The  bio.tools  registry of software tools and data resources for the life sciences

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Abstract

Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European enterprise to provide a catalogue ( https://bio.tools) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides a wide variety of practical information.

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Most cited references 21

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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Enis Afgan, Dannon Baker, Bérénice Batut … (2018)

Abstract Galaxy (homepage: https://galaxyproject.org, main public server: https://usegalaxy.org) is a web-based scientific analysis platform used by tens of thousands of scientists across the world to analyze large biomedical datasets such as those found in genomics, proteomics, metabolomics and imaging. Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making it simple to communicate analyses so that they can be reused and extended. During the last two years, the Galaxy team and the open-source community around Galaxy have made substantial improvements to Galaxy's core framework, user interface, tools, and training materials. Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed. The Galaxy community has led an effort to create numerous high-quality tutorials focused on common types of genomic analyses. The Galaxy developer and user communities continue to grow and be integral to Galaxy's development. The number of Galaxy public servers, developers contributing to the Galaxy framework and its tools, and users of the main Galaxy server have all increased substantially.

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ExPASy: SIB bioinformatics resource portal

Panu Artimo, Manohar Jonnalagedda, Konstantin Arnold … (2012)

ExPASy (http://www.expasy.org) has worldwide reputation as one of the main bioinformatics resources for proteomics. It has now evolved, becoming an extensible and integrative portal accessing many scientific resources, databases and software tools in different areas of life sciences. Scientists can henceforth access seamlessly a wide range of resources in many different domains, such as proteomics, genomics, phylogeny/evolution, systems biology, population genetics, transcriptomics, etc. The individual resources (databases, web-based and downloadable software tools) are hosted in a ‘decentralized’ way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions. Specifically, a single web portal provides a common entry point to a wide range of resources developed and operated by different SIB groups and external institutions. The portal features a search function across ‘selected’ resources. Additionally, the availability and usage of resources are monitored. The portal is aimed for both expert users and people who are not familiar with a specific domain in life sciences. The new web interface provides, in particular, visual guidance for newcomers to ExPASy.

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

Jon Ison, Matúš Kalaš, Inge Jonassen … (2013)

Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations. Availability: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl. Contact: jison@ebi.ac.uk

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Author and article information

Contributors

Jon Ison:

ORCID: http://orcid.org/0000-0001-6666-1520

jison@bioinformatics.dtu.dk

Journal

Journal ID (nlm-ta): Genome Biol

Journal ID (iso-abbrev): Genome Biol

Title: Genome Biology

Publisher: BioMed Central (London )

ISSN (Print): 1474-7596

ISSN (Electronic): 1474-760X

Publication date (Electronic): 12 August 2019

Publication date PMC-release: 12 August 2019

Publication date Collection: 2019

Volume: 20

Electronic Location Identifier: 164

Affiliations

[1 ]ISNI 0000 0001 2181 8870, GRID grid.5170.3, National Life Science Supercomputing Center, , Technical University of Denmark, ; Building 208, DK-2800 Kongens Lyngby, Denmark

[2 ]ISNI 0000 0001 0674 042X, GRID grid.5254.6, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, , University of Copenhagen, ; DK-2200 Copenhagen, Denmark

[3 ]ISNI 0000 0001 2353 6535, GRID grid.428999.7, Hub de Bioinformatique et de Biostatistiques, Institut Pasteur, C3BI USR, 3756 IP CNRS, ; Paris, France

[4 ]ISNI 0000 0004 1936 7443, GRID grid.7914.b, Computational Biology Unit, Department of Informatics, , University of Bergen, ; N-5020 Bergen, Norway

[5 ]ISNI 0000 0001 0728 0170, GRID grid.10825.3e, Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, , University of Southern Denmark, ; Campusvej 55, 5230 Odense, Denmark

[6 ]GRID grid.5963.9, Department of Computer Science, , Albert-Ludwigs-University Freiburg, ; Georges-Köhler-Allee 106, 79110 Freiburg, Germany

[7 ]ISNI 0000000121662407, GRID grid.5379.8, School of Computer Science, , The University of Manchester, ; Oxford Road, Manchester, M13 9PL UK

[8 ]ISNI 0000 0000 9709 7726, GRID grid.225360.0, The EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, ; Hinxton, Cambridge, CB10 1SD UK

[9 ]SIB Swiss Institute of Bioinformatics, Quartier Sorge - Batiment Amphipole, CH-1015 Lausanne, Switzerland

[10 ]ISNI 0000 0004 1936 9457, GRID grid.8993.b, Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Dept of Cell and Molecular Biology, , Uppsala University, ; S-75124 Uppsala, Sweden

