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Re: [Psidev-pi-dev] FW: Spec doc
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From: David C. <dc...@ma...> - 2008-12-04 12:22:53
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Hi Andy, Andreas,<br>
<br>
I assume that this is a typo below:<br>
<pre><span style="font-size: 8pt;" lang="EN-US"><pf:cvParam accession="PI:00999" name="search tolerance plus value" value=”0.5” cvRef="PSI-PI"<o:p></o:p></span></pre>
<p class="MsoNormal"><span
style="font-size: 8pt; font-family: "Courier New";" lang="EN-US">unitAccession="UO:0000221"
name="dalton" cvRef="UO" /><o:p></o:p></span></p>
<span style="color: rgb(31, 73, 125);"><o:p></o:p></span><br>
and the second cvRef is meant to be a unitCvRef??<br>
<br>
I've updated the Mascot_MSMS_example.axml, <br>
<small><tt> <FragmentTolerance><br>
<pf:cvParam accession="PI:00404" name="absolut mass unit"
value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
unitCvRef="UO" /><br>
<pf:cvParam accession="PI:00404" name="absolut mass unit"
value="0.5" cvRef="PSI-PI" unitAccession="UO:0000221" unitName="dalton"
unitCvRef="UO" /><br>
</FragmentTolerance><br>
<ParentTolerance><br>
<pf:cvParam accession="PI:00403" name="relative mass unit"
value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187"
unitName="percent" unitCvRef="UO" /><br>
<pf:cvParam accession="PI:00403" name="relative mass unit"
value="0.1" cvRef="PSI-PI" unitAccession="UO:0000187"
unitName="percent" unitCvRef="UO" /><br>
</ParentTolerance><br>
</tt></small><br>
<br>
but this doesn't validate:<br>
<br>
<pre><font color="red">Error: Unit CVTerm not allowed: UO:0000187 - percent of term PI:00403 - relative mass unit</font>
<font color="red">Error: Unit CVTerm not allowed: UO:0000221 - dalton of term PI:00404 - absolut mass unit</font>
<font color="red">Error: Value of CVTerm not allowed: 'PI:00403 - relative mass unit, value=0.1' at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance'</font>
<font color="red">Error: Value of CVTerm not allowed: 'PI:00404 - absolut mass unit, value=0.5' at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance'</font>
<font color="red">Error: Violated mapping rule 'R17a' number of term repeats at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/ParentTolerance'</font>
<font color="red">Error: Violated mapping rule 'R17b' number of term repeats at element '/AnalysisXML/AnalysisProtocolCollection/SpectrumIdentificationProtocol/FragmentTolerance'
</font></pre>
What am I doing wrong?<br>
<br>
I'm also slightly concerned about PSI-PI group getting the wrong(?)
