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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">
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<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superseded.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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http-equiv="Content-Type">
<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>
<br class="Apple-interchange-newline">
<blockquote type="cite">
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http-equiv="Content-Type">
<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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cite="mid:212e6e9c.000018f8.00000042@bmir-3880548.stanford.edu"
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<div class="WordSection1">
<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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