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

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...

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Detalles Bibliográficos
Autores principales: Kaleb, Klara, Vesztrocy, Alex Warwick, Altenhoff, Adrian, Dessimoz, Christophe
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2019
Materias:
Software Tool Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6464060/
https://www.ncbi.nlm.nih.gov/pubmed/31001419
http://dx.doi.org/10.12688/f1000research.17548.2
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author Kaleb, Klara
Vesztrocy, Alex Warwick
Altenhoff, Adrian
Dessimoz, Christophe
author_facet Kaleb, Klara
Vesztrocy, Alex Warwick
Altenhoff, Adrian
Dessimoz, Christophe
author_sort Kaleb, Klara
collection PubMed
description 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/.
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spelling pubmed-64640602019-04-17 Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python Kaleb, Klara Vesztrocy, Alex Warwick Altenhoff, Adrian Dessimoz, Christophe F1000Res Software Tool Article 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/. F1000 Research Limited 2019-03-29 /pmc/articles/PMC6464060/ /pubmed/31001419 http://dx.doi.org/10.12688/f1000research.17548.2 Text en Copyright: © 2019 Kaleb K et al. http://creativecommons.org/licenses/by/4.0/ 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.
spellingShingle Software Tool Article
Kaleb, Klara
Vesztrocy, Alex Warwick
Altenhoff, Adrian
Dessimoz, Christophe
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
title Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
title_full Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
title_fullStr Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
title_full_unstemmed Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
title_short Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python
title_sort expanding the orthologous matrix (oma) programmatic interfaces: rest api and the omadb packages for r and python
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6464060/
https://www.ncbi.nlm.nih.gov/pubmed/31001419
http://dx.doi.org/10.12688/f1000research.17548.2
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