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[bioontology-support] Submit MESH ontology into OntoPortal

Jennifer Leigh Vendetti vendetti at stanford.edu
Wed Jun 23 19:56:03 PDT 2021


Hello Bartłomiej,

I tested loading MESH into OntoPortal, version 3.0.2 (running from VMWare Fusion, version 11.5.6). I’m not sure what the exact steps are that you’re using, but I did the following:

* Downloaded MESH.ttl from BioPortal (https://bioportal.bioontology.org/ontologies/MESH)
* Created a new ontology entry in the www interface - please note that you need to choose “UMLS” as the “Format" for these TTL files from BioPortal.
* Verified that the success page was displayed after filling in the www interface forms for new ontology submission.

Do you have administrative access for your OntoPortal installation? If so, there are some pointers I could give in terms of where to locate the parsing log file for the ontology submission you created.

MESH is a large ontology and takes some time to process - for me it was about 1.5 hours. It’s also memory intensive - if the appliance ran out of memory, you may need to increase the memory for your virtual appliance, e.g., in VMWare Fusion you would right-click on the VM -> Settings… -> Processors & Memory.

Kind regards,
Jennifer


[cid:7F47A612-D69D-464B-9A49-D88C4F3C0950 at lan]


On Jun 23, 2021, at 7:11 PM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Hello Bartłomiej,

We have documented the ontology submission process for OntoPortal at https://ontoportal.github.io/administration/ontologies/, and in particular https://ontoportal.github.io/administration/ontologies/troubleshooting_submissions/ describes how to troubleshoot submissions. For your situation, you might want to start with the Check the ontology<https://ontoportal.github.io/administration/ontologies/troubleshooting_submissions/#check-the-ontology-other-ways-to-validate-an-ontology> section, to see ways to validate your ontology without even using OntoPortal.

The fact that Robot can convert the file to OWL suggests the file itself is valid. In this case I would check the logs to see if they have reported a specific problem, and read the section on parsing large ontologies, since MESH is a fairly large ontology. In some cases we have found compressing the ontology into a .zip file enables it to get past a critical ingestion bottleneck. (OntoPortal will automatically decompress any .zip files it receives.)

If none of these ideas help, please tell us what error you received during submission, as well as the logs from the parsing process (per the information in the troubleshooting document). Send this information to this support list, and we'll see what we can figure out.

John



On Jun 22, 2021, at 12:18 PM, Fajdek Bartłomiej <bartlomiej.fajdek at pw.edu.pl<mailto:bartlomiej.fajdek at pw.edu.pl>> wrote:

Dear Sir or Madame,

I have virtual machine with OntoPortal installed. Using www interface I am trying to submit MESH ontology without success.
I was trying to convert ttl file to owl using Robot but I received error during submision  to OntoPortal. I was also trying to submit ttl file. Could you please give me some advice how to submit MESH ontology to OntoPortal?

Yours sincerely,
Bartłomiej Fajdek, PhD

Warsaw University od Technology
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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360



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