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<div style="font-size:11pt; font-family:Calibri,sans-serif">Thanks Ray,<br>
<br>
This is great! :)<br>
<br>
Best wishes,<br>
<br>
Eamonn <br>
<br>
Sent from my Windows Phone</div>
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<span style="font-size:11pt; font-family:Calibri,sans-serif; font-weight:bold">From:
</span><span style="font-size:11pt; font-family:Calibri,sans-serif"><a href="mailto:ray.fergerson@stanford.edu">Ray Fergerson</a></span><br>
<span style="font-size:11pt; font-family:Calibri,sans-serif; font-weight:bold">Sent:
</span><span style="font-size:11pt; font-family:Calibri,sans-serif">‎04/‎03/‎2014 23:24</span><br>
<span style="font-size:11pt; font-family:Calibri,sans-serif; font-weight:bold">To:
</span><span style="font-size:11pt; font-family:Calibri,sans-serif"><a href="mailto:eamonn.maguire@st-annes.ox.ac.uk">Eamonn Maguire</a>;
<a href="mailto:jonquet@lirmm.fr">Clement Jonquet</a></span><br>
<span style="font-size:11pt; font-family:Calibri,sans-serif; font-weight:bold">Cc:
</span><span style="font-size:11pt; font-family:Calibri,sans-serif"><a href="mailto:support@bioontology.org">support@bioontology.org</a>;
<a href="mailto:isatools@googlegroups.com">ISA Team</a></span><br>
<span style="font-size:11pt; font-family:Calibri,sans-serif; font-weight:bold">Subject:
</span><span style="font-size:11pt; font-family:Calibri,sans-serif">RE: [bioontology-support] NCBO Annotator Excel plug-in</span><br>
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">The release today allows you to specify that you want the preferred name for every annotated class. Try this tomorrow.</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Ray</span></p>
<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"> </span></a></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt; font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt; font-family:"Tahoma","sans-serif""> bioontology-support-bounces@lists.stanford.edu [mailto:bioontology-support-bounces@lists.stanford.edu]
<b>On Behalf Of </b>Eamonn Maguire<br>
<b>Sent:</b> Tuesday, March 4, 2014 3:19 AM<br>
<b>To:</b> Clement Jonquet<br>
<b>Cc:</b> support@bioontology.org; ISA Team<br>
<b>Subject:</b> Re: [bioontology-support] NCBO Annotator Excel plug-in</span></p>
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<p class="MsoNormal">This email skipped under my radar, apologies.</p>
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<p class="MsoNormal">The current version still uses the old version of the annotator. As it stands, without the update to the annotator to include the term name in the response, it’s currently not usable (too slow to then search for each term, it’s preferred
 name). e.g. <a href="http://data.bioontology.org/annotator?text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye">http://data.bioontology.org/annotator?text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye.</a> -
 from the results here, there is no way of knowing what the actual term is - we have to do an additional query per term to figure that out - that’s way too many queries to have to do and would make the service unusable.</p>
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<p class="MsoNormal">Is there any chance this can be updated ASAP? We’re in the process of  releasing OntoMaton 2, which uses the new bioportal services, but we haven’t updated the annotator service as of yet, until this fix is made.</p>
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<p class="MsoNormal">Best wishes,</p>
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<p class="MsoNormal">Eamonn</p>
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<p class="MsoNormal">On 13 Feb 2014, at 08:54, Clement Jonquet <<a href="mailto:jonquet@lirmm.fr">jonquet@lirmm.fr</a>> wrote:</p>
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Thanks Trish for this response.</span><span lang="FR"></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Hi Eamonn,</span><span lang="FR"></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Do you confirm the Ontomaton tool is still available and use the new NCBO Annotator API (i.e., the one in BP 4.0) described at:</span><span lang="FR"></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D"><a href="http://data.bioontology.org/documentation#nav_annotator"><span style="color:purple">http://data.bioontology.org/documentation#nav_annotator</span></a></span><span lang="FR"></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">Regards</span><span lang="FR"></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt; font-family:"Calibri","sans-serif"; color:#1F497D">CJ</span><span lang="FR"></span></p>
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<p class="MsoNormal"><b><span lang="FR" style="font-size:11.0pt; font-family:"Calibri","sans-serif"">De :</span></b><span class="apple-converted-space"><span lang="FR" style="font-size:11.0pt; font-family:"Calibri","sans-serif""> </span></span><span lang="FR" style="font-size:11.0pt; font-family:"Calibri","sans-serif"">Trish
 Whetzel [<a href="mailto:plwhetzel@gmail.com"><span style="color:purple">mailto:plwhetzel@gmail.com</span></a>]<span class="apple-converted-space"> </span><br>
<b>Envoyé :</b><span class="apple-converted-space"> </span>jeudi 6 février 2014 17:21<br>
<b>À :</b><span class="apple-converted-space"> </span>Clement Jonquet<br>
<b>Cc :</b><span class="apple-converted-space"> </span><a href="mailto:support@bioontology.org"><span style="color:purple">support@bioontology.org</span></a><br>
