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] Can't generate ChEBI mappings in my OntoPortal 3 VM

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Sep 9 14:06:36 PDT 2020


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



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20200909/c5224c64/attachment.html>


More information about the bioontology-support mailing list