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 Genova, 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.; Wang, J.; Whitty, B.; Wong, D. T.; Wong-Erasmus, M.; Yao, L.; Youens-Clark, K.; Yung, C.; Zhang, J.; Kasprzyk, A.

doi:10.1093/database/bar041

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

Journal Article · Fri Sep 16 00:00:00 EDT 2011 · Database

DOI:https://doi.org/10.1093/database/bar041· OSTI ID:1625302

Guberman, J. M. ^[1]; Ai, J. ^[2]; Arnaiz, O. ^[3]; Baran, J. ^[4]; Blake, A. ^[5]; Baldock, R. ^[6]; Chelala, C. ^[7]; Croft, D. ^[8]; Cros, A. ^[4]; Cutts, R. J. ^[7]; Di Genova, A. ^[9]; Forbes, S. ^[10]; Fujisawa, T. ^[11]; Gadaleta, E. ^[7]; Goodstein, D. M. ^[12]; Gundem, G. ^[13]; Haggarty, B. ^[6]; Haider, S. ^[14]; Hall, M. ^[15]; Harris, T. ^[16] more »

Ontario Inst.e for Cancer Research, Toronto, ON (Canada); DOE/OSTI
Univ. of California, Los Angeles, CA (United States). School of Dentistry. Dental Research Inst.
Centre National de la Recherche Scientifique (CNRS), Paris (France). Centre de Genetique Moleculaire
Ontario Inst.e for Cancer Research, Toronto, ON (Canada)
Medical Rresearch Council (MRC) Harwell, Oxfordshire (United Kingdom)
Western General Hospital, Edinburgh, Scotland (United Kingdom). Inst. of Genetics and Molecular Medicine. Medical Research Council (MRC). Human Genetics Unit
Queen Mary Univ. of London (United Kingdom). Barts Cancer Inst. Centre for Molecular Oncology and Imaging
Wellcome Trust Genome Campus, Cambridge (United Kingdom). EMBL-European Bioinformatics Inst.
Univ. of Chile, Blanco Enclada (Chile). Center for Genome Regulation. Center for Mathematical Modeling
WEllcome Trust Sanger Inst., Cambridge (United Kingdom). Cancer Genome Project
Kasuza DNA Research Inst., Chiba (Japan)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Genomics Division
Universitat Pompeu Fabra, Barcelona (Spain). Dept. of Experimental and Health Sciences. Research Unit on Biomedical Informatics
Univ. of Cambridge (United Kingdom). Computer Lab.
The Jackson Lab., Bar Harbor, ME (United States). Mouse Genomic Informatics Group
Cold Spring Harbor Laboratory Cold Spring Harbor, NY (United States)
Univ. of Manchester (United Kingdom). Faculty of Life Sciences
Wellcome Trust Sanger Inst., Hinxton (United Kingdom)
Univ. of Tokyo (Japan)
Peking Univ., Beijing (China). College of Life Sciences. State Key Lab. of protein and Plant Gene Research. Center for Bioinformatics
Wellcome Trust Genome Campus, Cambridge (United Kingdom). EMBL-European Bioinformatics Inst. VectorBase
Wellcome Trust Genome Campus, Cambridge (United Kingdom). EMBL-European Bioinformatics Inst. HUGO Gene Nomenclature Committee (HGNC)
Institute National de la Recherche Agronomique (INRA), St-Gilles (France). Sigenae
Wellcome Trust Sanger Inst., Cambridge (United Kingdom). Wellcome Trust Genome Campus
Univ. of Rennes (France). Inserm U625
Wellcome Trust Sanger Inst., Cambridge (United Kingdom).Wellcome Trust Genome Campus. Cancer Genome Project
International Potato Center (CIP), Lima (Peru)
Wellcome Trust Sanger Inst., Hinxton (United Kingdom).Wellcome Trust Genome Campus.
Cold Spring Harbor Laboratory Cold Spring Harbor, NY (United States); Eagle Genomics Ltd., Cambridge (United Kingdom). Babraham Research Campus

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. Database URL: http://central.biomart.org.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1625302

Journal Information:: Database, Journal Name: Database Vol. 2011; ISSN 1758-0463

Publisher:: Oxford University Press - International Society for BiocurationCopyright Statement

Country of Publication:: United States

Language:: English

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