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Accessing the SEED Genome Databases via Web Services API: Tools for Programmers

Terry Disz12, Sajia Akhter3, Daniel Cuevas5, Robert Olson1, Ross Overbeek4, Veronika Vonstein4, Rick Stevens1 and Robert A Edwards135*

Author Affiliations

1 Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA

2 Computation Institute, University of Chicago, Chicago, IL 60637, USA

3 Computational Sciences Research Center, San Diego State University, San Diego, CA 92182, USA

4 Fellowship for the Interpretation of Genomes, Burr Ridge, IL, 60527, USA

5 Department of Computer Science, San Diego State University, San Diego, CA 92182, USA

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BMC Bioinformatics 2010, 11:319  doi:10.1186/1471-2105-11-319

Published: 14 June 2010

Abstract

Background

The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups.

Results

The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java.

Conclusions

We present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.