Tools and data services registry: a community effort to document bioinformatics resources

doi:10.1093/nar/gkv1116

. 2016 Jan 4;44(D1):D38-47.

doi: 10.1093/nar/gkv1116. Epub 2015 Nov 3.

Tools and data services registry: a community effort to document bioinformatics resources

Jon Ison¹, Kristoffer Rapacki², Hervé Ménager³, Matúš Kalaš⁴, Emil Rydza², Piotr Chmura², Christian Anthon⁵, Niall Beard⁶, Karel Berka⁷, Dan Bolser⁸, Tim Booth⁹, Anthony Bretaudeau¹⁰, Jan Brezovsky¹¹, Rita Casadio¹², Gianni Cesareni¹³, Frederik Coppens¹⁴, Michael Cornell¹⁵, Gianmauro Cuccuru¹⁶, Kristian Davidsen², Gianluca Della Vedova¹⁷, Tunca Dogan¹⁸, Olivia Doppelt-Azeroual³, Laura Emery⁸, Elisabeth Gasteiger¹⁹, Thomas Gatter²⁰, Tatyana Goldberg²¹, Marie Grosjean²², Björn Grüning²³, Manuela Helmer-Citterich²⁴, Hans Ienasescu²⁵, Vassilios Ioannidis¹⁹, Martin Closter Jespersen², Rafael Jimenez⁸, Nick Juty⁸, Peter Juvan²⁶, Maximilian Koch⁸, Camille Laibe⁸, Jing-Woei Li²⁷, Luana Licata¹³, Fabien Mareuil³, Ivan Mičetić²⁸, Rune Møllegaard Friborg²⁹, Sebastien Moretti³⁰, Chris Morris³¹, Steffen Möller³², Aleksandra Nenadic⁶, Hedi Peterson³³, Giuseppe Profiti¹², Peter Rice³⁴, Paolo Romano³⁵, Paola Roncaglia⁸, Rabie Saidi¹⁸, Andrea Schafferhans²¹, Veit Schwämmle³⁶, Callum Smith³⁷, Maria Maddalena Sperotto², Heinz Stockinger¹⁹, Radka Svobodová Vařeková³⁸, Silvio C E Tosatto²⁸, Victor de la Torre³⁹, Paolo Uva¹⁶, Allegra Via⁴⁰, Guy Yachdav²¹, Federico Zambelli⁴¹, Gert Vriend⁴², Burkhard Rost²¹, Helen Parkinson⁸, Peter Løngreen², Søren Brunak⁴³

Affiliations

¹ Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark jison@cbs.dtu.dk.
² Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark.
³ Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, France.
⁴ Computational Biology Unit, Department of Informatics, University of Bergen, Norway.
⁵ Department of Veterinary Clinical and Animal Sciences, Faculty for Health and Medical Sciences, University of Copenhagen, Denmark.
⁶ School of Computer Science, University of Manchester, UK.
⁷ Department of Physical Chemistry, RCPTM, Faculty of Science, Palacky University, Czech Republic.
⁸ The European Bioinformatics Institute (EMBL-EBI), UK.
⁹ NEBC Wallingford, Centre for Ecology and Hydrology, UK.
¹⁰ INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), France INRIA, IRISA, GenOuest Core Facility, France.
¹¹ Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Czech Republic.
¹² Bologna Biocomputing Group, University of Bologna, Italy.
¹³ Dept. of Biology, University of Rome Tor Vergata, Italy.
¹⁴ Department of Plant Systems Biology, VIB, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium.
¹⁵ Faculty of Life Sciences, University of Manchester, UK.
¹⁶ Bioinformatics, CRS4, Italy.
¹⁷ Dept. of Computer Science, Systems and Communication. Univ. Milano-Bicocca, Italy.
¹⁸ UniProt, European Bioinformatics Institute (EMBL-EBI), UK.
¹⁹ SIB Swiss Institute of Bioinformatics, Switzerland.
²⁰ Faculty of Technology and Center for Biotechnology, Universität Bielefeld, Germany.
²¹ Department of Informatics, Bioinformatics-I12, TUM, Germany.
²² Institut Français de Bioinformatique (French Institute of Bioinformatics), CNRS, UMS3601, France.
²³ Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79085 Freiburg.
²⁴ Centre for Molecular Bioinformatics, Dept. of Biology, University of Rome Tor Vergata, Italy.
²⁵ Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark.
²⁶ Centre for Functional Genomics and Biochips, Faculty of Medicine, University of Ljubljana, Slovenia.
²⁷ Faculty of Medicine, The Chinese University of Hong Kong, China Hong Kong Bioinformatics Centre, School of Life Sciences,The Chinese University of Hong Kong, China.
²⁸ Department of Biomedical Sciences, University of Padua, Italy.
²⁹ Bioinformatics Research Centre (BiRC), Denmark.
³⁰ SIB Swiss Institute of Bioinformatics, Switzerland Department of Ecology and Evolution, Biophore, Evolutionary Bioinformatics group, University of Lausanne, Switzerland.
³¹ STFC, Daresbury Laboratory, UK.
³² Department of Dermatology, University of Lübeck, Germany Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Germany.
³³ Institute of Computer Science, University of Tartu, Estonia.
³⁴ Department of Computing, William Penney Laboratory, Imperial College London, UK.
³⁵ IRCCS AOU San Martino IST, Italy.
³⁶ Protein Research Group, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Denmark.
³⁷ Instruct, WTCHG, UK.
³⁸ Central European Institute of Technology (CEITEC), Czech Republic.
³⁹ National Bioinformatics Institute Unit (INB), Fundacion Centro Nacional de Investigaciones Oncologicas, Spain.
⁴⁰ Dept. of Physics, Sapienza University, Italy.
⁴¹ Institute of Biomembranes and Bioenergetics, National Research Council (CNR), and Dept. of Biosciences, University of Milano, Italy.
⁴² Radboud University Medical Centre, CMBI, Netherlands.
⁴³ Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.

