The identification of orthologs is an important cornerstone for many comparative, evolutionary and functional genomics analyses. Yet, the true evolutionary history of genes is generally unknown. Because of the wide range of possible applications and taxonomic interests, benchmarking of orthology predictions remains a difficult challenge for methods developers and users.
This community developed web-service aims at simplifying and standardizing orthology benchmarking. And for the users, the benchmarks provide a way to identify the most effective methods for the problem at hand.
The associated paper to the service has been published open access in Nature Methods. If you use the orthology benchmark service, please consider citing it.
An orthology method developer should first infer the orthologs using the reference proteome dataset. The service will assess the induced pairwise orthologous relations. Therefore the method developer must provide the predictions in a format from which the pairwise orthologous predictions can be extracted in an unambiguous way.
Once the predictions have been uploaded, the service ensures that only predictions among valid reference proteomes are provided. Benchmarks are then selected and run in parallel. Finally, statistical analyses of method accuracy are performed on each benchmark dataset. The raw data and summary results in form of precision-recall curves are stored and provided to the submitter.
Orthology inference is most often based on molecular protein sequences. For a comparison of different orthology prediction methods, a common set of sequences must be established. Therefore, only identical proteins are mapped to each other.
To make comparisons of method easier, the orthology research community has agreed in 2009 to established a common QfO reference proteome dataset. Currently we are using the reference proteomes from 2018_04 and 2020_04 for benchmarking. The 2011 dataset can no longer be used for benchmarking, but the results of the public projects stay for reference.
We encourage to use always the newest dataset: Established resources should run their pipeline on all datasets, including the cutting edge dataset 2020_04. Emerging tools and resources should at least use the latest stable 2018_04 dataset, which allows to compare the predictions against a large set of established orthology inference resources.
All releases of the QfO Reference Proteomes are available from UniProtKB's archive FTP server. The currently recommended datasets for benchmarking are:
Our benchmarks assess orthology on the bases of protein pairs. Therefore, we ask our users to upload their prediction in a format from which we can extract pairwise relations in an unambiguous manner: We support
Adrian M Altenhoff, Brigitte Boeckmann, Salvador Capella-Gutierrez, Daniel A Dalquen, Todd DeLuca, Kristoffer Forslund, Jaime Huerta-Cepas, Benjamin Linard, Cécile Pereira, Leszek P Pryszcz, Fabian Schreiber, Alan Sousa da Silva, Damian Szklarczyk, Clément-Marie Train, Peer Bork, Odile Lecompte, Christian von Mering, Ioannis Xenarios, Kimmen Sjölander, Lars Juhl Jensen, Maria J Martin, Matthieu Muffato, Toni Gabaldón, Suzanna E Lewis, Paul D Thomas, Erik Sonnhammer, Christophe Dessimoz.
Standardized benchmarking in the quest for orthologs.
Nature Methods, 2016, 13, 425-430 Full text
Adrian M Altenhoff, Javier Garrayo-Ventas, Salvatore Cosentino, David Emms, Natasha M Glover, Ana Hernández-Plaza, Yannis Nevers, Vicky Sundesha, Damian Szklarczyk, José M Fernández, Laia Codó, the Quest for Orthologs Consortium, Josep Ll Gelpi, Jaime Huerta-Cepas, Wataru Iwasaki, Steven Kelly, Odile Lecompte, Matthieu Muffato, Maria J Martin, Salvador Capella-Gutierrez, Paul D Thomas, Erik Sonnhammer, Christophe Dessimoz
The Quest for Orthologs benchmark service and consensus calls in 2020.
Nucleic Acids Res, 2020, 48:W1, W538–W545 Full text
OpenEBench is an infra-structure designed to establish a continuous automated benchmarking system for bioinformatics methods, tools and web services. It is being developed so as to cater for the needs of the bioinformatics community, especially software developers who need an objective and quantitative way to inform their decisions as well as the larger community of end-users, in their search for unbiased and up-to-date evaluation of bioinformatics methods.
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