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

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

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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Main Authors: Klara Kaleb, Alex Warwick Vesztrocy, Adrian Altenhoff, Christophe Dessimoz
Format: Article
Language:English
Published: F1000 Research Ltd 2019-03-01
Series:F1000Research
Online Access:https://f1000research.com/articles/8-42/v2
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spelling doaj-800bafe308484009b8adb48219d4a2b72020-11-25T03:18:50ZengF1000 Research LtdF1000Research2046-14022019-03-01810.12688/f1000research.17548.220395Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python [version 2; peer review: 2 approved]Klara Kaleb0Alex Warwick Vesztrocy1Adrian Altenhoff2Christophe Dessimoz3Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UKCentre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, UKDepartment of Computer Science, ETH Zurich, Zurich, SwitzerlandDepartment of Computer Science, University College London, London, WC1E 6BT, SwitzerlandThe 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/.https://f1000research.com/articles/8-42/v2
collection DOAJ
language English
format Article
sources DOAJ
author Klara Kaleb
Alex Warwick Vesztrocy
Adrian Altenhoff
Christophe Dessimoz
spellingShingle Klara Kaleb
Alex Warwick Vesztrocy
Adrian Altenhoff
Christophe Dessimoz
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python [version 2; peer review: 2 approved]
F1000Research
author_facet Klara Kaleb
Alex Warwick Vesztrocy
Adrian Altenhoff
Christophe Dessimoz
author_sort Klara Kaleb
title Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python [version 2; peer review: 2 approved]
title_short Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python [version 2; peer review: 2 approved]
title_full Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python [version 2; peer review: 2 approved]
title_fullStr Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python [version 2; peer review: 2 approved]
title_full_unstemmed Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python [version 2; peer review: 2 approved]
title_sort expanding the orthologous matrix (oma) programmatic interfaces: rest api and the omadb packages for r and python [version 2; peer review: 2 approved]
publisher F1000 Research Ltd
series F1000Research
issn 2046-1402
publishDate 2019-03-01
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/.
url https://f1000research.com/articles/8-42/v2
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AT adrianaltenhoff expandingtheorthologousmatrixomaprogrammaticinterfacesrestapiandtheomadbpackagesforrandpythonversion2peerreview2approved
AT christophedessimoz expandingtheorthologousmatrixomaprogrammaticinterfacesrestapiandtheomadbpackagesforrandpythonversion2peerreview2approved
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