PMID: 26538599
PMCID: PMC4702812
DOI: 10.1093/nar/gkv1116

Tools and data services registry: a community effort to document bioinformatics resources

Jon Ison et al. Nucleic Acids Res. 2016.

. 2016 Jan 4;44(D1):D38-47.

doi: 10.1093/nar/gkv1116. Epub 2015 Nov 3.

Authors

Affiliations

¹ Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark jison@cbs.dtu.dk.
² Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark.
³ Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, France.
⁴ Computational Biology Unit, Department of Informatics, University of Bergen, Norway.
⁵ Department of Veterinary Clinical and Animal Sciences, Faculty for Health and Medical Sciences, University of Copenhagen, Denmark.
⁶ School of Computer Science, University of Manchester, UK.
⁷ Department of Physical Chemistry, RCPTM, Faculty of Science, Palacky University, Czech Republic.
⁸ The European Bioinformatics Institute (EMBL-EBI), UK.
⁹ NEBC Wallingford, Centre for Ecology and Hydrology, UK.
¹⁰ INRA, UMR Institut de Génétique, Environnement et Protection des Plantes (IGEPP), BioInformatics Platform for Agroecosystems Arthropods (BIPAA), France INRIA, IRISA, GenOuest Core Facility, France.
¹¹ Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Czech Republic.
¹² Bologna Biocomputing Group, University of Bologna, Italy.
¹³ Dept. of Biology, University of Rome Tor Vergata, Italy.
¹⁴ Department of Plant Systems Biology, VIB, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium.
¹⁵ Faculty of Life Sciences, University of Manchester, UK.
¹⁶ Bioinformatics, CRS4, Italy.
¹⁷ Dept. of Computer Science, Systems and Communication. Univ. Milano-Bicocca, Italy.
¹⁸ UniProt, European Bioinformatics Institute (EMBL-EBI), UK.
¹⁹ SIB Swiss Institute of Bioinformatics, Switzerland.
²⁰ Faculty of Technology and Center for Biotechnology, Universität Bielefeld, Germany.
²¹ Department of Informatics, Bioinformatics-I12, TUM, Germany.
²² Institut Français de Bioinformatique (French Institute of Bioinformatics), CNRS, UMS3601, France.
²³ Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79085 Freiburg.
²⁴ Centre for Molecular Bioinformatics, Dept. of Biology, University of Rome Tor Vergata, Italy.
²⁵ Bioinformatics Centre, Department of Biology, University of Copenhagen, Denmark.
²⁶ Centre for Functional Genomics and Biochips, Faculty of Medicine, University of Ljubljana, Slovenia.
²⁷ Faculty of Medicine, The Chinese University of Hong Kong, China Hong Kong Bioinformatics Centre, School of Life Sciences,The Chinese University of Hong Kong, China.
²⁸ Department of Biomedical Sciences, University of Padua, Italy.
²⁹ Bioinformatics Research Centre (BiRC), Denmark.
³⁰ SIB Swiss Institute of Bioinformatics, Switzerland Department of Ecology and Evolution, Biophore, Evolutionary Bioinformatics group, University of Lausanne, Switzerland.
³¹ STFC, Daresbury Laboratory, UK.
³² Department of Dermatology, University of Lübeck, Germany Institute for Biostatistics and Informatics in Medicine and Ageing Research, Rostock University Medical Center, Germany.
³³ Institute of Computer Science, University of Tartu, Estonia.
³⁴ Department of Computing, William Penney Laboratory, Imperial College London, UK.
³⁵ IRCCS AOU San Martino IST, Italy.
³⁶ Protein Research Group, Department for Biochemistry and Molecular Biology, University of Southern Denmark, Denmark.
³⁷ Instruct, WTCHG, UK.
³⁸ Central European Institute of Technology (CEITEC), Czech Republic.
³⁹ National Bioinformatics Institute Unit (INB), Fundacion Centro Nacional de Investigaciones Oncologicas, Spain.
⁴⁰ Dept. of Physics, Sapienza University, Italy.
⁴¹ Institute of Biomembranes and Bioenergetics, National Research Council (CNR), and Dept. of Biosciences, University of Milano, Italy.
⁴² Radboud University Medical Centre, CMBI, Netherlands.
⁴³ Center for Biological Sequence Analysis Department of Systems Biology, Technical University of Denmark, Denmark Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark.