[11 ]ISNI 0000 0001 2194 0956, GRID grid.10267.32, CEITEC - Central European Institute of Technology, , Masaryk University Brno, ; Kamenice 5, 625 00 Brno-Bohunice, Czech Republic

[12 ]ISNI 0000 0001 1015 3316, GRID grid.418095.1, Institute of Organic Chemistry and Biochemistry, , Czech Academy of Sciences, ; Flemingovo namesti 2, 160 00 Prague, Czech Republic

[13 ]ISNI 0000 0001 0943 7661, GRID grid.10939.32, ELIXIR-EE, Institute of Computer Science, , University of Tartu. J Liivi 2, ; Tartu, Estonia

[14 ]GRID grid.450126.4, Dutch Techcentre for Life Sciences, ; Jaarbeursplein 6, 3521 AL Utrecht, The Netherlands

[15 ]ISNI 0000 0004 0512 9137, GRID grid.20709.3c, CSC - IT Center for Science, ; PO BOX 405, FI-02101 Espoo, Finland

[16 ]ISNI 0000 0004 0387 1602, GRID grid.10097.3f, Barcelona Supercomputing Centre (BSC), ; 08034 Barcelona, Spain

[17 ]ISNI 0000 0000 9601 989X, GRID grid.425902.8, Institució Catalana de Recerca i Estudis Avançats (ICREA), ; Pg. Lluıs Companys 23, 08010 Barcelona, Spain

[18 ]ISNI 0000 0004 1937 0247, GRID grid.5841.8, Department of Biochemistry and Molecular Biomedicine, , University of Barcelona, INB / BSC-CNS, ; Barcelona, Spain

[19 ]ISNI 0000 0001 1940 4177, GRID grid.5326.2, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, , National Research Council (CNR), ; via Amendola 165/A, Bari, Italy

[20 ]ISNI 0000 0004 1757 2822, GRID grid.4708.b, Department of Biosciences, , University of Milano, ; Via Celoria 26, Milan, Italy

[21 ]ISNI 0000 0004 0635 706X, GRID grid.424165.0, Biomedical Sciences Research Centre, ; Alexander Fleming 34 Al. Fleming Str, 16672 Vari, Greece

[22 ]ISNI 0000 0001 0721 6013, GRID grid.8954.0, Faculty of Medicine / ELIXIR-SI, , University of Ljubljana, ; Vrazov trg 2, SI-1000 Ljubljana, Slovenia

[23 ]ISNI 0000 0001 2112 9282, GRID grid.4444.0, CNRS, UMS 3601, Institut Français de Bioinformatique, IFB-core, ; 2 rue Gaston Crémieux, F-91000 Evry, France

[24 ]ELIXIR-Hub, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK

[25 ]ISNI 0000 0001 2181 4263, GRID grid.9983.b, INESC-ID / Instituto Superior Técnico, ; R. Alves Redol 9, Lisbon, Portugal

[26 ]ISNI 0000 0004 0444 9382, GRID grid.10417.33, Radboud University Medical Centre, CMBI, ; Postbus 9101, 6500 HB Nijmegen, Netherlands

[27 ]ISNI 0000 0001 2298 7270, GRID grid.420225.3, Plateforme GenOuest Univ Rennes, Inria, CNRS, IRISA, ; F-35000 Rennes, France

[28 ]ISNI 0000 0001 2176 4817, GRID grid.5399.6, Aix-Marseille Univ, INSERM, lab. Theory and Approaches of Genome Complexity (TAGC), ; Marseille, France

[29 ]ISNI 0000 0001 2181 8870, GRID grid.5170.3, Department of Bio and Health Informatics, , Technical University of Denmark, ; Building 208, DK-2800 Kongens Lyngby, Denmark

Author information

Jon Ison http://orcid.org/0000-0001-6666-1520

Article

Publisher ID: 1772

DOI: 10.1186/s13059-019-1772-6

PMC ID: 6691543

PubMed ID: 31405382

SO-VID: ea2c405e-10bc-4552-9fec-d1d7597b5fe5

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

History

Date received : 12 April 2019

Date accepted : 22 July 2019

Funding

Funded by: ELIXIR-EXCELERATE under the European Union's Horizon 2020 research and innovation programme

Award ID: 676559

Award Recipient : Jon Ison

Funded by: The Danish Ministry of Higher Education and Science

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ScienceOpen disciplines: Genetics

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The bio.tools registry of software tools and data resources for the life sciences

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Most cited references 21

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

ExPASy: SIB bioinformatics resource portal

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

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