bio.tools: an expanded web service for research software in the life sciences
Nucleic Acids Research, vol. 54, pp. W4–W12
Abstract
Computational methods are central to the life sciences. The rapid growth and diversification of software tools and databases make it difficult to find, compare, and reuse methods for a given task. bio.tools is a community-driven registry designed to improve the visibility of research software and allow researchers to simplify access to the software ecosystem through structured, interoperable, and accessible metadata. Tools are annotated using the EDAM ontology and additional controlled vocabularies, enabling users to search and filter by scientific topics, operations, input/output data types, and data formats. bio.tools supports interactive exploration via rich tool landing pages and provides programmatic access through a documented API for search, retrieval, and registry statistics. The registry has expanded to almost 33,000 annotated tools through the combined contributions of thousands of community members and semi-automated literature mining that keep the registry up to date. Recent improvements to the registry include machine-assisted scoring to prioritise curator review, and consolidation of both its standards stack and software architecture. bio.tools has also become a foundational upstream metadata source that is reused by other services in the ELIXIR Research Software Ecosystem and beyond, to support synchronisation, cross-linking, and additional downstream services. bio.tools is freely available at https://bio.tools.
Authors 23
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University of Southern Denmark · Leiden University Medical Center
Affiliation as printed
Center for Proteomics and Metabolomics, Leiden University Medical Center , Postbus 9600, 2300 RC Leiden ,
Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, 5230 Odense ,
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Affiliation as printed
Independent Researcher , Timișoara ,
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University of Southern Denmark
Affiliation as printed
Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, 5230 Odense ,
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UiT The Arctic University of Norway
Affiliation as printed
Department of Chemistry, UiT The Arctic University of Norway , PO Box 6050 Stakkevollan, NO-9037 Tromsø ,
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University of Copenhagen · Novo Nordisk Foundation
Affiliation as printed
Novo Nordisk Foundation Centre for Protein Research , University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N ,
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University of Alaska Fairbanks
Affiliation as printed
University of Alaska Fairbanks , P.O. Box 757500, Fairbanks, AK 99775 ,
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Affiliation as printed
Australian BioCommons, University of Melbourne , 21 Bedford St (Level 2), North Melbourne, Victoria 3051 ,
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Affiliation as printed
ELIXIR Norway and Department of Informatics, University of Bergen , P.O. Box 7803N-5020 Bergen ,
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University of Southern Denmark
Affiliation as printed
Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, 5230 Odense ,
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University of Southern Denmark
Affiliation as printed
Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, 5230 Odense ,
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Affiliation as printed
Institute of Computer Science, University of Tartu , Ülikooli 18, 50090, Tartu ,
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University of Southern Denmark
Affiliation as printed
Department of Clinical Research, University of Southern Denmark , Campusvej 55, 5230 Odense ,
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Affiliation as printed
ELIXIR Norway and Department of Informatics, University of Bergen , P.O. Box 7803N-5020 Bergen ,
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Centre National de la Recherche Scientifique · Inserm · Institut Pasteur · Université Paris Cité · Commissariat à l'Énergie Atomique et aux Énergies Alternatives · Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement · Institut Français de Bioinformatique
Affiliation as printed
IFB-core, Institut Français de Bioinformatique (IFB), CNRS, INSERM, INRAE, CEA , 94800 Villejuif ,
Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub , 75015 Paris ,
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Leiden University Medical Center
Affiliation as printed
Center for Proteomics and Metabolomics, Leiden University Medical Center , Postbus 9600, 2300 RC Leiden ,
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University of Southern Denmark
Affiliation as printed
Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, 5230 Odense ,
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Masaryk University · Central European Institute of Technology – Masaryk University
Affiliation as printed
CEITEC - Central European Institute of Technology, Masaryk University , Brno 625 00 ,
National Centre for Biomolecular Research, Faculty of Science, Masaryk University , Brno 625 00 ,
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Masaryk University · Central European Institute of Technology – Masaryk University
Affiliation as printed
CEITEC - Central European Institute of Technology, Masaryk University , Brno 625 00 ,
National Centre for Biomolecular Research, Faculty of Science, Masaryk University , Brno 625 00 ,
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Affiliation as printed
Faculty of Informatics, Masaryk University , Brno 602 00 ,
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Leiden University Medical Center
Affiliation as printed
Biomedical Data Sciences, Leiden University Medical Center , Postbus 9600, 2300 RC Leiden ,
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University of Southern Denmark
Affiliation as printed
Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, 5230 Odense ,
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Masaryk University · Central European Institute of Technology – Masaryk University
Affiliation as printed
CEITEC - Central European Institute of Technology, Masaryk University , Brno 625 00 ,
National Centre for Biomolecular Research, Faculty of Science, Masaryk University , Brno 625 00 ,
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University of Southern Denmark
Affiliation as printed
Department of Biochemistry and Molecular Biology, University of Southern Denmark , Campusvej 55, 5230 Odense ,
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