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    <div class="moz-cite-prefix">Jennifer,<br>
      <br>
      No problem, OntoVIP can be changed into ONTOVIP.<br>
      <br>
      Best regards<br>
      <br>
      Bernard<br>
      <br>
      Le 01/02/2017 à 23:16, Jennifer Leigh Vendetti a écrit :<br>
    </div>
    <blockquote
      cite="mid:BD6ECD0B-CB99-43D9-8D85-0C78B758B841@stanford.edu"
      type="cite">
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      <div class="">Hello again Bernard,</div>
      <div class=""><br class="">
      </div>
      <div class="">I ran into a small complication with your OntoVIP
        ontology.</div>
      <div class=""><br class="">
      </div>
      <div class="">Several years ago, BioPortal’s backend code
        underwent a major refactor.  At the time, a new constraint was
        added that ontology acronyms must have all capital letters.
         Data migration scripts were run that should have cleaned up all
        existing acronyms with lowercase letters, but it seems your
        ontology was missed.  Before I can re-parse your ontology, I
        will need to change your ontology acronym to something with all
        capital letters (instead of “OntoVIP”).</div>
      <div class=""><br class="">
      </div>
      <div class="">Could you please confirm if you would like to use
        “ONTOVIP” as the new acronym?  Or, something else?</div>
      <div class=""><br class="">
      </div>
      <div class="">Best,</div>
      <div class="">Jennifer</div>
      <div class=""><br class="">
      </div>
      <div class=""><br class="">
      </div>
      <div class=""><br class="">
      </div>
      <br class="">
      <div>
        <blockquote type="cite" class="">
          <div class="">On Jan 31, 2017, at 6:45 PM, Jennifer Leigh
            Vendetti <<a moz-do-not-send="true"
              href="mailto:vendetti@stanford.edu" class="">vendetti@stanford.edu</a>>
            wrote:</div>
          <br class="Apple-interchange-newline">
          <div class="">
            <div style="word-wrap: break-word; -webkit-nbsp-mode: space;
              -webkit-line-break: after-white-space;" class="">
              Hello Bernard,
              <div class=""><br class="">
              </div>
              <div class="">The first 3 ontologies you list below are
                fully parsed and available in BioPortal now.</div>
              <div class=""><br class="">
              </div>
              <div class="">I should have the 4th one (OntoVIP) done by
                tomorrow.</div>
              <div class=""><br class="">
              </div>
              <div class="">Kind regards,</div>
              <div class="">Jennifer</div>
              <div class=""><br class="">
              </div>
              <div class=""><br class="">
              </div>
              <div class=""><br class="">
                <div class="">
                  <blockquote type="cite" class="">
                    <div class="">On Jan 31, 2017, at 4:40 AM, bernard
                      gibaud <<a moz-do-not-send="true"
                        href="mailto:bernard.gibaud@univ-rennes1.fr"
                        class="">bernard.gibaud@univ-rennes1.fr</a>>
                      wrote:</div>
                    <br class="Apple-interchange-newline">
                    <div class="">
                      <div bgcolor="#FFFFFF" text="#000000" class="">
                        <div class="moz-cite-prefix">Hello Jennifer,<br
                            class="">
                          <br class="">
                          The problem reported below was fixed.<br
                            class="">
                          <br class="">
                          Is it possible to reload the following
                          ontologies in the BioPortal:<br class="">
                          <a moz-do-not-send="true"
                            class="moz-txt-link-freetext"
                            href="https://bioportal.bioontology.org/ontologies/ONL-DP">https://bioportal.bioontology.org/ontologies/ONL-DP</a><br
                            class="">
                          <a moz-do-not-send="true"
                            class="moz-txt-link-freetext"
                            href="https://bioportal.bioontology.org/ontologies/ONL-MSA">https://bioportal.bioontology.org/ontologies/ONL-MSA</a><br
                            class="">
                          <a moz-do-not-send="true"
                            class="moz-txt-link-freetext"
                            href="https://bioportal.bioontology.org/ontologies/ONL-MR-DA">https://bioportal.bioontology.org/ontologies/ONL-MR-DA</a><br
                            class="">
                          <a moz-do-not-send="true"
                            class="moz-txt-link-freetext"
                            href="https://bioportal.bioontology.org/ontologies/OntoVIP">https://bioportal.bioontology.org/ontologies/OntoVIP</a><br
                            class="">
                          <br class="">
                          Actually they all imported the same file
                          'ontoneurolog-extension-of-dolce.owl', thus
