The Quest for Orthologs orthology benchmark service in 2022

Author:

Nevers Yannis12ORCID,Jones Tamsin E M3ORCID,Jyothi Dushyanth4,Yates Bethan3ORCID,Ferret Meritxell5,Portell-Silva Laura5,Codo Laia5ORCID,Cosentino Salvatore6,Marcet-Houben Marina57,Vlasova Anna57,Poidevin Laetitia8910,Kress Arnaud8910,Hickman Mark11,Persson Emma12,Piližota Ivana13,Guijarro-Clarke Cristina13,Altenhoff Adrian,Bruford Elspeth A,Cosentino Salvatore,Dessimoz Christophe,Ebersberger Ingo,Emms David M,Gabaldón Toni,Glover Natasha,Guijarro-Clarke Cristina,Hickman Mark,Hu Yanhui,Iwasaki Wataru,Jones Tamsin E M,Jyothi Dushyanth,Kress Arnaud,Lecompte Odile,Linard Benjamin,Marcet-Houben Marina,Martin Maria J,Nevers Yannis,Persson Emma,Piližota Ivana,Poidevin Laetitia,Roos David S,Sonhammer Erik,Thomas Paul D,Thybert David,Vandepoele Klaas,Vlasova Anna,Yates Bethan,Capella-Gutierrez Salvador,Codó Laia,Ferret Meritxell,Gonzalez-Uriarte Asier,Garrayo-Ventas Javier,Portell-Silva Laura,Repchevsky Dmitry,Sundesha Vicky,Iwasaki Wataru614ORCID,Lecompte Odile89,Sonnhammer Erik12ORCID,Roos David S11,Gabaldón Toni571516,Thybert David13,Thomas Paul D17ORCID,Hu Yanhui18ORCID,Emms David M19,Bruford Elspeth320ORCID,Capella-Gutierrez Salvador5ORCID,Martin Maria J4,Dessimoz Christophe122122ORCID,Altenhoff Adrian223,

Affiliation:

1. Department of Computational Biology, University of Lausanne , Lausanne , Switzerland

2. Swiss Institute for Bioinformatics, University of Lausanne , Lausanne, Switzerland

3. HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Genome Campus, Hinxton, UK

4. Protein Function development, European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Genome Campus, Hinxton, UK

5. Barcelona Supercomputing Centre (BSC-CNS) . Plaça Eusebi Güell, 1-3 08034 Barcelona , Spain

6. Department of Biological Sciences, Graduate School of Science, the University of Tokyo , Tokyo , Japan

7. Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology , Baldiri Reixac, 10, 08028 Barcelona , Spain

8. Department of Computer Science , ICube, UMR 7357, Centre de Recherche en Biomédecine de Strasbourg, , CNRS, Strasbourg , France

9. University of Strasbourg , ICube, UMR 7357, Centre de Recherche en Biomédecine de Strasbourg, , CNRS, Strasbourg , France

10. BiGEst-ICube Platform, ICube, UMR 7357, Centre de Recherche en Biomédecine de Strasbourg, University of Strasbourg , CNRS, Strasbourg , France

11. Department of Biology, University of Pennsylvania , Philadelphia, PA 19104,  USA

12. Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University , Solna , Sweden

13. European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Genome Campus, Hinxton, UK

14. Department of Integrated Biosciences, Graduate School of Frontier Sciences, the University of Tokyo , Kashiwa , Japan

15. Catalan Institution for Research and Advanced Studies (ICREA) , Barcelona , Spain

16. Centro de Investigaciones Biomédicas en Red de Enfermedades Infecciosas , Barcelona , Spain

17. Department of Population and Public Health Sciences, University of Southern California , Los Angeles,  CA 90032,  USA

18. Department of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University , Boston , MA 02115 , USA

19. Department of Plant Sciences, University of Oxford , Oxford  OX1 3RB, UK

20. Department of Haematology, University of Cambridge School of Clinical Medicine , Cambridge , UK

21. Department of Computer Science, University College London , London , UK

22. Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London , London , UK

23. Computer Science Department , ETH Zurich, Zurich , Switzerland

Abstract

Abstract The Orthology Benchmark Service (https://orthology.benchmarkservice.org) is the gold standard for orthology inference evaluation, supported and maintained by the Quest for Orthologs consortium. It is an essential resource to compare existing and new methods of orthology inference (the bedrock for many comparative genomics and phylogenetic analysis) over a standard dataset and through common procedures. The Quest for Orthologs Consortium is dedicated to maintaining the resource up to date, through regular updates of the Reference Proteomes and increasingly accessible data through the OpenEBench platform. For this update, we have added a new benchmark based on curated orthology assertion from the Vertebrate Gene Nomenclature Committee, and provided an example meta-analysis of the public predictions present on the platform.

Funder

European Molecular Biology Laboratory

National Institutes of Health

National Human Genome Research Institute

JSPS

JST

MEXT

Horizon 2020

ELIXIR

Wellcome

National Science Foundation

Wellcome Trust

Swiss National Science Foundation

Publisher

Oxford University Press (OUP)

Subject

Genetics

Reference37 articles.

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