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Re: [Psidev-pi-dev] Spec doc
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From: David C. <dc...@ma...> - 2008-10-17 08:43:30
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Hi Eric, <br>
<br>
Eric Deutsch wrote:
<blockquote cite="mid:1FA6C1F2633447F4BED00987D6AF412E@fozzie"
type="cite">
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<div class="Section1">
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;">Hi everyone,
I updated the current draft
of the on-line autogenerated schema docs to the latest svn. The result
is at:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><a moz-do-not-send="true"
href="http://www.peptideatlas.org/tmp/AnalysisXML_working.html">http://www.peptideatlas.org/tmp/AnalysisXML_working.html</a></span></font></p>
</div>
</blockquote>
That's looking great, thanks. I'll be starting to use it rather than
trawling through the schema...<br>
<br>
<blockquote cite="mid:1FA6C1F2633447F4BED00987D6AF412E@fozzie"
type="cite">
<div class="Section1">
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">It looks like the current
mapping file is just a template
without any term mappings themselves. Just as a test, I wrote into the
axml-mapping.xml file the mapping information for SearchType and it
seemed to
pull it out of the CV nicely:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><a moz-do-not-send="true"
href="http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType">http://www.peptideatlas.org/tmp/AnalysisXML_working.html#SearchType</a></span></font></p>
</div>
</blockquote>
Looks like it's going to be a very useful tool once the mapping file is
more complete.<br>
<blockquote cite="mid:1FA6C1F2633447F4BED00987D6AF412E@fozzie"
type="cite">
<div class="Section1">
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">The autogeneration pulls
examples out of one file. I
randomly chose Mascot_MSMS_example.axml. Is there a better instance
document to
automatically pull examples out of?</span></font></p>
</div>
</blockquote>
The X Tandem and Omssa examples will be rather similar to the Mascot
ones Since a simple ms-ms search result probably demonstrates the most
common 'use case' it may be the best example for the time being.
Presumably it takes the first occurrence of each element that it sees.
Maybe we should also try and make a 'search engine neutral' example.<br>
<br>
Cheers,<br>
<br>
David<br>
<br>
<blockquote cite="mid:1FA6C1F2633447F4BED00987D6AF412E@fozzie"
type="cite">
<div class="Section1">
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Regards,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;">Eric<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font color="navy" face="Arial" size="2"><span
style="font-size: 10pt; font-family: Arial; color: navy;"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><b><font face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma; font-weight: bold;">From:</span></font></b><font
face="Tahoma" size="2"><span
style="font-size: 10pt; font-family: Tahoma;"> Jones, Andy
[<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
<b><span style="font-weight: bold;">Sent:</span></b> Monday, October
13, 2008
7:07 AM<br>
<b><span style="font-weight: bold;">To:</span></b>
<a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b><span style="font-weight: bold;">Subject:</span></b>
[Psidev-pi-dev] Spec doc</span></font><font face="Times New Roman"
size="3"><span style="font-size: 12pt; font-family: "Times New Roman";"><o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Hi all,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">A new version of the spec
document has been uploaded by SVN (in the
specification_document directory), and previous versions have been put
in a
subfolder. I think the document is getting there... <o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Main tasks still to do:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Finish
section on use cases when we have finally agreed the list
online and made all the example files.<o:p></o:p></span></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Import
some parts of the example files to demonstrate a few specific
points<o:p></o:p></span></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Import
the autogenerated documentation<o:p></o:p></span></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Before we can submit, the main
outstanding issues are:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">CV
- looking through the CV there is still a fair bit of work to do,
there’s quite a few terms with missing or incorrect documentation<o:p></o:p></span></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Mapping
file<o:p></o:p></span></p>
<p class="msolistparagraph" style="text-indent: -0.25in;"><!--[if !supportLists]--><font
face="Calibri" size="2"><span style="font-size: 11pt;" lang="EN-GB"><span
style="">-<font face="Times New Roman" size="1"><span
style="font-family: "Times New Roman"; font-style: normal; font-variant: normal; font-weight: normal; font-size: 7pt; line-height: normal; font-size-adjust: none; font-stretch: normal;">
</span></font></span></span></font><!--[endif]--><span lang="EN-GB">Finish
example files.<o:p></o:p></span></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Prior to the call on Thurs, can
we have a think about how we plan to
get the CV into shape and discuss it as a main agenda item...<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Also new schema uploaded with a
few bits of improved documentation.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Cheers<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB">Andy<o:p></o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
<p class="MsoNormal" style="margin-left: 0.25in;"><font face="Calibri"
size="2"><span style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
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<p class="MsoNormal"><font face="Calibri" size="2"><span
style="font-size: 11pt;" lang="EN-GB"><o:p> </o:p></span></font></p>
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<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>
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Matrix Science Ltd. is registered in England and Wales
Company number 3533898</pre>
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