reputation. Martin, could you change PI:00404 from being a brand of
vodka to "absolute". Thanks.<br>
(I've still not installed OboEdit.)<br>
<br>
David<br>
<br>
Jones, Andy wrote:
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<div class="Section1">
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi all,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">New
schema uploaded:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Various
documentation changes, as
discussed below.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">PlusValue
/ MinusValue now
encoded as CVParams<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Made a
change to
AnalysisProtocolCollection and AnalysisCollection that prevented
GenericProtocol and GenericProtocolApplication being used – I’ve been
meaning
to fix this for a while. It also means the files are now restricted to
containing at most one ProteinDetection and one
ProteinDetectionApplication.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">In the
schema, we have some
fairly pointless abstract classes AnalysisProtocol and
AnalysisProtocolApplication. They were put in the schema at one stage
to
demonstrate how the format should be extended in the future, following
this
design pattern (or something like this...). I vote we get rid of them,
and
write in the spec document about future extension strategies.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Cheers<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andy<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">
Jones, Andy [<a class="moz-txt-link-freetext" href="mailto:And...@li...">mailto:And...@li...</a>] <br>
<b>Sent:</b> 02 December 2008 12:23<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-pi-dev] FW: Spec doc<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi David,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">The
changes relating the
instance docs are coming from the Mascot MS/MS example so these are for
you to
fix ;-)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Eric, are
you able to import
certain parts of the instance docs from other examples. Element
<DatabaseTranslation> could take examples from
Mascot_NA_example.axml? <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">I’ll make
the other recommended
changes to the XSD documentation (some of these require a fix to the
generating
script, which I’ve flagged to Eric separately).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Martin,
are you happy for us to
make the change relating to peptide mass documentation (see below).<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">>semiSpecific
- shouldn't
this be a boolean?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Agreed,
I’ll make this change.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">><PlusValue><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Eric is
right to query this part
of the schema. In fact, we’ve used the PropertyValue element only for
PlusValue
and MinusValue in the entire schema. Let’s make these CV terms:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<pre><span style="font-size: 8pt;" lang="EN-US"><pf:cvParam accession="PI:00999" name="search tolerance plus value" value=”0.5” cvRef="PSI-PI"<o:p></o:p></span></pre>
<p class="MsoNormal"><span
style="font-size: 8pt; font-family: "Courier New";" lang="EN-US">unitAccession="UO:0000221"
name="dalton" cvRef="UO" /><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andreas
can you add: “</span><span style="color: rgb(31, 73, 125);" lang="EN-US">search
tolerance plus value” and “search
tolerance minus value” to the CV and mapping file and I’ll change the
schema,
does this seem reasonable to everyone…?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"
lang="EN-US">Getting there…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"
lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"
lang="EN-US">Cheers<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"
lang="EN-US">Andy<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"><o:p> </o:p></span></p>
<div
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<div>
<div
style="border-style: solid none none; border-color: rgb(181, 196, 223) -moz-use-text-color -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif"; color: windowtext;"
lang="EN-US">
Pierre-Alain Binz [<a class="moz-txt-link-freetext" href="mailto:pie...@is...">mailto:pie...@is...</a>] <br>
<b>Sent:</b> 02 December 2008 11:17<br>
<b>To:</b> David Creasy<br>
<b>Cc:</b> <a class="moz-txt-link-abbreviated" href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-pi-dev] FW: Spec doc<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi,<br>
<br>
David Creasy wrote: <o:p></o:p></p>
<p class="MsoNormal">Hi Andy,<br>
<br>
Some minor changes:<o:p></o:p></p>
<pre>From:<o:p></o:p></pre>
<pre><pf:Person id="PERSON_DOC_OWNER" firstName="" lastName="Some Person" email=<a
moz-do-not-send="true" href="mailto:so...@so...">"so...@so..."</a>><o:p></o:p></pre>
<pre>to:<o:p></o:p></pre>
<pre><pf:Person id="PERSON_DOC_OWNER" firstName="Some" lastName="Person" email=<a
moz-do-not-send="true" href="mailto:so...@so...">"so...@so..."</a>><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Example Context: <o:p></o:p></pre>
<pre><pf:cv id="PSI-PI" fullName="PSI-PI" URI=<a
moz-do-not-send="true"
