Tools and data services registry

a community effort to document bioinformatics resources

Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Karol Rydza, Piotr Jaroslaw 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 & 49 others Tunca Dogan, Olivia Doppelt-Azeroual, Laura Emery, Elisabeth Gasteiger, Thomas Gatter, Tatyana Goldberg, Marie Grosjean, Björn Grüning, Manuela Helmer-Citterich, Hans 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

    Research output: Contribution to journalJournal articleResearchpeer-review

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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 September 2015, the registry includes 1633 resources, with depositions from 91 individual registrations including 40 institutional providers and 51 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 languageEnglish
    Article numbergkv1116
    JournalNucleic acids research
    Volume44
    Issue numberD1
    Pages (from-to)D38-D47
    ISSN0305-1048
    DOIs
    Publication statusPublished - 2016

    Bibliographical note

    © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

    This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

    Cite this

    Ison, Jon ; Rapacki, Kristoffer ; Ménager, Hervé ; Kalaš, Matúš ; Rydza, Emil Karol ; Chmura, Piotr Jaroslaw ; Anthon, Christian ; Beard, Niall ; Berka, Karel ; Bolser, Dan ; Booth, Tim ; Bretaudeau, Anthony ; Brezovsky, Jan ; Casadio, Rita ; Cesareni, Gianni ; Coppens, Frederik ; Cornell, Michael ; Cuccuru, Gianmauro ; Davidsen, Kristian ; Vedova, Gianluca Della ; Dogan, Tunca ; Doppelt-Azeroual, Olivia ; Emery, Laura ; Gasteiger, Elisabeth ; Gatter, Thomas ; Goldberg, Tatyana ; Grosjean, Marie ; Grüning, Björn ; Helmer-Citterich, Manuela ; Ienasescu, Hans ; Ioannidis, Vassilios ; Jespersen, Martin Closter ; Jimenez, Rafael ; Juty, Nick ; Juvan, Peter ; Koch, Maximilian ; Laibe, Camille ; Li, Jing-Woei ; Licata, Luana ; Mareuil, Fabien ; Mičetić, Ivan ; Friborg, Rune Møllegaard ; Moretti, Sebastien ; Morris, Chris ; Möller, Steffen ; Nenadic, Aleksandra ; Peterson, Hedi ; Profiti, Giuseppe ; Rice, Peter ; Romano, Paolo ; Roncaglia, Paola ; Saidi, Rabie ; Schafferhans, Andrea ; Schwämmle, Veit ; Smith, Callum ; Sperotto, Maria Maddalena ; Stockinger, Heinz ; Vařeková, Radka Svobodová ; Tosatto, Silvio C. E. ; de la Torre, Victor ; Uva, Paolo ; Via, Allegra ; Yachdav, Guy ; Zambelli, Federico ; Vriend, Gert ; Rost, Burkhard ; Parkinson, Helen ; Løngreen, Peter ; Brunak, Søren. / Tools and data services registry : a community effort to document bioinformatics resources. In: Nucleic acids research. 2016 ; Vol. 44, No. D1. pp. D38-D47.
    @article{1c377512a5e04f509ec9c53bfb6d4963,
    title = "Tools and data services registry: a community effort to document bioinformatics resources",
    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 September 2015, the registry includes 1633 resources, with depositions from 91 individual registrations including 40 institutional providers and 51 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.",
    author = "Jon Ison and Kristoffer Rapacki and Herv{\'e} M{\'e}nager and Mat{\'u}š Kalaš and Rydza, {Emil Karol} and Chmura, {Piotr Jaroslaw} and Christian Anthon and Niall Beard and Karel Berka and Dan Bolser and Tim Booth and Anthony Bretaudeau and Jan Brezovsky and Rita Casadio and Gianni Cesareni and Frederik Coppens and Michael Cornell and Gianmauro Cuccuru and Kristian Davidsen and Vedova, {Gianluca Della} and Tunca Dogan and Olivia Doppelt-Azeroual and Laura Emery and Elisabeth Gasteiger and Thomas Gatter and Tatyana Goldberg and Marie Grosjean and Bj{\"o}rn Gr{\"u}ning and Manuela Helmer-Citterich and Hans Ienasescu and Vassilios Ioannidis and Jespersen, {Martin Closter} and Rafael Jimenez and Nick Juty and Peter Juvan and Maximilian Koch and Camille Laibe and Jing-Woei Li and Luana Licata and Fabien Mareuil and Ivan Mičetić and Friborg, {Rune M{\o}llegaard} and Sebastien Moretti and Chris Morris and Steffen M{\"o}ller and Aleksandra Nenadic and Hedi Peterson and Giuseppe Profiti and Peter Rice and Paolo Romano and Paola Roncaglia and Rabie Saidi and Andrea Schafferhans and Veit Schw{\"a}mmle and Callum Smith and Sperotto, {Maria Maddalena} and Heinz Stockinger and Vařekov{\'a}, {Radka Svobodov{\'a}} and Tosatto, {Silvio C. E.} and {de la Torre}, Victor and Paolo Uva and Allegra Via and Guy Yachdav and Federico Zambelli and Gert Vriend and Burkhard Rost and Helen Parkinson and Peter L{\o}ngreen and S{\o}ren Brunak",
    note = "{\circledC} The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.",
    year = "2016",
    doi = "10.1093/nar/gkv1116",
    language = "English",
    volume = "44",
    pages = "D38--D47",
    journal = "Nucleic Acids Research",
    issn = "0305-1048",
    publisher = "Oxford University Press",
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    }

    Ison, J, Rapacki, K, Ménager, H, Kalaš, M, Rydza, EK, Chmura, PJ, 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, 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, gkv1116, pp. D38-D47. https://doi.org/10.1093/nar/gkv1116

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

    In: Nucleic acids research, Vol. 44, No. D1, gkv1116, 2016, p. D38-D47.

    Research output: Contribution to journalJournal articleResearchpeer-review

    TY - JOUR

    T1 - Tools and data services registry

    T2 - a community effort to document bioinformatics resources

    AU - Ison, Jon

    AU - Rapacki, Kristoffer

    AU - Ménager, Hervé

    AU - Kalaš, Matúš

    AU - Rydza, Emil Karol

    AU - Chmura, Piotr Jaroslaw

    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

    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

    N1 - © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

    PY - 2016

    Y1 - 2016

    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 September 2015, the registry includes 1633 resources, with depositions from 91 individual registrations including 40 institutional providers and 51 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 September 2015, the registry includes 1633 resources, with depositions from 91 individual registrations including 40 institutional providers and 51 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

    VL - 44

    SP - D38-D47

    JO - Nucleic Acids Research

    JF - Nucleic Acids Research

    SN - 0305-1048

    IS - D1

    M1 - gkv1116

    ER -