The MG-RAST API covers most of the functionality available through the MG-RAST website, with access to annotations, analyses, metadata and access to the MG-RAST user inbox to view contents as well as upload files. All sequence data and data products from intermediate stages in the analysis pipeline are available for download. Other resources provide services not available through the website, e.g. the m5nr resource lets you query the m5nr database.
Each query to the API is represented as a URI beginning with "http://api.mg-rast.org/" and has a defined structure to pass the requests and parameters to the API server.
The URI queries can be used from the command line, e.g. using curl, in a browser, or incorporated in a shell script or program.
Each URI has the form
"http://api.mg-rast.org/{version}/{resourcepath}?{querystring}"The {version} value (currently '1') explicitly directs the request to a specific version of the API, if it is omitted the latest API version will be used.
The resource path is constructed from the path parameters listed below to define a specific resource and the optional query string is used to filter the results obtained for the resource. For example:
http://api.mg-rast.org/1/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt
In this example the resource path "annotation/sequence/mgm4447943.3" defines a request for the annotated sequences for the MG-RAST job with ID 4447943.3.
The optional query string "evalue=10&type=organism&source=SwissProt" modifies the results by setting an evalue cutoff, annotation type and database source.
The API provides an authentication mechanism for access to private MG-RAST jobs and users' inbox. The 'auth_key' (or 'webkey') is a 25 character long string (e.g. 'j6FNL61ekNarTgqupMma6eMx5') which is used by the API to identify an MG-RAST user account and determine access rights to metagenomes. Note that the auth_key is valid for a limited time after which queries using the key will be rejected. You can create a new auth_key or view the expiration date and time of an existing auth_key on the MG-RAST website. An account can have only one valid auth_key and creating a new key will invalidate an existing key.
All public data in MG-RAST is available without an auth_key. All API queries for private data which either do not have an auth_key or use an invalid or expired auth_key will get a "insufficient permissions to view this data" response.
The auth_key can be included in the query string like:
http://api.mg-rast.org/1/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt&auth=j6FNL61ekNarTgqupMma6eMx5
or in a request using curl like:
curl -X GET -H "auth: j6FNL61ekNarTgqupMma6eMx5" "http://api.mg-rast.org/1/annotation/sequence/mgm4447943.3?evalue=10&type=organism&source=SwissProt"
Note that for the curl command the quotes are necessary for the query to be passed to the API correctly.
If an optional parameter passed through the query string has a list of values only the first will be used. When multiple values are required, e.g. for multiple md5 checksum values, they can be passed to the API like:
curl -X POST -d '{"data":["000821a2e2f63df1a3873e4b280002a8","15bf1950bd9867099e72ea6516e3d602"]}' "http://api.mg-rast.org/m5nr/md5"In some cases, the data requested is in the form of a list with a large number of entries. In these cases the limit and offset parameters can be used to step through the list, for example:
http://api.mg-rast.org/1/project?order=name&limit=20&offset=100
will limit the number of entries returned to 20 with an offset of 100. If these parameters are not provided default values of limit=10 and offset=0 are used. The returned JSON structure will contain the 'next' and 'prev' (previous) URIs to simplify stepping through the list.
The data returned may be plain text, compressed gzipped files or a JSON structure.
Most API queries are 'synchronous' and results are returned immediately. Some queries may require a substantial time to compute results, in these cases you can select the asynchronous option by adding '&asynchronous=1' to the end of the query string. This query will then return a URL which will return the query results when they are ready.
All annotations of a metagenome for a specific annotation type and source
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
tab delimited annotated sequence stream
This is a stream GET request.
negative exponent value for maximum e-value cutoff: default is 5
This is an optional parameter and may be passed in the query string.
text string to filter annotations by: only return those that contain text
This is an optional parameter and may be passed in the query string.
hierarchal level to filter annotations by, for organism or ontology only
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
percent value for minimum % identity cutoff: default is 60
This is an optional parameter and may be passed in the query string.
value for minimum alignment length cutoff: default is 15
This is an optional parameter and may be passed in the query string.
do not use any cutoffs. default is to use default cutoffs
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
M5NR version, default is 1
This is an optional parameter and may be passed in the query string.
unique metagenome identifier
This is a required parameter and must be passed as a REST parameter.
