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    <div class="moz-cite-prefix">Hi Ray,<br>
      <pre class="moz-signature" cols="72">
--</pre>
      On 12/12/2012 21:55, Ray Fergerson wrote:<br>
    </div>
    <blockquote
      cite="mid:a6d5ecad.000016dc.0000000e@BMIR-MSOB-245.stanford.edu"
      type="cite">
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      <div class="WordSection1">
        <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Eamonn,<o:p></o:p></span></p>
        <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
        <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">In
            OBI there are two terms “treatment” and “compound treatment
            design”. If the text that you supply is “compound treatment”
            then this results in a match on the first term but not the
            second.</span></p>
      </div>
    </blockquote>
    <br>
    I do not get this sorry. If what you say below (about the term has
    to be a synonym to be found) is the case, then I do not believe
    that  “compound treatment” is a  synonym of "treatment" that is why
    this is found and  “compound treatment design” is not.<br>
    If the Annotator is supposed to suggest terms you have to be able to
    find both “treatment” and “compound treatment design” and then you
    leave the user to choose which one is more relevant to their
    context.<br>
    <br>
    My two cents,<br>
    Susanna<br>
    <br>
    <blockquote
      cite="mid:a6d5ecad.000016dc.0000000e@BMIR-MSOB-245.stanford.edu"
      type="cite">
      <div class="WordSection1">
        <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
        <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
        <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">This
            seems reasonable and it is difficult to see how it could
            work differently. If the ontology contained the term “hay
            fever” and you supplied the text “hay” I don’t think that
            you should expect a match. The annotator is not a search
            system, it is a term matching system. “hay” is not the same
            term as “hay fever”.<o:p></o:p></span></p>
        <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
        <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">If
            “compound treatment” were a declared synonym of “compound
            treatment design” then it should be found. If it is really a
            synonym (unclear to me) but not declared to be one in the
            ontology that you are using then you could consider
            extending the ontology or contacting the authors and asking
            them to add a synonym.<o:p></o:p></span></p>
        <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
        <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Ray<o:p></o:p></span></p>
        <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
      </div>
    </blockquote>
    <br>
    <br>
    <blockquote
      cite="mid:a6d5ecad.000016dc.0000000e@BMIR-MSOB-245.stanford.edu"
      type="cite">
      <div class="WordSection1">
        <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
        <div>
          <div style="border:none;border-top:solid #B5C4DF
            1.0pt;padding:3.0pt 0in 0in 0in">
            <p class="MsoNormal" style="margin-left:.5in"><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"">
                <a class="moz-txt-link-abbreviated" href="mailto:bioontology-support-bounces@lists.stanford.edu">bioontology-support-bounces@lists.stanford.edu</a>
                [<a class="moz-txt-link-freetext" href="mailto:bioontology-support-bounces@lists.stanford.edu">mailto:bioontology-support-bounces@lists.stanford.edu</a>]
                <b>On Behalf Of </b>Meng, Fan<br>
                <b>Sent:</b> Wednesday, December 12, 2012 12:49 PM<br>
                <b>To:</b> Eamonn Maguire; Trish Whetzel; Dai, Manhong<br>
                <b>Cc:</b> ISA Team; <a class="moz-txt-link-abbreviated" href="mailto:support@bioontology.org">support@bioontology.org</a> Support<br>
                <b>Subject:</b> Re: [bioontology-support] Annotator
                query<o:p></o:p></span></p>
          </div>
        </div>
        <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
        <p class="MsoNormal" style="margin-left:.5in"><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Hi
            Eamonn and Trish:<o:p></o:p></span></p>
        <p class="MsoNormal" style="margin-left:.5in"><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
        <p class="MsoNormal" style="margin-left:.5in"><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Thanks
            a lot for  your messages. If the terms “"compound treatment"
            and"compound treatment design" are both in an ontology, I
            believe mgrep will only give the longest match by default
            but list both terms as matches will be possible.<o:p></o:p></span></p>
        <p class="MsoNormal" style="margin-left:.5in"><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">However,
            mgrep will not find them if none of them are in the
            ontologies you selected. <o:p></o:p></span></p>
        <p class="MsoNormal" style="margin-left:.5in"><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
        <p class="MsoNormal" style="margin-left:.5in"><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Manhong
