <br> <br> <br> <tt><font size="2">Hi all!<br> <br> To report modifications of resulting peptides we want to use unimod.<br> <br> I assembled a XSLT to transform the XML from<br> <a class="moz-txt-link-freetext" href="http://www.unimod.org/xml/unimod.xml">http://www.unimod.org/xml/unimod.xml</a><br> to a unimod.obo (e.g. with XMLSpy).<br> <br> For each (modification,specificity) pair an OBO term was created<br> (technically: a (umod:mod,spec_group) pair was transformed into a term with <br> a unique accession. For XSLT simplicity the accessions were created as<br> "PI-UNIMOD:"+record_id+"0"+spec_group, which creates gaps between<br> accession numbers, but ensures uniqueness).<br> <br> Only the umod:xref elements PMID, RESID and FindMod are transformed to Dbxrefs in <br> obo; some of them had an invalid type in the XML, which I corrected<br> (I will report these to the unimod people).<br> <br> Other umod:xrefs like "Misc. URL", "Book" or "Other" can be transformed<br> to property_values later.<br> <br> I added unimod.obo and unimodXML2OBO.xsl <br> to <a class="moz-txt-link-freetext" href="http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv">http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv</a><br> <br> Hope that helps...<br> <br> Bye<br> Martin<br> <br> <br> -------------------------------------------------------------------------<br> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge<br> Build the coolest Linux based applications with Moblin SDK & win great prizes<br> Grand prize is a trip for two to an Open Source event anywhere in the world<br> <a class="moz-txt-link-freetext" href="http://moblin-contest.org/redirect.php?banner_id=100&url=/">http://moblin-contest.org/redirect.php?banner_id=100&url=/</a><br> _______________________________________________<br> Psidev-pi-dev mailing list<br> <a class="moz-txt-link-abbreviated" href="mailto:Psi...@li...">Psi...@li...</a><br> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a><br> </font></tt> <br> <pre wrap=""> <hr size="4" width="90%"> ------------------------------------------------------------------------- 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 <a class="moz-txt-link-freetext" href="http://moblin-contest.org/redirect.php?banner_id=100&url=/">http://moblin-contest.org/redirect.php?banner_id=100&url=/</a></pre> <pre wrap=""> <hr size="4" width="90%"> _______________________________________________ Psidev-pi-dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Psi...@li...">Psi...@li...</a> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a> </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> |
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From: <cod...@go...> - 2008-11-19 19:41:55
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Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #21 by dcreasy: For the mapping file, PI:00088 needs to be allowed under: SequenceCollection/DBSequence We seem to have two sets of fragment types. For example [Term] id: PI:00220 name: frag: y ion is_a: PI:00221 ! fragmentation information [Term] id: PI:00262 name: param: y ion is_a: PI:00066 ! ions series considered in search Maybe this is OK, but maybe we can just have one lot? For the params, also need: "TODO: Need CV terms for a-NH3 and also a - NH3 if a significant and fragment includes RKNQ"; "TODO: Need CV terms for a-H20 and a - H2O if a significant and fragment includes STED"; "TODO: Need CV terms for b-NH2 and also b - NH3 if b significant and fragment includes RKNQ" "TODO: Need CV terms for b-H20 and b - H2O if b significant and fragment includes STED"; "TODO: Need CV terms for y - NH3 and also y - NH3 if y significant and fragment includes RKNQ"; "TODO: Need CV terms for y - H20 and also y - H2O if y significant and fragment includes STED"; "TODO: Need CV terms for internal yb"; "TODO: Need CV terms for z+1 series"; "TODO: Need CV terms for z+2 series"; I think that this one shouldn't require any value: id: PI:00020 name: DB filter taxonomy def: "The taxonomy filter applied (if any) to the database search." [PSI:PI] xref: value-type:xsd\:string "The allowed value-type for this CV term." is_a: PI:00019 ! database filtering See the relevant section of: http://code.google.com/p/psi-pi/wiki/NotesForDocumentation -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: Sean L S. <Sey...@ap...> - 2008-11-19 19:37:41
