This page describes installation and customization details to the NCBO Virtual Appliance to create an OOR instance.    (2X2W)

Download    (2X2X)

Download the OVF image for the NCBO Virtual Appliance. The URL is not public.    (2X2Y)

The current version (used in examples below) is ncbo-appliance-0.3.ova.    (2X2Z)

VM Conversion    (2X30)

The OVF image needs to be converted for the desired VM environment.    (2X31)

VMware    (2X32)

The image requires a 64-bit host with enabled support for Intel Virtualization Technology (VT).    (2XD5)

To convert the OVF image for execution under VMware:    (2X33)

  1. Download VMware OVF Tool from    (2X34)
  2. Run ovftool ncbo-appliance-0.3.ova .    (2X35)
  3. Execute the resulting ncbo-appliance-0.3/ncbo-appliance-0.3.vmx file under VMware, by double-clicking the file icon or opening it within VMware.    (2X36)
  4. Click through the initial Linux text screen setup questions.    (2X3S)

Xen    (2X37)

To convert the OVF image for execution under Xen:    (2X38)

  1. Download XenConvert from    (2X39)
  2. Run XenConvert under Windows. This requires access to a running XenServer.    (2X3A)

This hasn't yet been successfully accomplished.    (2X3B)

KVM    (34AO)

... (coming!)    (34AP)

Basic Customization: from BioPortal (ncbo-appliance) to an OOR instance    (30R7)

Banner, Logo, etc.    (2X3C)

  1. Login to the running image.    (2X3D)
  2. Edit /var/rails/BioPortal/current/config/bioportal_config.rb, changing at least    (2X3M)
  3. Replace the BioPortal logo with the OOR logo.    (2X3F)
    • public/maintenance/nav_logo.jpg (126x43) Medium logo using the color gradient    (2XCX)
    • public/maintenance/logo_background.jpg (1x43) The color gradient    (2XCY)
    • public/images/ncbo_logo_portal.gif (463x157) Large logo    (2XCZ)
    • public/images/logo.png (463x157) Large logo copy    (2XD0)
    • public/images/layout/logo_mini.png (85x20) Small logo using the color gradient    (2XD1)
    • public/images/layout/nav_logo.png (126x43) Medium logo copy    (2XD2)
  4. Replace the BioPortal IPR policy with the OOR or instance policy.    (2X3G)
    • The IPR license is at license.txt    (2XD3)
  5. "Send Feedback" form should be mailed to <support [at]>    (2YD1)
  6. Run ncborestart.    (2X3H)

Enable Google Analytics    (30RB)

Ontology Categories    (2X3P)

  1. Add OOR categories below per the instructions at    (2X3Q)
    1. You may need to download the MySQL JDBC driver and copy it to the Protege directory as driver.jar per    (317H)
    2. Use jdbc:mysql://localhost/bioportal_protege and run, e.g., ssh -L 3306:localhost:3306    (317I)
  2. Run ncborestart.    (2X3R)
  3. Verify the updated categories by opening the Browse panel and clicking the Filter by Category menu    (317J)

Support / Syndication / Social Network    (30RW)

Home Page Statistics    (32O9)

  1. Edit /srv/ncbo/rails/BioPortal/current/config/locales/en.rb to set :stats => ''.    (32OA)
  2. Manually edit :most_viewed in the same file, if desired for Most Viewed Ontologies.    (32OB)

reCaptcha    (34KM)

Other Updates    (3407)