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

. 2016 Jan 04 ; 44 (D1) : D38-47. [epub] 20151103

Jazyk angličtina Země Anglie, Velká Británie Médium print-electronic

Typ dokumentu časopisecké články, Research Support, N.I.H., Extramural, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid26538599

Grantová podpora
U41 HG002273 NHGRI NIH HHS - United States
5U41HG002273-14 NHGRI NIH HHS - United States

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.

Albert Ludwigs Universität Freiburg Fahnenbergplatz 79085 Freiburg

Bioinformatics Centre Department of Biology University of Copenhagen Denmark

Bioinformatics CRS4 Italy

Bioinformatics Research Centre Denmark

Bologna Biocomputing Group University of Bologna Italy

Center for Biological Sequence Analysis Department of Systems Biology Technical University of Denmark Denmark

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

Central European Institute of Technology Czech Republic

Centre d'Informatique pour la Biologie C3BI Institut Pasteur France

Centre for Functional Genomics and Biochips Faculty of Medicine University of Ljubljana Slovenia

Centre for Molecular Bioinformatics Dept of Biology University of Rome Tor Vergata Italy

Computational Biology Unit Department of Informatics University of Bergen Norway

Department of Biomedical Sciences University of Padua Italy

Department of Computing William Penney Laboratory Imperial College London UK

Department of Dermatology University of Lübeck Germany Institute for Biostatistics and Informatics in Medicine and Ageing Research Rostock University Medical Center Germany

Department of Informatics Bioinformatics I12 TUM Germany

Department of Physical Chemistry RCPTM Faculty of Science Palacky University Czech Republic

Department of Plant Systems Biology VIB Belgium Department of Plant Biotechnology and Bioinformatics Ghent University Belgium

Department of Veterinary Clinical and Animal Sciences Faculty for Health and Medical Sciences University of Copenhagen Denmark

Dept of Biology University of Rome Tor Vergata Italy

Dept of Computer Science Systems and Communication Univ Milano Bicocca Italy

Dept of Physics Sapienza University Italy

Faculty of Life Sciences University of Manchester UK

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

Faculty of Technology and Center for Biotechnology Universität Bielefeld Germany

INRA UMR Institut de Génétique Environnement et Protection des Plantes France INRIA IRISA GenOuest Core Facility France

Institut Français de Bioinformatique CNRS UMS3601 France

Institute of Biomembranes and Bioenergetics National Research Council and Dept of Biosciences University of Milano Italy

Institute of Computer Science University of Tartu Estonia

Instruct WTCHG UK

IRCCS AOU San Martino IST Italy

Loschmidt Laboratories Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX Masaryk University Czech Republic

National Bioinformatics Institute Unit Fundacion Centro Nacional de Investigaciones Oncologicas Spain

NEBC Wallingford Centre for Ecology and Hydrology UK

Protein Research Group Department for Biochemistry and Molecular Biology University of Southern Denmark Denmark

Radboud University Medical Centre CMBI Netherlands

School of Computer Science University of Manchester UK

SIB Swiss Institute of Bioinformatics Switzerland

SIB Swiss Institute of Bioinformatics Switzerland Department of Ecology and Evolution Biophore Evolutionary Bioinformatics group University of Lausanne Switzerland

STFC Daresbury Laboratory UK

The European Bioinformatics Institute UK

UniProt European Bioinformatics Institute UK

Zobrazit více v PubMed

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

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. PubMed PMC

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

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

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. PubMed PMC

Kasprzyk A. BioMart: driving a paradigm change in biological data management. Database. 2011;2011:bar049. PubMed PMC

Smedley D., Haider S., Durinck S., Pandini L., Provero P., Allen J., Arnaiz O., Awedh M.H., Baldock R., Barbiera G., et al. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Res. 2015;43:W589–W598. PubMed PMC

Chervitz S., Fuellen G., Dagdigian C., Brenner S., Birney E., Korf I. Bioperl: standard perl modules for bioinformatics. Bio Informatics Technology and Systems (BITS) 1998;10:1611–1618.

Pocock M., Down T., Hubbard T. BioJava: open source components for bioinformatics. ACM SIGBIO Newsl. 2000;20:10–12.

Chapman B., Chang J. Biopython: Python tools for computational biology. ACM SIGBIO Newsl. 2000;20:15–19.

Stajich J.E., Block D., Boulez K., Brenner S.E., Chervitz S.A., Dagdigian C., Fuellen G., Gilbert J.G., Korf I., Lapp H., et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002;12:1611–1618. PubMed PMC

Cock P.J.A., Antao T., Chang J.T., Chapman B.A., Cox C.J., Dalke A., Friedberg I., Hamelryck T., Kauff F., Wilczynski B., et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009;25:1422–1423. PubMed PMC

Goto N., Prins P., Nakao M., Bonnal R., Aerts J., Katayama T. BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics. 2010;26:2617–2619. PubMed PMC

Prlić A., Yates A., Bliven S.E., Rose P.W., Jacobsen J., Troshin P.V., Chapman M., Gao J., Koh C.H., Foisy S., et al. BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics. 2012;28:2693–2695. PubMed PMC

Bonnal R.J., Aerts J., Githinji G., Goto N., MacLean D., Miller C.A., Mishima H., Pagani M., Ramirez-Gonzalez R., Smant G., et al. Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics. Bioinformatics. 2012;28:1035–1037. PubMed PMC

