MetaBase-the wiki-database of biological databases

D.M. Bolser, P.Y.F.R.P. Chibon, N. Palopoli, S. Gong, D. Jacob, V.D. Del Angel, D. Swan, S. Bassi, V. Gonzalez, P. Suravajhala, S. Hwang, P. Romano, R. Edwards, B. Bishop, J. Eargle, T. Shtatland, N.J. Provart, D. Clements, D.P. Renfro, D. Bhak & 1 others J. Bhak

Research output: Contribution to journalArticleAcademicpeer-review

27 Citations (Scopus)

Abstract

Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project.
Original languageEnglish
Pages (from-to)D1250-D1254
JournalNucleic acids research
Volume40
Issue numberD1
DOIs
Publication statusPublished - 2012

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Databases
Chemical Databases
Biota
Nucleic Acid Databases
Research
Nucleic Acids
Molecular Biology
Technology

Keywords

  • web services
  • life sciences
  • information
  • collection
  • persistence
  • catalog

Cite this

Bolser, D. M., Chibon, P. Y. F. R. P., Palopoli, N., Gong, S., Jacob, D., Del Angel, V. D., ... Bhak, J. (2012). MetaBase-the wiki-database of biological databases. Nucleic acids research, 40(D1), D1250-D1254. https://doi.org/10.1093/nar/gkr1099
Bolser, D.M. ; Chibon, P.Y.F.R.P. ; Palopoli, N. ; Gong, S. ; Jacob, D. ; Del Angel, V.D. ; Swan, D. ; Bassi, S. ; Gonzalez, V. ; Suravajhala, P. ; Hwang, S. ; Romano, P. ; Edwards, R. ; Bishop, B. ; Eargle, J. ; Shtatland, T. ; Provart, N.J. ; Clements, D. ; Renfro, D.P. ; Bhak, D. ; Bhak, J. / MetaBase-the wiki-database of biological databases. In: Nucleic acids research. 2012 ; Vol. 40, No. D1. pp. D1250-D1254.
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Bolser, DM, Chibon, PYFRP, Palopoli, N, Gong, S, Jacob, D, Del Angel, VD, Swan, D, Bassi, S, Gonzalez, V, Suravajhala, P, Hwang, S, Romano, P, Edwards, R, Bishop, B, Eargle, J, Shtatland, T, Provart, NJ, Clements, D, Renfro, DP, Bhak, D & Bhak, J 2012, 'MetaBase-the wiki-database of biological databases', Nucleic acids research, vol. 40, no. D1, pp. D1250-D1254. https://doi.org/10.1093/nar/gkr1099

MetaBase-the wiki-database of biological databases. / Bolser, D.M.; Chibon, P.Y.F.R.P.; Palopoli, N.; Gong, S.; Jacob, D.; Del Angel, V.D.; Swan, D.; Bassi, S.; Gonzalez, V.; Suravajhala, P.; Hwang, S.; Romano, P.; Edwards, R.; Bishop, B.; Eargle, J.; Shtatland, T.; Provart, N.J.; Clements, D.; Renfro, D.P.; Bhak, D.; Bhak, J.

In: Nucleic acids research, Vol. 40, No. D1, 2012, p. D1250-D1254.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Bolser, D.M.

AU - Chibon, P.Y.F.R.P.

AU - Palopoli, N.

AU - Gong, S.

AU - Jacob, D.

AU - Del Angel, V.D.

AU - Swan, D.

AU - Bassi, S.

AU - Gonzalez, V.

AU - Suravajhala, P.

AU - Hwang, S.

AU - Romano, P.

AU - Edwards, R.

AU - Bishop, B.

AU - Eargle, J.

AU - Shtatland, T.

AU - Provart, N.J.

AU - Clements, D.

AU - Renfro, D.P.

AU - Bhak, D.

AU - Bhak, J.

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PY - 2012

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N2 - Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project.

AB - Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project.

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KW - life sciences

KW - information

KW - collection

KW - persistence

KW - catalog

U2 - 10.1093/nar/gkr1099

DO - 10.1093/nar/gkr1099

M3 - Article

VL - 40

SP - D1250-D1254

JO - Nucleic acids research

JF - Nucleic acids research

SN - 0305-1048

IS - D1

ER -

Bolser DM, Chibon PYFRP, Palopoli N, Gong S, Jacob D, Del Angel VD et al. MetaBase-the wiki-database of biological databases. Nucleic acids research. 2012;40(D1):D1250-D1254. https://doi.org/10.1093/nar/gkr1099