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[bioontology-support] batch endpoint

Wynne, Robert (NIH/NCI) [C] wynner at mail.nih.gov
Thu Sep 29 22:58:10 PDT 2016


Hello,

It appears the Modular_Component URI in this OWL1 file is the rdf:about of an owl:DeprecatedClass.

This is not exactly an owl:Class, and is likely the root cause of error.

You might want to specify "obsolete" instead of "class" for this particular URI.

And I don't think you're missing anything...

On first look, a json example in the documentation (http://data.bioontology.org/documentation) for owl:DeprecatedClass seems to be missing.

Although, there also does appear to be a way to recurse down a known deprecated branch (in this cased BRO:Deprecated_Resource).  See example: http://data.bioontology.org/ontologies/BRO/classes/http%3A%2F%2Fbioontology.org%2Fontologies%2FBiomedicalResourceOntology.owl%23Ontology_Development_and_Management/descendants  , but this approach may return more than what you want in a much larger ontology.

I haven't tried any of this, but if you're successful in your modified json request, would you mind attaching it as a reply for others?

Good luck!

Rob

From: Ben Leinfelder [mailto:leinfelder at nceas.ucsb.edu]
Sent: Thursday, September 29, 2016 8:04 PM
To: <support at bioontology.org> <support at bioontology.org>
Subject: [bioontology-support] batch endpoint

Hello,
I'm investigating BioPortal's "batch" endpoint - described here: http://data.bioontology.org/documentation#nav_batch - but haven't been able to retrieve results from it.

I've used your example, verbatim, to construct the json request and post it to the endpoint:
         curl -X POST -v -d @batch.json "http://data.bioontology.org/batch" -H "Authorization: apikey token=<my token>"
But get this response:
        {"errors":["Batch endpoint only support calls to owl:Class resources"],"status":422}

Am I missing something?

Thank you,
Ben Leinfelder

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