                          leading to the same error.<br class="">
                          <br class="">
                          Best regards,<br class="">
                          <br class="">
                          Bernard Gibaud<br class="">
                          <br class="">
                          <br class="">
                          <br class="">
                          Le 23/11/2016 à 08:26, bernard gibaud a
                          écrit :<br class="">
                        </div>
                        <blockquote
                          cite="mid:5bbaaaa9-b6d8-9896-d428-a02e49c4bca7@univ-rennes1.fr"
                          type="cite" class="">
                          <div class="moz-cite-prefix">Hello Christine,
                            Jennifer<br class="">
                            <br class="">
                            I will try to fix this problem. Actually
                            this problem did not cause any errors at the
                            time the ontology was shared.<br class="">
                            <br class="">
                            Best regards,<br class="">
                            <br class="">
                            Bernard Gibaud<br class="">
                            <br class="">
                            Le 22/11/2016 à 01:00, Jennifer Leigh
                            Vendetti a écrit :<br class="">
                          </div>
                          <blockquote
                            cite="mid:D818CA1C-BFD2-494B-9F05-B2F29770C9BF@stanford.edu"
                            type="cite" class="">
                            <div class="">Hello Christine,</div>
                            <div class=""><br class="">
                            </div>
                            <div class="">The reason for the 404
                              (“something has gone wrong") error is that
                              the PURL you list below resolves to what
                              is supposed to be the page that displays
                              the classes for the Mental State
                              Assessment ontology [1].  The classes page
                              is absent because the ontology source file
                              that was submitted to BioPortal has
                              invalid syntax and is unable to be parsed.
                               This is indicated by the “Error Rdf”
                              status listed on the ontology summary page
                              (<a moz-do-not-send="true"
                                href="http://bioportal.bioontology.org/ontologies/ONL-MSA"
                                class="">http://bioportal.bioontology.org/ontologies/ONL-MSA</a>).</div>
                            <div class=""><br class="">
                            </div>
                            <div class="">Normally if someone submits an
                              ontology with syntax errors, we try our
                              best to fix them and re-parse the ontology
                              to make it available to end-users.
                               However, this particular ontology imports
                              several other ontologies from a web URL
                              that we don’t host here at Stanford, and
                              the error is in one of the imports.</div>
                            <div class=""><br class="">
                            </div>
                            <div class="">I’m listing the syntax error
                              and suggested fix below, and I’ve cc’ed
                              the ontology contact person in the event
                              that Bernard is willing to submit a
                              corrected version.</div>
                            <div class=""><br class="">
                            </div>
                            <div class="">The error is on line 800 of
                              the ontoneurolog-extension-of-dolce.owl
                              ontology file (hosted at <a
                                moz-do-not-send="true"
href="http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl"
                                class="">http://neurolog.unice.fr/ontoneurolog/v3.0/ontoneurolog-extension-of-dolce.owl</a>).
                               The rdfs:comment is declared as datatype
                              XMLLiteral, but the content of the comment
                              doesn’t contain the required opening and
                              closing XML tags that are expected for
                              this particular datatype:</div>
                            <div class=""><br class="">
                            </div>
                            <div class="">
                              <div class=""><rdfs:comment
                                rdf:datatype="&rdf;XMLLiteral">[DEF]
                                ACTION A is generated, or is produced,
                                by ACTION B when A is done by doing B:
                                “doing A by doing B”.</div>
                              <div class="">[CIT] (Pacherie, 2008, p.