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Hi All, I'm rather confused by this decision. (1) Why don't we just use the MS mod synonym names that we already worked hard to establish (already have accessions as part of PSI-Mod), or is this what you mean by Unimod? If so, I don't think they should be called Unimod. (2) Are you really going to include the specificity in the accession assigned item? Or is this an issue about how modification search setting are indicated, not how modifications that have been detected are indicated in the results? I'll try to make the meeting tomorrow if it's easier to just set me straight by a short discussion than writing it out. Sean "Martin Eisenacher" <mar...@ru...> 11/19/2008 08:55 AM To psi...@li... cc Subject [Psidev-pi-dev] unimod.obo and XSLT Hi all! To report modifications of resulting peptides we want to use unimod. I assembled a XSLT to transform the XML from http://www.unimod.org/xml/unimod.xml to a unimod.obo (e.g. with XMLSpy). For each (modification,specificity) pair an OBO term was created (technically: a (umod:mod,spec_group) pair was transformed into a term with a unique accession. For XSLT simplicity the accessions were created as "PI-UNIMOD:"+record_id+"0"+spec_group, which creates gaps between accession numbers, but ensures uniqueness). Only the umod:xref elements PMID, RESID and FindMod are transformed to Dbxrefs in obo; some of them had an invalid type in the XML, which I corrected (I will report these to the unimod people). Other umod:xrefs like "Misc. URL", "Book" or "Other" can be transformed to property_values later. I added unimod.obo and unimodXML2OBO.xsl to http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv Hope that helps... Bye Martin ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Psidev-pi-dev mailing list Psi...@li... https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: David C. <dc...@ma...> - 2008-11-19 18:10:38
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Ooops! The title of the message and the timeanddate url below are correct, but it will be Thursday and not Wednesday Sorry for any confusion... David David Creasy wrote: > Hi everyone, > > There will be an AnalysisXML working group conference call on WEDNESDAY > (instead of Thursday) at: > http://www.timeanddate.com/worldclock/fixedtime.html?day=20&month=11&year=2008&hour=16&min=0&sec=0&p1=136 > > Minutes from last meeting at: > http://psidev.info/index.php?q=node/388 > > > Agenda: > 1. Review of minutes of last meeting > > 2. Status of mapping document, CV and examples. > > 3. Unimod .obo file. Martin has added unimod.obo and unimodXML2OBO.xsl > to http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv > Please review before the telecon. > > 4. Conformance to MIAPE: > http://psidev.info/index.php?q=node/386 > > 5. One week left to do the remaining tidy up before submission to the > document process. Clarify remaining tasks. > > > Dial in details: > > + Germany: 08001012079 > + Switzerland: 0800000860 > + UK: 08081095644 > + USA: 1-866-314-3683 > + Generic international: +44 2083222500 (UK number) > > access code: 297427 > -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
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From: David C. <dc...@ma...> - 2008-11-19 17:58:58
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Hi everyone, There will be an AnalysisXML working group conference call on WEDNESDAY (instead of Thursday) at: http://www.timeanddate.com/worldclock/fixedtime.html?day=20&month=11&year=2008&hour=16&min=0&sec=0&p1=136 Minutes from last meeting at: http://psidev.info/index.php?q=node/388 Agenda: 1. Review of minutes of last meeting 2. Status of mapping document, CV and examples. 3. Unimod .obo file. Martin has added unimod.obo and unimodXML2OBO.xsl to http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv Please review before the telecon. 4. Conformance to MIAPE: http://psidev.info/index.php?q=node/386 5. One week left to do the remaining tidy up before submission to the document process. Clarify remaining tasks. Dial in details: + Germany: 08001012079 + Switzerland: 0800000860 + UK: 08081095644 + USA: 1-866-314-3683 + Generic international: +44 2083222500 (UK number) access code: 297427 -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
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From: Martin E. <mar...@ru...> - 2008-11-19 16:54:54
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Hi all! To report modifications of resulting peptides we want to use unimod. I assembled a XSLT to transform the XML from http://www.unimod.org/xml/unimod.xml to a unimod.obo (e.g. with XMLSpy). For each (modification,specificity) pair an OBO term was created (technically: a (umod:mod,spec_group) pair was transformed into a term with a unique accession. For XSLT simplicity the accessions were created as "PI-UNIMOD:"+record_id+"0"+spec_group, which creates gaps between accession numbers, but ensures uniqueness). Only the umod:xref elements PMID, RESID and FindMod are transformed to Dbxrefs in obo; some of them had an invalid type in the XML, which I corrected (I will report these to the unimod people). Other umod:xrefs like "Misc. URL", "Book" or "Other" can be transformed to property_values later. I added unimod.obo and unimodXML2OBO.xsl to http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv Hope that helps... Bye Martin |
