DeCIFR REST API to TBAS V2

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The DeCIFR REST API service allows access to results of a previous run of T-BAS v2 via HTTP with a browser request, programmatically, or using a command line tool such as CURL.

REST allows the user to submit a query to retrieve specific metadata associated with a leaf on T-BAS reference tree or to retrieve the taxonomic assignment and metadata of an unknown placement on the tree.

For retrieving data using HTML requests the query of a resource starts with https://tools.decifr.hpc.ncsu.edu/rest/html/ in the URL name, followed by the T-BAS run number (e.g. YJCK3WI4) and a keyword of the type of data retrieved (e.g. placements). The full HTML request to retrieve the placement results in this example would look like this:

https://tools.decifr.hpc.ncsu.edu/rest/html/YJCK3WI4/placements

This will return the taxonomic assignments of all unknowns that were placed using the Pezizomycotina reference tree in run YJCK3WI4. The placements are shown in a web page as formatted JSON output files embedded in HTML. Other examples of information that can be retrieved are shown below.

Examples using HTML

Pages require login with T-BAS PIN.
List of placements on a treehttps://tools.decifr.hpc.ncsu.edu/rest/html/YJCK3WI4/placements
List of leaves (terminals) on a treehttps://tools.decifr.hpc.ncsu.edu/rest/html/YJCK3WI4/leaves
Metadata of a leafhttps://tools.decifr.hpc.ncsu.edu/rest/html/YJCK3WI4?query=Schizosaccharomyces_pombe
Metadata and taxonomy of a specific placementhttps://tools.decifr.hpc.ncsu.edu/rest/html/YJCK3WI4?placement=6407_endo

A query of a resource starting with https://tools.decifr.hpc.ncsu.edu/rest/json/ will return the requested data in JSON format. Authorization is by authentication header credentials submitted in the request.

Examples using JSON

Request requires username and password (Note this is not the same as T-BAS PIN).
List of placements on a tree as JSONhttps://tools.decifr.hpc.ncsu.edu/rest/json/YJCK3WI4/placements
List of leaves (terminals) on a tree as JSONhttps://tools.decifr.hpc.ncsu.edu/rest/json/YJCK3WI4/leaves

CURL is a command line tool that can be used to transfer data with URLs. CURL makes it easy to retrieve taxonomic assignment results from T-BAS into other tools and pipelines.

Examples using command line

Request requires username and password (Note this is not the same as T-BAS PIN).
List of placements on a tree as JSONcurl https://user:pass@tools.decifr.hpc.ncsu.edu/rest/json/YJCK3WI4/placements
List of leaves (terminals) on a tree as JSONcurl https://user:pass@tools.decifr.hpc.ncsu.edu/rest/json/YJCK3WI4/leaves

Links for example data

list of leaves or terminals list of placements