MG-RAST Overview

RESTful Metagenomics RAST object and resource API For usage note that required parameters need to be passed as path parameters, optional parameters need to be query parameters. If an optional parameter has a list of option values, the first displayed will be used as default.


annotation

Description

All annotations of a metagenome for a specific annotation type and source

info - request

Description

Returns description of parameters and attributes.

This is a synchronous GET request. This request has no parameters.

sequence - request

Description

tab deliminted annotated sequence stream

This is a stream GET request.

Parameters

Example

Return Attributes

similarity - request

Description

tab deliminted blast m8 with annotation

This is a stream GET request.

Parameters

Example

Return Attributes


compute

Description

Calculate various statistics for given input data.

info - request

Description

Returns description of parameters and attributes.

This is a synchronous GET request. This request has no parameters.

alphadiversity - request

Description

Calculate alpha diversity value for given ID and taxon level.

This is a synchronous GET request.

Parameters

Example

Return Attributes

normalize - request

Description

Calculate normalized values for given input data.

This is a synchronous POST request.

Parameters

Example

Return Attributes

significance - request

Description

Calculate significance values for given input data.

This is a synchronous POST request.

Parameters

Example

Return Attributes

heatmap - request

Description

Calculate a dendogram for given input data.

This is a synchronous POST request.

Parameters

Example

Return Attributes

pcoa - request

Description

Calculate a PCoA for given input data.

This is a synchronous POST request.

Parameters

Example

Return Attributes


download

Description

An analysis file from the processing of a metagenome from a specific stage in its analysis

info - request

Description

Returns description of parameters and attributes.

This is a synchronous GET request. This request has no parameters.

instance - request

Description

Returns a single sequence file.

This is a synchronous GET request.

Parameters

Example

Return Attributes

setlist - request

Description

Returns a list of sets of sequence files for the given id.

This is a synchronous GET request.

Parameters

Example

Return Attributes


inbox

Description

inbox receives user inbox data upload, requires authentication, see http://blog.metagenomics.anl.gov/mg-rast-v3-2-faq/#api_submission for details

info - request

Description

Returns description of parameters and attributes.

This is a synchronous GET request. This request has no parameters.

view - request

Description

lists the contents of the user inbox

This is a synchronous GET request.

Parameters

Example

Return Attributes

upload - request

Description

receives user inbox data upload

This is a synchronous POST request.

Parameters

Example

Return Attributes


library

Description

A library of metagenomic samples from some environment

info - request

Description

Returns description of parameters and attributes.

This is a synchronous GET request. This request has no parameters.

query - request

Description

Returns a set of data matching the query criteria.

This is a synchronous GET request.

Parameters

Example

Return Attributes

instance - request

Description

Returns a single data object.

This is a synchronous GET request.

Parameters

Example

Return Attributes


m5nr

Description

M5NR provides data through a comprehensive non-redundant protein / rRNA database

info - request

Description

Returns description of parameters and attributes.

This is a synchronous GET request. This request has no parameters.

ontology - request

Description

Return functional hierarchy

This is a synchronous GET request.

Parameters

Example

Return Attributes

taxonomy - request

Description

Return organism hierarchy

This is a synchronous GET request.

Parameters

Example

Return Attributes

sources - request

Description

Return all sources in M5NR

This is a synchronous GET request.

Parameters

Example

Return Attributes

accession - request

Description

Return annotation of given source protein ID

This is a synchronous GET request.

Parameters

Example

Return Attributes

alias - request

Description

Return annotations for alias IDs containing the given text

This is a synchronous GET request.

Parameters

Example

Return Attributes

md5 - request

Description

Return annotation(s) or sequence of given md5sum (M5NR ID)

This is a synchronous GET request.

Parameters

Example

Return Attributes

function - request

Description

Return annotations for function names containing the given text

This is a synchronous GET request.

Parameters

Example

Return Attributes

organism - request

Description

Return annotations for organism names containing the given text

This is a synchronous GET request.

Parameters

Example

Return Attributes

sequence - request

Description

Return annotation(s) for md5sum (M5NR ID) of given sequence

This is a synchronous GET request.

Parameters

Example

Return Attributes

accession - request

Description

Return annotations of given source protein IDs

This is a synchronous POST request.

Parameters

Example

Return Attributes

alias - request

Description

Return annotations for aliases containing the given texts

This is a synchronous POST request.

Parameters

Example

Return Attributes

md5 - request

Description

Return annotations or sequences of given md5sums (M5NR ID)

This is a synchronous POST request.

