Difference between revisions of "Category:NCBO Virtual Appliance"

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The NCBO Virtual Appliance image contains a pre-installed, pre-configured version of commonly-used open source NCBO software running on a Linux operating system. The image was created using VMWare and is available for download by contacting support@bioontology.org.
+
== OntoPortal Virtual Appliance version 3.0 coming soon ==
  
The following software is included on the image:
+
After briefly putting out a Release Candidate 1 for the v3.0 Virtual Appliance, we have identified a few more features that we want to complete before making the Appliance available.
* NCBO Web Services (BioPortal Core)
+
 
* BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)
+
We intend to release a Virtual Appliance 3.0 later this fall; watch this space for news.
* BioPortal Admin (a UI for administering BioPortal Ontology Services)
+
 
 +
== OntoPortal Virtual Appliance v2.5 is 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 BioPortal's v5.x software infrastructure, including the use of an RDF triplestore as the primary data storage mechanism.
 +
 
 +
== 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 v2.5:
 +
* Ontologies API (REST service)
 
* Annotator
 
* Annotator
* Resource Index
+
* 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 Resource Index.
+
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 ==
 
== Getting Started ==
* To obtain the Virtual Appliance, contact [mailto:support@bioontology.org NCBO Support] and include your BioPortal username. You can create a BioPortal account at: http://bit.ly/bioportal-account
+
=== VMWare Virtual Appliance ===
* The download is provided as a tar archive containing several files. One of these is an Open Virtualization Format (OVF) file that may need to be [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_use_the_OVF_image_with_my_virtualization_software.3F_.28VMWare.2C_VirtualBox.2C_KVM.2C_Xen.2C_etc.29 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 as this hostname as 'example'.
+
To obtain the VMWare Virtual Appliance, contact [mailto:support@bioontology.org 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 [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#How_can_I_use_the_OVF_image_with_my_virtualization_software.3F_.28VMWare.2C_VirtualBox.2C_KVM.2C_Xen.2C_etc.29 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'''
 
* '''Change default passwords'''
 
** Operating System
 
** Operating System
 
*** Username: <code>root</code>
 
*** Username: <code>root</code>
 
*** Password: password is prompted on the first boot
 
*** Password: password is prompted on the first boot
** BioPortal Admin User
+
** OntoPortal Admin User
 
*** Username: <code>admin</code>
 
*** Username: <code>admin</code>
 
*** Password: <code>changeme</code>
 
*** Password: <code>changeme</code>
* Add an ontology using the BioPortal Admin User here: http://{YourDomainName}/ontologies/new
+
 
** BioPortal Ontology Services can be configured to automatically process new ontologies every hour at 30 minutes past the hour (see [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#When_are_new_ontologies_parsed.3F documentation for enabling the scheduler]). This processing includes:
+
=== 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 [https://aws.amazon.com/marketplace/seller-profile/ref=dtl_pcp_sold_by?ie=UTF8&id=76948a46-8f8a-4a68-9a5c-3e3ff6b82d10 BioOntology AWS Market Place].  Please contact [mailto:support@bioontology.org 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 [http://www.bioontology.org/wiki/index.php/Virtual_Appliance_FAQ#When_are_new_ontologies_parsed.3F documentation for enabling the scheduler]). This processing includes:
 
*** Parsing any new, unparsed ontologies
 
*** Parsing any new, unparsed ontologies
 
*** Calculating a set of metrics for these ontologies
 
*** Calculating a set of metrics for these ontologies
 
*** Indexing these ontologies for use with search
 
*** Indexing these ontologies for use with search
* Parsing, indexing, metrics calculation, and ontology deletion can all be manually triggered or re-triggered using the BioPortal Admin user interface, which is available here: http://example:8080/bioportal_admin
+
*** Processing the ontology for use with the annotator
* REST services are available at the following locations. The URLs below are for the root of the REST service and generally will not return information. Please read the documentation for guidelines on how to interact with the services, including sample URLs:
+
* REST services are available at the following location:
** NCBO Web Services - http://example:8080/bioportal ([http://www.bioontology.org/wiki/index.php/BioPortal_REST_services documentation])
+
** http://{ip_address_of_appliance}:8080
** Annotator - http://example:8080/obs/annotator ([http://www.bioontology.org/wiki/index.php/Annotator_User_Guide documentation])
+
** http://{ip_address_of_appliance}:8080/documentation
** Resource Index - http://example:8080/resource_index ([http://www.bioontology.org/wiki/index.php/Resource_Index_REST_Web_Service_User_Guide documentation])
+
  
 
== System Requirements ==
 
== System Requirements ==
Line 38: Line 70:
  
 
* Minimum
 
* Minimum
** 1 CPU (2 GHz)
+
** 2 CPU (2 GHz)
 
** 4GB RAM
 
** 4GB RAM
** Hard disk space: 3GB
+
** Hard disk space: 20GB
  
 
* Recommended for heavier usage
 
* Recommended for heavier usage
** 2 CPU (3 GHz)
+
** 4 CPU (3 GHz)  
** 6GB RAM (When using more than 4GB RAM, you should configure Tomcat to use the additional memory)
+
** 8GB RAM (or more depending on the size/number of ontologies)
** Hard disk space: 10GB (or more depending on number/size of ontologies)
+
** Hard disk space: 20GB (or more depending on number/size of ontologies)
 
