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[bioontology-support] problems with loading NCBITAXON ontology

Coonen Maarten (FACBURFHML) m.coonen at
Mon May 2 00:58:36 PDT 2016

Dear Jennifer,

Thank you for your quick response and efforts to reproduce my issue!
I think I was not clear regarding the virtual machine’s RAM memory. My VM-host machine is much larger;, I specifically allocated 16 GB RAM and 4 CPU-cores to the virtual guest machine running the BioPortal appliance.

Today I tried to parse the ontology manually by following these steps:

It starts with the Java call that runs multi-core for about 5 minutes, which results in a xrdf output file
(I, [2016-05-02T09:28:44.547947 #5525]  INFO -- : Output size 1470168001 in `/srv/ncbo/repository/NCBITAXON/1/owlapi.xrdf`)

Then a ruby process starts, which runs single core at 100% CPU for about 15 minutes. Then it terminates with the message “Killed” (see the lines below, which I copied from the console)

isOBO false

I, [2016-05-02T09:28:44.547947 #5525]  INFO -- : Output size 1470168001 in `/srv/ncbo/repository/NCBITAXON/1/owlapi.xrdf`

Any suggestions?
Best regards,

From: Jennifer Leigh Vendetti [mailto:vendetti at]
Sent: zaterdag 30 april 2016 02:38
To: Coonen Maarten (FACBURFHML) <m.coonen at>
Cc: support at
Subject: Re: [bioontology-support] problems with loading NCBITAXON ontology

Hello Maarten,

I looked at both of the ontologies you mention below.


Internally, BioPortal uses the OWL API [1] for parsing ontologies.  The API is written in Java.  When we launch the parsing process, we set the maximum heap size to 10.24GB (java -Xmx10240M ...).  I tried loading this ontology using the OWL API with the same heap size setting outside of BioPortal and I get an out of memory error:

java.lang.OutOfMemoryError: GC overhead limit exceeded

I tried upping the heap size to 15GB, but I still got an out of memory error.

I also tried loading the ontology in the Protege ontology editing environment [2] and I was unsuccessful there as well:

Got xpc error message: Connection interrupted
2016-04-29 17:14:31.361 java[11459:904759] Communications error: <OS_xpc_error: <error: 0x7fff78dacb90> { count = 1, contents =
"XPCErrorDescription" => <string: 0x7fff78dacf40> { length = 22, contents = "Connection interrupted" }
It seems that the OWL API is having trouble loading this ontology.  I could try posting a message on their developers list to see if they have any insight on this.


Loading this ontology worked fine for me using the default 10.24G heap space setting.  It’s less clear to me why this case is failing for you.  You mentioned that your physical host machine has 16 GB RAM.  Could you tell us how much RAM you’ve allocated to the virtual guest machine running the BioPortal appliance?



On Apr 29, 2016, at 7:22 AM, Coonen Maarten (FACBURFHML) <m.coonen at<mailto:m.coonen at>> wrote:

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

<NCBITAXON OBO parsing.log><BFO SUCCESS parsing.log><NCBITAXON OWL parsing.log>_______________________________________________
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