title: A RESTful API for accessing microbial community data for MG-RAST.
abstract: Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MG-RAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, as well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http://kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase's microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service.
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America; Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Andreas
authors.initials: A
authors.lastname: Wilke
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America; Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Jared
authors.initials: J
authors.lastname: Bischof
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America; Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Travis
authors.initials: T
authors.lastname: Harrison
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America.
authors.forename: Tom
authors.initials: T
authors.lastname: Brettin
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America; Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Mark
authors.initials: M
authors.lastname: D'Souza
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America; Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Gerlach
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America; Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Hunter
authors.initials: H
authors.lastname: Matthews
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America; Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Tobias
authors.initials: T
authors.lastname: Paczian
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America; Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Jared
authors.initials: J
authors.lastname: Wilkening
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America; Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Glass
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America; Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Narayan
authors.initials: N
authors.lastname: Desai
authors.affiliation: Mathematics and Computer Science Division, Argonne National Laboratory, Lemont, Illinois, United States of America; Computation Institute, University of Chicago, Chicago, Illinois, United States of America.
authors.forename: Folker
authors.initials: F
authors.lastname: Meyer
mesh_terms: D003628:Database Management Systems; D030541:Databases, Genetic; D016680:Genome, Bacterial / Q000235:genetics*; D020407:Internet; D056186:Metagenomics / Q000379:methods*; D058977:Molecular Sequence Annotation / Q000379:methods; D012984:Software; D014584:User-Computer Interface