            wrote the mgrep program and I believe it is possible to
            include that option although we may need to generate more
            complex dictionaries. Manhong can certainly provide better
            insights on this issue.<o:p></o:p></span></p>
        <p class="MsoNormal" style="margin-left:.5in"><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
        <p class="MsoNormal" style="margin-left:.5in"><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Best,<o:p></o:p></span></p>
        <p class="MsoNormal" style="margin-left:.5in"><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black"><o:p> </o:p></span></p>
        <p class="MsoNormal" style="margin-left:.5in"><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Fan<o:p></o:p></span></p>
        <p class="MsoNormal" style="margin-left:.5in"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
        <p class="MsoNormal" style="margin-left:.5in"><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"">
            Eamonn Maguire [<a moz-do-not-send="true"
              href="mailto:eamonnmag@gmail.com">mailto:eamonnmag@gmail.com</a>]
            <br>
            <b>Sent:</b> Wednesday, December 12, 2012 12:48 PM<br>
            <b>To:</b> Trish Whetzel<br>
            <b>Cc:</b> Meng, Fan; <a moz-do-not-send="true"
              href="mailto:support@bioontology.org">support@bioontology.org</a>
            Support; ISA Team<br>
            <b>Subject:</b> Re: [bioontology-support] Annotator query<o:p></o:p></span></p>
        <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
        <div>
          <p class="MsoNormal" style="margin-left:.5in">Hi Trish, <o:p></o:p></p>
        </div>
        <div>
          <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
        </div>
        <div>
          <p class="MsoNormal" style="margin-left:.5in">Thanks for your
            reply. It would be great if this feature were integrated in
            to the annotator. Some users have been asking us why the
            annotator doesn't find things they expect it to, so it's
            good to have a response to this. I understand why you do it
            the way you do but I'd assume that an indexing system such
            as Lucene could help improve the speed for these types of
            lookups.<o:p></o:p></p>
        </div>
        <div>
          <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
        </div>
        <div>
          <p class="MsoNormal" style="margin-left:.5in">Thanks again,<o:p></o:p></p>
        </div>
        <div>
          <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
        </div>
        <div>
          <p class="MsoNormal" style="margin-left:.5in">Eamonn<o:p></o:p></p>
        </div>
        <div>
          <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
        </div>
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                    <p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Arial","sans-serif"">--</span></b><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
                  </div>
                  <div>
                    <p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Arial","sans-serif"">Eamonn
                          Maguire</span></b><span
style="font-size:10.0pt;font-family:"Arial","sans-serif""><br>
                      </span><span
style="font-size:8.5pt;font-family:"Arial","sans-serif"">Oxford
                        e-Research Centre & Computer Science
                        Department</span><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
                  </div>
                  <div>
                    <p class="MsoNormal"><span
style="font-size:8.5pt;font-family:"Arial","sans-serif"">University
                        of Oxford</span><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
                  </div>
                  <div>
                    <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
                  </div>
                  <div>
                    <p class="MsoNormal"><span
style="font-size:8.0pt;font-family:"Arial","sans-serif"">7
                        Keble Road, Oxford, OX1 3QG</span><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
                  </div>
                  <div>
                    <p class="MsoNormal"><b><span
style="font-size:8.0pt;font-family:"Arial","sans-serif"">T:</span></b><span
style="font-size:8.0pt;font-family:"Arial","sans-serif""> 01865
                        (2) 610788 <b>M:</b> 07526 924483</span><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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        <p style="margin-left:.5in"><span style="color:#A0A0A8">On
            Wednesday, 12 December 2012 at 17:45, Trish Whetzel wrote:<o:p></o:p></span></p>
        <blockquote style="border:none;border-left:solid windowtext
          1.0pt;padding:0in 0in 0in
          8.0pt;margin-left:0in;margin-top:5.0pt;margin-bottom:5.0pt">
          <div>
            <div>
              <div>
                <p class="MsoNormal" style="margin-left:.5in">Hi Eamonn, <o:p></o:p></p>
              </div>
              <div>
                <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
              </div>
              <div>
                <p class="MsoNormal" style="margin-left:.5in">I am not
                  aware of any parameters that can be altered with the
                  Annotator to get a match based on the scenario below.
