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Re: [Psidev-pi-dev] unimod.obo and XSLT
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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> |
