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    Thanks,<br>
    <br>
    Jie<br>
    <br>
    On 4/10/2012 8:32 PM, Chris Mungall wrote:
    <blockquote cite="mid:8D1C4E21-7681-4449-98AD-361F17FE96EB@lbl.gov"
      type="cite">
      <div><br>
      </div>
      <div>Yes, this is equivalent to what I suggested - see table 16.</div>
      <a moz-do-not-send="true"
        href="http://www.w3.org/TR/owl2-mapping-to-rdf/">http://www.w3.org/TR/owl2-mapping-to-rdf/</a>
      <div><br>
      </div>
      <div>The main point is to avoid oboInOwl:Obsolete. This was
        introduced in the legacy oboInOwl mapping and has now been
        superseded.<br>
        <div><br>
          <div>
            <div>On Apr 10, 2012, at 4:04 PM, Jie Zheng wrote:</div>
            <br class="Apple-interchange-newline">
            <blockquote type="cite">
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              <div bgcolor="#FFFFFF" text="#000000"> Hi Chris,<br>
                <br>
                I defined the obsolete property or class as the
                subProperty or subClass of <a moz-do-not-send="true"
                  class="moz-txt-link-rfc2396E"
                  href="http://www.w3.org/2002/07/owl#DeprecatedProperty">"http://www.w3.org/2002/07/owl#DeprecatedProperty"</a>
                or <a moz-do-not-send="true"
                  class="moz-txt-link-rfc2396E"
                  href="http://www.w3.org/2002/07/owl#DeprecatedClass">"http://www.w3.org/2002/07/owl#DeprecatedClass"</a>.
                <br>
                <br>
                This is how I did:<br>
                    <owl:ObjectProperty rdf:about=<a
                  moz-do-not-send="true" class="moz-txt-link-rfc2396E"
                  href="http://purl.obolibrary.org/obo/IAO_0000222">"http://purl.obolibrary.org/obo/IAO_0000222"</a>><br>
                        <rdfs:label
                rdf:datatype=<a moz-do-not-send="true"
                  class="moz-txt-link-rfc2396E"
                  href="http://www.w3.org/2001/XMLSchema#string">"http://www.w3.org/2001/XMLSchema#string"</a>>obsolete_describes</rdfs:label><br>
                          <rdfs:subPropertyOf rdf:resource=<a
                  moz-do-not-send="true" class="moz-txt-link-rfc2396E"
                  href="http://www.w3.org/2002/07/owl#DeprecatedProperty">"http://www.w3.org/2002/07/owl#DeprecatedProperty"</a>/><br>
                        <obo:IAO_0000231 rdf:resource=<a
                  moz-do-not-send="true" class="moz-txt-link-rfc2396E"
                  href="http://purl.obolibrary.org/obo/IAO_0000103">"http://purl.obolibrary.org/obo/IAO_0000103"</a>/><br>
                    </owl:ObjectProperty><br>
                <br>
                As Bioportal developers pointed out, I misused it.
                Should I use it as:<br>
                <owl:DeprecatedProperty rdf:ID=<a
                  moz-do-not-send="true" class="moz-txt-link-rfc2396E"
                  href="http://purl.obolibrary.org/obo/IAO_0000222">"http://purl.obolibrary.org/obo/IAO_0000222"</a>><br>
                        <rdfs:label
                rdf:datatype=<a moz-do-not-send="true"
                  class="moz-txt-link-rfc2396E"
                  href="http://www.w3.org/2001/XMLSchema#string">"http://www.w3.org/2001/XMLSchema#string"</a>>obsolete_describes</rdfs:label><br>
                        <obo:IAO_0000231 rdf:resource=<a
                  moz-do-not-send="true" class="moz-txt-link-rfc2396E"
                  href="http://purl.obolibrary.org/obo/IAO_0000103">"http://purl.obolibrary.org/obo/IAO_0000103"</a>/><br>
                 </owl:DeprecatedProperty><br>
                <br>
                Thanks,<br>
                <br>
                Jie<br>
                <br>
                <br>
                <br>
                On 4/10/2012 6:54 PM, Chris Mungall wrote:
                <blockquote
                  cite="mid:647E28E0-FE4A-4F22-AF0D-AB3EC2B30C4D@lbl.gov"
                  type="cite">
                  <div><br>
                  </div>
                  <div>oboInOwl:obsolete should be declared obsolete, I
                    don't recommend reverting to this.</div>
                  <div><br>
                  </div>
                  <div>You should use the owl:deprecated annotation
                    property. This is the standard way to translate
                    obsolete classes in the obo2owl translation. Tim
                    added support for this in Protege.</div>
                  <div><br>
                  </div>
                  <div><br>
                  </div>
                  <div>
                    <div>On Apr 10, 2012, at 3:27 PM, Jie Zheng wrote:</div>
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                    <blockquote type="cite">
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                      <div bgcolor="#FFFFFF" text="#000000"> Hi Ray,<br>
                        <br>
                        Thanks for identified the bug. We have tried to
                        open OBI in both Protege 3 and Protege 4. Both
                        worked fine. The issue cause by replacing
                        oboInOwl:obsolete root terms by Owl:deprecate.