                                198): “At least three cases [of
                                productions] must be distinguished. The
                                first is indeed causal generation. Doing
                                A by doing B counts as an instance of
                                causal generation when the production of
                                B causes the production of A. For
                                instance, turning the light by flipping
                                a switch or breaking the glass by
                                dropping it on a hard surface count as
                                instances of causal generation. The
                                second case is conventional generation,
                                where doing B (in circumstances C)
                                counts as doing A in virtue of a rule or
                                convention that stipulates that is so
                                counts. Thus, signalling a left turn by
                                extending one’s left arm or voting in
                                favour of the motion by raising one’s
                                hand are instances of conventional
                                generation. The third case is
                                circumstantial generation, where doing B
                                counts as doing A only if certain
                                circumstances obtain. For instance, one
                                breaks the world record for in the 100 m
                                for men by running it in 9,77 s only in
                                circumstances where no one has yet run
                                this distance in 9,77 a or
                                less.”</rdfs:comment></div>
                            </div>
                            <div class=""><br class="">
                            </div>
                            <div class="">Possible fixes are a) remove
                              the XMLLiteral datatype declaration, e.g.:</div>
                            <div class=""><br class="">
                            </div>
                            <div class=""><rdfs:comment>[DEF]
                              ACTION A is
                              generated…</rdfs:comment></div>
                            <div class=""><br class="">
                            </div>
                            <div class="">… or b) add the desired start
                              and end tags to the comment, e.g.:</div>
                            <div class=""><br class="">
                            </div>
                            <div class="">
                              <div class=""><rdfs:comment
                                rdf:datatype="&rdf;XMLLiteral”><b
                                  class=""><p></b>[DEF] ACTION A
                                is generated…<b class=""></p></b></rdfs:comment></div>
                            </div>
                            <div class=""><br class="">
                            </div>
                            <div class="">Kind regards,</div>
                            <div class="">Jennifer</div>
                            <div class=""><br class="">
                            </div>
                            <div class="">[1] <a moz-do-not-send="true"
href="http://bioportal.bioontology.org/ontologies/ONL-MSA?p=classes&conceptid=root"
                                class="">http://bioportal.bioontology.org/ontologies/ONL-MSA?p=classes&conceptid=root</a></div>
                            <div class=""><br class="">
                            </div>
                            <div class="">Screen shot of the syntax
                              error as seen in the Protege ontology
                              editing environment:</div>
                            <div class=""><br class="">
                            </div>
                            <div class=""><br class="">
                            </div>
                            <div class=""><span
                                id="cid:part4.5FD2EE15.364461DC@univ-rennes1.fr"
                                class=""><Mail Attachment.png></span></div>
                            <div class=""><br class="">
                            </div>
                            <div class=""><br class="">
                            </div>
                            <br class="">
                            <div class="">
                              <blockquote type="cite" class="">
                                <div class="">On Nov 21, 2016, at 8:59
                                  AM, <a moz-do-not-send="true"
                                    href="mailto:support@bioontology.org"
                                    class="">
                                    support@bioontology.org</a> wrote:</div>
                                <br class="Apple-interchange-newline">
                                <div class="">
                                  <div class="">
                                    <p class="">Name: Christine Girges </p>
                                    <p class="">Email: <a
                                        moz-do-not-send="true"
                                        href="mailto:c.girges@ucl.ac.uk"
