GeneDB-an annotation database for pathogens

Flora J. Logan-Klumpler; Nishadi De Silva; Ulrike Boehme; Matthew B. Rogers; Giles Velarde; Jacqueline A. McQuillan; Tim Carver; Martin Aslett; Christian Olsen; Sandhya Subramanian; Isabelle Phan; Carol Farris; Siddhartha Mitra; Gowthaman Ramasamy; Haiming Wang; Adrian Tivey; Andrew Jackson; Robin Houston; Julian Parkhill; Matthew Holden; Omar S. Harb; Brian P. Brunk; Peter J. Myler; David Roos; Mark Carrington; Deborah F. Smith; Christiane Hertz-Fowler; Matthew Berriman

doi:10.1093/nar/gkr1032

GeneDB-an annotation database for pathogens

Flora J. Logan-Klumpler, Nishadi De Silva, Ulrike Boehme, Matthew B. Rogers, Giles Velarde, Jacqueline A. McQuillan, Tim Carver, Martin Aslett, Christian Olsen, Sandhya Subramanian, Isabelle Phan, Carol Farris, Siddhartha Mitra, Gowthaman Ramasamy, Haiming Wang, Adrian Tivey, Andrew Jackson, Robin Houston, Julian Parkhill, Matthew HoldenOmar S. Harb, Brian P. Brunk, Peter J. Myler, David Roos, Mark Carrington, Deborah F. Smith, Christiane Hertz-Fowler, Matthew Berriman

Research output: Contribution to journal › Article › peer-review

Abstract

GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome projects with curated annotation, which is readily accessible from a web based resource. The development of the database in recent years has focused on providing database-driven annotation tools and pipelines, as well as catering for increasingly frequent assembly updates. The website has been significantly redesigned to take advantage of current web technologies, and improve usability. The current release stores 41 data sets, of which 17 are manually curated and maintained by biologists, who review and incorporate data from the scientific literature, as well as other sources. GeneDB is primarily a production and annotation database for the genomes of predominantly pathogenic organisms.

Original language	English
Pages (from-to)	D98-D108
Number of pages	11
Journal	Nucleic Acids Research
Volume	40
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkr1032
Publication status	Published - Jan 2012

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Logan-Klumpler, F. J., De Silva, N., Boehme, U., Rogers, M. B., Velarde, G., McQuillan, J. A., Carver, T., Aslett, M., Olsen, C., Subramanian, S., Phan, I., Farris, C., Mitra, S., Ramasamy, G., Wang, H., Tivey, A., Jackson, A., Houston, R., Parkhill, J., ... Berriman, M. (2012). GeneDB-an annotation database for pathogens. Nucleic Acids Research, 40(D1), D98-D108. https://doi.org/10.1093/nar/gkr1032

@article{4cb4782044f4447db128ff85af897d93,

title = "GeneDB-an annotation database for pathogens",

abstract = "GeneDB (http://www.genedb.org) is a genome database for prokaryotic and eukaryotic pathogens and closely related organisms. The resource provides a portal to genome sequence and annotation data, which is primarily generated by the Pathogen Genomics group at the Wellcome Trust Sanger Institute. It combines data from completed and ongoing genome projects with curated annotation, which is readily accessible from a web based resource. The development of the database in recent years has focused on providing database-driven annotation tools and pipelines, as well as catering for increasingly frequent assembly updates. The website has been significantly redesigned to take advantage of current web technologies, and improve usability. The current release stores 41 data sets, of which 17 are manually curated and maintained by biologists, who review and incorporate data from the scientific literature, as well as other sources. GeneDB is primarily a production and annotation database for the genomes of predominantly pathogenic organisms.",

author = "Logan-Klumpler, {Flora J.} and {De Silva}, Nishadi and Ulrike Boehme and Rogers, {Matthew B.} and Giles Velarde and McQuillan, {Jacqueline A.} and Tim Carver and Martin Aslett and Christian Olsen and Sandhya Subramanian and Isabelle Phan and Carol Farris and Siddhartha Mitra and Gowthaman Ramasamy and Haiming Wang and Adrian Tivey and Andrew Jackson and Robin Houston and Julian Parkhill and Matthew Holden and Harb, {Omar S.} and Brunk, {Brian P.} and Myler, {Peter J.} and David Roos and Mark Carrington and Smith, {Deborah F.} and Christiane Hertz-Fowler and Matthew Berriman",

year = "2012",

month = jan,

doi = "10.1093/nar/gkr1032",

language = "English",

volume = "40",

pages = "D98--D108",

journal = "Nucleic Acids Research",

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Logan-Klumpler, FJ, De Silva, N, Boehme, U, Rogers, MB , Velarde, G, McQuillan, JA, Carver, T, Aslett, M, Olsen, C, Subramanian, S, Phan, I, Farris, C, Mitra, S, Ramasamy, G, Wang, H, Tivey, A, Jackson, A, Houston, R, Parkhill, J, Holden, M, Harb, OS, Brunk, BP, Myler, PJ, Roos, D, Carrington, M, Smith, DF, Hertz-Fowler, C & Berriman, M 2012, 'GeneDB-an annotation database for pathogens', Nucleic Acids Research, vol. 40, no. D1, pp. D98-D108. https://doi.org/10.1093/nar/gkr1032

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AU - Logan-Klumpler, Flora J.

AU - De Silva, Nishadi

AU - Boehme, Ulrike

AU - Rogers, Matthew B.

AU - Velarde, Giles

AU - McQuillan, Jacqueline A.

AU - Carver, Tim

AU - Aslett, Martin

AU - Olsen, Christian

AU - Subramanian, Sandhya

AU - Phan, Isabelle

AU - Farris, Carol

AU - Mitra, Siddhartha

AU - Ramasamy, Gowthaman

AU - Wang, Haiming

AU - Tivey, Adrian

AU - Jackson, Andrew

AU - Houston, Robin

AU - Parkhill, Julian

AU - Holden, Matthew

AU - Harb, Omar S.

AU - Brunk, Brian P.

AU - Myler, Peter J.

AU - Roos, David

AU - Carrington, Mark

AU - Smith, Deborah F.

AU - Hertz-Fowler, Christiane

AU - Berriman, Matthew

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VL - 40

SP - D98-D108

JO - Nucleic Acids Research

JF - Nucleic Acids Research

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ER -

GeneDB-an annotation database for pathogens

Abstract

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