Category:NCBO Virtual Appliance

ONTOPORTAL VIRTUAL APPLIANCE v2.5 IS NOW AVAILABLE

The OntoPortal Virtual Appliance is the (rebranded) update of the BioPortal Virtual Appliance originally developed by the National Center for Biomedical Ontologies (NCBO). Our current Virtual Appliance software is based on NCBO's v4.x software infrastructure, including the use of an RDF triplestore as the primary data storage mechanism. Please read below as much of the Appliance workflow has changed.

Virtual Appliance Basics

The OntoPortal Virtual Appliance is a copy of the BioPortal software that you can run on your own Linux system. You have to install it following the instructions below, and upload your own ontologies (and/or copies of ours, if they are public).

The OntoPortal Virtual Appliance image contains a pre-installed, pre-configured version of commonly-used open source software running on a Linux operating system.

It is available as a VMWare Virtual Appliance OVF, as well as an Amazon Web Service AMI, and can be obtained by contacting us following the instructions under Getting Started below.

The following software is included on the image as of v2.4:

• Ontologies API (REST service)
• Annotator
• Recommender
• OntoPortal Web User Interface (including UIs for ontology browse, Annotator and Recommender, ontology tree visualization, graph visualization with BioMixer, and widgets)
• API services

Please see below for how-to documentation for managing the software and running data population for Annotator and Recommender.

You may also want to visit the Virtual Appliance FAQ for additional information on the Virtual Appliance, as well as the other pages in this category (bottom of the page).

Getting Started

VMWare Virtual Appliance

To obtain the VMWare Virtual Appliance, contact OntoPortal Support to initiate your request. You'll then be asked privately for your BioPortal account username, project goals, and reason for preferring the local installation.

• If you don't have a BioPortal account, you can create one at: http://bit.ly/bioportal-account.
• If your email doesn't include your organization or other means of identifying you, we will ask for that as well.
• The overall transaction can take a few working days, depending on resource availability.

The download is provided as a zip archive containing several files. One of these is an Open Virtualization Format (OVF) file that may need to be converted to work in your virtualization environment.

• You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer to this hostname as 'example'.
• Change default passwords
  • Operating System
    • Username: root
    • Password: password is prompted on the first boot
  • OntoPortal Admin User
    • Username: admin
    • Password: changeme

Amazon AWS AMI

For users who want to run their OntoPortal instance on Amazon Web Services, an Amazon Machine Instance (AMI) is available on the BioOntology AWS Market Place. Please contact OntoPortal Support for more information.

Once the instance is running, enter the public DNS provided by Amazon into your browser to access BioPortal web interface. The default application administrator is 'admin' and the initial password is the Instance ID. You can also SSH to the machine using the username 'ec2-user' and your Amazon private key.

General Instruction

Virtual Appliance Web UI can be accessed at http://{ip_address_of_appliance}. You can get IP address of the Appliance by using the following command in the terminal 'ip addr show eth0'

• Add an ontology using the OntoPortal Admin User here: http://{ip_address_of_appliance}/ontologies/new
  • The ncbo_cron project is configured to automatically process new ontologies every 5 minutes (see documentation for enabling the scheduler). This 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
• REST services are available at the following location:
  • http://{ip_address_of_appliance}:8080
  • http://{ip_address_of_appliance}:8080/documentation

System Requirements

The following requirements are for the resources that you devote to your Appliance instance, not for the machine running your host environment. For example, if you are using a system with 4GB of RAM, then you will need to devote all of that RAM to your guest Appliance.

Note: these requirements are for basic usage. System requirements will vary greatly depending on the size of the ontologies you work with, the number of ontologies in the system, and the number of concurrent requests that the system needs to respond to. It can also vary depending on how the ontologies are used. For example, the search index can be RAM-intensive but parsing ontologies can be CPU-intensive. You will need to experiment with your Appliance resource settings to find what works for your scenario.

• Minimum
  • 2 CPU (2 GHz)
  • 4GB RAM
  • Hard disk space: 20GB

• Recommended for heavier usage
  • 4 CPU (3 GHz)
  • 8GB RAM (or more depending on the size/number of ontologies)
  • Hard disk space: 20GB (or more depending on number/size of ontologies)

Image Format and Operating System Details

The OntoPortal Virtual Appliance image was created using the Open Virtualization Format, which should allow the machine to be used in a variety of environments.

The operating system is CentOS 6.9 64-bit running:

• Tomcat 6.0.26
• Solr 6.6
• Java 8
• MySQL 5.1.x
• Rails 4.2.x
• Ruby 2.3.6
• memcached
• redis 2.3.11
• nginx 1.12.1
• 4store
• Passenger/Apache

The following applications use these services/runtime environments:

• Sinatra, Ruby, 4store, redis
  • Ontologies API
  • Annotator
  • Recommender
• Rails, Ruby, memcached, mysql
  • BioPortal Web User Interface (including ontology visualization, Flex widgets, biomixer, Annotator)
• Tomcat, Solr
  • Search index

Basic System Administration

• Most of our administration scripts and build environment assume that you will be running as the root user.
• We assume familiarity with basic CentOS Linux administration
• 2 text editors are originally installed: nano and vim
• All services required for OntoPortal Stack are automatically started on boot. For troubleshooting purposes you can manually stop/start services:
  • bprestart: manually restart services required for Ontoportal Stack.
  • bpstart: manually start services.
  • bpstop: manually stop services
• Start individual services:
  • /sbin/service httpd start
  • /sbin/service memcached start
  • /sbin/service tomcat6 start
  • /sbin/service mgrep start
  • /sbin/service 4s-httpd-ontologies_api start
  • /sbin/service unicorn start
• Stop individual services:
  • /sbin/service httpd stop
  • /sbin/service memcached stop
  • /sbin/service tomcat6 stop
  • /sbin/service mgrep stop
  • /sbin/service 4s-httpd-ontologies_api stop
  • /sbin/service unicorn stop

License

The Virtual Appliance software is released with the 2-clause BSD license. Source code is included on the Virtual Appliance.

Archival

For documentation of previous (v1.0) Virtual Appliances, please see our archive.