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

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.

Silvio C. E. Tosatto | Anthony Bretaudeau | Burkhard Rost | Chris Morris | Dan M. Bolser | Karel Berka | Gianluca Della Vedova | Rafael C. Jimenez | Vassilios Ioannidis | Allegra Via | Radka Svobodová Vareková | Frederik Coppens | Søren Brunak | Jon C. Ison | Helen E. Parkinson | Manuela Helmer-Citterich | Aleksandra Nenadic | Jan Brezovsky | Gert Vriend | Rita Casadio | Paolo Romano | Martin Closter Jespersen | Luana Licata | Elisabeth Gasteiger | Sébastien Moretti | Paolo Uva | Gianni Cesareni | Tim Booth | Camille Laibe | Steffen Möller | Veit Schwämmle | Hervé Ménager | Heinz Stockinger | Rabie Saidi | Victor de la Torre | Federico Zambelli | Giuseppe Profiti | Ivan Micetic | Kristian Davidsen | Tunca Dogan | Maximilian Koch | Björn A. Grüning | Paola Roncaglia | Guy Yachdav | Peter M. Rice | Laura Emery | Andrea Schafferhans | Rune Møllegaard Friborg | Jing-Woei Li | Hedi Peterson | Fabien Mareuil | Tatyana Goldberg | Laura R. Emery | Peter Løngreen | Marie Grosjean | Matús Kalas | Kristoffer Rapacki | Olivia Doppelt-Azeroual | Maria Sperotto | Niall Beard | Gianmauro Cuccuru | Emil Rydza | Piotr Chmura | Christian Anthon | Michael Cornell | Thomas Gatter | Hans Ienasescu | Nick S. Juty | Peter Juvan | Callum Smith | B. Rost | S. Brunak | G. D. Vedova | H. Parkinson | P. Juvan | R. Casadio | G. Vriend | Steffen Möller | M. Helmer-Citterich | Callum Smith | G. Cesareni | H. Stockinger | P. Rice | N. Juty | R. Jimenez | K. Berka | R. Vareková | Marie Grosjean | R. M. Friborg | Peter Løngreen | L. Licata | A. Schafferhans | K. Rapacki | M. C. Jespersen | E. Gasteiger | D. Bolser | C. Laibe | P. Roncaglia | F. Zambelli | A. Via | Tim Booth | S. Tosatto | Giuseppe Profiti | Olivia Doppelt-Azeroual | J. Ison | Tatyana Goldberg | V. Schwämmle | B. Grüning | A. Bretaudeau | M. Sperotto | P. Uva | Hedi Peterson | J. Brezovsky | Thomas Gatter | Fabien Mareuil | P. Romano | V. Ioannidis | S. Moretti | Chris Morris | M. Koch | Guy Yachdav | Rabie Saidi | I. Mičetić | Emil Rydza | A. Nenadic | N. Beard | G. Cuccuru | K. Davidsen | Matúš Kalaš | H. Ménager | P. Chmura | Tunca Dogan | Christian Anthon | Hans Ienasescu | Frederik Coppens | Michael Cornell | Jing-Woei Li | R. Jiménez

[1]  Dan M. Bolser,et al.  The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis , 2011, Nucleic Acids Res..

[2]  Maria Jesus Martin,et al.  BioJS: an open source JavaScript framework for biological data visualization , 2013, Bioinform..

[3]  Dawn Field,et al.  Open software for biologists: from famine to feast , 2006, Nature Biotechnology.

[4]  Mike May,et al.  LIFE SCIENCE TECHNOLOGIES: Big biological impacts from big data , 2014 .

[5]  Steve Pettifer,et al.  EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats , 2013, Bioinform..

[6]  Pietro Liò,et al.  The BioMart community portal: an innovative alternative to large, centralized data repositories , 2015, Nucleic Acids Res..

[7]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[8]  Aleksandra Pawlik,et al.  A Quick Guide for Building a Successful Bioinformatics Community , 2015, PLoS Comput. Biol..