href="http://www.psidev.info/not_sure_of_url_to_cv.obo"><b><span
style="color: red;">MailScanner has detected a possible fraud attempt from "www.psidev.info" claiming to be</span></b> "http://www.psidev.info/not_sure_of_url_to_cv.obo"</a>></pf:cv><o:p></o:p></pre>
<pre>We only want the cv psidev.info when we finally release. Guess it's OK to leave this as it is at the moment.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Element <AnalysisSoftware><o:p></o:p></pre>
<pre>Definition: A data set containing spectra data (consisting of one or more spectra). <o:p></o:p></pre>
<pre>Definition looks like a copy and paste of something quite different!<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Element <pf:ContactRole><o:p></o:p></pre>
<pre>Definition: The Contact that provided the document instance. <o:p></o:p></pre>
<pre>We use the contact role in several different places. Definition needs to be a bit more general? <o:p></o:p></pre>
<pre>In the example it is for a software vendor.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Element <pf:Person><o:p></o:p></pre>
<pre>Example needs filling out a bit with some fictitious person.<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Element <Peptide><o:p></o:p></pre>
<pre>sequenceMass xsd:double - The sum of the unmodified (poly)peptide sequence residues, exclusive of the termini masses in Daltons.<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<p class="MsoNormal">Oh dear. Some of the examples are inclusive of
the termini
masses and any modifications, others are not. In theory, it's possible
to
calculate the mass given the modification delta and the
CTermGain="OH" NTermGain="H" from the enzyme. However,
that's not trivial in a case of multiple enzymes. I'd suggest we change
the
definition to include the termini and mods. Martin (whose examples
followed the
documentation) may think differently?<o:p></o:p></p>
<p class="MsoNormal" style="margin-bottom: 12pt;">I aggree: with
termini and
mods. Calculated neutral mass in Da (not m/z), monoisotopic, 6digits
after
unit?<o:p></o:p></p>
<p class="MsoNormal"><br>
<br>
Element <Inputs><br>
Definition: The inputs to the analyses including the
databases searched and the spectral data <br>
The example shows the input file to the process that created the
analysisXML
document (the Mascot .dat file)<br>
The global definition needs changing. Also, need to add a definition
for
SpectraData.<br>
<br>
<br>
Element <DatabaseTranslation><br>
Could take examples from Mascot_NA_example.axml<br>
<br>
<br>
Element <Enzyme><br>
missedCleavages xsd:int
optional URI of the analysis software e.g. manufacturer's
website<br>
semiSpecific - shouldn't this be a boolean?<br>
<br>
<br>
Element <PlusValue><br>
unitName xsd:string - The
name of the unit.<br>
Shame that it doesn't pull out the allowed CV from the mapping file:<br>
<br>
<CvTerm termAccession="UO:0000221" useTermName="false"
useTerm="true" termName="dalton"
cvIdentifierRef="UO" /><br>
<CvTerm termAccession="UO:0000166" useTermName="false"
useTerm="false" termName="parts per notation"
cvIdentifierRef="UO" /><br>
<br>
Element <SpectrumIdentificationItem><br>
Has an attribute of rank and also a CV item. From the minutes here:<br>
<a moz-do-not-send="true"
href="http://psidev.info/index.php?q=node/380">http://psidev.info/index.php?q=node/380</a><br>
Looks as though we agreed it should be an attribute and removed from
the CV<br>
<br>
Cheers,<br>
David<br>
<br>
Jones, Andy wrote: <o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi all,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Eric has
re-generated the schema
documentation for us. This is getting fairly close to a version I can
cut and
paste into the spec doc. Let me know if you have any comments,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Cheers</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andy</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<div
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<div>
<div
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<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US"> Eric Deutsch [<a moz-do-not-send="true"
href="mailto:ede...@sy...">mailto:ede...@sy...</a>]
<br>
<b>Sent:</b> 01 December 2008 09:23<br>
<b>To:</b> Jones, Andy<br>
<b>Cc:</b> 'Eric Deutsch'<br>
<b>Subject:</b> RE: [Psidev-pi-dev] Spec doc</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US">Hi Andy, sorry for the delay, US holiday over here. You
will find
updated HTML documentation at:</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"><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><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">A version that is suitable
for cut-n-paste
into a word doc is at:</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"><a moz-do-not-send="true"
href="http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html">http://www.peptideatlas.org/tmp/AnalysisXML_working_simple.html</a></span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">I fixed some of the problems.
The main
problem I still know about is that in the subelement listing, any
subelements
that are double-tall nested substitution grouped elements do not have
their definition
visible. If one clicks on the subelement, the main element does have a
definition. So it’s there, but my program is stymied by the various
levels.
