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

Miller, Mark markampa at pennmedicine.upenn.edu
Wed Sep 9 14:14:46 PDT 2020


Thanks for the quick reply.

How much memory do you recommend for these parse jobs? I’ll be doing DrOn soon, too. How could I tell if I’m not allocating enough memory?

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!

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

Thanks,
Mark

On Sep 9, 2020, at 5:06 PM, Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:

Hello Mark,


On Sep 9, 2020, at 6:45 AM, Miller, Mark <markampa at pennmedicine.upenn.edu<mailto:markampa at pennmedicine.upenn.edu>> wrote:

Currently, one of my main uses for BioPortal/OntoPortal is retrieving all mappings between ChEBI, DrOn, and RxNorm. I prefer to do that from the VM because it’s faster and I can load new versions as soon as they become available. And it’s better citizenship, right?


Yes, thank you!



I recently upgraded to OntoPortal 3, and I can’t seem to get mappings to or from ChEBI.


I have OntoPortal version 3.0.2 installed on my laptop. I uploaded CHEBI and RXNORM, and was able to reproduce this issue.

I can retrieve mappings for individual classes, but not ontology level mappings. In other words, this call to get all mappings between RXNORM and CHEBI returns an empty set:

http://192.168.86.40:8080/mappings?ontologies=RXNORM,CHEBI

… but calls to get mappings for an individual class like “cystine” do return results:

http://192.168.86.40:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_17376/mappings



Are there caches that can be cleared besides the four on the Admin page?


No, that covers clearing of all the caches.



Is there some way to force a rebuild of the mappings? I have tried re-processing and re-annotating from the Ontology Administration page.


I had to reprocess both ontologies because initially I hadn’t allocated enough memory to the virtual machine. It doesn’t appear that reprocessing addresses this issue.

Apologies for the inconvenience, but I’ll have to continue to troubleshoot on our end to see if I can find the root cause of the issue. I’ll update you when I know something more.

Kind regards,
Jennifer




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