Accessing the SEED Genome Databases via Web Services API: Tools for Programmers
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 commonmore »
- Authors:
-
- Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Division; Univ. of Chicago, IL (United States). Computation Inst.
- 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
- Publication Date:
- Research Org.:
- Argonne National Laboratory (ANL), Argonne, IL (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Institutes of Health (NIH); National Institute of Allergy and Infectious Diseases (NIAID)
- OSTI Identifier:
- 1626269
- Grant/Contract Number:
- AC02-06CH11357; HHSN266200400042C
- Resource Type:
- Accepted Manuscript
- Journal Name:
- BMC Bioinformatics
- Additional Journal Information:
- Journal Volume: 11; Journal Issue: 1; Journal ID: ISSN 1471-2105
- Publisher:
- BioMed Central
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Biochemistry & Molecular Biology; Biotechnology & Applied Microbiology; Mathematical & Computational Biology; Application Programming Interface; Microbial Genome; Simple Object Access Protocol; Seed Family; Seed Database
Citation Formats
Disz, Terry, Akhter, Sajia, Cuevas, Daniel, Olson, Robert, Overbeek, Ross, Vonstein, Veronika, Stevens, Rick, and Edwards, Robert A. Accessing the SEED Genome Databases via Web Services API: Tools for Programmers. United States: N. p., 2010.
Web. doi:10.1186/1471-2105-11-319.
Disz, Terry, Akhter, Sajia, Cuevas, Daniel, Olson, Robert, Overbeek, Ross, Vonstein, Veronika, Stevens, Rick, & Edwards, Robert A. Accessing the SEED Genome Databases via Web Services API: Tools for Programmers. United States. https://doi.org/10.1186/1471-2105-11-319
Disz, Terry, Akhter, Sajia, Cuevas, Daniel, Olson, Robert, Overbeek, Ross, Vonstein, Veronika, Stevens, Rick, and Edwards, Robert A. Mon .
"Accessing the SEED Genome Databases via Web Services API: Tools for Programmers". United States. https://doi.org/10.1186/1471-2105-11-319. https://www.osti.gov/servlets/purl/1626269.
@article{osti_1626269,
title = {Accessing the SEED Genome Databases via Web Services API: Tools for Programmers},
author = {Disz, Terry and Akhter, Sajia and Cuevas, Daniel and Olson, Robert and Overbeek, Ross and Vonstein, Veronika and Stevens, Rick and Edwards, Robert A.},
abstractNote = {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.},
doi = {10.1186/1471-2105-11-319},
journal = {BMC Bioinformatics},
number = 1,
volume = 11,
place = {United States},
year = {Mon Jun 14 00:00:00 EDT 2010},
month = {Mon Jun 14 00:00:00 EDT 2010}
}
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