<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 This was introduced in the legacy oboInOwl mapping and has now been superseded.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>
<br class="Apple-interchange-newline">
<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:
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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>
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