BioMart Central Portal: an open database network for the biological community

Guberman, J. M., Ai, J., Arnaiz, O., Baran, J., Blake, A., Baldock, R., Chelala, C., Croft, D., Cros, A., Cutts, R. J., Di Génova, A., Forbes, S., Fujisawa, T., Gadaleta, E., Goodstein, D. M., Gundem, G., Haggarty, B., Haider, S., Hall, M., Harris, T., Haw, R., Hu, S., Hubbard, S., Hsu, J., Iyer, V., Jones, P., Katayama, T., Kinsella, R., Kong, L., Lawson, D., Liang, Y., Lopez-Bigas, N., Luo, J., Lush, M., Mason, J., Moreews, F., Ndegwa, N., Oakley, D., Perez-Llamas, C., Primig, M., Rivkin, E., Rosanoff, S., Shepherd, R., Simon, R., Skarnes, B., Smedley, D., Sperling, L., Spooner, W., Stevenson, P., Stone, K., Teague, J., Wang, J., Whitty, B., Wong, D. T., Wong-Erasmus, M., Yao, L., Youens-Clark, K., Yung, C., Zhang, J., Kasprzyk, A. (2011) BioMart Central Portal: an open database network for the biological community. Database : the journal of biological databases and curation, 2011. ISSN 17580463 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/21930507
DOI: 10.1093/database/bar041

Abstract

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.

Item Type: Paper
Uncontrolled Keywords: animal article bacterium computer interface data base factual database fungus genome human international cooperation Internet medical research virus Animals Bacteria Biomedical Research Database Management Systems Databases, Factual Fungi Humans User-Computer Interface Viruses
Subjects: bioinformatics
bioinformatics > genomics and proteomics > databases
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > databases > databases
CSHL Authors:
Communities: CSHL labs > Ware lab
Depositing User: Matt Covey
Date: 2011
Date Deposited: 07 Feb 2013 16:04
Last Modified: 07 Feb 2013 16:04
PMCID: PMC3263598
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27129

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