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/.
Highlights
Orthologs are pairs of protein coding genes that have common ancestry and have diverged due to speciation events[1]
We start by describing the Orthologous Matrix (OMA) Representational State Transfer (REST) Application Programming Interface (API), before moving on to detail the OmaDB Bioconductor package, and outline the omadb Python package
Since the backend of the OMA browser is almost fully based on Python and its frontend is supported by the Django web framework[8], we have opted to use the Django Rest Framework (DRF) to implement a REST API in our latest release[4]
Summary
Orthologs are pairs of protein coding genes that have common ancestry and have diverged due to speciation events[1]. The detection of orthologs is of fundamental importance in many fields in biology, such as comparative genomics, as it allows us to propagate existing biological knowledge to ever growing newly sequenced data[2,3]. The Orthologous Matrix (OMA) is a method and resource for the inference of orthologs among complete genomes[4]. The OMA browser has supported multiple ways of exporting the underlying data from its beginning. Early OMA database releases offered an Application Programming Interface (API) in the form of the Simple Object Access Protocol (SOAP). The complexity and limited adoption of SOAP has prompted us to recently switch to the simpler, faster, and more widely used Representational State Transfer (REST) protocol for the OMA API4. We provide a description of this new OMA REST API
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