                                        class="">
                                        c.girges@ucl.ac.uk</a> </p>
                                    <p class="">Location: <a
                                        moz-do-not-send="true"
                                        href="https://bioportal.bioontology.org/ontologies/ONL-MSA"
                                        class="">
https://bioportal.bioontology.org/ontologies/ONL-MSA</a> </p>
                                    <p class=""><br class="">
                                      <strong class="">Feedback:</strong>
                                    </p>
                                    <p class="">The following link does
                                      not work:</p>
                                    <p class=""><a
                                        moz-do-not-send="true"
                                        href="http://purl.bioontology.org/ontology/ONL-MSA"
                                        class="">http://purl.bioontology.org/ontology/ONL-MSA</a></p>
                                    <p class="">I receive this error
                                      message:</p>
                                    <p class="">We're sorry but
                                      something has gone wrong. We have
                                      been notified of this error.</p>
                                    <div class=""><br
                                        class="webkit-block-placeholder">
                                    </div>
                                  </div>
_______________________________________________<br class="">
                                  bioontology-support mailing list<br
                                    class="">
                                  <a moz-do-not-send="true"
                                    href="mailto:bioontology-support@lists.stanford.edu"
                                    class="">bioontology-support@lists.stanford.edu</a><br
                                    class="">
                                  <a moz-do-not-send="true"
                                    class="moz-txt-link-freetext"
                                    href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</a><br
                                    class="">
                                </div>
                              </blockquote>
                            </div>
                            <br class="">
                          </blockquote>
                          <br class="">
                          <p class=""><br class="">
                          </p>
                          <pre class="moz-signature" cols="72">-- 
Bernard Gibaud
Equipe INSERM MediCIS 
Unite U1099 LTSI, Universite de Rennes 1
Faculte de Medecine
2, Avenue du Pr. Leon Bernard
CS 34317
35043 Rennes Cedex, France
France
Tel +33 (0) 2 23 23 45 90 ou +33 (0) 2 23 23 47 18 (secr)
email: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:bernard.gibaud@univ-rennes1.fr">bernard.gibaud@univ-rennes1.fr</a>
page web: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://medicis.univ-rennes1.fr/members/bernard.gibaud/index">https://medicis.univ-rennes1.fr/members/bernard.gibaud/index</a>

</pre>
                        </blockquote>
                        <br class="">
                        <p class=""><br class="">
                        </p>
                        <pre class="moz-signature" cols="72">-- 
Bernard Gibaud
Equipe INSERM MediCIS 
Unite U1099 LTSI, Universite de Rennes 1
Faculte de Medecine
2, Avenue du Pr. Leon Bernard
CS 34317
35043 Rennes Cedex, France
France
Tel +33 (0) 2 23 23 45 90 ou +33 (0) 2 23 23 47 18 (secr)
email: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:bernard.gibaud@univ-rennes1.fr">bernard.gibaud@univ-rennes1.fr</a>
page web: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://medicis.univ-rennes1.fr/members/bernard.gibaud/index">https://medicis.univ-rennes1.fr/members/bernard.gibaud/index</a>

</pre>
                      </div>
                    </div>
                  </blockquote>
                </div>
                <br class="">
              </div>
            </div>
            _______________________________________________<br class="">
            bioontology-support mailing list<br class="">
            <a moz-do-not-send="true"
              href="mailto:bioontology-support@lists.stanford.edu"
              class="">bioontology-support@lists.stanford.edu</a><br
              class="">
<a class="moz-txt-link-freetext" href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</a><br
              class="">
          </div>
        </blockquote>
      </div>
      <br class="">
    </blockquote>
    <br>
    <p><br>
    </p>
    <pre class="moz-signature" cols="72">-- 
Bernard Gibaud
Equipe INSERM MediCIS 
Unite U1099 LTSI, Universite de Rennes 1
Faculte de Medecine
2, Avenue du Pr. Leon Bernard
CS 34317
35043 Rennes Cedex, France
France
Tel +33 (0) 2 23 23 45 90 ou +33 (0) 2 23 23 47 18 (secr)
email: <a class="moz-txt-link-abbreviated" href="mailto:bernard.gibaud@univ-rennes1.fr">bernard.gibaud@univ-rennes1.fr</a>
page web: <a class="moz-txt-link-freetext" href="https://medicis.univ-rennes1.fr/members/bernard.gibaud/index">https://medicis.univ-rennes1.fr/members/bernard.gibaud/index</a>

</pre>
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