+
== Population Workflows ==
+
When storing an ontology using the BioPortal Ontology Services, some amount of processing is done automatically so that the ontologies can be visualized using the Web UI. However, the Annotator and Resource Index require separate, manual data population workflows in order to function with the provided ontologies. Details on running these populations can be found in the "Howto" sections located at the bottom of this page.
+
 
+
 
+
NOTE: Loading ontologies [1] developed using the NCI version of Protege will require an additional manual pre-processing step to remove XML tags added into the synonym and definition property values. This pre-processing step is especially important for populating the correct synonym value into the Annotator workflow. The code to pre-process ontologies developed using the NCI version of Protege is located at:
+
https://bmir-gforge.stanford.edu/gf/project/bp_helper_tools/scmsvn/?action=browse&path=%2Ftrunk%2FNCItProcessor%2F, the code can be checked out via anonymous SVN.
+
 
+
[1] The NCI Thesaurus and the NanoParticle Ontology are developed using the NCI version of Protege
+
  
 
== Image Format and Operating System Details ==
 
== Image Format and Operating System Details ==
The NCBO Appliance image was created using the [http://www.vmware.com/appliances/getting-started/learn/ovf.html Open Virtualization Format], which should allow the machine to be used in a variety of environments.
+
The OntoPortal Virtual Appliance image was created using the [http://www.vmware.com/appliances/getting-started/learn/ovf.html 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 operating system is CentOS 5.7 64-bit running Tomcat 6.0.26, Java 6, MySQL 5.1.x, PHP 5.1.6, Rails 2.3.x, and Ruby Enterprise Edition 1.8.7, and memcached.
 
  
 
The following applications use these services/runtime environments:
 
The following applications use these services/runtime environments:
* Tomcat, Java
+
* Sinatra, Ruby, 4store, redis
** BioPortal Ontology Services (BioPortal Core)
+
** Ontologies API
** BioPortal Admin (a UI for administering BioPortal Ontology Services)
+
** Annotator
** Annotator and Recommender
+
** Recommender
** Resource Index
+
* Rails, Ruby, memcached, mysql
* Rails, Ruby, memcached
+
** BioPortal Web User Interface (including ontology visualization, Flex widgets, biomixer, Annotator)
** BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)
+
* Tomcat, Solr
* PHP
+
** Search index
** Resource Index UI
+
* 4store
+
** Mappings
+
  
 
== Basic System Administration ==
 
== Basic System Administration ==
 
* Most of our administration scripts and build environment assume that you will be running as the root user.
 
* Most of our administration scripts and build environment assume that you will be running as the root user.
* Helper commands:
+
* We assume familiarity with basic CentOS Linux administration
** <code>ncbostart</code>: the required services are started on boot automatically, but if they need to be started automatically
+
* 2 text editors are originally installed: nano and vim
** <code>ncbostop</code>: manually stop services
+
* All services required for OntoPortal Stack are automatically started on boot.  For troubleshooting purposes you can manually stop/start services:
** <code>ncborestart</code>: manually start/stop services
+
** <code>bprestart</code>: manually restart services required for Ontoportal Stack. 
 +
** <code>bpstart</code>: manually start services
 +
** <code>bpstop</code>: manually stop services
 
* Start individual services:
 
* Start individual services:
 
** <code>/sbin/service httpd start</code>
 
** <code>/sbin/service httpd start</code>
Line 85: Line 119:
 
** <code>/sbin/service tomcat6 start</code>
 
** <code>/sbin/service tomcat6 start</code>
 
** <code>/sbin/service mgrep start</code>
 
** <code>/sbin/service mgrep start</code>
** <code>/sbin/service 4store start</code>
+
** <code>/sbin/service 4s-httpd-ontologies_api start</code>
 +
** <code>/sbin/service unicorn start</code>
 
* Stop individual services:
 
* Stop individual services:
 
** <code>/sbin/service httpd stop</code>
 
** <code>/sbin/service httpd stop</code>
Line 91: Line 126:
 
** <code>/sbin/service tomcat6 stop</code>
 
** <code>/sbin/service tomcat6 stop</code>
 
** <code>/sbin/service mgrep stop</code>
 
** <code>/sbin/service mgrep stop</code>
** <code>/sbin/service 4store stop</code>
+
** <code>/sbin/service 4s-httpd-ontologies_api stop</code>
 +
** <code>/sbin/service unicorn stop</code>
  
 
== License ==
 
== License ==
All NCBO software is released with the 2-clause BSD license. Source code is included on the Virtual Appliance.
+
 
 +
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 [http://www.bioontology.org/wiki/index.php?title=Category:NCBO_Virtual_Appliance&oldid=12610 archive].

Latest revision as of 09:25, 18 October 2019

Contents

[edit] OntoPortal Virtual Appliance version 3.0 coming soon

After briefly putting out a Release Candidate 1 for the v3.0 Virtual Appliance, we have identified a few more features that we want to complete before making the Appliance available.

We intend to release a Virtual Appliance 3.0 later this fall; watch this space for news.

[edit] OntoPortal Virtual Appliance v2.5 is 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 BioPortal's v5.x software infrastructure, including the use of an RDF triplestore as the primary data storage mechanism.

[edit] 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 v2.5:

  • 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).

[edit] Getting Started

[edit] 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

[edit] 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.

[edit] 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'

[edit] 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)

[edit] 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

[edit] 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

[edit] License

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

[edit] Archival

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

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