Literature DB >> 31624831

Community curation of bioinformatics software and data resources.

Jon Ison1, Hervé Ménager2, Bryan Brancotte2, Erik Jaaniso3, Ahto Salumets3, Tomáš Raček4,5, Anna-Lena Lamprecht6, Magnus Palmblad7, Matúš Kalaš8, Piotr Chmura9, John M Hancock10, Veit Schwämmle11, Hans-Ioan Ienasescu1.   

Abstract

The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided under a single portal (https://bio.tools). We describe here the practical means by which scientific communities, including individual developers and projects, through major service providers and research infrastructures, can describe their own bioinformatics resources and share these via bio.tools.
© The Author(s) 2019. Published by Oxford University Press.

Entities:  

Keywords:  bioinformatics; community driven; curation; database; registry; software

Year:  2020        PMID： 31624831      PMCID： PMC7947956          DOI： 10.1093/bib/bbz075

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN： 1467-5463            Impact factor:   11.622


  18 in total

1.  Predicting Secretory Proteins with SignalP.

Authors:  Henrik Nielsen
Journal:  Methods Mol Biol       Date:  2017

2.  ExPASy: SIB bioinformatics resource portal.

Authors:  Panu Artimo; Manohar Jonnalagedda; Konstantin Arnold; Delphine Baratin; Gabor Csardi; Edouard de Castro; Séverine Duvaud; Volker Flegel; Arnaud Fortier; Elisabeth Gasteiger; Aurélien Grosdidier; Céline Hernandez; Vassilios Ioannidis; Dmitry Kuznetsov; Robin Liechti; Sébastien Moretti; Khaled Mostaguir; Nicole Redaschi; Grégoire Rossier; Ioannis Xenarios; Heinz Stockinger
Journal:  Nucleic Acids Res       Date:  2012-05-31       Impact factor: 16.971

3.  Semantics-based composition of EMBOSS services.

Authors:  Anna-Lena Lamprecht; Stefan Naujokat; Tiziana Margaria; Bernhard Steffen
Journal:  J Biomed Semantics       Date:  2011-03-07

4.  Europe PMC: a full-text literature database for the life sciences and platform for innovation.

Authors: 
Journal:  Nucleic Acids Res       Date:  2014-11-06       Impact factor: 16.971

5.  OMICtools: an informative directory for multi-omic data analysis.

Authors:  Vincent J Henry; Anita E Bandrowski; Anne-Sophie Pepin; Bruno J Gonzalez; Arnaud Desfeux
Journal:  Database (Oxford)       Date:  2014-07-14       Impact factor: 3.451

6.  The EBI search engine: EBI search as a service-making biological data accessible for all.

Authors:  Young M Park; Silvano Squizzato; Nicola Buso; Tamer Gur; Rodrigo Lopez
Journal:  Nucleic Acids Res       Date:  2017-07-03       Impact factor: 16.971

7.  ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.

Authors:  L Larcombe; R Hendricusdottir; T K Attwood; F Bacall; N Beard; L J Bellis; W B Dunn; J M Hancock; A Nenadic; C Orengo; B Overduin; S-A Sansone; M Thurston; M R Viant; C L Winder; C A Goble; C P Ponting; G Rustici
Journal:  F1000Res       Date:  2017-06-21

8.  Automated workflow composition in mass spectrometry-based proteomics.

Authors:  Magnus Palmblad; Anna-Lena Lamprecht; Jon Ison; Veit Schwämmle
Journal:  Bioinformatics       Date:  2019-02-15       Impact factor: 6.937

9.  EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.

Authors:  Jon Ison; Matús Kalas; Inge Jonassen; Dan Bolser; Mahmut Uludag; Hamish McWilliam; James Malone; Rodrigo Lopez; Steve Pettifer; Peter Rice
Journal:  Bioinformatics       Date:  2013-03-11       Impact factor: 6.937

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

Authors:  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 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
Journal:  Nucleic Acids Res       Date:  2015-11-03       Impact factor: 16.971
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  3 in total

1.  biotoolsSchema: a formalized schema for bioinformatics software description.

Authors:  Jon Ison; Hans Ienasescu; Emil Rydza; Piotr Chmura; Kristoffer Rapacki; Alban Gaignard; Veit Schwämmle; Jacques van Helden; Matúš Kalaš; Hervé Ménager
Journal:  Gigascience       Date:  2021-01-27       Impact factor: 6.524

2.  APE in the Wild: Automated Exploration of Proteomics Workflows in the bio.tools Registry.

Authors:  Vedran Kasalica; Veit Schwämmle; Magnus Palmblad; Jon Ison; Anna-Lena Lamprecht
Journal:  J Proteome Res       Date:  2021-03-15       Impact factor: 4.466

3.  Perspectives on automated composition of workflows in the life sciences.

Authors:  Anna-Lena Lamprecht; Magnus Palmblad; Jon Ison; Veit Schwämmle; Mohammad Sadnan Al Manir; Ilkay Altintas; Christopher J O Baker; Ammar Ben Hadj Amor; Salvador Capella-Gutierrez; Paulos Charonyktakis; Michael R Crusoe; Yolanda Gil; Carole Goble; Timothy J Griffin; Paul Groth; Hans Ienasescu; Pratik Jagtap; Matúš Kalaš; Vedran Kasalica; Alireza Khanteymoori; Tobias Kuhn; Hailiang Mei; Hervé Ménager; Steffen Möller; Robin A Richardson; Vincent Robert; Stian Soiland-Reyes; Robert Stevens; Szoke Szaniszlo; Suzan Verberne; Aswin Verhoeven; Katherine Wolstencroft
Journal:  F1000Res       Date:  2021-09-07
  3 in total

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