                  The dictionary that the Annotator uses is based on the
                  preferred names and synonyms of ontology terms and
                  there has to be an exact match in the input text to
                  the dictionary term to return a match .. good for
                  speed of annotation but does not handle term
                  variations in the matching step unless the variation
                  is included in the ontology itself.<o:p></o:p></p>
              </div>
              <div>
                <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
              </div>
              <div>
                <p class="MsoNormal" style="margin-left:.5in">Last I
                  talked with the developers of the entity recognizer
                  that the Annotator uses, called Mgrep, they have
                  developed some methods to account for term
                  permutations and there was an interest to collect use
                  cases to test further. I have included Fan Meng in
                  this response in case this is of interest to pursue
                  further.<o:p></o:p></p>
              </div>
              <div>
                <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
              </div>
              <div>
                <p class="MsoNormal" style="margin-left:.5in">Best,<o:p></o:p></p>
              </div>
              <div>
                <p class="MsoNormal" style="margin-left:.5in">Trish <o:p></o:p></p>
              </div>
              <div>
                <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
              </div>
              <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
              <div>
                <div>
                  <p class="MsoNormal" style="margin-left:.5in">On Dec
                    12, 2012, at 4:17 AM, Eamonn Maguire wrote:<o:p></o:p></p>
                </div>
                <p class="MsoNormal"
style="mso-margin-top-alt:0in;margin-right:0in;margin-bottom:12.0pt;margin-left:.5in"><o:p> </o:p></p>
                <div>
                  <div>
                    <p class="MsoNormal" style="margin-left:.5in">Hi
                      all, <o:p></o:p></p>
                  </div>
                  <div>
                    <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
                  </div>
                  <div>
                    <p class="MsoNormal" style="margin-left:.5in">I have
                      a query about the annotator. <o:p></o:p></p>
                  </div>
                  <div>
                    <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
                  </div>
                  <div>
                    <p class="MsoNormal" style="margin-left:.5in">It
                      appears that if we search on something like
                      "compound treatment", we don't get a hit for
                      "compound treatment design" for instance from
                      OBI/EFO. Do you have any idea about how we can get
                      the search results to return a better match? Or if
                      it's possible?<o:p></o:p></p>
                  </div>
                  <div>
                    <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
                  </div>
                  <div>
                    <p class="MsoNormal" style="margin-left:.5in">Many
                      thanks,<o:p></o:p></p>
                  </div>
                  <div>
                    <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
                  </div>
                  <div>
                    <p class="MsoNormal" style="margin-left:.5in">Eamonn<o:p></o:p></p>
                  </div>
                  <div>
                    <div>
                      <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
                    </div>
                    <table class="MsoNormalTable"
                      style="margin-left:.5in;z-index:auto" border="0"
                      cellpadding="0" cellspacing="0">
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                          <td style="padding:0in 0in 0in 0in">
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                              <p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Arial","sans-serif"">--</span></b><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
                            </div>
                            <div>
                              <p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Arial","sans-serif"">Eamonn
                                    Maguire</span></b><span
style="font-size:10.0pt;font-family:"Arial","sans-serif""><br>
                                </span><span
style="font-size:8.5pt;font-family:"Arial","sans-serif"">Oxford
                                  e-Research Centre & Computer
                                  Science Department</span><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
                            </div>
                            <div>
                              <p class="MsoNormal"><span
style="font-size:8.5pt;font-family:"Arial","sans-serif"">University
                                  of Oxford</span><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
                            </div>
                            <div>
                              <p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p> </o:p></span></p>
                            </div>
                            <div>
                              <p class="MsoNormal"><span
style="font-size:8.0pt;font-family:"Arial","sans-serif"">7
                                  Keble Road, Oxford, OX1 3QG</span><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
                            </div>
                            <div>
                              <p class="MsoNormal"><b><span
style="font-size:8.0pt;font-family:"Arial","sans-serif"">T:</span></b><span
style="font-size:8.0pt;font-family:"Arial","sans-serif""> 01865
                                  (2) 610788 <b>M:</b> 07526 924483</span><span
style="font-size:11.0pt;font-family:"Calibri","sans-serif""><o:p></o:p></span></p>
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                  </div>
                  <p class="MsoNormal" style="margin-left:.5in">_______________________________________________<br>
                    bioontology-support mailing list<br>
                    <a moz-do-not-send="true"
                      href="mailto:bioontology-support@lists.stanford.edu">bioontology-support@lists.stanford.edu</a><br>
                    <a moz-do-not-send="true"
                      href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</a><o:p></o:p></p>
                </div>
              </div>
              <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
            </div>
          </div>
        </blockquote>
        <div>
          <p class="MsoNormal" style="margin-left:.5in"><o:p> </o:p></p>
        </div>
      </div>
      -- <br>
      ISA support team:<br>
      - Philippe Rocca-Serra<br>
      - Eamonn Maguire<br>
      - Alejandra Gonzalez-Beltran<br>
      - Susanna-Assunta Sansone<br>
      ***<br>
      <a class="moz-txt-link-abbreviated" href="http://www.isa-tools.org">www.isa-tools.org</a><br>
      <a class="moz-txt-link-abbreviated" href="http://www.isacommons.org">www.isacommons.org</a><br>
       <br>
       <br>
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