Parameters

Example

Return Attributes

function - request

Description

Return annotations for function names containing the given texts

This is a synchronous POST request.

Parameters

Example

Return Attributes

organism - request

Description

Return annotations for organism names containing the given texts

This is a synchronous POST request.

Parameters

Example

Return Attributes

sequence - request

Description

Return annotations for md5s (M5NR ID) of given sequences

This is a synchronous POST request.

Parameters

Example

Return Attributes


matrix

Description

A profile in biom format that contains abundance counts

info - request

Description

Returns description of parameters and attributes.

This is a synchronous GET request. This request has no parameters.

organism - request

Description

Returns a BIOM object.

This is a synchronous or asynchronous GET request.

Parameters

Example

Return Attributes

function - request

Description

Returns a BIOM object.

This is a synchronous or asynchronous GET request.

Parameters

Example

Return Attributes

feature - request

Description

Returns a BIOM object.

This is a synchronous or asynchronous GET request.

Parameters

Example

Return Attributes


metadata

Description

Metagenomic metadata is data providing information about one or more aspects of a set sequences from a sample of some environment

info - request

Description

Returns description of parameters and attributes.

This is a synchronous GET request. This request has no parameters.

template - request

Description

Returns static template for metadata object relationships and types

This is a synchronous GET request.

Parameters

Example

Return Attributes

cv - request

Description

Returns static controlled vocabularies used in metadata. By default returns all CVs at latest version. If label and version options used, returns those specific values.

This is a synchronous GET request.

Parameters

Example

Return Attributes

ontology - request

Description

Returns static ontology used in metadata for the given name and version.

This is a synchronous GET request.

Parameters

Example

Return Attributes

export - request

Description

Returns full nested metadata for a project in same format as template, or metadata for a single metagenome.

This is a synchronous GET request.

Parameters

Example

Return Attributes

import - request

Description

Create project with given metadata spreadsheet and metagenome IDs, either upload or shock node

This is a synchronous POST request.

Parameters

Example

Return Attributes

update - request

Description

Update project with given metadata spreadsheet and metagenome IDs, either upload or shock node

This is a synchronous POST request.

Parameters

Example

Return Attributes

validate - request

Description

Validate given metadata spreadsheet, either upload or shock node

This is a synchronous POST request.

Parameters

Example

Return Attributes

validate - request

Description

Validate given metadata value

This is a synchronous GET request.

Parameters

Example

Return Attributes


metagenome

Description

A metagenome is an analyzed set sequences from a sample of some environment

info - request

Description

Returns description of parameters and attributes.

This is a synchronous GET request. This request has no parameters.

query - request

Description

Returns a set of data matching the query criteria.

This is a synchronous GET request.

Parameters

Example

Return Attributes

instance - request

Description

Returns a single data object.

This is a synchronous GET request.

Parameters

Example

Return Attributes


profile

Description

A profile in biom format that contains abundance and similarity values

info - request

Description

Returns description of parameters and attributes.

This is a synchronous GET request. This request has no parameters.

instance - request

Description

Returns a single data object in BIOM format

This is a synchronous GET request.

Parameters

Return Attributes


project

Description

A project is a composition of samples, libraries and metagenomes being analyzed in a global context.

info - request

Description

Returns description of parameters and attributes.

This is a synchronous GET request. This request has no parameters.

query - request

Description

Returns a set of data matching the query criteria.

This is a synchronous GET request.

Parameters

Example

Return Attributes

instance - request

Description

Returns a single data object.

This is a synchronous GET request.

Parameters

Example

Return Attributes


sample

Description

A metagenomic sample from some environment.

info - request

Description

Returns description of parameters and attributes.

This is a synchronous GET request. This request has no parameters.

query - request

Description

Returns a set of data matching the query criteria.

This is a synchronous GET request.

Parameters

Example

Return Attributes

instance - request

Description

Returns a single data object.

This is a synchronous GET request.

Parameters

Example

Return Attributes


server

Description

The server resource returns information about a server.

info - request

Description

Returns the server information.

This is a synchronous GET request. This request has no parameters.

instance - request

Description

Returns a single user object.

This is a synchronous GET request.

Parameters

Example

Return Attributes


validation

Description

validates templates for correct structure and data to fit a valid template

info - request

Description

Returns description of parameters and attributes.

This is a synchronous GET request. This request has no parameters.

template - request

Description

Checks if the referenced JSON structure is a valid template

This is a synchronous GET request.

Parameters

Example

Return Attributes

data - request

Description

Returns a single data object.

This is a synchronous GET request.

Parameters

Example

Return Attributes