                        Same should define the deprecated term as
                        <owl:DeprecatedClass rdf:ID="OBSOLETE_TERM"
                        />. For making sure everything worked well, I
                        reverted to oboInOwl:obsolete root terms. Hope
                        parsing go through this time.<br>
                        <br>
                        Thanks,<br>
                        <br>
                        Jie<br>
                        <br>
                        <br>
                        On 4/10/2012 4:33 PM, Ray Fergerson wrote:
                        <blockquote
                          cite="mid:212e6e9c.000018f8.00000042@bmir-3880548.stanford.edu"
                          type="cite">
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                            <p class="MsoNormal"><span style="font-size:
                                11pt; font-family:
                                "Cambria","serif";
                                color: windowtext;">Jie,<o:p></o:p></span></p>
                            <p class="MsoNormal"><span style="font-size:
                                11pt; font-family:
                                "Cambria","serif";
                                color: windowtext;"><o:p> </o:p></span></p>
                            <p class="MsoNormal"><span style="font-size:
                                11pt; font-family:
                                "Cambria","serif";
                                color: windowtext;">It took a while to
                                track this down; the cause was quite
                                obscure. Unfortunately the ontology has
                                bugs in it that u</span><span
                                style="font-size: 11pt; font-family:
                                "Cambria","serif";
                                color: windowtext;">nfortunately neither
                                Protégé 4 nor the OWL api catch. The
                                errors result in incorrect query-time
                                behavior on Protégé.</span><span
                                style="font-size: 11pt; font-family:
                                "Cambria","serif";
                                color: windowtext;"><o:p></o:p></span></p>
                            <p class="MsoPlainText"><o:p> </o:p></p>
                            <p class="MsoNormal"><span style="font-size:
                                11pt; font-family:
                                "Cambria","serif";
                                color: windowtext;">The message below is
                                from Tim Redmond (resident Protégé &
                                OWL expert) that should explain how to
                                fix the ontology.</span><span
                                style="font-size: 11pt; font-family:
                                "Cambria","serif";
                                color: windowtext;"><o:p></o:p></span></p>
                            <p class="MsoPlainText"><o:p> </o:p></p>
                            <p class="MsoPlainText">Ray<o:p></o:p></p>
                            <p class="MsoPlainText"><o:p> </o:p></p>
                            <p class="MsoPlainText">----------------------------<o:p></o:p></p>
                            <p class="MsoPlainText"><o:p> </o:p></p>
                            <p class="MsoPlainText">Message for obi
                              folk:<o:p></o:p></p>
                            <p class="MsoPlainText"><o:p> </o:p></p>
                            <p class="MsoPlainText">The provided
                              ontologies were not in OWL 2 because of
                              their use of<o:p></o:p></p>
                            <p class="MsoPlainText">reserved names. 
                              While the deviation is not serious, it
                              turns out -<o:p></o:p></p>
                            <p class="MsoPlainText">unfortunately - that
                              Protege 3 is sensitive to this deviation. 
                              <o:p></o:p></p>
                            <p class="MsoPlainText"><o:p> </o:p></p>
                            <p class="MsoPlainText">The reserved names
                              in question are owl:DeprecatedClass and<o:p></o:p></p>
                            <p class="MsoPlainText">owl:DeprecatedProperty. 
                              These two terms can be used in the RDF/XML<o:p></o:p></p>
                            <p class="MsoPlainText">serialization but
                              should not appear in the OWL ontology
                              itself.  These<o:p></o:p></p>
                            <p class="MsoPlainText">terms can appear in
                              the RDF/XML serialization in the following
                              two<o:p></o:p></p>
                            <p class="MsoPlainText">ways:<o:p></o:p></p>
                            <p class="MsoPlainText"><o:p> </o:p></p>
                            <p class="MsoPlainText">    *:x rdf:type
                              owl:DeprecatedClass .<o:p></o:p></p>
                            <p class="MsoPlainText">    *:x rdf:type
                              owl:DeprecatedProperty .<o:p></o:p></p>
                            <p class="MsoPlainText"><o:p> </o:p></p>
                            <p class="MsoPlainText">In the provided
                              ontlogies this usage pattern does not
                              appear.  However<o:p></o:p></p>
                            <p class="MsoPlainText">these names appear
                              in disjoint classes axioms, SubClassOf
                              axioms,<o:p></o:p></p>
                            <p class="MsoPlainText">declaration axioms,
                              SubObjectPropertyOf axioms and
                              ObjectProperty<o:p></o:p></p>
                            <p class="MsoPlainText">domain and range
                              axioms.<o:p></o:p></p>
                            <p class="MsoPlainText"><o:p> </o:p></p>
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