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

[Jennifer Leigh Vendetti]

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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