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<font face="Calibri" size="3">> The OWL 2 spec makes a distinction between datatype and class:<br>
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Yes. And that's also partly why owl:Class != rdfs:Class.<br>
But I don't think that's the issue here.<br>
It's about how a datatype is formally defined.<br>
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RDFS says that all datatypes are subclasses of rdfs:Literal which makes complete sense.<br>
I think there may be a question whether that should be captured using the rdfs:subClassOf axiom.
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Else this is where Bioportal might be too fierce. <br>
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Anyway, the inclusion of a definition of xsd:dateTimeStamp in this ontology is not necessary since it is defined elsewhere (in the xsd spec) so I will see if we can get it removed from the RDF sources.<br>
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Simon<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Samson Tu <swt@stanford.edu><br>
<b>Sent:</b> Sunday, 11 February 2018 4:43:18 PM<br>
<b>To:</b> Cox, Simon (L&W, Clayton)<br>
<b>Cc:</b> Samson Tu; John Graybeal; bioontology-support@lists.stanford.edu<br>
<b>Subject:</b> Re: [bioontology-support] labels for Time ontology</font>
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<div>The OWL 2 spec makes a distinction between datatype and class:
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<div class="">"<i class="" style="font-family:sans-serif">Datatypes</i><span class="" style="font-family:sans-serif; font-size:medium; background-color:rgb(255,255,255)"> are entities that refer to sets of data values. </span>Thus, datatypes are analogous to
 classes, the main difference being that the former contain data values such as strings and numbers, rather than individuals.Ē [1]</div>
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<div class="">Maybe the issue is whether the Time ontology is meant to be an RDF schema or an OWL ontology. These are two different specifications.</div>
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<div class="">The OWL API loads the ontology didnít throw an error. Itís the Bioportal hierarchy display code that had problem. I agree that the Bioportal hierarchy display code should be more forgiving. Maybe that should be an issue  tracker item.</div>
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<div class="" style="margin:0px; line-height:normal"><i class="">With best regards,</i></div>
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<div class="" style="margin:0px; line-height:normal"><span class="" style="font-size:12px">[1] <a href="https://www.w3.org/TR/owl2-syntax/#Datatypes" class="">https://www.w3.org/TR/owl2-syntax/#Datatypes</a></span></div>
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<div class="">On Feb 10, 2018, at 10:10 PM, <a href="mailto:simon.cox@csiro.au" class="">
simon.cox@csiro.au</a> wrote:</div>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">I donít think you are correct.</span></div>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">The RDFS Spec is quite explicit on this [1]: ďEach instance of rdfs:Datatype is a subclass of rdfs:Literal.Ē</span></div>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">                                                                                                                                                                                                         </span></div>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">The offending lines in the OWL-Time rdf are</span></div>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">xsd:dateTimeStamp</span></div>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">  rdf:type rdfs:Datatype ;              #i.e xsd:dateTimeStamp is an instance of rdfs:Datatype</span></div>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">  rdfs:label "dateTimeStamp" ;</span></div>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">  rdfs:subClassOf rdfs:Literal ;     #... and is a subclass of rdfs:Literal</span></div>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">I guess the explanation in the RDFS spec means that the sub-class axiom is strictly not needed, since it is an entailment of typing axiom anyway, but it should not cause
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">[1]<span class="Apple-converted-space"> </span><a href="https://www.w3.org/TR/rdf-schema/#ch_datatype" class="" style="color:purple; text-decoration:underline">https://www.w3.org/TR/rdf-schema/#ch_datatype</a></span></div>
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<b class=""><span lang="EN-US" class="" style="font-size:11pt; font-family:Calibri,sans-serif">From:</span></b><span lang="EN-US" class="" style="font-size:11pt; font-family:Calibri,sans-serif"><span class="Apple-converted-space"> </span>Samson Tu [<a href="mailto:swt@stanford.edu" class="" style="color:purple; text-decoration:underline">mailto:swt@stanford.edu</a>]<span class="Apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Saturday, 10 February, 2018 05:59<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Cox, Simon (L&W, Clayton) <<a href="mailto:Simon.Cox@csiro.au" class="" style="color:purple; text-decoration:underline">Simon.Cox@csiro.au</a>><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span>Samson Tu <<a href="mailto:swt@stanford.edu" class="" style="color:purple; text-decoration:underline">swt@stanford.edu</a>>; John Graybeal <<a href="mailto:jgraybeal@stanford.edu" class="" style="color:purple; text-decoration:underline">jgraybeal@stanford.edu</a>>;<span class="Apple-converted-space"> </span><a href="mailto:bioontology-support@lists.stanford.edu" class="" style="color:purple; text-decoration:underline">bioontology-support@lists.stanford.edu</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [bioontology-support] labels for Time ontology</span></div>
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Hi,<span class="Apple-converted-space"> </span></div>
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I am not sure this is the reason for the failure to render the Time class hierarchy in Bioportal. The ontology includes a (xsd:dateTimeStamp rdfs:subClassOf rdfs:Literal) axiom. This mixing of datatype and class is not right.  </div>
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<i class="">With best regards,</i></div>
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<i class="">Samson</i></div>
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On Feb 8, 2018, at 9:49 PM,<span class="Apple-converted-space"> </span><a href="mailto:simon.cox@csiro.au" class="" style="color:purple; text-decoration:underline">simon.cox@csiro.au</a><span class="Apple-converted-space"> </span>wrote:</div>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">John Ė there are rdfs:label annotations on every class and property Ö<span class="apple-converted-space"> </span><a href="https://www.w3.org/2006/time" class="" style="color:purple; text-decoration:underline"><span class="" style="color:purple">https://www.w3.org/2006/time</span></a><span class="apple-converted-space"> </span>...
