Location: Plant, Soil and Nutrition ResearchTitle: The BioMart community portal: an innovative alternative to large, centralized data repositories Author
|Smedley, Damian - Wellcome Trust Sanger Institute|
|Haider, Syed - University Of Oxford|
|Spooner, William - Cold Spring Harbor Laboratory|
|Youens-clark, Ken - Cold Spring Harbor Laboratory|
|Kasprzyk, Arek - Translational Genomics Research Institute|
Submitted to: Nucleic Acids Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/2/2015
Publication Date: 7/1/2015
Publication URL: http://DOI: 10/1093/nar/gkv350
Citation: Smedley, D., Haider, S., Spooner, W., Ware, D., Youens-Clark, K., Kasprzyk, A. 2015. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Research. 43(W1):W589-598.
Interpretive Summary: Like a super-market, BioMart is a “Mart” that offers customized downloads of various biological datasets. The BioMart community portal is a new centralized data repository for biomedical databases that includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information, etc. The portal provides a unified interface to all available resources, which are independently administered and funded by their host scientific organizations. It averages over one million requests per day. 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, while adhering to the open source philosophy that promotes code reuse.
Technical Abstract: The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.