This is fixable, but probably not before submission.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">If you send me screen-capture
images to embed
in some elements, that can be done if you like.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">If there are still other
outstanding
issues, please let me know</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">Regards,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US">Eric</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US"> </span><o:p></o:p></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
<div>
<div class="MsoNormal" style="text-align: center;" align="center"><span
style="font-size: 12pt; font-family: "Times New Roman","serif";"
lang="EN-US">
<hr align="center" size="2" width="100%"></span></div>
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US"> Jones, Andy [<a moz-do-not-send="true"
href="mailto:And...@li...">mailto:And...@li...</a>]
<br>
<b>Sent:</b> Thursday, November 27, 2008 4:56 AM<br>
<b>To:</b> Eric Deutsch<br>
<b>Subject:</b> RE: [Psidev-pi-dev] Spec doc</span><o:p></o:p></p>
</div>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi Eric,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Any
chance you could look at the
generated documentation this week? We’re aiming to submit the specs to
the
document process by Monday...</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Thanks</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andy</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
<div>
<div
style="border-style: solid none none; border-color: -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US"> Eric Deutsch [<a moz-do-not-send="true"
href="mailto:ede...@sy...">mailto:ede...@sy...</a>]
<br>
<b>Sent:</b> 21 November 2008 17:44<br>
<b>To:</b> Jones, Andy<br>
<b>Cc:</b> 'Eric Deutsch'<br>
<b>Subject:</b> RE: [Psidev-pi-dev] Spec doc</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US">Hi Andy, yes, I will fix the bugs and regenerate the docs
from the
latest schema and files early next week.</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US">I will also have a look at TPP related materials for
AnalysisXML
and get back to you.</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US">Sorry I’ve missed the calls. That time is very awkward
for me and
I’ve occasionally been confused by Wednesday/Thursday switches.</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US">Regards,</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US">Eric</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US"> </span><o:p></o:p></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
<div>
<div class="MsoNormal" style="text-align: center;" align="center"><span
style="font-size: 12pt; font-family: "Times New Roman","serif";"
lang="EN-US">
<hr align="center" size="2" width="100%"></span></div>
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US"> Jones, Andy [<a moz-do-not-send="true"
href="mailto:And...@li...">mailto:And...@li...</a>]
<br>
<b>Sent:</b> Friday, November 21, 2008 2:09 AM<br>
<b>To:</b> Eric Deutsch<br>
<b>Subject:</b> RE: [Psidev-pi-dev] Spec doc</span><o:p></o:p></p>
</div>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Hi Eric,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Would you
be able to do a couple
of updates to the auto-generated docs? There’s a couple of errors to
fix.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">When
there is an instance of:
<xsd:element ref="pf:DatabaseReference" minOccurs="0">,
would you be able to retrieve the documentation in the table from the
referenced element.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Also,
when an element is
inherited from, documentation for inherited attributes does not appear
in the
table (e.g. see Specificity rule, no docs for cvRef, unitName etc.) –
unless we
were missing documentation for these attributes when it was last
generated?.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">There are
also a few instances
of elements imported from the FuGE-light schema which are completely
empty, no
attributes or documentation e.g. Organization or Person.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">We’re
aiming to submit the specs
to the PSI process by the end of month (i.e. a week on Monday), so if
you would
be able to look at this fairly soon it would be very much appreciated!
