Pieter Verschaffelt1,2, Philippe Van Thienen1, Tim Van Den Bossche2,3, Felix Van der Jeugt1, Caroline De Tender1,4, Lennart Martens2,3, Peter Dawyndt1, Bart Mesuere1,2. 1. Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent 9000, Belgium. 2. VIB - UGent Center for Medical Biotechnology, Ghent, Belgium. 3. CompOmics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium. 4. Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Merelbeke 9820, Belgium.
Abstract
SUMMARY: Unipept is an ecosystem of tools developed for fast metaproteomics data-analysis consisting of a web application, a set of web services (application programming interface, API) and a command-line interface (CLI). After the successful introduction of version 4 of the Unipept web application, we here introduce version 2.0 of the API and CLI. Next to the existing taxonomic analysis, version 2.0 of the API and CLI provides access to Unipept's powerful functional analysis for metaproteomics samples. The functional analysis pipeline supports retrieval of Enzyme Commission numbers, Gene Ontology terms and InterPro entries for the individual peptides in a metaproteomics sample. This paves the way for other applications and developers to integrate these new information sources into their data processing pipelines, which greatly increases insight into the functions performed by the organisms in a specific environment. Both the API and CLI have also been expanded with the ability to render interactive visualizations from a list of taxon ids. These visualizations are automatically made available on a dedicated website and can easily be shared by users. AVAILABILITY AND IMPLEMENTATION: The API is available at http://api.unipept.ugent.be. Information regarding the CLI can be found at https://unipept.ugent.be/clidocs. Both interfaces are freely available and open-source under the MIT license. CONTACT: pieter.verschaffelt@ugent.be. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: Unipept is an ecosystem of tools developed for fast metaproteomics data-analysis consisting of a web application, a set of web services (application programming interface, API) and a command-line interface (CLI). After the successful introduction of version 4 of the Unipept web application, we here introduce version 2.0 of the API and CLI. Next to the existing taxonomic analysis, version 2.0 of the API and CLI provides access to Unipept's powerful functional analysis for metaproteomics samples. The functional analysis pipeline supports retrieval of Enzyme Commission numbers, Gene Ontology terms and InterPro entries for the individual peptides in a metaproteomics sample. This paves the way for other applications and developers to integrate these new information sources into their data processing pipelines, which greatly increases insight into the functions performed by the organisms in a specific environment. Both the API and CLI have also been expanded with the ability to render interactive visualizations from a list of taxon ids. These visualizations are automatically made available on a dedicated website and can easily be shared by users. AVAILABILITY AND IMPLEMENTATION: The API is available at http://api.unipept.ugent.be. Information regarding the CLI can be found at https://unipept.ugent.be/clidocs. Both interfaces are freely available and open-source under the MIT license. CONTACT: pieter.verschaffelt@ugent.be. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Tim Van Den Bossche; Benoit J Kunath; Kay Schallert; Stephanie S Schäpe; Paul E Abraham; Jean Armengaud; Magnus Ø Arntzen; Ariane Bassignani; Dirk Benndorf; Stephan Fuchs; Richard J Giannone; Timothy J Griffin; Live H Hagen; Rashi Halder; Céline Henry; Robert L Hettich; Robert Heyer; Pratik Jagtap; Nico Jehmlich; Marlene Jensen; Catherine Juste; Manuel Kleiner; Olivier Langella; Theresa Lehmann; Emma Leith; Patrick May; Bart Mesuere; Guylaine Miotello; Samantha L Peters; Olivier Pible; Pedro T Queiros; Udo Reichl; Bernhard Y Renard; Henning Schiebenhoefer; Alexander Sczyrba; Alessandro Tanca; Kathrin Trappe; Jean-Pierre Trezzi; Sergio Uzzau; Pieter Verschaffelt; Martin von Bergen; Paul Wilmes; Maximilian Wolf; Lennart Martens; Thilo Muth Journal: Nat Commun Date: 2021-12-15 Impact factor: 14.919