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    <p>Thank you very much, it really worked.</p>
    <p>Kind regards, Carlos Oscar<br>
    </p>
    <div class="moz-cite-prefix">El 28/07/2020 a las 18:13, Michael Dorf
      escribió:<br>
    </div>
    <blockquote type="cite"
      cite="mid:8615803C-0030-42E0-B6AA-8B2CEF22060A@stanford.edu">
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      Hi Carlos,
      <div class=""><br class="">
      </div>
      <div class="">It looks like the ontology has loaded correctly, but
        it hasn’t had a chance to propagate through our caching layers.
        I’ve cleared the system caches manually, and the ontology now
        appears and functions correctly. </div>
      <div class=""><br class="">
      </div>
      <div class="">Let me know if you are still seeing any issues.</div>
      <div class=""><br class="">
      </div>
      <div class="">Thank you,</div>
      <div class=""><br class="">
      </div>
      <div class="">Michael</div>
      <div class=""><br class="">
      </div>
      <div class=""><br class="">
      </div>
      <div class=""><br class="">
        <div class="">
          <div><br class="">
            <blockquote type="cite" class="">
              <div class="">On Jul 28, 2020, at 4:25 AM, Carlos Oscar
                Sorzano <<a href="mailto:coss@cnb.csic.es" class=""
                  moz-do-not-send="true">coss@cnb.csic.es</a>> wrote:</div>
              <br class="Apple-interchange-newline">
              <div class="">
                <div class="">
                  <p class="">Dear Jennifer,</p>
                  <p class="">presumably I have uploaded now a true OWL
                    file, but BioPortal cannot show yet the classes.
                    Would you mind having a look? And thank you very
                    much.</p>
                  <p class="">Kind regards, Carlos Oscar<br class="">
                  </p>
                  <div class="moz-cite-prefix">On 7/24/20 8:53 PM,
                    Jennifer Leigh Vendetti wrote:<br class="">
                  </div>
                  <blockquote type="cite"
                    cite="mid:15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu"
                    class="">
                    Hello Carlos Oscar,
                    <div class=""><br class="">
                    </div>
                    <div class="">I looked at the contents of your
                      ontology source file. You mentioned that it’s an
                      OWL file, but the contents appear to be in OBO
                      format, i.e., see the following snippet from the
                      top of your ontology showing OBO-style term
                      stanzas:</div>
                    <div class=""><br class="">
                    </div>
                    <div class="">
                      <div class=""><font class="" color="#0433ff">format-version:
                          1.2</font></div>
                      <div class=""><font class="" color="#0433ff">ontology:
                          <a
href="http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2"
                            class="" moz-do-not-send="true">
http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2</a></font></div>
                      <div class=""><font class="" color="#0433ff">owl-axioms:
                          Prefix(owl:=<<a
                            href="http://www.w3.org/2002/07/owl#"
                            class="" moz-do-not-send="true">http://www.w3.org/2002/07/owl#</a>>)\nPrefix(rdf:=<<a
href="http://www.w3.org/1999/02/22-rdf-syntax-ns#" class=""
                            moz-do-not-send="true">http://www.w3.org/1999/02/22-rdf-syntax-ns#</a>>)\nPrefix(xml:=<<a
                            href="http://www.w3.org/XML/1998/namespace"
                            class="" moz-do-not-send="true">http://www.w3.org/XML/1998/namespace</a>>)\nPrefix(xsd:=<<a
                            href="http://www.w3.org/2001/XMLSchema#"
                            class="" moz-do-not-send="true">http://www.w3.org/2001/XMLSchema#</a>>)\nPrefix(rdfs:=<<a
                            href="http://www.w3.org/2000/01/rdf-schema#"
                            class="" moz-do-not-send="true">http://www.w3.org/2000/01/rdf-schema#</a>>)\n\n\nOntology(\nDeclaration(AnnotationProperty(<<a
href="http://www.geneontology.org/formats/oboInOwl#id" class=""
                            moz-do-not-send="true">http://www.geneontology.org/formats/oboInOwl#id</a>>))\n\n\nAnnotationAssertion(<<a
href="http://www.geneontology.org/formats/oboInOwl#id" class=""
                            moz-do-not-send="true">http://www.geneontology.org/formats/oboInOwl#id</a>>
                          <<a
href="http://purl.obolibrary.org/obo/http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2#ProtMovies"
                            class="" moz-do-not-send="true">http://purl.obolibrary.org/obo/http://www.semanticweb.org/coss/ontologies/2020/2/untitled-ontology-2#ProtMovies</a>>
                          \"ProtProcessMovies\"^^xsd:string)\n)</font></div>
                      <div class=""><font class="" color="#0433ff"><br
                            class="">
                        </font></div>
                      <div class=""><font class="" color="#0433ff">[Term]</font></div>
                      <div class=""><font class="" color="#0433ff">id:
                          Acquisition</font></div>
                      <div class=""><font class="" color="#0433ff">comment:
                          Contains acquisition parameters such as
                          magnification, voltage, spherical aberration,
                          amplitude contrast, dose per frame and inital
