Abstract
BackgroundThe MG-RAST API provides search capabilities and delivers organism and function data as well as raw or annotated sequence data via the web interface and its RESTful API. For casual users, however, RESTful APIs are hard to learn and work with.ResultsWe created the graphical MG-RAST API explorer to help researchers more easily build and export API queries; understand the data abstractions and indices available in MG-RAST; and use the results presented in-browser for exploration, development, and debugging.ConclusionsThe API explorer lowers the barrier to entry for occasional or first-time MG-RAST API users.
Highlights
The MG-RAST application programming interface (API) provides search capabilities and delivers organism and function data as well as raw or annotated sequence data via the web interface and its RESTful API
In addition to storing metadata about the datasets, MG-RAST stores the results of the sequence analysis, indexed to allow querying by organism name, taxonomic names from the National Center for Biotechnology Information (NCBI) taxonomy, or protein function
Private datasets can be securely accessed by adding “&auth = MGRKEY” to Uniform resource locator (URL) used in any browser or – H “Authorization: mgrast MGRKEY” to the command line for curl, where MGRKEY is replaced by the text of the MG-RAST authentication key, a password-like string that is available from the user’s upload page
Summary
Environmental DNA sequence analysis (i.e., metagenomics) is gaining popularity and is frequently used by researchers who are not specialists in genomics or bioinformatics [1]. Remote computation, data management, and indexing of large-scale metagenomic data are a growing community need and will be key features of any future bioinformatics landscape. Hosted services such as MG-RAST [5], the EBI Metagenomics Portal [5], and the U.S Department of Energy’s JGI IMG/M [6] provide web interfaces to access the data, computational results, and search results. These interfaces often are limited to predefined queries, even if the underlying data and indexing support additional query capabilities. Like all of MG-RAST, the API explorer is available as open source software on GitHub at https://github.com/ MG-RAST under a BSD-style license
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