This attribute has an object structure:
tab delimited annotated sequence stream
This is a stream POST request.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
md5 to get hits for
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
M5NR version, default is 1
This parameter must be passed in the message body.
unique metagenome identifier
This is a required parameter and must be passed as a REST parameter.
This attribute has an object structure:
tab delimited blast m8 with annotation
This is a stream GET request.
negative exponent value for maximum e-value cutoff: default is 5
This is an optional parameter and may be passed in the query string.
text string to filter annotations by: only return those that contain text
This is an optional parameter and may be passed in the query string.
hierarchal level to filter annotations by, for organism or ontology only
This is an optional parameter and may be passed in the query string.
percent value for minimum % identity cutoff: default is 60
This is an optional parameter and may be passed in the query string.
value for minimum alignment length cutoff: default is 15
This is an optional parameter and may be passed in the query string.
do not use any cutoffs. default is to use default cutoffs
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
M5NR version, default is 1
This is an optional parameter and may be passed in the query string.
unique metagenome identifier
This is a required parameter and must be passed as a REST parameter.
This attribute has an object structure:
tab delimited blast m8 with annotation
This is a stream POST request.
md5 to get hits for
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
M5NR version, default is 1
This parameter must be passed in the message body.
unique metagenome identifier
This is a required parameter and must be passed as a REST parameter.
This attribute has an object structure:
Calculate various statistics for given input data.
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Calculate alpha diversity value for given ID and taxon level.
This is a synchronous or asynchronous GET request.
M5NR annotation version, default 1
This is an optional parameter and may be passed in the query string.
if true return process id to query status resource for results, default is false
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
unique object identifier
This is a required parameter and must be passed as a REST parameter.
alpha diversity value
unique metagenome identifier
resource location of this object instance
Calculate rarefaction x-y coordinates for given ID and taxon level.
This is a synchronous or asynchronous GET request.
if true also return alphadiversity, default is false
This is an optional parameter and may be passed in the query string.
M5NR annotation version, default 1
This is an optional parameter and may be passed in the query string.
if true return process id to query status resource for results, default is false
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
force rerun and set retry number, default is zero - no retry
This is an optional parameter and may be passed in the query string.
number of sequences in metagenome
This is an optional parameter and may be passed in the query string.
unique object identifier
This is a required parameter and must be passed as a REST parameter.
rarefaction value
unique metagenome identifier
resource location of this object instance
Produce NCBI-BLAST sequence alinments for given md5sum and its hits.
This is a synchronous or asynchronous GET request.
M5NR annotation version, default 1
This is an optional parameter and may be passed in the query string.
if true return process id to query status resource for results, default is false
This is an optional parameter and may be passed in the query string.
exponent value for evalue cutoff, default is 5 (e-5)
This is an optional parameter and may be passed in the query string.
md5sum of M5NR feature to search against
This is an optional parameter and may be passed in the query string.
if true input md5sum is RNA feature, default is false (md5sum is protein)
This is an optional parameter and may be passed in the query string.
unique object identifier
This is a required parameter and must be passed as a REST parameter.
text blob of BLAT sequence alignment
unique metagenome identifier
resource location of this object instance
Calculate normalized values for given input data.
This is a synchronous POST request.
column id
This parameter must be passed in the message body.
raw value
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
row id
This parameter must be passed in the message body.
column id
normalized value
row id
Calculate a distance matrix for given input data.
This is a synchronous POST request.
column id
This parameter must be passed in the message body.
raw or normalized value
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
option to use raw data (not normalize)
This parameter must be passed in the message body.
row id
This parameter must be passed in the message body.
column id
distance value
row id
Calculate a dendrogram for given input data.
This is a synchronous POST request.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
column id
This parameter must be passed in the message body.
raw or normalized value
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
option to use raw data (not normalize)
This parameter must be passed in the message body.
row id
This parameter must be passed in the message body.
dendrogram object for columns
column id index
column id
normalized value
dendrogram object for rows
row id index
row id
Calculate a PCoA for given input data.
This is a synchronous POST request.
column id
This parameter must be passed in the message body.
raw or normalized value
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
option to use raw data (not normalize)
This parameter must be passed in the message body.
row id
This parameter must be passed in the message body.
This attribute has an object structure:
average principal component value
An analysis file from the processing of a metagenome from a specific stage in its analysis
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Returns a darkmatter sequence file.
