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Unipept CLI 2.0 : adding support for visualisations and functional annotations

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Abstract
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.
Keywords
Statistics and Probability, Computational Theory and Mathematics, Biochemistry, Molecular Biology, Computational Mathematics, Computer Science Applications

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MLA
Verschaffelt, Pieter, et al. “Unipept CLI 2.0 : Adding Support for Visualisations and Functional Annotations.” BIOINFORMATICS, 2020, doi:10.1093/bioinformatics/btaa553.
APA
Verschaffelt, P., Van Thienen, P., Van Den Bossche, T., Van der Jeugt, F., De Tender, C., Martens, L., … Mesuere, B. (2020). Unipept CLI 2.0 : adding support for visualisations and functional annotations. BIOINFORMATICS. https://doi.org/10.1093/bioinformatics/btaa553
Chicago author-date
Verschaffelt, Pieter, Philippe Van Thienen, Tim Van Den Bossche, Felix Van der Jeugt, Caroline De Tender, Lennart Martens, Peter Dawyndt, and Bart Mesuere. 2020. “Unipept CLI 2.0 : Adding Support for Visualisations and Functional Annotations.” BIOINFORMATICS. https://doi.org/10.1093/bioinformatics/btaa553.
Chicago author-date (all authors)
Verschaffelt, Pieter, Philippe Van Thienen, Tim Van Den Bossche, Felix Van der Jeugt, Caroline De Tender, Lennart Martens, Peter Dawyndt, and Bart Mesuere. 2020. “Unipept CLI 2.0 : Adding Support for Visualisations and Functional Annotations.” BIOINFORMATICS. doi:10.1093/bioinformatics/btaa553.
Vancouver
1.
Verschaffelt P, Van Thienen P, Van Den Bossche T, Van der Jeugt F, De Tender C, Martens L, et al. Unipept CLI 2.0 : adding support for visualisations and functional annotations. BIOINFORMATICS. 2020;
IEEE
[1]
P. Verschaffelt et al., “Unipept CLI 2.0 : adding support for visualisations and functional annotations,” BIOINFORMATICS, 2020.
@article{8667500,
  abstract     = {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.},
  author       = {Verschaffelt, Pieter and Van Thienen, Philippe and Van Den Bossche, Tim and Van der Jeugt, Felix and De Tender, Caroline and Martens, Lennart and Dawyndt, Peter and Mesuere, Bart},
  issn         = {1367-4803},
  journal      = {BIOINFORMATICS},
  keywords     = {Statistics and Probability,Computational Theory and Mathematics,Biochemistry,Molecular Biology,Computational Mathematics,Computer Science Applications},
  language     = {eng},
  pages        = {3},
  title        = {Unipept CLI 2.0 : adding support for visualisations and functional annotations},
  url          = {http://dx.doi.org/10.1093/bioinformatics/btaa553},
  year         = {2020},
}

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