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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: 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 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: Henning H. <hen...@go...> - 2008-11-20 11:13:44
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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: David C. <dc...@ma...> - 2008-11-20 13:19:42
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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 |
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From: Martin E. <mar...@ru...> - 2008-11-20 14:25:37
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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 |
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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>
</body>
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From: Martin E. <mar...@ru...> - 2008-11-20 17:40:34
|
Hi!
I updated the XSLT and unimod.obo in the svn as discussed in the conference.
For an excerpt of the oxidation term (the specificities are property_values) see below.
Of course, the 'property_value: spec_groupX="X"' entries can be dropped.
The names are unique as the UNIMOD ids are.
Bye
Martin
[Term]
id: UNIMOD:35
name: Oxidation
def: "Oxidation or Hydroxylation" [FindMod:HYDR RESID:AA0322 PMID:11212008 PMID:11120890 FindMod:DOPA FindMod:CSEA
PMID:14661084 RESID:AA0026 PMID:15569593 RESID:AA0205 RESID:AA0215 RESID:AA0029 RESID:AA0030 PMID:9004526 RESID:AA0028
PMID:11461766 RESID:AA0027 RESID:AA0235 RESID:AA0146 PMID:14661085 PMID:12781462 PMID:2057999 ]
property_value: record_id="35"
property_value: delta_mono_mass="15.994915"
property_value: delta_avge_mass="15.9994"
property_value: delta_composition="O"
property_value: username_of_poster="unimod"
property_value: group_of_poster="admin"
property_value: date_time_posted="2002-08-19 19:17:11"
property_value: date_time_modified="2008-02-15 05:37:07"
property_value: approved="false"
property_value: spec_group1="1"
property_value: spec_hidden_1="true"
property_value: spec_site_1="D"
property_value: spec_position_1="Anywhere"
property_value: spec_classification_1="Post-translational"
property_value: spec_group2="2"
property_value: spec_hidden_2="true"
property_value: spec_site_2="K"
property_value: spec_position_2="Anywhere"
property_value: spec_classification_2="Post-translational"
.
Von: David Creasy [mailto:dc...@ma...]
Gesendet: Thursday, November 20, 2008 4:36 PM
An: Martin Eisenacher
Cc: 'Sean L Seymour'; psi...@li...
Betreff: Re: AW: [Psidev-pi-dev] unimod.obo and XSLT
Hi Martin, (& Sean)
Yes, you did exactly what we agreed, but maybe we were wrong....
I don't think that we need to include the specificity in the CV. So, for the found modifications we have:
<Peptide id="peptide_2_4" sequenceMass="1614.774567" sequenceLength="13">
<Modification location="1" residues="M" monoisotopicMassDelta="15.994919">
<pf:cvParam accession="Oxidation" name="Oxidation" cvRef="PSI-MS-MOD" />
</Modification>
<Modification location="9" residues="M" monoisotopicMassDelta="15.994919">
<pf:cvParam accession="Oxidation" name="Oxidation" cvRef="PSI-MS-MOD" />
</Modification>
<peptideSequence>MIKTGESGMTVFR</peptideSequence>
</Peptide>
Which is fine (and as in the current schema). Having the specificity in the CV is a duplication here.
However, for the search modification we currently have:
<SearchModification fixedMod="false" >
<ModName accession="MOD:TODO" name="Oxidation (M)" cvRef="UNIMOD" />
<MassDelta value="15.994919" unitAccession="UO:0000221" unitName="Da" />
<SpecificityRule accession="PI:00188" cvRef="PSI-PI" name="modification specificity variable" />
</SearchModification>
and we have the following CV:
id: PI:00187, name: modification specificity fixed
id: PI:00188, name: modification specificity variable
id: PI:00189, name: modification specificity N-term
id: PI:00190, name: modification specificity C-term
How about we add a residues attribute to SearchModification and then remove all specificity from the CV? Does this sound
reasonable Sean?
Note that the PSI-MS-MOD names don't include any specificities.
(Also, we seem to now have a duplication of CV and attributes for fixed/variable...).
Can we discuss further on the call?
David
Martin Eisenacher wrote:
Hi!
(btw, I don't think that the .obo file is correct - I don't think that want new ID's)
You mean, we want to use the original unimod.xml-record_id?
But we agreed to have one OBO term for each (modification,specificity) pair.
Bye
Martin
"Martin Eisenacher" <mailto:mar...@ru...> <mar...@ru...>
11/19/2008 08:55 AM
To
psi...@li...
cc
Subject
[Psidev-pi-dev] unimod.obo and XSLT
Hi all!
To report modifications of resulting peptides we want to use unimod.
I assembled a XSLT to transform the XML from
http://www.unimod.org/xml/unimod.xml
to a unimod.obo (e.g. with XMLSpy).
For each (modification,specificity) pair an OBO term was created
(technically: a (umod:mod,spec_group) pair was transformed into a term with
a unique accession. For XSLT simplicity the accessions were created as
"PI-UNIMOD:"+record_id+"0"+spec_group, which creates gaps between
accession numbers, but ensures uniqueness).
Only the umod:xref elements PMID, RESID and FindMod are transformed to Dbxrefs in
obo; some of them had an invalid type in the XML, which I corrected
(I will report these to the unimod people).
Other umod:xrefs like "Misc. URL", "Book" or "Other" can be transformed
to property_values later.
I added unimod.obo and unimodXML2OBO.xsl
to http://code.google.com/p/psi-pi/source/browse/#svn/trunk/cv
Hope that helps...
Bye
Martin
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Psi...@li...
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________________________________________
-------------------------------------------------------------------------
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Grand prize is a trip for two to an Open Source event anywhere in the world
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________________________________________
_______________________________________________
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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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