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accessing the seed genome databases via web services api tools for programmers通过web服务api访问种子基因组数据库程序员的工具.pdf

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accessing the seed genome databases via web services api tools for programmers通过web服务api访问种子基因组数据库程序员的工具

Disz et al. BMC Bioinformatics 2010, 11:319 /1471-2105/11/319 S O F T W A R E Open Access Software Accessing the SEED Genome Databases via Web Services API: Tools for Programmers 1,2 3 5 1 4 4 1 Terry Disz , Sajia Akhter , Daniel Cuevas , Robert Olson , Ross Overbeek , Veronika Vonstein , Rick Stevens and Robert A Edwards*1,3,5 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 acc