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

Disz, Terry; Akhter, Sajia; Cuevas, Daniel; Olson, Robert; Overbeek, Ross; Vonstein, Veronika; Stevens, Rick; Edwards, Robert A.

doi:10.1186/1471-2105-11-319

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

Journal Article · Mon Jun 14 00:00:00 EDT 2010 · BMC Bioinformatics

DOI:https://doi.org/10.1186/1471-2105-11-319· OSTI ID:1626269

Disz, Terry ^[1]; Akhter, Sajia ^[2]; Cuevas, Daniel ^[3]; Olson, Robert ^[4]; Overbeek, Ross ^[5]; Vonstein, Veronika ^[5]; Stevens, Rick ^[4]; Edwards, Robert A. ^[6]

Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division; Univ. of Chicago, IL (United States). Computation Inst.; DOE/OSTI
San Diego State Univ., CA (United States). Computational Sciences Research Center
San Diego State Univ., CA (United States). Dept. of Computer Science
Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division
Fellowship for the Interpretation of Genomes, Burr Ridge, IL (United States)
Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division; San Diego State Univ., CA (United States). Computational Sciences Research Center and Dept. of Computer Science

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.

View Accepted Manuscript (DOE)

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States)

Sponsoring Organization:: National Institute of Allergy and Infectious Diseases (NIAID); National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-06CH11357

OSTI ID:: 1626269

Journal Information:: BMC Bioinformatics, Journal Name: BMC Bioinformatics Journal Issue: 1 Vol. 11; ISSN 1471-2105

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

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

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