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. 2019 Jan 10:8:42.
doi: 10.12688/f1000research.17548.2. eCollection 2019.

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

Klara Kaleb  1 , Alex Warwick Vesztrocy  1   2 , Adrian Altenhoff  2   3 , Christophe Dessimoz  1   2   4   5   6
Affiliations

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

Klara Kaleb et al. F1000Res. .

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/.

Keywords: API; R; REST; bioconductor; comparative genomics; hierarchical orthologous groups; oma; orthologous matrix; orthologs; paralogs; python.

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Conflict of interest statement

No competing interests were disclosed.

Figures

Figure 1.
Figure 1.. Showcase of the OMA REST API documentation page, with an example of the interactive query and response.
Figure 2.
Figure 2.. Species taxonomy tree obtained using example 3.
Figure 3.
Figure 3.. Distribution of evolutionary distances (in PAM units; 27) human-dog (red) and human-mouse (blue) pairs, obtained using example 4.
See this image and copyright information in PMC

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