An evaluation of EDAM coverage in the Tools Ecosystem and prototype integration of Galaxy and WorkflowHub systems

Abstract

Here we report the results of a project started at the BioHackathon Europe 2022. Its goals were to cross-compare and analyze the metadata centralized in the Tools Ecosystem, and linked to the EDAM ontology, as well as to explore methods for connecting tools used in registered Galaxy workflows (i.e. WorkflowHub entries) to the annotations available in bio.tools.

Authors 12

1. Lucie Lamothe

   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 ( INRAE Domaine de Vilvert 78352 JOUY-EN-JOSAS CEDEX - France)

2. Jennifer Rugaard Bregndahl Jensen

   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 ( INRAE Domaine de Vilvert 78352 JOUY-EN-JOSAS CEDEX - France)

3. Hans Ienasescu

   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 ( INRAE Domaine de Vilvert 78352 JOUY-EN-JOSAS CEDEX - France)

4. Ove Gustafsson

   The University of Melbourne

   Affiliation as printed

   University of Melbourne (Parkville VIC 3010 - Australia)

5. Alban Gaignard

   Institut du Thorax · Nantes Université

   Affiliation as printed

   Institut du Thorax [Nantes] (France)

6. Dmitry Repchevsky

   Barcelona Supercomputing Center · Instituto de Salud Carlos III

   Affiliation as printed

   BSC-CNS - Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (Plaça d'Eusebi Güell, 1-3, Les Corts, 08034 Barcelona - Spain)

   NB-ISCIII - Spanish National Bioinformatics Institute [Barcelona, Spain] (Spain)

7. Radka Svobodová Vařeková

   Central European Institute of Technology · Masaryk University · Central European Institute of Technology – Masaryk University

   Affiliation as printed

   CEITEC MU - Central European Institute of Technology [Brno] (Masaryk University, Kamenice 753/5 625 00 Brno - Czech Republic)

8. Tomáš Raček

   Central European Institute of Technology · Masaryk University · Central European Institute of Technology – Masaryk University

   Affiliation as printed

   CEITEC MU - Central European Institute of Technology [Brno] (Masaryk University, Kamenice 753/5 625 00 Brno - Czech Republic)

9. Matej Antol

   Central European Institute of Technology · Masaryk University · Central European Institute of Technology – Masaryk University

   Affiliation as printed

   CEITEC MU - Central European Institute of Technology [Brno] (Masaryk University, Kamenice 753/5 625 00 Brno - Czech Republic)

10. Magnus Palmblad Aachen

    Leiden University · Leiden University Medical Center

    Affiliation as printed

    LUMC - Leiden University Medical Center (Leids Universitair Medisch Centrum, Universiteit Leiden - 1233 ZA, Leiden - Netherlands)

11. Matúš Kalaš

    University of Bergen

    Affiliation as printed

    UiB - University of Bergen (Universitetet i Bergen | Postboks 7800, NO-5020 Bergen - Norway)

12. Hervé Ménager

    Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement · Institut Français de Bioinformatique

    Affiliation as printed

    Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB (Département de biologie computationnelle (ex C3BI), 25-28 rue du Docteur Roux, 75724 Paris cedex 15 - France)

    IFB-CORE - Institut Français de Bioinformatique ( INRAE Domaine de Vilvert 78352 JOUY-EN-JOSAS CEDEX - France)