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

Area of Science:

• Bioinformatics
• Genomics
• Computational Biology

Background:

• The Orthologous Matrix (OMA) is a key resource for identifying orthologs across diverse genomes.
• Efficient programmatic access to OMA data is crucial for large-scale comparative genomics studies.

Purpose of the Study:

• To introduce new programmatic interfaces for the OMA resource.
• To enhance the accessibility and usability of OMA ortholog data for researchers.

Main Methods:

• Development and release of a REST API for the OMA database.
• Creation of user-friendly R (OmaDB) and Python (omadb) packages.
• Integration of these tools with existing bioinformatics platforms like Bioconductor and PyPI.

Main Results:

• A publicly accessible REST API is now available at https://omabrowser.org/api.
• The OmaDB R package is available via Bioconductor.
• The omadb Python package is distributed through the Python Package Index (PyPI).

Conclusions:

• The new programmatic interfaces significantly improve the integration of OMA ortholog data into computational pipelines.
• These tools lower the barrier for researchers to utilize comprehensive orthology information in their analyses.
• Expanded programmatic access is expected to foster wider adoption and application of OMA data in genomic research.