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[bioontology-support] [External] Can't generate ChEBI mappings in my OntoPortal 3 VM

Miller, Mark markampa at pennmedicine.upenn.edu
Tue Sep 15 12:07:51 PDT 2020


The mappings in my OntoPortal VM have indeed resolved themselves.  Thanks.

-Mark


On Sep 9, 2020, at 7:44 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hi Mark,


On Sep 9, 2020, at 2:14 PM, Miller, Mark <markampa at pennmedicine.upenn.edu<mailto:markampa at pennmedicine.upenn.edu>> wrote:

How much memory do you recommend for these parse jobs?


There are some general system requirements documented here:

https://ontoportal.github.io/administration/general/system_requirements/

However, it depends on the size of the ontology. We recently corresponded with someone that uploaded SNOMED CT (roughly 1.47 GB ontology source file), and they needed to allocate 32 GB to the appliance. Anything less resulted in out of memory errors.

For my installation, I have 28 GB allocated, which is the maximum my development laptop can handle without keeling over. For smaller ontologies, you wouldn’t need as much.


I’ll be doing DrOn soon, too. How could I tell if I’m not allocating enough memory?


If processing fails due to an out of memory error, there could be a message to that effect in the parsing log file for the ontology. The Admin -> Ontology Administration page has a URL column with “Log” links that allow you to view the parsing log file. Just make sure to look at the timestamps for the processing, as multiple runs of processing the same ontology will output log data into that same file.

Alternatively, if you have access to the administration console for the appliance, you can navigate to the submission directory on the command line and view the parsing log in a text editor:

https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#is-there-a-log-file-for-parsing



Can you point me towards documentation about triggering reprocessing? I think I saw it before, but now that the documentation is so much more comprehensive, it can be hard to find things!


Sure, no problem.

From the OntoPortal application, you can kick off a reprocessing of an ontology using the Admin -> Ontology Administration page. You would select the row for the desired ontology, choose “Process" from the “Apply to Selected Rows” dropdown box, then click the Go button.

Alternatively, you can use these instructions to reprocess the ontology from the command line:

https://ontoportal.github.io/administration/ontologies/submitting_ontologies/#manually-reparsing-as-a-developer-in-the-scripting-environment

I use this approach because I can watch the log output and see immediately if errors are written out.


I have loaded the Consumer Health Vocabulary Ontology (OCHV) since I sent the first message and am characterizing the mapping success now.

It’s not apparent to me that this problem is specific to any one ontology. I’ve uploaded five separate ontologies, and there are no ontology-level mappings for any of them.

Kind regards,
Jennifer


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