Also,
any chance that you can get someone to generate the TPP and SpectraST
examples
at your end. It’s no disaster if we submit to the process without these
but it
would be beneficial.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Cheers</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);">Andy</span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="color: rgb(31, 73, 125);"> </span><o:p></o:p></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
<div>
<div
style="border-style: solid none none; border-color: -moz-use-text-color; border-width: 1pt medium medium; padding: 3pt 0cm 0cm;">
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US"> Eric Deutsch [<a moz-do-not-send="true"
href="mailto:ede...@sy...">mailto:ede...@sy...</a>]
<br>
<b>Sent:</b> 17 October 2008 07:43<br>
<b>To:</b> <a moz-do-not-send="true"
href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> Re: [Psidev-pi-dev] Spec doc</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US">Hi everyone, I updated the current draft of the on-line
autogenerated schema docs to the latest svn. The result is at:</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";"
lang="EN-US"><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><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";"
lang="EN-US">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:</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";"
lang="EN-US"><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><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";"
lang="EN-US">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><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";"
lang="EN-US">Regards,</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";"
lang="EN-US">Eric</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif";"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size: 10pt; font-family: "Arial","sans-serif"; color: navy;"
lang="EN-US"> </span><o:p></o:p></p>
<div
style="border-style: none none none solid; border-color: -moz-use-text-color -moz-use-text-color -moz-use-text-color blue; border-width: medium medium medium 1.5pt; padding: 0cm 0cm 0cm 4pt;">
<div>
<div class="MsoNormal" style="text-align: center;" align="center"><span
style="font-size: 12pt; font-family: "Times New Roman","serif";"
lang="EN-US">
<hr align="center" size="2" width="100%"></span></div>
<p class="MsoNormal"><b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US">From:</span></b><span
style="font-size: 10pt; font-family: "Tahoma","sans-serif";"
lang="EN-US"> Jones, Andy [<a moz-do-not-send="true"
href="mailto:And...@li...">mailto:And...@li...</a>]
<br>
<b>Sent:</b> Monday, October 13, 2008 7:07 AM<br>
<b>To:</b> <a moz-do-not-send="true"
href="mailto:psi...@li...">psi...@li...</a><br>
<b>Subject:</b> [Psidev-pi-dev] Spec doc</span><o:p></o:p></p>
</div>
<p class="MsoNormal"><span lang="EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal">Hi all,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">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></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Main tasks still to do:<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;">Finish
section on use
cases when we have finally agreed the list online and made all the
example
files.<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;">Import some
parts of the
example files to demonstrate a few specific points<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;">Import the
autogenerated
documentation<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Before we can submit, the main outstanding
issues are:<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;">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></p>
<p class="MsoListParagraph" style="text-indent: -18pt;">Mapping file<o:p></o:p></p>
<p class="MsoListParagraph" style="text-indent: -18pt;">Finish
example files.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">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></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Also new schema uploaded with a few bits of
improved
documentation.<o:p></o:p></p>
<p class="MsoNormal">Cheers<o:p></o:p></p>
<p class="MsoNormal">Andy<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal" style="margin-left: 18pt;"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;">
<hr align="center" size="4" width="90%">
</pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>-------------------------------------------------------------------------<o:p></o:p></pre>
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<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;">
<hr align="center" size="4" width="90%">
</pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre style="text-align: center;"><o:p> </o:p></pre>
<pre><o:p> </o:p></pre>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Psidev-pi-dev mailing list<o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="mailto:Psi...@li...">Psi...@li...</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true"
href="https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev">https://lists.sourceforge.net/lists/listinfo/psidev-pi-dev</a><o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<p class="MsoNormal" style="margin-bottom: 12pt;"><span
style="font-size: 12pt; font-family: "Times New Roman","serif";"><o:p> </o:p></span></p>
<pre>-- <o:p></o:p></pre>
<pre>David Creasy<o:p></o:p></pre>
<pre>Matrix Science<o:p></o:p></pre>
<pre>64 Baker Street<o:p></o:p></pre>
<pre>London W1U 7GB, UK<o:p></o:p></pre>
<pre>Tel: +44 (0)20 7486 1050<o:p></o:p></pre>
<pre>Fax: +44 (0)20 7224 1344<o:p></o:p></pre>
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This SF.Net email is sponsored by the Moblin Your Move Developer's challenge
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Grand prize is a trip for two to an Open Source event anywhere in the world
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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>
<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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