BioPortal Virtual Appliance Release Notes

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This page contains software release notes for the BioPortal Virtual Appliance.

Please see the main release notes page to access release notes for the Stanford-hosted BioPortal application.

BioPortal Virtual Appliance 2.5 RC1 (2017-Aug)


  • Web UI is updated to V5.1.1 which is a major overhaul of the user interface. It has been refactored for rails 4.x support and adopted bootstrap UI framework.
  • Bundled-in UMLS Semantic Network (STY) ontology was updated to version 2016AA
  • Appliance includes scripts for facilitating minor in-place updates of the appliance components such as bioportal_web_up, ontologies_api and ncbo_cron. This is an experimental feature and not guaranteed to work for major appliance upgrades.

Please refer to the main release notes page for more detailed information on the new features and bug fixes introduced in various Bioportal components.

Known issues

  • Web UI layout is not customized for the Appliance. It contains original footer and header tool menu has a link to non-functioning resource index tool.


  • bioportal_web_ui v5.1.1
  • ontologies_api v5.4.0
  • ncbo_cron v5.4.0

Application Stack

  • CentOS 6.9
  • Apache httpd 2.2.15
  • Apache Tomcat 6
  • Solr 4.10.4
  • MySQL 5.1
  • Ruby 2.3.3
  • Passenger 5.1.6
  • Redis 3.2.9
  • Memcached 1.4.4
  • 4store v1.1.5-122-g1788d29
  • nginx 1.12.1

BioPortal Virtual Appliance 2.4 (2015-Apr)


  • Ontologies API (REST service) v4.15.3
  • Annotator
  • Recommender
  • BioPortal Web User Interface (including ontology visualization, widgets, and Annotator UI) v4.15.5
  • BioMixer

Note that release 4.15 was a silent release, implying that it contained bug fixes and other non-visible changes, and the third release number (.3, .5) indicates a patch number.

Application server stack

  • CentOS 6.6
  • Apache httpd 2.2.15
  • Apache Tomcat 6.0.24
  • Solr 4.10.4
  • MySQL 5.1.73
  • Ruby 2.1.5
  • Passenger 4.0.57
  • Redis 2.8.18
  • Memcached 1.4.4
  • 4store v1.1.5-122-g1788d29
  • nginx 1.6.3