OntoPortal Administration Guide

Installation and maintenance documentation for OntoPortal. It focuses on system administration. This software is provided by the OntoPortal Alliance.

There are different ways to install OntoPortal.

• The recommended approach is by getting and installing the OntoPortal Virtual Appliance as provided by Stanford BMIR which keeps trace of all the uses and assigns free licenses. This Appliance is based on BioPortal codebase and packaged roughly once a year. For this, please contact Alex Skrenchuk at alex.skrenchuk@stanford.edu.

• A custom version of the OntoPortal Virtual Appliance is distributed by INRAE MISTEA which is based on AgroPortal codebase. For this, please contact Clement Jonquet at clement.jonquet@inrae.fr.

• The ontoportal_docker repository provides a containerized installation of OntoPortal intended primarily for developers and evaluation purposes, rather than production deployments. While it is actively maintained, we currently offer only limited support for this installation method.

• The ontoportal-deployment repository provides deployment resources for setting up a containerized OntoPortal instance using Docker and Kubernetes. It is designed for more robust and scalable deployments, including production environments, although it requires familiarity with container orchestration and infrastructure management.

The documentation generally holds for any version of OntoPortal Virtual Appliance which current version is Release 4.1. When something is specific for a version of the Appliance the page displays alternative pages.

This software is provided by the Stanford Center for Biomedical Informatics Research (BMIR) and the OntoPortal Alliance.

To use this software, you must have a license. Licenses are provided free to individual users for their own research, and to non-profit and educational institutions. See our licensing page for more information.

Table of contents

• General Information - General and reference information about the OntoPortal Appliance
  • Introduction - Description of the OntoPortal Virtual Appliance
  • System Requirements - Resources you need to run the Virtual Appliance
  • Licensing - How we license the Virtual Appliance
  • History - How the Appliance got to this point
• Joining OntoPortal - How to join the OntoPortal Alliance or the OntoPortal Federation
  • Joining the Alliance - First steps to set up and customize your own OntoPortal-based portal
  • Joining the Federation - How to connect your OntoPortal-based portal to the OntoPortal Federation
• Installation Steps - Key steps to install the OntoPortal Appliance
  • Getting Started - First steps toward installing the Virtual Appliance
  • Initial Installation - First steps to install your appliance
  • Initial Configuration - Configuring settings after installation
  • Advanced Configuration - Configuring more advanced settings
  • Registration Process - How to register your Appliance
  • TLS and HTTPS - Enable HTTPS and manage TLS certificates
  • Setting Up Tools - Configuring the various OntoPortal tools
  • Branding Customizations - Configuring OntoPortal for your own project
  • Troubleshooting Installations - Figuring out why your installation didn't work
  • Virtualization Environments - How to use the OVF image with your virtualization software
  • AllegroGraph Configuration - Configuring your system to run AllegroGraph
  • 4store Configuration - Configuring your system to use 4store as RDF backend
  • Virtuoso Configuration - Configuring your system to use Virtuoso as RDF backend
  • Enable Recaptcha - enable Recaptcha verification for forms in Ontoportal
• Managing Content - Working with ontologies in the OntoPortal Appliance
  • Submitting Ontologies - How to submit ontology files to your repository
  • Copying External Ontologies - How to copy ontologies from another OntoPortal-based repository to your repository
  • Submitting UMLS Content - How to submit UMLS content to your repository
  • Configuring Ontology Permissions - How to manage access to your repository's ontologies
  • Managing Ontologies - How to manage your repository's ontologies
  • Parseable Ontologies - The types of ontologies that OntoPortal can handle
  • Ontology Limitations - Kinds of ontologies that OntoPortal can't handle
  • Troubleshooting Submissions - Figuring out why your submission didn't work
• System Management - Keeping your OntoPortal Virtual Appliance running smoothly
  • Monitoring Operations - Ways to monitor the OntoPortal Appliance
  • Routine Administrative Operations - Performing routine tasks in the OntoPortal system
  • Scheduled Maintenance - OntoPortal tasks you might want to do every so often
  • Annotator Management - Operations on the solr search index
  • Search Index Management - Operations on the solr search index
  • Google Analytics Management - Setting up Google Analytics tracking for your Appliance
  • Troubleshooting Operations - Solving problems with the Appliance
  • Appliance Upgrade - Procedure for upgrading Appliance to new version
  • Appliance Upgrade v2.5 to v3.1 - Procedure for upgrading Appliance from v2.5 to v3.1
  • ncbo-cron Reference - Advanced information about ncbo-cron
  • Solr Reference - Advanced information about Solr
  • 4store Reference - Advanced information about 4store
  • SPARQL Endpoint Reference - About the OntoPortal SPARQL endpoint
  • Triple Store Rebuild Reference - Advanced information about rebuilding the triple store
• Frequently Asked Questions (FAQ) - Various common questions about the Appliance