BioMart Course


BioMart Course Overview

BioMart is a generic data management system which offers a range of advanced query interfaces and administration tools. The BioMart project provides free software and data services to the international scientific community in order to foster scientific collaboration and facilitate the scientific discovery process. The project adheres to the open source philosophy that promotes collaboration and code reuse.

Using BioMart’s unique data federation technology, a Central Portal was established to provide a convenient single point of access to all of these data, which is distributed worldwide.

The system comes with built-in support for query-optimization and database federation. BioMart provides users with the ability to conduct fast, powerful queries using either web, graphical, or text based applications, or programmatically using web service or software libraries written in Perl and Java. For data providers, the system simplifies the task of integrating their own data with other datasets hosted on the network.

BioMart is a community-driven project to provide a single point of access to distributed research data. The BioMart project contributes open source software and data services to the international scientific community.

Anyone who is working on Maintenance project where the underlying ETL tool is Ab Initio. Anyone who wanted to better their ETL skill sets by learning the happening tool in the Market. Knowledge in the database and/or data warehouse.

Knowledge about different components and its purpose. Build a graph adhering the business requirement. How to blend different tools for different requirement. Complete understanding of Data Warehousing and ETL terminologies.

You will be hired as data analyst, ETL developer in the companies like Apollo, biotech labs, shantha biotech and more.

Quick start, deploy biomart webserver, configure deployment, security, external plugins, extending query handling, preconfigured portal deployment, biomart api, troubleshooting installation

BioMart Course Syllabus



  • The MartConfigurator window
  • Importing data sources
  • Adding a new URL Mart
  • Adding a new RDBMS Source
  • Adding a new Relational Mart
  • Adding a new Source Schema (“Virtual Mart
  • Manipulating a Mart using the Schema Editor
  • Materializing a Virtual Mart
  • Adding marts from Registry File
  • Creating and modifying an access point
  • Creating a report
  • Creating links between sources
  • Creating a link index
  • Changing the GUI type for a config
  • MartSearch MartAnalysis
  • MartForm
  • MartWizard
  • MartExplorer
  • User management
  • Hiding an access point




  • Secure web connections (HTTPS)
  • Authenticated remote access


  • Creating a new plugin
  • Front-end files (client side component
  • Configure
  • Using the new plugin
  • An advanced example
  • Change plugin URL
  • Modify index.jsp
  • New stylesheet
  • New JavaScript file
  • Redeploy
  • Custom Processors (server side component)


  • Introduction
  • Configuration
  • Implementing a Dino
  • Dependency Injection
  • Enrichment
  • BED format, downstream, upstream support


  • ICGC
  • Changing connection parameters
  • Quick deployment
  • Configuring site appearance
  • Configuring the location dropdown
  • Security
  • Advanced deployment


  • Query XML
  • Processors
  • Specifying Response Format
  • Status Codes
  • Resources
  • Portal
  • Marts
  • Datasets
  • Filters
  • Attributes
  • Containers
  • Linkable Datasets
  • Querying
  • Simple Example
  • Accessing SOAP API Using Java
  • Accessing SOAP API Using Python
  • Semantic Web API
  • Meta-Data Retrieval: Working with Ontologies
  • Semantic Querying: Using SPARQL
  • Java API
  • MartRegistryFactory
  • Portal
  • Root GUI Container
  • Marts
  • Datasets
  • Filters
  • Attributes
  • Containers
  • Linkables Datasets
  • Query
  • Set Processor
  • Set Limit
  • Enable Header
  • Set Client Name
  • Add Dataset
  • QueryDataset
  • Add Filter
  • Add Attribute
  • Return Query
  • Simple Example
  • Portal Access
  • Querying


  • System checks
  • *Nix/OS X users
  • Windows users
  • Testing Environment