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[bioontology-support] Question about migrating ontologies from BioPortal to local VM

Fri Feb 7 15:02:55 PST 2020

Hi BioPortal,

This is Jahoon, a student worker from Health Data Compass.

I have installed the virtual appliance and tried to migrate ontologies from BioPortal to the VM using the Ruby script provided.
It seems like many ontologies migrated have missing classes. On the UI, they have "no submission available".

I have checked if my ontologies have fully parsed in the virtual appliance by following the instruction on your wiki:
I am currently using this URL: http://{your_appliance_ip_or_domain_name}:8080/ontologies/{ontology_acronym}/latest_submission?include=all<http://%7byour_appliance_ip_or_domain_name%7d:8080/ontologies/%7bontology_acronym%7d/latest_submission?include=all> to check parsing status.
I have migrated FB-CV ontology, and the submission status of FB-CV ontology is "Uploaded" at the REST service. However, when I click any other links, such as properties, classes, single class, etc, it has an error below.

*        errors": [
o   "Ontology FB-CV submission not found."
*        "status": 404
I have cleared the memcached-based UI cache, but it wasn't helpful.

I also have checked parsing.log file in /srv/ncbo/repository/{ontology acronym}. It says,
"Starting to process /ontologies/FB-CV/submissions/8"
"Pull location found, but no file in the upload file path"

What should I do to fix this migration issue?

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