<b>Objet :</b><span class="apple-converted-space"> </span>Re: [bioontology-support] NCBO Annotator Excel plug-in</span><span lang="FR"></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="FR">Hi Clement,</span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="FR">As I recall, the Excel plugin for the Annotator was no longer being maintained. However, you might be interested to check-out OntoMaton [1], which is an Excel GoogleDoc script that incorporates
 the BioPortal Search and Annotator services.</span></p>
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<p class="MsoNormal"><span lang="FR">Cheers,</span></p>
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<p class="MsoNormal"><span lang="FR">Trish<span class="apple-converted-space"> </span><br>
[1]<span class="apple-converted-space"> </span><a href="http://isatools.wordpress.com/2012/07/13/introducing-ontomaton-ontology-search-tagging-for-google-spreadsheets/"><span style="color:purple">http://isatools.wordpress.com/2012/07/13/introducing-ontomaton-ontology-search-tagging-for-google-spreadsheets/</span></a></span></p>
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<p class="MsoNormal"><span lang="FR">On Thu, Feb 6, 2014 at 12:23 AM, Clement Jonquet <<a href="mailto:jonquet@lirmm.fr" target="_blank"><span style="color:purple">jonquet@lirmm.fr</span></a>> wrote:</span></p>
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<p class="MsoNormal"><span lang="FR">Hi all,</span></p>
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<p class="MsoNormal"><span lang="FR"> </span></p>
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<p class="MsoNormal">We used to have an Excel plugin for the Annotator.<span lang="FR"></span></p>
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<p class="MsoNormal">Does anyone have updates on this ?<span lang="FR"></span></p>
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<p class="MsoNormal"> <span lang="FR"></span></p>
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<p class="MsoNormal">Is it still available ?<span lang="FR"></span></p>
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<p class="MsoNormal">Is it compatible with Annotator 2 ?<span lang="FR"></span></p>
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<p class="MsoNormal"> <span lang="FR"></span></p>
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<p class="MsoNormal">Clement<span lang="FR"></span></p>
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<p class="MsoNormal">---------------------------------------------------------------------------------------------------------------------------<span lang="FR"></span></p>
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<p class="MsoNormal">Dr.<span class="apple-converted-space"> </span><b>Clement JONQUET</b>  - <span class="apple-converted-space"> </span><i>PhD in Informatics  -  Assistant Professor</i><span lang="FR"></span></p>
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<p class="MsoNormal"><i>PI of the<span class="apple-converted-space"> </span><a href="http://www.lirmm.fr/sifr/" target="_blank"><span style="color:purple">SIFR project</span></a>: Semantic Indexing of French Biomedical Data Resources (ANR, UM2, CNRS, IBC)</i><span lang="FR"></span></p>
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<p class="MsoNormal"><i>Organizer of<span class="apple-converted-space"> </span><a href="http://www.meetup.com/webscience-montpellier/" target="_blank"><span style="color:purple">Web Science Montpellier</span></a><span class="apple-converted-space"> </span>Meetup</i><span lang="FR"></span></p>
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<p class="MsoNormal"> <span lang="FR"></span></p>
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<p class="MsoNormal"><a href="mailto:jonquet@lirmm.fr" target="_blank"><span style="color:purple">jonquet@lirmm.fr</span></a><span lang="FR"></span></p>
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<p class="MsoNormal"><a href="http://www.lirmm.fr/~jonquet" target="_blank"><span style="color:purple">http://www.lirmm.fr/~jonquet</span></a><span lang="FR"></span></p>
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<p class="MsoNormal"> <span lang="FR"></span></p>
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<p class="MsoNormal">               <span class="apple-converted-space"> </span><b>University of Montpellier</b>                          Tel:                      <a href="tel:%2B33%2F4%2067%2014%2097%2043" target="_blank"><span style="color:purple">+33/4
 67 14 97 43</span></a><span lang="FR"></span></p>
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<p class="MsoNormal">                LIRMM                                                            Fax:                     <a href="tel:%2B33%2F4%2067%C2%A0%2041%2085%2000" target="_blank"><span style="color:purple">+33/4 67  41 85 00</span></a>          <span lang="FR"></span></p>
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<p class="MsoNormal">                161 rue Ada                                                   Skype:                 clementpro<br>
                34095 Montpellier Cdx 5                            Twitter:              <span class="apple-converted-space"> </span><a href="http://twitter.com/jonquet_lirmm" target="_blank"><span style="color:purple">@jonquet_lirmm</span></a><span lang="FR"></span></p>
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<p class="MsoNormal">                France                                                            Google:              <span class="apple-converted-space"> </span><a href="mailto:jonquet.lirmm@gmail.com" target="_blank"><span style="color:purple">jonquet.lirmm@gmail.com</span></a><span lang="FR"></span></p>
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_______________________________________________<br>
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