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The Quest for Orthologs orthology benchmark service in 2022

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Nevers, Yannis, Jones, Tamsin E M, Jyothi, Dushyanth, Yates, Bethan, Ferret, Meritxell, Portell-Silva, Laura, Codo, Laia, Cosentino, Salvatore +61 more·2022·Nucleic Acids Research
DOI 10.1093/nar/gkac330PMC PMC9252809
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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.

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Authors
Nevers, Y., Jones, T. E. M., Jyothi, D., Yates, B., Ferret, M., Portell-Silva, L., Codo, L., Cosentino, S., Marcet-Houben, M., Vlasova, A., Poidevin, L., Kress, A., Hickman, M., Persson, E., Piližota, I., Guijarro-Clarke, C., the OpenEBench team the Quest for Orthologs Consortium, Altenhoff, A., Bruford, E. A., Cosentino, S., Dessimoz, C., Ebersberger, I., Emms, D. M., Gabaldón, T., Glover, N., Guijarro-Clarke, C., Hickman, M., Hu, Y., Iwasaki, W., Jones, T. E. M., Jyothi, D., Kress, A., Lecompte, O., Linard, B., Marcet-Houben, M., Martin, M. J., Nevers, Y., Persson, E., Piližota, I., Poidevin, L., Roos, D. S., Sonhammer, E., Thomas, P. D., Thybert, D., Vandepoele, K., Vlasova, A., Yates, B., Capella-Gutierrez, S., Codó, L., Ferret, M., Gonzalez-Uriarte, A., Garrayo-Ventas, J., Portell-Silva, L., Repchevsky, D., Sundesha, V., Iwasaki, W., Lecompte, O., Sonnhammer, E., Roos, D. S., Gabaldón, T., Thybert, D., Thomas, P. D., Hu, Y., Emms, D. M., Bruford, E., Capella-Gutierrez, S., Martin, M. J., Dessimoz, C., & Altenhoff, A.
Affiliations
  • Barcelona Supercomputing Centre (BSC-CNS) . Plaça Eusebi Güell, 1-3 08034 Barcelona , Spain
  • Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier (FR)
  • Stockholm University (SE)
  • HUGO Gene Nomenclature Committee (HGNC), European Molecular Biology Laboratory, European Bioinformatics Institute , Wellcome Genome Campus, Hinxton, UK
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2022-05-12
Volume
50
Issue
W1
Pages
W623-W632
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkac330
PMC
PMC9252809
OpenAlex
W4280527426
Cited by
74
References
2
Citations by year
2026: 8 · 2025: 16 · 2024: 29 · 2023: 19 · 2022: 2
FWCI
1.92
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Oxford University Research Archive (ORA) (University of Oxford) (publishedVersion)
  • SERVAL (Université de Lausanne) (publishedVersion, cc-by)
  • HAL (submittedVersion, cc-by)
  • Ghent University Academic Bibliography (Ghent University) (submittedVersion, cc-by)
  • IRIS (submittedVersion, cc-by)
  • Apollo (University of Cambridge) (submittedVersion, cc-by)
  • HAL (submittedVersion)
  • UCL Discovery (University College London) (submittedVersion)
  • UPCommons institutional repository (Universitat Politècnica de Catalunya) (submittedVersion, cc-by)
  • Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
  • Apollo (cc-by)
  • ETH Zürich Research Collection
Funders
  • European Molecular Biology Laboratory
  • National Institutes of Health (U24HG007822, 75N93019C00077)
  • National Human Genome Research Institute (U24HG003345)
  • JSPS (16H06279, 19H05688)
  • JST (JPMJCR19S2)
  • MEXT (JPMXD1521474594)
  • Horizon 2020 (676559, 637765)
  • ELIXIR
  • Wellcome (208349/Z/17/Z)
  • National Science Foundation (1917302)
  • Wellcome Trust (WT-218288, WT-212929)
  • Swiss National Science Foundation (186397, 205085)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
Keywords
orthology inference, benchmark dataset, reference proteomes, comparative genomics, phylogenetic analysis
MeSH terms
Phylogeny, Proteome, Genomics

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