<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>Yes, this is equivalent to what I suggested - see table 16.</div><a 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 This was introduced in the legacy oboInOwl mapping and has now been superseded.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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    Hi Chris,<br>
    <br>
    I defined the obsolete property or class as the subProperty or
    subClass of <a 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 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 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 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 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 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 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 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 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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              <div class="WordSection1"><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif";color:windowtext">Jie,<o:p></o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Cambria","serif";color:windowtext"><o:p> </o:p></span></p><p class="MsoNormal"><span style="font-size:11.0pt;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:11.0pt;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:11.0pt;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:11.0pt;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:11.0pt;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>
              </div>
            </blockquote>
            <br>
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    <br>
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