transmart-metacore-plugin is a grails plugin to enable MetaCore capabilities within TranSMART. In current release (v16.2), user can do MetaCore enrichment analysis using this plugin after biomarker discover analysis.
The plugin must be enabled in transmart configuration file ("Config.groovy"). User needs restart the tomcat server after modify the configuration. Depends on the MetaCore credential users have, there are three types of configuration.
//For a demo without MetaCore credential:
com.thomsonreuters.transmart.metacoreSettingsMode = 'demo'
com.thomsonreuters.transmart.demoEnrichmentURL = 'http://pathwaymaps.com'
//For a user with their individual credential:
com.thomsonreuters.transmart.metacoreAnalyticsEnable = true
com.thomsonreuters.transmart.metacoreSettingsMode = ‘user'
// For a system-wide credential for MetaCore:
com.thomsonreuters.transmart.metacoreSettingsMode = 'system'
com.thomsonreuters.transmart.metacoreURL = 'https://portal.genego.com'
com.thomsonreuters.transmart.metacoreDefaultLogin = '***'
com.thomsonreuters.transmart.metacoreDefaultPassword = '***'
Here is a simple use case using the "demo" configuration*. This use case is just to demonstrate the procedure of this plugin. It is not to validate any scientific questions.
This use case uses GSE20141 dataset provided by tranSMART community. User can download it from tranSMART Curated Data Repository.
1. Generate two dataset using GSE20141, one is for Parkinson Disease Group and another one is for normal group.
2. Go to "Advanced Workflow" → "Marker Selection", then select the expression data from GSE20141
3. Keep the default setting for this demo, click the "Run" button. Once the analysis is complete successfully, user should see a "Run MetaCore Enrichment Analysis" button on top the Table of Top Markers. Click on this button to run the MetaCore enrichment analysis.
4. Once the enrichment analysis is complete, the top enrichment pathways should be list on top the table. Each pathway is linked to its description.
*This use case was based on a conference call with Clarivate/MetaCore team for tranSMART integration. Thanks for the help from Sirimon O’Charoen and Taylor Horsfield at Clarivate/MetaCore.