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

被引：82

作者：

Ison, Jon ^{[1
]}

Rapacki, Kristoffer ^{[1
]}

Menager, Herve ^{[2
]}

Kalas, Matus ^{[3
]}

Rydza, Emil ^{[1
]}

Chmura, Piotr ^{[1
]}

Anthon, Christian ^{[4
]}

Beard, Niall ^{[5
]}

Berka, Karel ^{[6
]}

Bolser, Dan ^{[7
]}

Booth, Tim ^{[8
]}

Bretaudeau, Anthony ^{[9
,10
]}

Brezovsky, Jan ^{[11
,12
]}

Casadio, Rita ^{[13
]}

Cesareni, Gianni ^{[14
]}

Coppens, Frederik ^{[15
,16
]}

Cornell, Michael ^{[17
]}

Cuccuru, Gianmauro ^{[18
]}

Davidsen, Kristian ^{[1
]}

Della Vedova, Gianluca ^{[19
]}

Dogan, Tunca ^{[20
]}

Doppelt-Azeroual, Olivia ^{[2
]}

Emery, Laura ^{[7
]}

Gasteiger, Elisabeth ^{[21
]}

Gatter, Thomas ^{[22
,23
]}

Goldberg, Tatyana ^{[24
]}

Grosjean, Marie ^{[25
]}

Gruening, Bjoern ^{[26
]}

Helmer-Citterich, Manuela ^{[27
]}

Ienasescu, Hans ^{[28
]}

Ioannidis, Vassilios ^{[21
]}

Jespersen, Martin Closter ^{[1
]}

Jimenez, Rafael ^{[7
]}

Juty, Nick ^{[7
]}

Juvan, Peter ^{[29
]}

Koch, Maximilian ^{[7
]}

Laibe, Camille ^{[7
]}

Li, Jing-Woei ^{[30
,31
]}

Licata, Luana ^{[14
]}

Mareuil, Fabien ^{[2
]}

Micetic, Ivan ^{[32
]}

Friborg, Rune Mollegaard ^{[33
]}

Moretti, Sebastien ^{[21
,34
]}

Morris, Chris ^{[35
]}

Moeller, Steffen ^{[36
,37
]}

Nenadic, Aleksandra ^{[5
]}

Peterson, Hedi ^{[38
]}

Profiti, Giuseppe ^{[13
]}

Rice, Peter ^{[39
]}

Romano, Paolo ^{[40
]}

机构：

[1] Tech Univ Denmark, Dept Syst Biol, Ctr Biol Sequence Anal, Lyngby, Denmark

[2] Inst Pasteur, C3BI, Ctr Informat Biol, Paris, France

[3] Univ Bergen, Dept Informat, Computat Biol Unit, N-5020 Bergen, Norway

[4] Univ Copenhagen, Fac Hlth & Med Sci, Dept Vet Clin & Anim Sci, DK-1168 Copenhagen, Denmark

[5] Univ Manchester, Sch Comp Sci, Manchester M13 9PL, Lancs, England

[6] Palacky Univ, Fac Sci, RCPTM, Dept Phys Chem, Olomouc, Czech Republic

[7] European Bioinformat Inst EMBL EBI, London, England

[8] NEBC Wallingford, Ctr Ecol & Hydrol, Wallingford, Oxon, England

[9] INRA, UMR Inst Genet Environm & Protect Plantes IGEPP, BioInformat Platform Agroecosyst Arthropods BIPAA, Angers, France

[10] INRIA, IRISA, GenOuest Core Facil, Lyon, France

[11] Masaryk Univ, Dept Expt Biol, Loschmidt Labs, CS-60177 Brno, Czech Republic

[12] Masaryk Univ, Res Ctr Tox Cpds Environm RECETOX, CS-60177 Brno, Czech Republic

