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

Autor: Kaleb K; Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK., Vesztrocy AW; Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.; Swiss Institute of Bioinformatics, Lausanne, Switzerland., Altenhoff A; Swiss Institute of Bioinformatics, Lausanne, Switzerland.; Department of Computer Science, ETH Zurich, Zurich, Switzerland., Dessimoz C; Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UK.; Swiss Institute of Bioinformatics, Lausanne, Switzerland.; Department of Computer Science, University College London, London, WC1E 6BT, Switzerland.; Department of Computational Biology, University of Lausanne, Lausanne, 1015, Switzerland.; Center for Integrative Genomics, University of Lausanne, Lausanne, 1015, Switzerland.
Jazyk: angličtina
Zdroj: F1000Research [F1000Res] 2019 Jan 10; Vol. 8, pp. 42. Date of Electronic Publication: 2019 Jan 10 (Print Publication: 2019).
DOI: 10.12688/f1000research.17548.2
Abstrakt: 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/.
Competing Interests: No competing interests were disclosed.
Databáze: MEDLINE
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