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<div class=Section1>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Trish, it’s all there in the
header:<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>.<o:p></o:p></span></font></p>

<pre><font size=2 face="Courier New"><span style='font-size:10.0pt'>remark: namespace: MS<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>remark: version: 2.13.0<o:p></o:p></span></font></pre><pre><font
size=2 face="Courier New"><span style='font-size:10.0pt'>remark: release date: 2009-06-11<o:p></o:p></span></font></pre>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thanks!<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Eric<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>

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face="Times New Roman"><span style='font-size:12.0pt'>

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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> Trish Whetzel
[mailto:whetzel@stanford.edu] <br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, June 16, 2009 11:57
AM<br>
<b><span style='font-weight:bold'>To:</span></b> 'Eric Deutsch';
support@bioontology.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> RE: [bioontology-support]
MS ontology</span></font><o:p></o:p></p>

</div>

<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'>Sounds good. <o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'><o:p> </o:p></span></font></p>

<pre><font size=2 color="#1f497d" face=Calibri><span style='font-size:11.0pt;
font-family:Calibri;color:#1F497D'>One question on the ontology metadata, I see that the release date is specified here “</span></font>remark: release date: 2009-06-11<font
size=2 color="#1f497d" face=Calibri><span style='font-size:11.0pt;font-family:
Calibri;color:#1F497D'>”, however where is the ontology version stated?<o:p></o:p></span></font></pre><pre><font
size=2 color="#1f497d" face=Calibri><span style='font-size:11.0pt;font-family:
Calibri;color:#1F497D'><o:p> </o:p></span></font></pre><pre><font size=2
color="#1f497d" face=Calibri><span style='font-size:11.0pt;font-family:Calibri;
color:#1F497D'>Trish<o:p></o:p></span></font></pre>

<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'><o:p> </o:p></span></font></p>

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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> Eric Deutsch
[mailto:edeutsch@systemsbiology.org] <br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, June 16, 2009 11:29
AM<br>
<b><span style='font-weight:bold'>To:</span></b> <st1:PersonName w:st="on">'Trish
 Whetzel'</st1:PersonName>; support@bioontology.org<br>
<b><span style='font-weight:bold'>Cc:</span></b> 'Eric Deutsch'<br>
<b><span style='font-weight:bold'>Subject:</span></b> RE: [bioontology-support]
MS ontology<o:p></o:p></span></font></p>

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</div>

<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Trish, thanks. If you’re happy to
do so, why don’t we email <a href="mailto:support@bioontology.org">support@bioontology.org</a>
whenever there’s a new version and have you take care of it. Later
we’ll try to come up with an easier solution.<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thank you!<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Eric<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>

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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> Trish Whetzel
[mailto:whetzel@stanford.edu] <br>
<b><span style='font-weight:bold'>Sent:</span></b> Tuesday, June 16, 2009 10:31
AM<br>
<b><span style='font-weight:bold'>To:</span></b> 'Eric Deutsch';
support@bioontology.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> RE: [bioontology-support]
MS ontology</span></font><o:p></o:p></p>

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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'>Hi Eric, <o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'>Thanks for the
pointer to the new file. Currently there are 2 ways that the file can be
updated for ontologies that are not within the obo sourceforge cvs
directory.  The ways to update the file in BioPortal are either for us to
load the file when there is a new version given some sort of alert of the new
file (email, RSS, etc) or someone from PSI can load the file. It is very easy
to load a new version and takes only ~5 minutes from downloading the file from
the source location to uploading into BioPortal.  Do you have a preference
on how the file is updated; we are happy to load the file given notice of a new
version. <o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'>Trish<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 color="#1f497d" face=Calibri><span
style='font-size:11.0pt;font-family:Calibri;color:#1F497D'><o:p> </o:p></span></font></p>

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<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
bioontology-support-bounces@lists.stanford.edu
[mailto:bioontology-support-bounces@lists.stanford.edu] <b><span
style='font-weight:bold'>On Behalf Of </span></b>Eric Deutsch<br>
<b><span style='font-weight:bold'>Sent:</span></b> Monday, June 15, 2009 1:49
PM<br>
<b><span style='font-weight:bold'>To:</span></b> support@bioontology.org<br>
<b><span style='font-weight:bold'>Cc:</span></b> Eric Deutsch<br>
<b><span style='font-weight:bold'>Subject:</span></b> [bioontology-support] MS
ontology<o:p></o:p></span></font></p>

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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi, I notice that the MS ontology:<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><a href="http://bioportal.bioontology.org/ontologies/39281">http://bioportal.bioontology.org/ontologies/39281</a><o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>is quite out of date. The latest is much newer an available
from our CVS:<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><a
href="http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo">http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo</a><o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Can we get the BioPortal site updated?<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>What needs to happen for our ontology to get automatically
updated whenever we can a new version?<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Thanks!<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Eric<o:p></o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>

<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><o:p> </o:p></span></font></p>

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