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From: <cod...@go...> - 2008-11-19 16:21:12
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Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #20 by eisenachM: In the CV there is a "search engine specific score" branch containing e.g. "mascot:expectation value" and others. It is good to have the search engine specific scores under one parent term, but most of them should (additionally) be child terms of "peptide result information" or "protein result information". I think that would improve the validator mapping. We can give them multiple parents... -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2008-11-19 16:16:05
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Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #19 by eisenachM: There is a "spectrum descriptions" branch with "spectrum quality descriptions". If it is calculated by a search engine, I would prefer to move the branch directly below "search result details" and rename it to "spectrum result information". -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2008-11-19 16:12:02
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Issue 30: Specifying the enzyme rules used in the search http://code.google.com/p/psi-pi/issues/detail?id=30 Comment #39 by eisenachM: There is a "spectrum descriptions" branch with "spectrum quality descriptions". If it is calculated by a search engine, I would prefer to move the branch directly below "search result details" and rename it to "spectrum result information". -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: David C. <dc...@ma...> - 2008-11-17 14:23:01
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I've updated: http://psidev.info/index.php?q=node/386 There are quite a few missing 'ticks' for the examples. (Less for the ones that I'm responsible for because I made the changes as I filled in the table!). If you make changes to the examples to fill in more gaps, either let me know or edit the table as described at the top of that page. There are still a few TODOs in the table, and I've not completed the 3 items for section 4 because I'm not clear how we are describing this in AnalysisXML. Perhaps we can discuss at the next telecon David Jones, Andy wrote: > Hi all, > > New schema uploaded: > > - Removed runtimeParams and analysisParams from SpectrumIdentificatino and > ProteinDetection > > - Added creationDate to AnalysisXML root node > > > Cheers > Andy > >> -----Original Message----- >> From: David Creasy [mailto:dc...@ma...] >> Sent: 12 November 2008 17:56 >> To: psi...@li... >> Subject: Re: [Psidev-pi-dev] PSI-PI Working group conference call on Wednesday >> 12th November at 4:00pm UK time >> >> Minutes available here: >> >> http://psidev.info/index.php?q=node/388 >> (Please let me know of any corrections) >> >> Next meeting: >> http://www.timeanddate.com/worldclock/fixedtime.html?day=20&month=11&year=2 >> 008&hour=16&min=0&sec=0&p1=136 >> >> >> David Creasy wrote: >>> Hi everyone, >>> >>> There will be an AnalysisXML working group conference call on WEDNESDAY >>> (instead of Thursday) at: >>> >> http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2 >> 008&hour=16&min=0&sec=0&p1=136 >>> >>> Minutes from last meeting at: >>> http://psidev.info/index.php?q=node/384 >>> >>> >>> Agenda: (strangely identical to last week, although progress has been >>> made!) >>> 1. Review of minutes of last meeting >>> >>> 2. Status of mapping document and CV >>> >>> 3. Issue 30: Enzymes >>> http://code.google.com/p/psi-pi/issues/detail?id=30 >>> Almost complete now? >>> http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 >>> >>> 4. Other items on the issues list: >>> http://code.google.com/p/psi-pi/issues/list >>> >>> Dial in details: >>> >>> + Germany: 08001012079 >>> + Switzerland: 0800000860 >>> + UK: 08081095644 >>> + USA: 1-866-314-3683 >>> + Generic international: +44 2083222500 (UK number) >>> >>> access code: 297427 >>> >> -- >> David Creasy >> Matrix Science >> 64 Baker Street >> London W1U 7GB, UK >> Tel: +44 (0)20 7486 1050 >> Fax: +44 (0)20 7224 1344 >> >> dc...@ma... >> http://www.matrixscience.com >> >> Matrix Science Ltd. is registered in England and Wales >> Company number 3533898 >> >> ------------------------------------------------------------------------- >> This SF.Net email is sponsored by the Moblin Your Move Developer's challenge >> Build the coolest Linux based applications with Moblin SDK & win great prizes >> Grand prize is a trip for two to an Open Source event anywhere in the world >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ >> _______________________________________________ >> Psidev-pi-dev mailing list >> Psi...@li... >> https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
