Paper Info
Title
Accessing the SEED genome databases via Web services API: tools for programmers.
Abstract
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.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.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.
Year
DOI
Venue
2010
10.1186/1471-2105-11-319
BMC Bioinformatics
Keywords
Field
DocType
bioinformatics,metagenomics,programming language,genome annotation,algorithms,user interface,microarrays,genome,genome sequence,web service
Genome,World Wide Web,Annotation,Genome project,Computer science,Metagenomics,SOAP,Application programming interface,Bioinformatics,Web service,Vertebrate and Genome Annotation Project,Database
Journal
Volume
Issue
ISSN
11
1
1471-2105
Citations 
PageRank 
References 
14
0.73
9
Authors
8
Name
Order
Citations
PageRank
Terry Disz140728.23
Sajia Akhter2140.73
Daniel Cuevas3141.07
Robert Olson450838.89
Ross A. Overbeek5760234.40
Veronika Vonstein614510.65
Rick Stevens7140.73
Rick L. Stevens81327135.40