<div dir="ltr"><div><div><div>Hi Clement, <br><br></div>Eamonn is with a different group now. I added in Philippe, who I think is still in the same group.<br><br></div>Cheers, <br></div>Trish <br><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Oct 30, 2015 at 9:52 AM, Clement Jonquet <span dir="ltr"><<a href="mailto:jonquet@lirmm.fr" target="_blank">jonquet@lirmm.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div link="blue" vlink="purple" lang="FR"><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d">Hi all, <u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">I am re-opening that thread question Eamonn about the possibility to use OntoMaton with another BioPortal appliance.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">We are working on a agronomic/plant specific version of BioPortal, called AgroPortal and some of our users at INRA will love to see the Plugin being able to talk to our /search and /annotator services.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">We have made some improvement to the Annotator (e.g., scoring) but we are completely backward compatible with NCBO. So I guess this would be just a small change in the code to hit another web service endpoint.<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Eamonn, does it sound reasonable to you ? <u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Can you point us to the exact spot in the GitHub OntoMaton repo here to change?<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"><u></u> <u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">By,<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Clement<u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"><u></u> <u></u></span></p><div><div style="border:none;border-top:solid #e1e1e1 1.0pt;padding:3.0pt 0cm 0cm 0cm"><p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">De :</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Eamonn Maguire [mailto:<a href="mailto:eamonn.maguire@st-annes.ox.ac.uk" target="_blank">eamonn.maguire@st-annes.ox.ac.uk</a>] <br><b>Envoyé :</b> mercredi 5 mars 2014 02:40<br><b>À :</b> Ray Fergerson <<a href="mailto:ray.fergerson@stanford.edu" target="_blank">ray.fergerson@stanford.edu</a>>; Clement Jonquet <<a href="mailto:jonquet@lirmm.fr" target="_blank">jonquet@lirmm.fr</a>><br><b>Cc :</b> <a href="mailto:support@bioontology.org" target="_blank">support@bioontology.org</a>; ISA Team <<a href="mailto:isatools@googlegroups.com" target="_blank">isatools@googlegroups.com</a>><br><b>Objet :</b> RE: [bioontology-support] NCBO Annotator Excel plug-in<u></u><u></u></span></p></div></div><div><div class="h5"><p class="MsoNormal"><u></u> <u></u></p><div><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">Thanks Ray,<br><br>This is great! :)<br><br>Best wishes,<br><br>Eamonn <br><br>Sent from my Windows Phone<u></u><u></u></span></p></div></div><div><div class="MsoNormal" style="text-align:center" align="center"><span lang="EN-US"><hr align="center" size="2" width="100%"></span></div><p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">From: </span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US"><a href="mailto:ray.fergerson@stanford.edu" target="_blank">Ray Fergerson</a></span><span lang="EN-US"><br></span><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">Sent: </span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">‎04/‎03/‎2014 23:24</span><span lang="EN-US"><br></span><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">To: </span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US"><a href="mailto:eamonn.maguire@st-annes.ox.ac.uk" target="_blank">Eamonn Maguire</a>; <a href="mailto:jonquet@lirmm.fr" target="_blank">Clement Jonquet</a></span><span lang="EN-US"><br></span><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">Cc: </span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US"><a href="mailto:support@bioontology.org" target="_blank">support@bioontology.org</a>; <a href="mailto:isatools@googlegroups.com" target="_blank">ISA Team</a></span><span lang="EN-US"><br></span><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">Subject: </span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif" lang="EN-US">RE: [bioontology-support] NCBO Annotator Excel plug-in</span><span lang="EN-US"><u></u><u></u></span></p></div><div><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">The release today allows you to specify that you want the preferred name for every annotated class. Try this tomorrow.</span><span lang="EN-US"><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><span lang="EN-US"><u></u><u></u></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Ray</span><span lang="EN-US"><u></u><u></u></span></p><p class="MsoNormal"><a name="150b9aa5ec38a33a__MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span></a><span lang="EN-US"><u></u><u></u></span></p><div><div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0cm 0cm 0cm"><p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif" lang="EN-US">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma",sans-serif" lang="EN-US"> <a href="mailto:bioontology-support-bounces@lists.stanford.edu" target="_blank">bioontology-support-bounces@lists.stanford.edu</a> [<a href="mailto:bioontology-support-bounces@lists.stanford.edu" target="_blank">mailto:bioontology-support-bounces@lists.stanford.edu</a>] <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> <a href="mailto:support@bioontology.org" target="_blank">support@bioontology.org</a>; ISA Team<br><b>Subject:</b> Re: [bioontology-support] NCBO Annotator Excel plug-in</span><span lang="EN-US"><u></u><u></u></span></p></div></div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p><p class="MsoNormal"><span lang="EN-US">This email skipped under my radar, apologies.<u></u><u></u></span></p><div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">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" target="_blank">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.<u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">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.<u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">Best wishes,<u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">Eamonn<u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p><div><div><div><p class="MsoNormal"><span lang="EN-US">On 13 Feb 2014, at 08:54, Clement Jonquet <<a href="mailto:jonquet@lirmm.fr" target="_blank">jonquet@lirmm.fr</a>> wrote:<u></u><u></u></span></p></div><p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="EN-US"><u></u> <u></u></span></p><div><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Thanks Trish for this response.