This is a synchronous GET request.
unique metagenome identifier
This is a required parameter and must be passed as a REST parameter.
unique metagenome identifier
md5sum of file
name of the file
size of file in bytes
cv
resource location of this object instance
An analysis file from the processing of a metagenome from a specific stage in its analysis
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Returns a single sequence file.
This is a synchronous GET request.
file name or identifier
This is an optional parameter and may be passed in the query string.
if true return one time link for download and not file stream
This is an optional parameter and may be passed in the query string.
unique metagenome identifier
This is a required parameter and must be passed as a REST parameter.
requested analysis file
Summary of MG-RAST analysis-pipeline workflow and commands.
This is a synchronous GET request.
optional: AWE ID of MG-RAST metagenome
This is an optional parameter and may be passed in the query string.
if true (and user is admin) delete original document from AWE on completion.
This is an optional parameter and may be passed in the query string.
if true, recreate document in Shock from AWE.
This is an optional parameter and may be passed in the query string.
unique metagenome identifier
This is a required parameter and must be passed as a REST parameter.
requested workflow file
Returns a list of sets of sequence files for the given id.
This is a synchronous GET request.
stage name or identifier
This is an optional parameter and may be passed in the query string.
unique metagenome identifier
This is a required parameter and must be passed as a REST parameter.
unique identifier of file in stage
name of the analysis file
unique metagenome identifier
three digit numerical identifier of the stage
name of the stage in processing of this file
type of the analysis file within a stage, i.e. passed or removed for quality control steps
url for retrieving this analysis file
inbox receives user inbox data upload, requires authentication, see http://blog.metagenomics.anl.gov/mg-rast-v3-2-faq/#api_submission for details
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
lists the contents of the user inbox
This is a synchronous GET request.
RFC 4122 UUID for file
This is an optional parameter and may be passed in the query string.
This attribute has an object structure:
user id
status message
timestamp for return of this query
user login
view status of AWE inbox actions
This is a synchronous GET request.
If true show the given state
This is an optional parameter and may be passed in the query string.
If true show the given state
This is an optional parameter and may be passed in the query string.
If true show the given state
This is an optional parameter and may be passed in the query string.
If true show the given state
This is an optional parameter and may be passed in the query string.
If true show the given state
This is an optional parameter and may be passed in the query string.
If true show the given state
This is an optional parameter and may be passed in the query string.
user id
status message
timestamp for return of this query
user login
receives user inbox data upload, auto-uncompress if has .gz or .bz2 file extension
This is a synchronous POST request.
file to upload to inbox
This parameter must be passed in the message body.
user id
status message
timestamp for return of this query
user login
delete indicated file from inbox
This is a synchronous DELETE request.
RFC 4122 UUID for file
This is a required parameter and must be passed as a REST parameter.
user id
status message
timestamp for return of this query
user login
unpacks an archive upload into mutlple inbox files. supports: .zip, .tar, .tar.gz, .tar.bz2
This is a synchronous POST request.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
If true keeps archive file when complete, default is to delete.
This is an optional parameter and may be passed in the query string.
RFC 4122 UUID for file
This is a required parameter and must be passed as a REST parameter.
This attribute has an object structure:
user id
status message
timestamp for return of this query
user login
get basic file info - returns results and updates shock node
This is a synchronous GET request.
RFC 4122 UUID for file
This is a required parameter and must be passed as a REST parameter.
user id
key value pairs describing file info
status message
timestamp for return of this query
user login
validate metadata spreadsheet in inbox
This is a synchronous GET request.
RFC 4122 UUID for file
This is a required parameter and must be passed as a REST parameter.
user id
status message
timestamp for return of this query
user login
runs sequence stats on file in user inbox - submits AWE job
This is a asynchronous GET request.
RFC 4122 UUID for sequence file
This is a required parameter and must be passed as a REST parameter.
url/id of awe job
user id
status message
timestamp for return of this query
user login
cancel (delete) given AWE job ID
This is a synchronous GET request.
RFC 4122 UUID for AWE job
This is a required parameter and must be passed as a REST parameter.
user id
status message
timestamp for return of this query
user login
rename indicated file from inbox
This is a synchronous POST request.
RFC 4122 UUID for file
This parameter must be passed in the message body.
new name for file
This parameter must be passed in the message body.
user id
status message
timestamp for return of this query
user login
create fastq file from sff file - submits AWE job
This is a asynchronous POST request.
