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[bioontology-support] problems with loading NCBITAXON ontology

Coonen Maarten (FACBURFHML) m.coonen at maastrichtuniversity.nl
Fri Apr 29 07:22:05 PDT 2016


Dear Bioontology support,

I'm using the Bioportal VM Appliance and am currently running into some issues with loading a specific ontology.
I've successfully added several ontologies (EFO, OBI, NCIT etc...) using the Pull URL mechanism, but the NCBITAXON ontology keeps erroring out.

Here is what I've tried:

NCBITAXON in obo-format
Pull URL: http://www.berkeleybop.org/ontologies/ncbitaxon.obo
I can see the ruby and java processes using CPU- and RAM-resources in top immediately after submitting the ontology-information. However, after 2 hours the processes stop and the log-file indicates a time-out.
The xrdf file has not been created.
Status in Bioportal web UI: Uploaded, XRDF parse error (or something similar)

NCBITAXON in owl-format
Pull URL: http://www.berkeleybop.org/ontologies/ncbitaxon.owl
Just as with the obo-format, CPU- and RAM-resources are being used. After a few minutes an xrdf file appears in the repository directory, but then the process stops without any information.
Status in Bioportal web UI: Uploaded


The specs of the machine that runs the VM appliance:
4 cores
16 GB RAM
8.2 GB of free HDD space


I've also attached the parsing.log files for both failed NCBITAXON formats and one succesfull BFO import.


I hope you can help me to solve this issue.
Best regards,

Maarten Coonen
Data Architect
Research IT, Maastricht University Medical Center+
m.coonen at maastrichtuniversity.nl<mailto:m.coonen at maastrichtuniversity.nl>
maarten.coonen at mumc.nl<mailto:maarten.coonen at mumc.nl>
www.mumc.nl<http://www.mumc.nl/> <http://www.maastrichtuniversity.nl/>
Tel: +31 (0)43 388 4754

Peter Debyelaan 15, 6229 HX Maastricht
P.O. Box 616, 6200 MD Maastricht
The Netherlands

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