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[bioontology-support] Submit MESH ontology into OntoPortal

John Graybeal jgraybeal at
Tue Jun 29 17:08:01 PDT 2021

Bartlomiej, and copying BioPortal support for the record,

The LOOM algorithm automatically runs when ontologies are submitted, in the default configuration for OntoPortal. So you should see those mapping appear as ontologies are submitted.

You can also submit mappings via the API, just as with BioPortal:

We have example code for programmatically creating mappings in our GitHub sample code repository:


On Jun 29, 2021, at 12:28 AM, Fajdek Bartłomiej <bartlomiej.fajdek at<mailto:bartlomiej.fajdek at>> wrote:

Hello John,

I have another question about ontoportal. Is it possible to submit mappings to local ontoportal instance?
Or maybe is it possible to run algorithm LOOM or any other to create mappings between ontologies that are submitted to the system.

Best regards,
Bartłomiej Fajdek

From: John Graybeal <jgraybeal at<mailto:jgraybeal at>>
Sent: Thursday, June 24, 2021 4:11 AM
To: Fajdek Bartłomiej <bartlomiej.fajdek at<mailto:bartlomiej.fajdek at>>
Cc: support at<mailto:support at>
Subject: Re: [bioontology-support] Submit MESH ontology into OntoPortal

Hello Bartłomiej,

We have documented the ontology submission process for OntoPortal at, and in particular describes how to troubleshoot submissions. For your situation, you might want to start with the Check the 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.


On Jun 22, 2021, at 12:18 PM, Fajdek Bartłomiej <bartlomiej.fajdek at<mailto:bartlomiej.fajdek at>> 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
bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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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