                          dose, optics group, and beam tilt</font></div>
                      <div class=""><font class="" color="#0433ff">is_a:
                          EMObject</font></div>
                      <div class=""><font class="" color="#0433ff"><br
                            class="">
                        </font></div>
                      <div class=""><font class="" color="#0433ff">[Term]</font></div>
                      <div class=""><font class="" color="#0433ff">id:
                          AtomStruct</font></div>
                      <div class=""><font class="" color="#0433ff">comment:
                          File representing an atomic structure (PDB,
                          mmCIF, ...)</font></div>
                      <div class=""><font class="" color="#0433ff">is_a:
                          EMObject</font></div>
                      <div class=""><font class="" color="#0433ff">property_value:
                          hasVolume "Volume"</font></div>
                      <div class=""><br class="">
                      </div>
                      <div class="">The first line indicates that the
                        ontology file is written in OBO format version
                        1.2, however the rest of the header tags aren’t
                        valid according to OBO file format documentation
                        here:</div>
                      <div class=""><br class="">
                      </div>
                      <div class=""><a
href="https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1"
                          class="" moz-do-not-send="true">https://owlcollab.github.io/oboformat/doc/GO.format.obo-1_2.html#S.2.1</a></div>
                      <div class=""><br class="">
                      </div>
                      <div class="">Could you provide more detail about
                        how this ontology was generated? Do you have an
                        OBO source file that you attempted to convert to
                        a different format using the Protege desktop
                        application? Also, I do see an error message in
                        the Protege log when opening your ontology in
                        the desktop version (Window -> Show log…).</div>
                      <div class=""><br class="">
                      </div>
                      <div class=""><span
                          id="cid:part11.97196242.4073B62F@cnb.csic.es"><Screenshot
                          2020-07-24 11.52.33.png></span></div>
                      <div class=""><br class="">
                      </div>
                      <div class="">Kind regards,</div>
                      <div class="">Jennifer</div>
                      <div class=""><br class="">
                      </div>
                      <div class=""><br class="">
                        <blockquote type="cite" class="">
                          <div class="">On Jul 23, 2020, at 10:43 PM,
                            Carlos Oscar Sorzano <<a
                              href="mailto:coss@cnb.csic.es" class=""
                              moz-do-not-send="true">coss@cnb.csic.es</a>>
                            wrote:</div>
                          <br class="Apple-interchange-newline">
                          <div class="">
                            <div class="">Dear colleagues,<br class="">
                              <br class="">
                              I uploaded yesterday an ontology file for
                              Cryo Electron Microscopy (<a
href="http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root"
                                class="" moz-do-not-send="true">http://bioportal.bioontology.org/ontologies/CRYOEM/?p=classes&conceptid=root</a>).
                              The OWL file was generated with Protege
                              and it does not show any obvious error in
                              Protege. However, when it is read at
                              BioPortal there is some problem because we
                              see the error message "Problem retrieving
                              classes" (see previous link). The file is
                              partly parsed because it shows some
                              metrics, but we must have something wrong
                              with the file. Could you help us with any
                              hint?<br class="">
                              <br class="">
                              Kind regards and thanks, Carlos Oscar<br
                                class="">
_______________________________________________<br class="">
                              bioontology-support mailing list<br
                                class="">
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                                href="mailto:bioontology-support@lists.stanford.edu"
                                class="" moz-do-not-send="true">bioontology-support@lists.stanford.edu</a><br
                                class="">
                              <a class="moz-txt-link-freetext"
                                href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support"
                                moz-do-not-send="true">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</a><br
                                class="">
                            </div>
                          </div>
                        </blockquote>
                      </div>
                      <br class="">
                    </div>
                  </blockquote>
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