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[bioontology-support] [BioPortal] Feedback from Mike Hucka

Michael Hucka mhucka at caltech.edu
Thu Oct 20 21:47:25 PDT 2016


Hi,

Thanks for the fix, and for the detailed explanation.  I can confirm it works for me now.

Best regards,
MH

On Wed, 19 Oct 2016 00:39:56 +0000, Jennifer Leigh Vendetti wrote:
> Hi Mike,
> 
> The SWO ontology is now parsed and available in BioPortal.  Apologies 
> that it took a bit of time to track down the problem - I ended up 
> having to consult with one of the ontology experts on the Protege 
> team here at Stanford.  I’ve included a longer explanation of what 
> went awry below if anyone is curious.
> 
> Best,
> Jennifer
> 
> ―――――――――――――――――――――――――――――――――――――
> 
> The issue in loading this ontology boiled down to an annotation on an 
> annotation that contains a blank <rdf:Description> element.  See 
> relevant snippet beginning on line 1340 of the original ontology 
> source file:
> 
> <swo:SWO_0000144>
>   <rdf:Description/>
> </swo:SWO_0000144>
> 
> Internally, BioPortal uses the OWL API [1] to parse ontologies.  When 
> the OWL API encounters a blank element such as this, it generates an 
> ID, i.e.:
> 
> <swo:SWO_0000144>
>   <rdf:Description rdf:nodeID="_:genid28”/>
> </swo:SWO_0000144>
> 
> This doesn’t create any problems when loading the ontology into an 
> ontology editing environment like Protege [2].  However, BioPortal 
> has a second step in the loading process where we use the Raptor RDF 
> parser [3] to generate RDF triples from ontology data, that we then 
> load into the triplestore that backs the BioPortal application.  The 
> Raptor parser is unhappy with the generated ID:
> 
> rapper: Error - Illegal rdf:nodeID value '_:genid28’
> 
> … as the ‘:’ character is illegal in rdf:nodeIDs.
> 
> I modified the original source file to remove the blank 
> <rdf:Description> element, i.e. line 1340 now looks like this:
> 
> <swo:SWO_0000144></swo:SWO_0000144>
> 
> This approach preserved the annotation on an annotation (no change to 
> the meaning of the ontology), and avoids the issue with an invalid 
> node ID.  I’ve included before and after pictures from Protege below 
> to show that the annotation hierarchy is preserved properly.
> 
> [1] https://github.com/owlcs/owlapi/wiki
> [2] http://protege.stanford.edu/
> [3] http://librdf.org/raptor/rapper.html
> 
> 
> [cid:F01B6384-D652-4E2A-A87F-1B2214379DC6 at stanford.edu]
> 
> 
> [cid:F3ACC16A-0BB1-4739-8605-DA8019BCAD33 at stanford.edu]
> 
> 
> 
> 
> On Oct 10, 2016, at 11:52 AM, Michael Hucka 
> <mhucka at caltech.edu<mailto:mhucka at caltech.edu>> wrote:
> 
> Hi,
> 
> Thanks!
> 
> MH
> 
> On Mon, 10 Oct 2016 17:40:33 +0000, Jennifer Leigh Vendetti wrote:
> Hi Mike,
> 
> Thanks for reporting this and apologies for the difficulties with
> this ontology.  I’ve entered an issue in our tracker (NCBO-1825), and
> we’re looking into this now.
> 
> Kind regards,
> Jennifer
> 
> 
> On Oct 9, 2016, at 4:44 PM,
> support at bioontology.org<mailto:support at bioontology.org><mailto:support at bioontology.org> 
> wrote:
> 
> 
> Name: Mike Hucka
> 
> Email: 
> mhucka at caltech.edu<mailto:mhucka at caltech.edu><mailto:mhucka at caltech.edu>
> 
> Location: http://bioportal.bioontology.org/404?p=classes&conceptid=root
> 
> Feedback:
> 
> There is something wrong with the SWO ontology. When I visit the link
> from the page at
> 
> https://bioportal.bioontology.org/ontologies/SWO
> 
> it sends me to
> http://bioportal.bioontology.org/ontologies/SWO?p=classes&conceptid=root
> 
> which apparently does not exist.
> 
> Mike
> 
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