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A RESTful API for accessing microbial community data for MG-RAST.

Andreas Wilke1, Jared Bischof1, Travis Harrison1

  • 1Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America; Computation Institute, University of Chicago, Chicago, Illinois, United States of America.

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Summary
This summary is machine-generated.

The MG-RAST system now offers a web services API, expanding data access and enabling third-party analysis for metagenomic sequencing projects. This enhances the utility of MG-RAST for researchers and developers.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Microbial Genomics

Background:

  • Metagenomic sequencing generates vast datasets, with MG-RAST annotating over 110,000 datasets by summer 2013.
  • Existing MG-RAST infrastructure has limitations in comparative analysis and comprehensive tool availability for growing user demands.
  • Increased adoption of metagenomic sequencing necessitates improved data accessibility and analytical capabilities.

Purpose of the Study:

  • To enhance data retrieval and analysis capabilities for the MG-RAST platform.
  • To enable the integration of third-party analysis tools with MG-RAST data.
  • To provide programmatic access to MG-RAST data and analysis results.

Main Methods:

  • Implementation of a RESTful web services API for MG-RAST.
  • Exposing all MG-RAST data and objects as JSON objects via the API.
  • Developing the API as part of the DOE Systems Biology Knowledgebase (KBase) project.

Main Results:

  • The API provides comprehensive access to sequence data, quality control results, and annotations.
  • All MG-RAST data and pipeline-generated objects are accessible through the API.
  • Code examples in multiple languages are provided to facilitate user adoption and integration.

Conclusions:

  • The new web services API significantly expands access to MG-RAST data.
  • The API enhances the utility of MG-RAST by supporting third-party tools and advanced analyses.
  • This development serves as a foundation for KBase's microbial community analysis capabilities.