Search Mailing List Archives
[bioontology-support] [Obi-devel] [BioPortal] Ontology for Biomedical Investigations Parsing Failed
jiezheng at pcbi.upenn.edu
Tue Apr 10 16:04:49 PDT 2012
I defined the obsolete property or class as the subProperty or subClass
of "http://www.w3.org/2002/07/owl#DeprecatedProperty" or
This is how I did:
As Bioportal developers pointed out, I misused it. Should I use it as:
On 4/10/2012 6:54 PM, Chris Mungall wrote:
> oboInOwl:obsolete should be declared obsolete, I don't recommend
> reverting to this.
> 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.
> On Apr 10, 2012, at 3:27 PM, Jie Zheng wrote:
>> Hi Ray,
>> 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.
>> On 4/10/2012 4:33 PM, Ray Fergerson wrote:
>>> It took a while to track this down; the cause was quite obscure.
>>> Unfortunately the ontology has bugs in it that unfortunately neither
>>> Protégé 4 nor the OWL api catch. The errors result in incorrect
>>> query-time behavior on Protégé.
>>> The message below is from Tim Redmond (resident Protégé & OWL
>>> expert) that should explain how to fix the ontology.
>>> Message for obi folk:
>>> The provided ontologies were not in OWL 2 because of their use of
>>> reserved names. While the deviation is not serious, it turns out -
>>> unfortunately - that Protege 3 is sensitive to this deviation.
>>> The reserved names in question are owl:DeprecatedClass and
>>> owl:DeprecatedProperty. These two terms can be used in the RDF/XML
>>> serialization but should not appear in the OWL ontology itself. These
>>> terms can appear in the RDF/XML serialization in the following two
>>> *:x rdf:type owl:DeprecatedClass .
>>> *:x rdf:type owl:DeprecatedProperty .
>>> In the provided ontlogies this usage pattern does not appear. However
>>> these names appear in disjoint classes axioms, SubClassOf axioms,
>>> declaration axioms, SubObjectPropertyOf axioms and ObjectProperty
>>> domain and range axioms.
>> Better than sec? Nothing is better than sec when it comes to
>> monitoring Big Data applications. Try Boundary one-second
>> resolution app monitoring today. Free.
>> Obi-devel mailing list
>> Obi-devel at lists.sourceforge.net
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the bioontology-support