[9]  Jean YH Yang,et al.  Bioconductor: open software development for computational biology and bioinformatics , 2004, Genome Biology.

[10]  Scott McMillan,et al.  The Bioinformatics Links Directory: a Compilation of Molecular Biology Web Servers , 2005, Nucleic Acids Res..

[11]  Aleksandra Pawlik,et al.  BioJS: an open source standard for biological visualisation – its status in 2014 , 2014, F1000Research.

[12]  Aidan Budd,et al.  Ten Simple Rules for Organizing an Unconference , 2015, PLoS Comput. Biol..

[13]  Michael Y. Galperin,et al.  The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection , 2014, Nucleic Acids Res..

[14]  Arek Kasprzyk,et al.  BioMart: driving a paradigm change in biological data management , 2011, Database J. Biol. Databases Curation.

[15]  Alex Bateman,et al.  Ten Simple Rules for Editing Wikipedia , 2010, PLoS Comput. Biol..

[16]  Michelle D. Brazas,et al.  A decade of web server updates at the bioinformatics links directory: 2003–2012 , 2012, Nucleic Acids Res..

[17]  Carole A. Goble,et al.  BioCatalogue: a universal catalogue of web services for the life sciences , 2010, Nucleic Acids Res..

[18]  Andreas Prlic,et al.  Sequence analysis , 2003 .

[19]  Terri K. Attwood,et al.  The EMBRACE web service collection , 2010, Nucleic Acids Res..

[20]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[21]  Daniel MacLean,et al.  Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics , 2012, Bioinform..

[22]  Matthew R. Pocock,et al.  The Bioperl toolkit: Perl modules for the life sciences. , 2002, Genome research.

[23]  Jon C. Ison,et al.  Using registries to integrate bioinformatics tools and services into workbench environments , 2016, International Journal on Software Tools for Technology Transfer.

[24]  Andreas D. Baxevanis,et al.  The Molecular Biology Database Collection: an online compilation of relevant database resources , 2000, Nucleic Acids Res..

[25]  Olivier Sallou,et al.  Community-driven development for computational biology at Sprints, Hackathons and Codefests , 2014, BMC Bioinformatics.

[26]  Robert Schmieder,et al.  SEQanswers: an open access community for collaboratively decoding genomes , 2012, Bioinform..

[27]  Jeffrey Chang,et al.  Biopython: Python tools for computational biology , 2000, SIGB.

[28]  Burkhard Rost,et al.  Anatomy of BioJS, an open source community for the life sciences , 2015, eLife.

[29]  Steve Pettifer,et al.  An active registry for bioinformatics web services , 2009, Bioinform..

[30]  Matthew R. Pocock,et al.  BioJava: open source components for bioinformatics , 2000, SIGB.

[31]  Carole A. Goble,et al.  Community-driven computational biology with Debian Linux , 2010, BMC Bioinformatics.

[32]  Brent S. Pedersen,et al.  BioStar: An Online Question & Answer Resource for the Bioinformatics Community , 2011, PLoS Comput. Biol..

[33]  Rafael C. Jimenez,et al.  The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases , 2013, Nucleic Acids Res..

[34]  Greg Wilson,et al.  Software Carpentry: lessons learned , 2013, F1000Research.

[35]  Pjotr Prins,et al.  BioRuby: bioinformatics software for the Ruby programming language , 2010, Bioinform..

[36]  Christian Burks,et al.  Molecular Biology Database List , 1999, Nucleic Acids Res..

[37]  Andreas Prlic,et al.  BioJava: an open-source framework for bioinformatics in 2012 , 2012, Bioinform..

[38]  Olivier Sallou,et al.  Sprints, Hackathons and Codefests as community gluons in computational biology , 2013 .

[39]  Greg Wilson,et al.  Software Carpentry: lessons learned , 2014, F1000Research.