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Submitting Ontologies

You can add an ontology using the OntoPortal Admin User at http://{ip_address_of_appliance}/ontologies/new. The ncbo_cron project is configured to automatically process any new ontologies every 5 minutes (see the documentation for enabling the scheduler).

The ontology processing includes:

  • Parsing any new, unparsed ontologies
  • Calculating a set of metrics for these ontologies
  • Indexing these ontologies for use with search
  • Processing the ontology for use with the annotator

As an OntoPortal user with the UI

A regular usar of OntoPortal can submit ontologies by going to the Browse page and clicking on the Submit Ontology button.

The first metadata form asks about characterists of the ontology. Once this form is complete, the user is prompted for information about the first submission (version) of the ontology.

Detailed information for submitting ontologies can be found online in the documentation found at your appliance at https://{my_appliance_hostname}/documentation, or in the BioPortal documentation on submissions.

As an OntoPortal user with the API

Information on submitting ontologies via the API is provided at the BioPortal API documentation on submissions, or in your own OntoPortal installation’s API documentation.

Manually reparsing (as a developer) in the scripting environment

The ncbo_ontology_process script can be used to easily submit an ontology, if the dependencies associated with deploying the system are in place.

To manually reparse an ontology, you need to ssh into the system and run ncbo_ontology_process script after switching to ontoportal user:

# from the shell:
sudo su - ontoportal
cd /srv/ontoportal/ncbo_cron
bin/ncbo_ontology_process -o ONTOLOGY_ACRONYM

How do I know if an ontology has parsed?

The OntoPortal Web UI will cache old information about ontologies for 60 seconds. After parsing is complete, just refresh the ontology summary page to see the status for the most recent submission listed under the “Submissions” table.

In addition, you can look at the REST service directly, which will always give you the most updated information. To do this, visit the following URL:

http://{your_appliance_ip_or_domain_name}:8080/ontologies/{ontology_acronym}/latest_submission?include=all

You can look for the submissionStatus attribute to get the status.

If you are looking at an ontology that should have been parsed some time ago, you can look at the Ontology Administration tab of the Administration Console page. See Troubleshooting Submissions for more information.

Is there a log file for parsing?

Parsing progress is logged in the ontology submission repository folder:

OntoPortal versions 3.0 and higher: /srv/ontoportal/data/repository/{ontology acronym}/{submission id}
Older versions: /srv/ncbo/repository/{ontology acronym}/{submission id}

You can also see the latest log from the Ontology Administration tab of the Administration Console page. See Troubleshooting Submissions for more information

For further information about ontology parsing, please see Parseable Ontologies and Troubleshooting Submissions