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[bioontology-support] while trying to make an update: "We're sorry but something has gone wrong. We have been notified of this error."

Egon Willighagen egon.willighagen at gmail.com
Tue Oct 17 21:48:17 PDT 2017


On Tue, Oct 17, 2017 at 11:24 PM, Jennifer Leigh Vendetti
<vendetti at stanford.edu> wrote:
> I looked at the submission information for WIKIPATHWAYS. It’s currently
> configured to pull from this URL:
>
> http://vocabularies.wikipathways.org/wp.rdf
>
> Accessing that URL results in a 404 error. You could either specify a
> working URL, or create a new submission with a one-time file upload if you
> no longer plan to make the ontology file available at a URL.

Yes, this was exactly what I was trying to fix. We changed our set up,
now some time ago, but we had forgotten to update this part. I would
very much appreciate if you could debug it; we have a rather
non-conventional set up :)

First, while it is an OWL ontology (well, more like an thesaurus,
actually), it is stored as HTML+RDFa:
https://vocabularies.wikipathways.org/wp

So, the URL to get the ontology in another format is different:
http://www.w3.org/2012/pyRdfa/extract?uri=http://vocabularies.wikipathways.org/wp#

That returns a Turtle file, also attached. So, there are enough
aspects where I think it may go wrong :)

Looking forward to hearing your analysis,

Egon

-- 
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/u/egonwillighagen
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