Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] problems with loading NCBITAXON ontology

Coonen Maarten (FACBURFHML) m.coonen at
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:
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:
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
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<mailto:m.coonen at>
maarten.coonen at<mailto:maarten.coonen at><> <>
Tel: +31 (0)43 388 4754

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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: NCBITAXON OBO parsing.log
Type: application/octet-stream
Size: 4297 bytes
Desc: NCBITAXON OBO parsing.log
URL: <>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: BFO SUCCESS parsing.log
Type: application/octet-stream
Size: 15799 bytes
Desc: BFO SUCCESS parsing.log
URL: <>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: NCBITAXON OWL parsing.log
Type: application/octet-stream
Size: 2739 bytes
Desc: NCBITAXON OWL parsing.log
URL: <>

More information about the bioontology-support mailing list