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

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

doi:10.1093/nar/gkv1116

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

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

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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.

Original language	English
Journal	Nucleic Acids Research
Volume	44
Issue number	D1
Pages (from-to)	D38-D47
Number of pages	10
ISSN	0305-1048
DOIs	https://doi.org/10.1093/nar/gkv1116
Publication status	Published - 4 Jan 2016

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Ison_2016_Tools_and_dataFinal published version, 749 KBLicence: CC BY

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Ison, J., Rapacki, K., Ménager, H., Kalaš, M., Rydza, E., Chmura, P., Anthon, C., Beard, N., Berka, K., Bolser, D., Booth, T., Bretaudeau, A., Brezovsky, J., Casadio, R., Cesareni, G., Coppens, F., Cornell, M., Cuccuru, G., Davidsen, K., ... Brunak, S. (2016). Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research, 44(D1), D38-D47. https://doi.org/10.1093/nar/gkv1116

Ison, J, Rapacki, K, Ménager, H, Kalaš, M, Rydza, E, Chmura, P, Anthon, C, Beard, N, Berka, K, Bolser, D, Booth, T, Bretaudeau, A, Brezovsky, J, Casadio, R, Cesareni, G, Coppens, F, Cornell, M, Cuccuru, G, Davidsen, K, Vedova, GD, Dogan, T, Doppelt-Azeroual, O, Emery, L, Gasteiger, E, Gatter, T, Goldberg, T, Grosjean, M, Grüning, B, Helmer-Citterich, M, Ienasescu, H-I, Ioannidis, V, Jespersen, MC, Jimenez, R, Juty, N, Juvan, P, Koch, M, Laibe, C, Li, J-W, Licata, L, Mareuil, F, Mičetić, I, Friborg, RM, Moretti, S, Morris, C, Möller, S, Nenadic, A, Peterson, H, Profiti, G, Rice, P, Romano, P, Roncaglia, P, Saidi, R, Schafferhans, A, Schwämmle, V, Smith, C, Sperotto, MM, Stockinger, H, Vařeková, RS, Tosatto, SCE, de la Torre, V, Uva, P, Via, A, Yachdav, G, Zambelli, F, Vriend, G, Rost, B, Parkinson, H, Løngreen, P & Brunak, S 2016, 'Tools and data services registry: a community effort to document bioinformatics resources', Nucleic Acids Research, vol. 44, no. D1, pp. D38-D47. https://doi.org/10.1093/nar/gkv1116

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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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AU - Ison, Jon

AU - Rapacki, Kristoffer

AU - Ménager, Hervé

AU - Kalaš, Matúš

AU - Rydza, Emil

AU - Chmura, Piotr

AU - Anthon, Christian

AU - Beard, Niall

AU - Berka, Karel

AU - Bolser, Dan

AU - Booth, Tim

AU - Bretaudeau, Anthony

AU - Brezovsky, Jan

AU - Casadio, Rita

AU - Cesareni, Gianni

AU - Coppens, Frederik

AU - Cornell, Michael

AU - Cuccuru, Gianmauro

AU - Davidsen, Kristian

AU - Vedova, Gianluca Della

AU - Dogan, Tunca

AU - Doppelt-Azeroual, Olivia

AU - Emery, Laura

AU - Gasteiger, Elisabeth

AU - Gatter, Thomas

AU - Goldberg, Tatyana

AU - Grosjean, Marie

AU - Grüning, Björn

AU - Helmer-Citterich, Manuela

AU - Ienasescu, Hans-Ioan

AU - Ioannidis, Vassilios

AU - Jespersen, Martin Closter

AU - Jimenez, Rafael

AU - Juty, Nick

AU - Juvan, Peter

AU - Koch, Maximilian

AU - Laibe, Camille

AU - Li, Jing-Woei

AU - Licata, Luana

AU - Mareuil, Fabien

AU - Mičetić, Ivan

AU - Friborg, Rune Møllegaard

AU - Moretti, Sebastien

AU - Morris, Chris

AU - Möller, Steffen

AU - Nenadic, Aleksandra

AU - Peterson, Hedi

AU - Profiti, Giuseppe

AU - Rice, Peter

AU - Romano, Paolo

AU - Roncaglia, Paola

AU - Saidi, Rabie

AU - Schafferhans, Andrea

AU - Schwämmle, Veit

AU - Smith, Callum

AU - Sperotto, Maria Maddalena

AU - Stockinger, Heinz

AU - Vařeková, Radka Svobodová

AU - Tosatto, Silvio C. E.

AU - de la Torre, Victor

AU - Uva, Paolo

AU - Via, Allegra

AU - Yachdav, Guy

AU - Zambelli, Federico

AU - Vriend, Gert

AU - Rost, Burkhard

AU - Parkinson, Helen

AU - Løngreen, Peter

AU - Brunak, Søren

PY - 2016/1/4

Y1 - 2016/1/4

N2 - 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.

AB - 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.

U2 - 10.1093/nar/gkv1116

DO - 10.1093/nar/gkv1116

M3 - Journal article

C2 - 26538599

SN - 0305-1048

VL - 44

SP - D38-D47

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -

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

Abstract

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