 So Iím not sure what the issue is? Ė Simon</span></div>
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<b class=""><span lang="EN-US" class="" style="font-size:11pt; font-family:Calibri,sans-serif">From:</span></b><span class="apple-converted-space"><span lang="EN-US" class="" style="font-size:11pt; font-family:Calibri,sans-serif"> </span></span><span lang="EN-US" class="" style="font-size:11pt; font-family:Calibri,sans-serif">John
 Graybeal [<a href="mailto:jgraybeal@stanford.edu" class="" style="color:purple; text-decoration:underline"><span class="" style="color:purple">mailto:jgraybeal@stanford.edu</span></a>]<span class="apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="apple-converted-space"> </span>Friday, 9 February, 2018 16:35<br class="">
<b class="">To:</b><span class="apple-converted-space"> </span><a href="mailto:bioontology-support@lists.stanford.edu" class="" style="color:purple; text-decoration:underline"><span class="" style="color:purple">bioontology-support@lists.stanford.edu</span></a><br class="">
<b class="">Cc:</b><span class="apple-converted-space"> </span>Cox, Simon (L&W, Clayton) <<a href="mailto:Simon.Cox@csiro.au" class="" style="color:purple; text-decoration:underline"><span class="" style="color:purple">Simon.Cox@csiro.au</span></a>><br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>labels for Time ontology</span></div>
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Simon,<span class="apple-converted-space"> </span></div>
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(not sure if you got copied on that first response, which is below)</div>
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Is it reasonable to think the Time ontology might get labels any time soon, which would save us from having to troubleshoot this?  (Just a shot in the dark, in case there are plans.)</div>
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John</div>
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On Feb 8, 2018, at 5:54 PM, Jennifer Leigh Vendetti <<a href="mailto:vendetti@stanford.edu" class="" style="color:purple; text-decoration:underline"><span class="" style="color:purple">vendetti@stanford.edu</span></a>> wrote:</div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">Hello Simon,</span></div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">On Feb 8, 2018, at 4:18 PM,<span class="apple-converted-space"> </span><a href="mailto:support@bioontology.org" class="" style="color:purple; text-decoration:underline"><span class="" style="color:purple">support@bioontology.org</span></a><span class="apple-converted-space"> </span>wrote:</span></div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">Name: Simon Cox</span></div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif"><a href="mailto:simon.cox@csiro.au" class="" style="color:purple; text-decoration:underline"><span class="" style="color:purple">Email: simon.cox@csiro.au</span></a></span></div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">Location: http%3A%2F%<a href="http://2fbioportal.bioontology.org/" class="" style="color:purple; text-decoration:underline"><span class="" style="color:purple">2Fbioportal.bioontology.org</span></a>%2Fontologies%2FTIME</span></div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">I tried to register the W3C OWL-Time ontology last year.<span class="apple-converted-space"> </span><br class="">
Its listed here<span class="apple-converted-space"> </span><a href="http://bioportal.bioontology.org/ontologies/TIME" class="" style="color:purple; text-decoration:underline"><span class="" style="color:purple">http://bioportal.bioontology.org/ontologies/TIME</span></a><span class="apple-converted-space"> </span><br class="">
Something went wrong, but I do not understand the error message.<span class="apple-converted-space"> </span><br class="">
In particular the class tree does not render properly.<span class="apple-converted-space"> </span><br class="">
This is now a W3C 'Recommendation' so I think merits listing in BioPortal.<span class="apple-converted-space"> </span><br class="">
Any comments?<span class="apple-converted-space"> </span></span></div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">I looked at the latest submission for the TIME ontology. During the parsing process in BioPortal, we have some code that generates labels for any classes donít have labels declared. After
 generating that data, an error occurs when the system attempts to load it into the triplestore. The error is rather deep in the stack, and it wasnít immediately obvious to me what the problem is. Iíve entered an issue in our tracker:</span></div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif"><a href="https://github.com/ncbo/bioportal-project/issues/66" class="" style="color:purple; text-decoration:underline"><span class="" style="color:purple">https://github.com/ncbo/bioportal-project/issues/66</span></a></span></div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">Ö so that we can spend some time debugging.</span></div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">Kind regards,</span></div>
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<span class="" style="font-size:9pt; font-family:Helvetica,sans-serif">Jennifer</span></div>
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bioontology-support mailing list<br class="">
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</span><a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support" class="" style="color:purple; text-decoration:underline"><span class="" style="font-size:9pt; font-family:Helvetica,sans-serif; color:purple">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</span></a></div>
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Stanford Center for Biomedical Informatics Research<br class="">
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</span><a href="https://mailman.stanford.edu/mailman/listinfo/bioontology-support" class="" style="color:purple; text-decoration:underline"><span class="" style="font-size:10.5pt; font-family:Helvetica,sans-serif; color:purple">https://mailman.stanford.edu/mailman/listinfo/bioontology-support</span></a></div>
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