[13] Univ Bologna, Bologna Biocomp Grp, I-40126 Bologna, Italy

[14] Univ Roma Tor Vergata, Dept Biol, Rome, Italy

[15] VIB, Dept Plant Syst Biol, Brussels, Belgium

[16] Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9000 Ghent, Belgium

[17] Univ Manchester, Fac Life Sci, Manchester M13 9PL, Lancs, England

[18] CRS4, Bioinformat, Rome, Italy

[19] Univ Milano Bicocca, Dept Comp Sci Syst & Commun, Milan, Italy

[20] European Bioinformat Inst EMBL EBI, UniProt, London, England

[21] Swiss Inst Bioinformat, Zurich, Switzerland

[22] Univ Bielefeld, Fac Technol, Bielefeld, Germany

[23] Univ Bielefeld, Ctr Biotechnol, Bielefeld, Germany

[24] TUM, Dept Informat, Bioinformat I12, Berlin, Germany

[25] CNRS, UMS3601, French Inst Bioinformat, F-75700 Paris, France

[26] Univ Freiburg, Fahnenbergpl, D-79085 Freiburg, Germany

[27] Univ Roma Tor Vergata, Dept Biol, Ctr Mol Bioinformat, Rome, Italy

[28] Univ Copenhagen, Dept Biol, Bioinformat Ctr, DK-1168 Copenhagen, Denmark

[29] Univ Ljubljana, Fac Med, Ctr Funct Genom & Biochips, Ljubljana 61000, Slovenia

[30] Chinese Univ Hong Kong, Fac Med, Hong Kong, Hong Kong, Peoples R China

[31] Chinese Univ Hong Kong, Sch Life Sci, Hong Kong Bioinformat Ctr, Hong Kong, Hong Kong, Peoples R China

[32] Univ Padua, Dept Biomed Sci, I-35100 Padua, Italy

[33] Bioinformat Res Ctr BiRC, Lyngby, Denmark

[34] Univ Lausanne, Dept Ecol & Evolut, Biophore, Evolutionary Bioinformat Grp, CH-1015 Lausanne, Switzerland

[35] Daresbury Lab, STFC, Warrington, Cheshire, England

[36] Univ Lubeck, Dept Dermatol, Lubeck, Germany

[37] Univ Rostock, Med Ctr, Inst Biostat & Informat Med & Ageing Res, D-18055 Rostock, Germany

[38] Univ Tartu, Inst Comp Sci, Tartu, Estonia

[39] Univ London Imperial Coll Sci Technol & Med, William Penney Lab, Dept Comp, London SW7 2AZ, England

[40] IRCCS AOU San Martino IST, Rome, Italy

[41] Univ Southern Denmark, Dept Biochem & Mol Biol, Prot Res Grp, Odense, Denmark

[42] WTCHG, Instruct, London, England

[43] Cent European Inst Technol CEITEC, Brno, Czech Republic

[44] Fdn Ctr Nacl Invest Oncol, Natl Bioinformat Inst Unit INB, Madrid, Spain

[45] Univ Roma La Sapienza, Dept Phys, I-00185 Rome, Italy

[46] CNR, Inst Biomembranes & Bioenerget, I-00185 Rome, Italy

[47] Univ Milan, Dept Biosci, I-20122 Milan, Italy

[48] Radboud Univ Nijmegen, Med Ctr, CMBI, NL-6525 ED Nijmegen, Netherlands

[49] Univ Copenhagen, Novo Nordisk Fdn, Ctr Prot Res, Fac Hlth & Med Sci, DK-1168 Copenhagen, Denmark

来源：

NUCLEIC ACIDS RESEARCH | 2016年 / 44卷 / D1期

关键词：

MOLECULAR-BIOLOGY; SOFTWARE-DEVELOPMENT; COMPILATION; SEQANSWERS; FRAMEWORK;

D O I：

10.1093/nar/gkv1116

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：D38 / D47

页数：10

共 38 条

[1] Activities at the Universal Protein Resource (UniProt) [J].

Apweiler, Rolf ;

Bateman, Alex ;

Martin, Maria Jesus ;

O'Donovan, Claire ;

Magrane, Michele ;

Alam-Faruque, Yasmin ;

Alpi, Emanuele ;

Antunes, Ricardo ;

Arganiska, Joanna ;

Casanova, Elisabet Barrera ;

Bely, Benoit ;

Bingley, Mark ;

Bonilla, Carlos ;

Britto, Ramona ;

Bursteinas, Borisas ;

Chan, Wei Mun ;

Chavali, Gayatri ;

Cibrian-Uhalte, Elena ;

Da Silva, Alan ;

