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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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