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From: Jones, A. <And...@li...> - 2008-11-14 16:32:54
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Hi all, New schema uploaded: - Removed runtimeParams and analysisParams from SpectrumIdentificatino and ProteinDetection - Added creationDate to AnalysisXML root node Cheers Andy > -----Original Message----- > From: David Creasy [mailto:dc...@ma...] > Sent: 12 November 2008 17:56 > To: psi...@li... > Subject: Re: [Psidev-pi-dev] PSI-PI Working group conference call on Wednesday > 12th November at 4:00pm UK time > > Minutes available here: > > http://psidev.info/index.php?q=node/388 > (Please let me know of any corrections) > > Next meeting: > http://www.timeanddate.com/worldclock/fixedtime.html?day=20&month=11&year=2 > 008&hour=16&min=0&sec=0&p1=136 > > > David Creasy wrote: > > Hi everyone, > > > > There will be an AnalysisXML working group conference call on WEDNESDAY > > (instead of Thursday) at: > > > http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2 > 008&hour=16&min=0&sec=0&p1=136 > > > > > > Minutes from last meeting at: > > http://psidev.info/index.php?q=node/384 > > > > > > Agenda: (strangely identical to last week, although progress has been > > made!) > > 1. Review of minutes of last meeting > > > > 2. Status of mapping document and CV > > > > 3. Issue 30: Enzymes > > http://code.google.com/p/psi-pi/issues/detail?id=30 > > Almost complete now? > > http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 > > > > 4. Other items on the issues list: > > http://code.google.com/p/psi-pi/issues/list > > > > Dial in details: > > > > + Germany: 08001012079 > > + Switzerland: 0800000860 > > + UK: 08081095644 > > + USA: 1-866-314-3683 > > + Generic international: +44 2083222500 (UK number) > > > > access code: 297427 > > > > -- > David Creasy > Matrix Science > 64 Baker Street > London W1U 7GB, UK > Tel: +44 (0)20 7486 1050 > Fax: +44 (0)20 7224 1344 > > dc...@ma... > http://www.matrixscience.com > > Matrix Science Ltd. is registered in England and Wales > Company number 3533898 > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > Psidev-pi-dev mailing list > Psi...@li... > https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev |
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From: David C. <dc...@ma...> - 2008-11-12 17:56:06
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Minutes available here: http://psidev.info/index.php?q=node/388 (Please let me know of any corrections) Next meeting: http://www.timeanddate.com/worldclock/fixedtime.html?day=20&month=11&year=2008&hour=16&min=0&sec=0&p1=136 David Creasy wrote: > Hi everyone, > > There will be an AnalysisXML working group conference call on WEDNESDAY > (instead of Thursday) at: > http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2008&hour=16&min=0&sec=0&p1=136 > > > Minutes from last meeting at: > http://psidev.info/index.php?q=node/384 > > > Agenda: (strangely identical to last week, although progress has been > made!) > 1. Review of minutes of last meeting > > 2. Status of mapping document and CV > > 3. Issue 30: Enzymes > http://code.google.com/p/psi-pi/issues/detail?id=30 > Almost complete now? > http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 > > 4. Other items on the issues list: > http://code.google.com/p/psi-pi/issues/list > > Dial in details: > > + Germany: 08001012079 > + Switzerland: 0800000860 > + UK: 08081095644 > + USA: 1-866-314-3683 > + Generic international: +44 2083222500 (UK number) > > access code: 297427 > -- David Creasy Matrix Science 64 Baker Street London W1U 7GB, UK Tel: +44 (0)20 7486 1050 Fax: +44 (0)20 7224 1344 dc...@ma... http://www.matrixscience.com Matrix Science Ltd. is registered in England and Wales Company number 3533898 |
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From: <cod...@go...> - 2008-11-12 17:05:39
