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[bioontology-support] Submit MESH ontology into OntoPortal

John Graybeal jgraybeal at stanford.edu
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:
    http://data.bioontology.org/documentation#Mapping

We have example code for programmatically creating mappings in our GitHub sample code repository:
   https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/CreateMapping.java

John



On Jun 29, 2021, at 12:28 AM, Fajdek Bartłomiej <bartlomiej.fajdek at pw.edu.pl<mailto:bartlomiej.fajdek at pw.edu.pl>> 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 stanford.edu<mailto:jgraybeal at stanford.edu>>
Sent: Thursday, June 24, 2021 4:11 AM
To: Fajdek Bartłomiej <bartlomiej.fajdek at pw.edu.pl<mailto:bartlomiej.fajdek at pw.edu.pl>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Submit MESH ontology into OntoPortal

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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