PMID: 26538599
PMCID: PMC4702812
DOI: 10.1093/nar/gkv1116

Abstract

Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.

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Figures

**Figure 1.**
EDAM concepts. EDAM includes four main sub-ontologies defining common concepts within bioinformatics: topics, operations, data (including identifiers, the fifth sub-ontology) and data formats. EDAM provides the core scientific concepts for describing registry entries.

**Figure 2.**
ELIXIR registry query user interface. The query interface (https://bio.tools) provides features to search the registry, display what fields of information are shown, and filter and sort the results by various attributes.

See this image and copyright information in PMC

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References

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[1] May M. Life science technologies: Big biological impacts from big data. Science. 2014;344:1298–1300.

[2] May M. Life science technologies: Big biological impacts from big data. Science. 2014;344:1298–1300.

[3] Parnell L.D., Lindenbaum P., Shameer K., Dall'Olio G.M., Swan D.C., Jensen L.J., Cockell S.J., Pedersen B.S., Mangan M.E., Miller C.A., et al. BioStar: an online question & answer resource for the bioinformatics community. PLoS Comput. Biol. 2011;7:e1002216. - PMC - PubMed

[4] Parnell L.D., Lindenbaum P., Shameer K., Dall'Olio G.M., Swan D.C., Jensen L.J., Cockell S.J., Pedersen B.S., Mangan M.E., Miller C.A., et al. BioStar: an online question & answer resource for the bioinformatics community. PLoS Comput. Biol. 2011;7:e1002216. - PMC - PubMed

[5] Logan D.W., Sandal M., Gardner P.P., Manske M., Bateman A. Ten simple rules for editing Wikipedia. PLoS Comput. Biol. 2010;6:e1000941. - PMC - PubMed

[6] Logan D.W., Sandal M., Gardner P.P., Manske M., Bateman A. Ten simple rules for editing Wikipedia. PLoS Comput. Biol. 2010;6:e1000941. - PMC - PubMed

[7] The UniProt Consortium. Activities at the Universal Protein Resource (UniProt) Nucleic Acids Res. 2014;42:D191–D198. - PMC - PubMed

[8] The UniProt Consortium. Activities at the Universal Protein Resource (UniProt) Nucleic Acids Res. 2014;42:D191–D198. - PMC - PubMed

[9] Orchard S., Ammari M., Aranda B., Breuza L., Briganti L., Broackes-Carter F., Campbell N.H., Chavali G., Chen C., Del-Toro N. The MIntAct project'IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 2013;42:D358–D363. - PMC - PubMed

[10] Orchard S., Ammari M., Aranda B., Breuza L., Briganti L., Broackes-Carter F., Campbell N.H., Chavali G., Chen C., Del-Toro N. The MIntAct project'IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 2013;42:D358–D363. - PMC - PubMed

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Tools and data services registry: a community effort to document bioinformatics resources

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Tools and data services registry: a community effort to document bioinformatics resources

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