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Issue 35: reporting ambiguous modifications http://code.google.com/p/psi-pi/issues/detail?id=35 Comment #13 by eisenachM: TeleCon 5th of Nov, 2008: We allow Modifications without CVParam, reporting a mass shift. To clarify comment 12: If there are search engines (we don't know such engines at the moment), that report ambiguous modifications by stating more than one modification name, these concrete modification names are lost. Issue attribute updates: Status: Fixed -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: <cod...@go...> - 2008-11-12 16:29:19
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Issue 42: Issues with the CV http://code.google.com/p/psi-pi/issues/detail?id=42 Comment #18 by a.bertsch0815: update list of unused cv terms Attachments: unused_cv_terms.txt 12.2 KB -- You received this message because you are listed in the owner or CC fields of this issue, or because you starred this issue. You may adjust your issue notification preferences at: http://code.google.com/hosting/settings |
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From: Pierre-Alain B. <pie...@is...> - 2008-11-12 16:25:45
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Hi, David Creasy wrote: > Hi Pierre-Alain, > > Pierre-Alain Binz wrote: >> Thanks David. >> FYI, for mzML, we had generated a excel mapping spreadsheet (if you >> want to see it...) > Yes please. (I can't see it on psidev.info). you can find a temp version at ftp://ftp.genebio.com/div/MIAPE-mzML-mapping.01.xls > >> >> The format is ok for me. About the notes: the descriptions of what >> should be the content from a MIAPE point of view are in the MIAPE >> document, in the Annex table. > Oh yes... > >> >> Note also that for mzML-MIAPE MS mapping, there were a few items not >> covered by MIAPE, and also not covered by mzML. The latest have >> either been annotated for a future version of mzML (similar to the >> quantitation in AnalysisXML), or just left out and annotated as such >> (for instance flow rates, detector sensitivity). Either they are >> independant or an estimation that looks more like an interpretation. >> We there need to decide whether those should be taken out of MIAPE or >> not. > We will aim to add anything missing (apart from quantitation) before > submission to the document process. > >> >> I have commented two of the notes. If there are unclear items, just >> put a note in and I can clarify > Yes please! I can't remember what we intended from "Location of the > files generated". The definition is: > "The location of the data generated. If made available in a public > repository, describe the URI (for instance an url, or the url of the > repository and the information on how to retrieve the data). If not > made available for public access, describe the contact person > reference or source and the internal coordinates of the data." > > But _what_ data does this refer to? The peak list, the analysisXML > document, intermediate files like Sequest .out files or any/all of > these? If it's the analysisXML file, you presumably have it and you > must know where you got it from ;) the files used to generate the AnalysisXML file... > >> >> One more: for mzML, we have two (at least) levels of stringency for >> the validators: basic semantic and MIAPE compliance. Therefore we can >> deal with legacy being compliant woth the format, even if it does not >> comply with MIAPE > Sounds good, > > David voila, Pierre-Alain >> >> >> Cheers >> Pierre-Alain >> >> David Creasy wrote: >>> I've started on the MIAPE conformance doc: >>> >>> http://psidev.info/index.php?q=node/386 >>> >>> Can we discuss whether this is a suitable format on the call later. >>> (Looks as though we may have a couple of things to add to the >>> schema...) >>> >>> Thanks, >>> David >>> >>> David Creasy wrote: >>> >>>> Hi everyone, >>>> >>>> There will be an AnalysisXML working group conference call on >>>> WEDNESDAY >>>> (instead of Thursday) at: >>>> http://www.timeanddate.com/worldclock/fixedtime.html?day=12&month=11&year=2008&hour=16&min=0&sec=0&p1=136 >>>> >>>> >>>> Minutes from last meeting at: >>>> http://psidev.info/index.php?q=node/384 >>>> >>>> >>>> Agenda: (strangely identical to last week, although progress has >>>> been made!) >>>> 1. Review of minutes of last meeting >>>> >>>> 2. Status of mapping document and CV >>>> >>>> 3. Issue 30: Enzymes >>>> http://code.google.com/p/psi-pi/issues/detail?id=30 >>>> Almost complete now? >>>> http://code.google.com/p/psi-pi/issues/detail?id=30&can=1#c37 >>>> >>>> 4. Other items on the issues list: >>>> http://code.google.com/p/psi-pi/issues/list >>>> >>>> Dial in details: >>>> >>>> + Germany: 08001012079 >>>> + Switzerland: 0800000860 >>>> + UK: 08081095644 >>>> + USA: 1-866-314-3683 >>>> + Generic international: +44 2083222500 (UK number) >>>> >>>> access code: 297427 >>>> >>>> >>> >>> > |
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