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What is NeuroCommons Project?

As articulated in the Science Commons mission statement video, NeuroCommons project within Science Commons aimed at creating openly accessible neuroscience and computational biology knowledgebases on the Web.

NeuroCommons Installation on Virtuoso EC2 AMI instance

OpenLink Software provides a backup up of the current NeuroCommons Database as hosted on the live service at http://sparql.neurocommons.org/, that users can restore into a Virtuoso EC2 AMI instance in the cloud, providing them with an instance of NeuroCommons for their own use.

Installation

  1. Start a Virtuoso EC2 AMI instance. Note a Virtuoso Release 5 AMI instance ( ami-ids ami-59628630 or ami-c46084ad ) must be used with this backup. We recommended a 64-bit large image AMI instance with 8GB of memory be used, which is a m1.large EC2 instance type.



  2. Note for best performance particularly under extensive usage it is recommended the 16GB m1.xlarge EC2 instance type be used.
  3. Load the Virtuoso Conductor Administration interface of the running EC2 AMI instance with a URL of the form http://your-ec2-instance-cname/conductor.



  4. From the Virtuoso Conductor, navigate to the "System Admin" -> "Packages" tab to obtain a list of available Virtuoso packages (VADs) to install.



  5. Click the "Install" button to initiate installation of the "EC2 Extensions" VAD package for use in performing backup and restore tasks.



  6. Click the "Proceed" button to install the "EC2 Extensions" VAD package.
  7. Go to the URL http://your-ec2-instance-cname/ec2exts to load the Virtuoso Extensions for Amazon EC2 Images login page and log in as the "dba" user.



  8. From the Virtuoso Extensions for Amazon EC2 Images main page, click the "Restore a Remote Backup" link.



  9. On the "Restore a Remote Backup" page, set the follow options. 

    Protocol: WebDAV/HTTP
Host: s3.amazonaws.com
Path or Bucket: neurocommons-virtuoso-bundle
Backup File Prefix: neurocommons-bundle



  10. Click the "Restore" button to begin the restoration of the NeuroCommons database from backup.


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  11. Click on the "Continue" button to begin the re-assembly of the database from the restored backup files. Output similar to the following will be displayed when the re-assembly of the database is complete.

Once complete the server will have been restarted automatically with the restored NeuroCommons database ready for use.

Usage Examples

You can then access pages such as these on your NeuroCommons server:
  • NeuroCommons SPARQL endpoint — http://your-ec2-instance-cname/nsparql.html



  • NeuroCommons XHTML Description page — http://your-ec2-instance-cname/commons/record/pmid/12477932



Safeguarding Your SPARQL End-point

Important — The following section should be added to the Virtuoso configuration file (/opt/virtuoso/database/virtuoso.ini) to control and safeguard your SPARQL end-point against overzealous usage: 

[SPARQL]
MaxCacheExpiration         = 1    ; Cache Expiration time in seconds that overrides Sponger's default cache invalidation scheme
ExternalQuerySource        = 1
ExternalXsltSource         = 1
ResultSetMaxRows           = 100000
;DefaultGraph               = http://demo.openlinksw.com/dataspace/person/demo
MaxQueryCostEstimationTime = 10000    ; in seconds
MaxQueryExecutionTime      = 30    ; in seconds
;ImmutableGraphs            = http://unknown:8890/dataspace
;PingService                = http://rpc.pingthesemanticweb.com/
DefaultQuery               = select distinct ?URI ?ObjectType where {?URI a ?ObjectType} limit 50
DeferInferenceRulesInit    = 0  ;  Defer Loading of inference rules at start up

Details about these settings can be found in the Virtuoso Online Documentation in the SPARQL Configuration File section. The "DeferInferenceRulesInit = 1" setting is important when hosting large RDF data sets like NeuroCommons, as it defers the load of the inference rules which can take quite some time (up to an hour) during server startup.

OAuth support can be used to secure the SPARQL endpoint by installing the oauth_dav.vad VAD package. This allows the /sparql endpoint to be disabled or mapped to the Virtuoso OAuth SPARQL service thereby requiring an API key to use the endpoint as detailed in the Virtuoso OAuth documentation.

Virtuoso Web Services ACLs can be used to control (limit) access to the SPARQL endpoint as detailed in the documentation link.

NeuroCommons VAD Application Package

For those running a NeuroCommons Virtuoso EC2 AMI instance created before December 8, 2008, you will need to update your NeuroCommons VAD Application package to obtain the latest enhancements, by taking the following steps

  1. Download the NeuroCommons VAD Application (neurocommons_dav.vad) package.
  2. Navigate to the "System Admin" -> "Packages" tab of the Virtuoso Conductor.



  3. Scroll down to the "Install Package" section of the tab, use the "Upload Package" option "browse" button.



  4. Navigate to the location of the downloaded neurocommons_dav.vad file and click the "open" button to select it.



  5. Click the "Proceed" button to begin the installation process.



Related

  • The NeuroCommons SPARQL endpoint can be accessed on http://your-ec2-instance-cname/sparql
  • The OpenLink Interactive SPARQL Query Builder can be accessed on http://your-ec2-instance-cname/isparql, enabling the visual construction of queries (Graph Patterns).
  • OAuth support can be used to secure the SPARQL endpoint by installing the policy manager_dav.vad VAD package. This allows the /sparql endpoint to be disabled or mapped to the Virtuoso OAuth SPARQL service thereby requiring an API key to use the endpoint as detailed in the Virtuoso OAuth documentation.
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