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[bioontology-support] problems with loading NCBITAXON ontology

Jennifer Leigh Vendetti vendetti at stanford.edu
Fri Apr 29 17:37:32 PDT 2016


Hello Maarten,

I looked at both of the ontologies you mention below.


NCBITAXON in OBO format

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.


NCBITAXON in OWL format

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?

Jennifer


[1] http://owlapi.sourceforge.net/
[2] http://protege.stanford.edu/products.php



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

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