BioMart is an open-source tool designed to help scientists navigate the vast and growing sea of biological research data. It provides a single point of access to distributed research information, making it easier for researchers to find, integrate, and analyze biological data. BioMart is a community-driven project that contributes both software and data services to the international scientific community, supporting global research efforts.
What is BioMart and Why Was it Created?
Biological research generates an enormous amount of data daily, ranging from genetic sequences to protein structures and disease associations. This information is often fragmented and stored in various specialized databases across different institutions and geographical regions. This dispersed nature of data creates a significant hurdle for researchers who need to combine information from multiple sources to gain a comprehensive understanding of biological processes or diseases.
Before BioMart, accessing and integrating this scattered data was a time-consuming and complex task. Researchers often needed to learn multiple query interfaces or possess advanced programming skills. The lack of a unified system meant manually collating information, which hindered efficient analysis and slowed the pace of discovery.
BioMart was created to address this problem by providing a centralized and integrated solution for biological data access. It acts as a federated database system, presenting data hosted on different servers as if it were a single, unified database. This allows researchers to access and cross-reference information from disparate sources through one user-friendly interface.
The project originated at the European Bioinformatics Institute (EBI) as a data management solution for the Human Genome Project. Since its inception, BioMart has evolved into a multi-institute collaboration spanning five continents, becoming a widely adopted system for managing various types of biological databases. It simplifies data management for providers and empowers biologists to create complex, customized datasets without extensive bioinformatics support.
The Types of Biological Data BioMart Handles
BioMart enables users to query and retrieve a wide array of biological data, making it a comprehensive resource for diverse research needs. One primary category is gene information, which includes details about gene IDs, their precise locations on chromosomes, and associated variations. Researchers can also access information about protein domains and sequences, understanding the building blocks and functions of proteins.
Beyond individual genes and proteins, BioMart handles data related to biological pathways, which illustrate how molecules interact in various cellular processes. It also provides access to disease associations, allowing scientists to link genetic or protein data to specific conditions. The system can provide information on regulatory features, which control gene activity, and homology data, showing evolutionary relationships between genes or proteins across different species.
For instance, within the Ensembl BioMart, users can access data from specific “marts” or databases like Ensembl Genes, Ensembl Variation, and Ensembl Regulation. The Ensembl Genes mart, for example, allows retrieval of gene, transcript, and protein data, along with external references and microarray information. The Ensembl Variation mart provides germline and somatic variants, including structural variations, phenotypes, and citations.
BioMart also integrates data from external projects like PRIDE (proteomics data) and Reactome (pathways data). This means researchers can explore diverse biological information, such as human somatic mutation data from COSMIC or Genome-Wide Association Studies (GWAS) data, all from a single platform.
How BioMart Simplifies Data Access for Researchers
BioMart simplifies data access by offering user-friendly interfaces that empower researchers to construct complex data queries without requiring advanced programming skills. The system provides graphical user interfaces and application programming interfaces (APIs), allowing queries to be performed conveniently. This ease of use removes technical barriers that often prevent biologists from directly interacting with large datasets.
Researchers can navigate through the BioMart web interface, selecting desired databases and datasets, such as “Ensembl Genes” and a specific species like “Human genes.” They can then apply filters to narrow down their search, for example, by inputting a list of known gene IDs or restricting the query to a specific chromosomal region. This intuitive filtering process allows for highly specific data extraction.
The system’s ability to link data across different biological domains is a powerful feature, streamlining complex research tasks. For instance, a researcher can easily find genes associated with a particular disease and then retrieve the specific proteins these genes produce. This cross-referencing capability enables scientists to integrate information that might otherwise be siloed in separate databases.
BioMart also supports the automation of queries, offering “scripting at the click of a button” functionality once a query has been defined. This automation is particularly useful for batch retrieval of data, where the same query needs to be run for multiple biological entities. The efficiency of BioMart allows scientists to focus more on analysis and less on data retrieval.
BioMart’s Role in Advancing Scientific Discovery
BioMart plays a substantial role in accelerating scientific discovery by making vast biological datasets more accessible and interconnected. By facilitating the integration of diverse information, it empowers researchers to uncover previously hidden relationships and patterns within complex biological systems. This unified access to data can lead to breakthroughs in understanding disease mechanisms and identifying potential targets for new therapies.
For example, researchers can use BioMart to identify specific genes or proteins that are overexpressed in cancer cells, which could then be investigated as potential drug targets. The ability to cross-reference gene expression data with disease annotations and protein functions allows for a more comprehensive approach to drug discovery. This streamlined access to integrated data supports the development of personalized medicine, tailoring treatments based on an individual’s unique genetic profile.
BioMart also fosters collaboration among scientists worldwide by providing a common platform for data sharing and analysis. Its open-source nature and federated model allow different research groups to contribute and access data independently while still benefiting from a unified interface. This collaborative environment enables researchers to build upon each other’s work more effectively, accelerating the pace of scientific progress on a global scale.
The continuous expansion of the BioMart community, with over 800 different biological datasets from 30 scientific organizations, demonstrates its growing impact. This extensive network of interconnected data sources supports a wide range of analyses, from annotating microarray results to selecting single nucleotide polymorphisms (SNPs) for candidate gene screening. BioMart’s role in democratizing access to complex biological information is paving the way for a deeper understanding of life and advancements in human health.