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Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python

Kaleb, K; Warwick Vesztrocy, A; Altenhoff, A; Dessimoz, C; (2019) Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python. (F1000Research 8:42). F1000 Research Ltd. Green open access

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Abstract

The Orthologous Matrix (OMA) is a well-established resource to identify orthologs among many genomes. Here, we present two recent additions to its programmatic interface, namely a REST API, and user-friendly R and Python packages called OmaDB . These should further facilitate the incorporation of OMA data into computational scripts and pipelines. The REST API can be freely accessed at https://omabrowser.org/api . The R OmaDB package is available as part of Bioconductor at http://bioconductor.org/packages/OmaDB/ , and the omadb Python package is available from the Python Package Index (PyPI) at https://pypi.org/project/omadb/ .

Type: Working / discussion paper
Title: Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
Open access status: An open access version is available from UCL Discovery
DOI: 10.12688/f1000research.17548.1
Publisher version: https://doi.org/10.12688/f1000research.17548.1
Language: English
Additional information: Copyright: © 2019 Kaleb K et al. This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Keywords: orthologs, paralogs, hierarchical orthologous groups, comparative genomics, orthologous matrix, oma, API, R, python, REST, bioconductor
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
UCL > Provost and Vice Provost Offices > UCL BEAMS
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences
UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Mathematics
URI: https://discovery.ucl.ac.uk/id/eprint/10066392
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