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

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State: Public
Version: Final published version
License: CC BY 4.0
Serval ID
serval:BIB_DA9EB0198996
Type
Article: article from journal or magazin.
Collection
Publications
Title
Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python.
Journal
F1000Research
Author(s)
Kaleb K., Vesztrocy A.W., Altenhoff A., Dessimoz C.
ISSN
2046-1402 (Electronic)
ISSN-L
2046-1402
Publication state
Published
Issued date
2019
Peer-reviewed
Oui
Volume
8
Pages
42
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
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
Pubmed
Open Access
Yes
Create date
03/05/2019 16:41
Last modification date
10/10/2019 5:10
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