<html>
  <head>
    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
  </head>
  <body>
    <p>Thank you, Jennifer. I will check the configuration of Protege
      and see if I can save a truly OWL file. At least I have now
      something to look at.</p>
    <p>Kind regards, Carlos Oscar<br>
    </p>
    <div class="moz-cite-prefix">El 24/07/2020 a las 20:53, Jennifer
      Leigh Vendetti escribió:<br>
    </div>
    <blockquote type="cite"
      cite="mid:15D2C6A1-C747-4738-896A-B97FDC9E1F2E@stanford.edu">
      <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
      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=""><img apple-inline="yes"
            id="F4C310D6-0CD9-4460-83EA-0D91A00DF052"
            src="cid:part11.71328C0B.C44D9018@cnb.csic.es" class=""></div>
        <div class=""><br class="">
        </div>
        <div class="">Kind regards,</div>
        <div class="">Jennifer</div>
        <div class=""><br class="">
        </div>
        <div><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="">
                <a 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">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</a><br
                  class="">
              </div>
            </div>
          </blockquote>
        </div>
        <br class="">
      </div>
    </blockquote>
  </body>
</html>