Li J.-W., Schmieder R., Ward R.M., Delenick J., Olivares E.C., Mittelman D. SEQanswers: an open access community for collaboratively decoding genomes. Bioinformatics. 2012;28:1272–1273. PubMed PMC

Wilson G. Software Carpentry: lessons learned. F1000Research. 2014;3 PubMed PMC

Burks C. Molecular Biology Database List. Nucleic Acids Res. 1999;27:1–9. PubMed PMC

Baxevanis A.D. The molecular biology database collection: an online compilation of relevant database resources. Nucleic Acids Res. 2000;28:1–7. PubMed PMC

Galperin M.Y., Rigden D.J., Fernández-Suárez X.M. The 2015 Nucleic Acids Research Database Issue and molecular biology database collection. Nucleic Acids Res. 2015;43:D1–D5. PubMed PMC

Fox J.A., Butland S.L., McMillan S., Campbell G., Ouellette B. F.F. The Bioinformatics Links Directory: a compilation of molecular biology web servers. Nucleic Acids Res. 2005;33:W3–W24. PubMed PMC

Brazas M.D., Yim D., Yeung W., Ouellette B.F.F. A decade of web server updates at the bioinformatics links directory: 2003–2012. Nucleic Acids Res. 2012;40:W3–W12. PubMed PMC

Pettifer S., Thorne D., McDermott P., Attwood T., Baran J., Bryne J.C., Hupponen T., Mowbray D., Vriend G. An active registry for bioinformatics web services. Bioinformatics. 2009;25:2090–2091. PubMed PMC

Pettifer S., Ison J., Kalaš M., Thorne D., McDermott P., Jonassen I., Liaquat A., Fernández J.M., Rodriguez J.M., Partners I., et al. The EMBRACE web service collection. Nucleic Acids Res. 2010;38:W683–W688. PubMed PMC

Bhagat J., Tanoh F., Nzuobontane E., Laurent T., Orlowski J., Roos M., Wolstencroft K., Aleksejevs S., Stevens R., Pettifer S., et al. BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Res. 2010;38:W689–W694. PubMed PMC

Gentleman R., Carey V., Bates D., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004;5:R80. PubMed PMC

Field D., Tiwari B., Booth T., Houten S., Swan D., Bertrand N., Thurston M. Open software for biologists: from famine to feast. Nat. Biotechnol. 2006;24:801–803. PubMed

Möller S., Krabbenhöft H., Tille A., Paleino D., Williams A., Wolstencroft K., Goble C., Holland R., Belhachemi D., Plessy C. Community-driven computational biology with Debian Linux. BMC Bioinformatics. 2010;11:S5. PubMed PMC

Gómez J., García L.J., Salazar G.A., Villaveces J., Gore S., García A., Martín M.J., Launay G., Alcántara R., del Toro N., et al. BioJS: an open source JavaScript framework for biological data visualization. Bioinformatics. 2013;29:1103–1104. PubMed PMC

Corpas M., Jimenez R., Carbon S.J., García A., Garcia L., Goldberg T., Gomez J., Kalderimis A., Lewis S.E., Mulvany I., et al. BioJS: an open source standard for biological visualisation—its status in 2014 [version 1; referees: 2 approved] F1000Research. 2014;3:55. PubMed PMC

Yachdav G., Goldberg T., Wilzbach S., Dao D., Shih I., Choudhary S., Crouch S., Franz M., García A., García L.J., et al. Anatomy of BioJS, an open source community for the life sciences. eLife. 2015;4:e07009. PubMed PMC

Li J.-W., Robison K., Martin M., Sjödin A., Usadel B., Young M., Olivares E.C., Bolser D.M. The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis. Nucleic Acids Res. 2012;40:D1313–D1317. PubMed PMC

Ison J., Kalaš M., Jonassen I., Bolser D., Uludag M., McWilliam H., Malone J., Lopez R., Pettifer S., Rice P. EDAM: An ontology of bioinformatics operations, types of data and identifiers, topics, and formats. Bioinformatics. 2013;29:1325–1332. PubMed PMC

Budd A., Corpas M., Brazas M.D., Fuller J.C., Goecks J., Mulder N.J., Michaut M., Ouellette B.F., Pawlik A., Blomberg N. A quick guide for building a successful bioinformatics community. PLoS Comput. Biol. 2015;11:e1003972. PubMed PMC

Möller S., Afgan E., Banck M., Cock P., Kalaš M., Kaján L., Prins P., Quinn J., Sallou O., Strozzi F., et al. Sprints, Hackathons and Codefests as community gluons in computational biology. EMBnet.J. 2013;19:40–42.

Möller S., Afgan E., Banck M., Bonnal R. J.P., Booth T., Chilton J., Cock P. J.A., Gumbel M., Harris N., Holland R., et al. Community-driven development for computational biology at Sprints, Hackathons and Codefests. BMC Bioinformatics. 2014;15:S7. PubMed PMC

Budd A., Dinkel H., Corpas M., Fuller J.C., Rubinat L., Devos D.P., Khoueiry P.H., Förstner K.U., Georgatos F., Rowland F., et al. Ten simple rules for organizing an unconference. PLoS Comput. Biol. 2015;11:e1003905. PubMed PMC

Ménager H., Kalaš M., Rapacki K., Ison J. Using registries to integrate bioinformatics tools and services into workbench environments. International Journal on Software Tools for Technology Transfer. 2015:1–6.

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...