F1000Research (Mar 2019)

Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python [version 2; peer review: 2 approved]

  • Klara Kaleb,
  • Alex Warwick Vesztrocy,
  • Adrian Altenhoff,
  • Christophe Dessimoz

DOI
https://doi.org/10.12688/f1000research.17548.2
Journal volume & issue
Vol. 8

Abstract

Read online

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/.