De Giorgi, Maurizio ;

Dogan, Tunca ;

Fazzini, Francesco ;

Gane, Paul ;

Castro, Leyla Garcia ;

Garmiri, Penelope ;

Hatton-Ellis, Emma ;

Hieta, Reija ;

Huntley, Rachael ;

Legge, Duncan ;

Liu, Wudong ;

Luo, Jie ;

MacDougall, Alistair ;

Mutowo, Prudence ;

Nightingale, Andrew ;

Orchard, Sandra ;

Pichler, Klemens ;

Poggioli, Diego ;

Pundir, Sangya ;

Pureza, Luis ;

Qi, Guoying ;

Rosanoff, Steven ;

Saidi, Rabie ;

Sawford, Tony ;

Shypitsyna, Aleksandra ;

Turner, Edward ;

Volynkin, Vladimir ;

Wardell, Tony ;

Watkins, Xavier ;

Zellner, Hermann ;

Corbett, Matt .

NUCLEIC ACIDS RESEARCH, 2014, 42 (D1) :D191-D198

[2] The Molecular Biology Database Collection: an online compilation of relevant database resources [J].

Baxevanis, AD .

NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :1-7

[3] BioCatalogue: a universal catalogue of web services for the life sciences [J].

Bhagat, Jiten ;

Tanoh, Franck ;

Nzuobontane, Eric ;

Laurent, Thomas ;

Orlowski, Jerzy ;

Roos, Marco ;

Wolstencroft, Katy ;

Aleksejevs, Sergejs ;

Stevens, Robert ;

Pettifer, Steve ;

Lopez, Rodrigo ;

Goble, Carole A. .

NUCLEIC ACIDS RESEARCH, 2010, 38 :W689-W694

[4] Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics [J].

Bonnal, Raoul J. P. ;

Aerts, Jan ;

Githinji, George ;

Goto, Naohisa ;

MacLean, Dan ;

Miller, Chase A. ;

Mishima, Hiroyuki ;

Pagani, Massimiliano ;

Ramirez-Gonzalez, Ricardo ;

Smant, Geert ;

Strozzi, Francesco ;

Syme, Rob ;

Vos, Rutger ;

Wennblom, Trevor J. ;

Woodcroft, Ben J. ;

Katayama, Toshiaki ;

Prins, Pjotr .

BIOINFORMATICS, 2012, 28 (07) :1035-1037

[5] A decade of web server updates at the bioinformatics links directory: 2003-2012 [J].

Brazas, Michelle D. ;

Yim, David ;

Yeung, Winston ;

Ouellette, B. F. Francis .

NUCLEIC ACIDS RESEARCH, 2012, 40 (W1) :W3-W12

[6] Ten Simple Rules for Organizing an Unconference [J].

Budd, Aidan ;

Dinkel, Holger ;

Corpas, Manuel ;

Fuller, Jonathan C. ;

Rubinat, Laura ;

Devos, Damien P. ;

Khoueiry, Pierre H. ;

Foestner, Konrad U. ;

Georgatos, Fotis ;

Rowland, Francis ;

Sharan, Malvika ;

Binder, Janos X. ;

Grace, Tom ;

Traphagen, Karyn ;

Gristwood, Adam ;

Wood, Natasha T. .

PLOS COMPUTATIONAL BIOLOGY, 2015, 11 (01)

[7] A Quick Guide for Building a Successful Bioinformatics Community [J].

Budd, Aidan ;

Corpas, Manuel ;

Brazas, Michelle D. ;

Fuller, Jonathan C. ;

Goecks, Jeremy ;

Mulder, Nicola J. ;

Michaut, Magali ;

Ouellette, B. F. Francis ;

Pawlik, Aleksandra ;

Blomberg, Niklas .

PLOS COMPUTATIONAL BIOLOGY, 2015, 11 (02)

[8] Molecular Biology Database List [J].

Burks, C .

NUCLEIC ACIDS RESEARCH, 1999, 27 (01) :1-9

[9]

Chapman B., 2000, SIGBIO Newsletter, V20, P15, DOI 10.1145/360262.360268

[10]

Chervitz S., 1998, BIO INFORMATICS TECH, V10, P1611

← 1 2 3 4 →