</span><span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Hi Eamonn,</span><span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">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="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"><a href="http://data.bioontology.org/documentation#nav_annotator" target="_blank"><span style="color:purple">http://data.bioontology.org/documentation#nav_annotator</span></a></span><span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">Regards</span><span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US">CJ</span><span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1f497d" lang="EN-US"> </span><span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">De :</span></b><span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Trish Whetzel [<a href="mailto:plwhetzel@gmail.com" target="_blank"><span style="color:purple">mailto:plwhetzel@gmail.com</span></a>]<span> </span><br><b>Envoyé :</b><span> </span>jeudi 6 février 2014 17:21<br><b>À :</b><span> </span>Clement Jonquet<br><b>Cc :</b><span> </span><a href="mailto:support@bioontology.org" target="_blank"><span style="color:purple">support@bioontology.org</span></a><br><b>Objet :</b><span> </span>Re: [bioontology-support] NCBO Annotator Excel plug-in</span><span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"> <span lang="EN-US"><u></u><u></u></span></p></div><div><div><div><p class="MsoNormal" style="margin-bottom:12.0pt">Hi Clement,<span lang="EN-US"><u></u><u></u></span></p></div><p class="MsoNormal" style="margin-bottom:12.0pt">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 lang="EN-US"><u></u><u></u></span></p></div><div><div><p class="MsoNormal">Cheers,<span lang="EN-US"><u></u><u></u></span></p></div></div><div><p class="MsoNormal">Trish<span> </span><br>[1]<span> </span><a href="http://isatools.wordpress.com/2012/07/13/introducing-ontomaton-ontology-search-tagging-for-google-spreadsheets/" target="_blank"><span style="color:purple">http://isatools.wordpress.com/2012/07/13/introducing-ontomaton-ontology-search-tagging-for-google-spreadsheets/</span></a><span lang="EN-US"><u></u><u></u></span></p></div></div><div><p class="MsoNormal" style="margin-bottom:12.0pt"> <span lang="EN-US"><u></u><u></u></span></p><div><div><p class="MsoNormal">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 lang="EN-US"><u></u><u></u></span></p></div><blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt"><div><div><p class="MsoNormal">Hi all,<span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"> <span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">We used to have an Excel plugin for the Annotator.<u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">Does anyone have updates on this ?<u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">Is it still available ?<u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">Is it compatible with Annotator 2 ?<u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">Clement<u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p></div><div><p class="MsoNormal"> <span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">---------------------------------------------------------------------------------------------------------------------------<u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">Dr.<span> </span><b>Clement JONQUET</b>  - <span> </span><i>PhD in Informatics  -  Assistant Professor</i><u></u><u></u></span></p></div><div><p class="MsoNormal"><i><span lang="EN-US">PI of the<span> </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)</span></i><span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><i><span lang="EN-US">Organizer of<span> </span><a href="http://www.meetup.com/webscience-montpellier/" target="_blank"><span style="color:purple">Web Science Montpellier</span></a><span> </span>Meetup</span></i><span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US"><a href="mailto:jonquet@lirmm.fr" target="_blank"><span style="color:purple">jonquet@lirmm.fr</span></a><u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US"><a href="http://www.lirmm.fr/~jonquet" target="_blank"><span style="color:purple">http://www.lirmm.fr/~jonquet</span></a><u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">               <span> </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><u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">                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>          <u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">                161 rue Ada                                                   Skype:                 clementpro<br>                34095 Montpellier Cdx 5                            Twitter:              <span> </span><a href="http://twitter.com/jonquet_lirmm" target="_blank"><span style="color:purple">@jonquet_lirmm</span></a><u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">                France                                                            Google:              <span> </span><a href="mailto:jonquet.lirmm@gmail.com" target="_blank"><span style="color:purple">jonquet.lirmm@gmail.com</span></a><u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US">----------------------------------------------------------------------------------------------------------------------<u></u><u></u></span></p></div><table align="left" border="0" cellpadding="0" cellspacing="0"><tbody><tr style="height:76.5pt"><td style="width:14.25pt;padding:0cm 0cm 0cm 0cm;height:76.5pt" width="19"></td></tr><tr><td style="padding:0cm 0cm 0cm 0cm"></td><td style="padding:0cm 0cm 0cm 0cm"><div><p class="MsoNormal"><image001.png><u></u><u></u></p></div></td></tr></tbody></table><div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p></div><div><p class="MsoNormal"> <span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"> <span lang="EN-US"><u></u><u></u></span></p></div><div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p></div></div><p class="MsoNormal" style="margin-bottom:12.0pt"><br>_______________________________________________<br>bioontology-support mailing list<br><a href="mailto:bioontology-support@lists.stanford.edu" target="_blank"><span style="color:purple">bioontology-support@lists.stanford.edu</span></a><br><a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support" target="_blank"><span style="color:purple">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</span></a><span lang="EN-US"><u></u><u></u></span></p></blockquote></div></div></div></div><p class="MsoNormal"><span lang="EN-US"> <u></u><u></u></span></p></div></div></div></div></div></div></div></div><br>_______________________________________________<br>
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