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

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/.

SUBMITTER: Kaleb K

PROVIDER: S-EPMC6464060 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the <i>OmaDB</i> packages for R and Python.

Kaleb Klara K Vesztrocy Alex Warwick AW Altenhoff Adrian A Dessimoz Christophe C

F1000Research 20190110

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 <i>OmaDB</i>. 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://bioconducto ...[more]

PMID: 31001419

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