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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."

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Oct 18 18:00:07 PDT 2017


Hi Egon,


On Oct 17, 2017, at 9:48 PM, Egon Willighagen <egon.willighagen at gmail.com<mailto:egon.willighagen at gmail.com>> wrote:

On Tue, Oct 17, 2017 at 11:24 PM, Jennifer Leigh Vendetti
<vendetti at stanford.edu<mailto: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 :)


Thanks for those additional details.

I tracked down the source of the “We’re sorry but something has gone wrong…” error. The contact field on the latest submission of WIKIPATHWAYS contained an empty array. There’s a bug in the user interface that fails to display the necessary fields to fill in contact data when an empty array is encountered. A more detailed explanation is available in the issue I entered in our tracker: https://github.com/ncbo/bioportal_web_ui/issues/65. We’ll work on getting this fixed.

In the mean time - to get your latest submission up and going - I manually added contact data to the submission object, and entered the new pull URL that you listed above (http://www.w3.org/2012/pyRdfa/extract?uri=http://vocabularies.wikipathways.org/wp#). The system didn’t encounter any issues fetching or parsing the TTL file, so the ontology data is now available via the UI and the REST endpoint:

https://bioportal.bioontology.org/ontologies/WIKIPATHWAYS?p=classes
http://data.bioontology.org/ontologies/WIKIPATHWAYS/classes

One small issue is that there was some kind of error calculating/generating the diff file. I haven’t had a chance to look at that yet.

Kind regards,
Jennifer

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