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[bioontology-support] MONDO ontology submission 39 empty on bioontology? (http://data.bioontology.org/ontologies/MONDO/classes)

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Jun 6 15:19:45 PDT 2019


Hi again Brian,

After some initial investigation, it’s apparent that our system is struggling to handle mondo.owl, and diagnosing / fixing the issue isn’t altogether trivial. I’ve uploaded the OBO version of MONDO (mondo.obo) until such time that we’re able to have a more in depth look at the issue. BioPortal processes mondo.obo w/out issue, so the classes are fully available from the UI and/or the REST endpoint, e.g.:

https://bioportal.bioontology.org/ontologies/MONDO?p=classes

http://data.bioontology.org/ontologies/MONDO/classes/

http://data.bioontology.org/ontologies/MONDO/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMONDO_0004992/ancestors<http://data.bioontology.org/ontologies/MONDO/classes/http://purl.obolibrary.org/obo/MONDO_0004992/ancestors>

Jennifer



On Jun 4, 2019, at 1:20 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Brian,

Thanks for reporting that. I’ve entered an issue in our tracker so that we can have a look: https://github.com/ncbo/bioportal-project/issues/125.

Apologies for the inconvenience.

Jennifer


On Jun 4, 2019, at 10:30 AM, Brian Walsh <walsbr at ohsu.edu<mailto:walsbr at ohsu.edu>> wrote:


Receiving 404 errors attempting to look up a MONDO class by id

curl http://data.bioontology.org/ontologies/MONDO/classes/MONDO:0004992/ancestors?apikey=XXXXXXXXX
{"errors":["Resource 'MONDO:0004992' not found in ontology MONDO submission 39"],"status":404}

When I examine

http://data.bioontology.org/ontologies/MONDO/classes

It looks like all pages are empty?


Thanks very much,

-Brian


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