RFC 4122 UUID for sff file
This parameter must be passed in the message body.
url/id of awe job
user id
status message
timestamp for return of this query
user login
demultiplex seq file with barcode file - submits AWE job
This is a asynchronous POST request.
RFC 4122 UUID for barcode mapping file
This parameter must be passed in the message body.
RFC 4122 UUID for index file (optional)
This parameter must be passed in the message body.
RFC 4122 UUID for second index file, for double barcodes (optional)
This parameter must be passed in the message body.
If true barcodes in mapping file are reverse compliment, default is false
This parameter must be passed in the message body.
RFC 4122 UUID for sequence file
This parameter must be passed in the message body.
url/id of awe job
user id
status message
timestamp for return of this query
user login
merge overlapping paired-end fastq files - submits AWE job
This is a asynchronous POST request.
prefix for output file, default is a random uuid
This parameter must be passed in the message body.
RFC 4122 UUID for pair 1 file
This parameter must be passed in the message body.
RFC 4122 UUID for pair 2 file
This parameter must be passed in the message body.
If true retain non-overlapping sequences, default is false
This parameter must be passed in the message body.
url/id of awe job
user id
status message
timestamp for return of this query
user login
merge overlapping paired-end fastq files and demultiplex based on index file - submits AWE job
This is a asynchronous POST request.
RFC 4122 UUID for barcode mapping file
This parameter must be passed in the message body.
RFC 4122 UUID for index file
This parameter must be passed in the message body.
RFC 4122 UUID for second index file, for double barcodes (optional)
This parameter must be passed in the message body.
RFC 4122 UUID for pair 1 file
This parameter must be passed in the message body.
RFC 4122 UUID for pair 2 file
This parameter must be passed in the message body.
If true barcodes in mapping file are reverse compliment, default is false
This parameter must be passed in the message body.
If true retain non-overlapping sequences, default is false
This parameter must be passed in the message body.
url/id of awe job
user id
status message
timestamp for return of this query
user login
A library of metagenomic sequences from some environment linked to a specific sample
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Returns a set of data matching the query criteria.
This is a synchronous GET request.
maximum number of items requested
This is an optional parameter and may be passed in the query string.
zero based index of the first data object to be returned
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This attribute has an object structure:
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
name of the attribute the returned data is ordered by
link to the next set or null if this is the last set
total number of available data items
Returns a single data object.
This is a synchronous GET request.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
unique object identifier
This is a required parameter and must be passed as a REST parameter.
time the object was first created
unique object identifier
key value pairs describing metadata
reference to the related metagenome object
human readable identifier
reference to the project object
reference to the related sample object
a list of references to the related sequence sets
resource location of this object instance
version of the object
M5NR provides data through a comprehensive non-redundant protein / rRNA database
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Return functional hierarchy
This is a synchronous GET request.
if true, return full compressed ontology, other options ignored
This is an optional parameter and may be passed in the query string.
if true return only those ontologies that exactly match filter, default is false
This is an optional parameter and may be passed in the query string.
text of ontology group (filter_level) to filter by
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
M5NR version, default 1
This is an optional parameter and may be passed in the query string.
This attribute has an object structure:
resource location of this object instance
version of M5NR
Return organism hierarchy
This is a synchronous GET request.
if true, return full compressed taxonomy, other options ignored
This is an optional parameter and may be passed in the query string.
if true return only those taxonomies that exactly match filter, default is false
This is an optional parameter and may be passed in the query string.
text of taxonomy group (filter_level) to filter by
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
M5NR version, default 1
This is an optional parameter and may be passed in the query string.
This attribute has an object structure:
resource location of this object instance
version of M5NR
Return all sources in M5NR
This is a synchronous GET request.
M5NR version, default 1
This is an optional parameter and may be passed in the query string.
source object
resource location of this object instance
version of M5NR
Return annotation of given source protein ID
This is a synchronous GET request.
maximum number of items requested
This is an optional parameter and may be passed in the query string.
zero based index of the first data object to be returned
This is an optional parameter and may be passed in the query string.
name of the attribute the returned data is ordered by
This is an optional parameter and may be passed in the query string.
M5NR version, default 1
This is an optional parameter and may be passed in the query string.
unique identifier from source DB
This is a required parameter and must be passed as a REST parameter.
This attribute has an object structure:
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
link to the next set or null if this is the last set
total number of available data items
resource location of this object instance
version of M5NR
Return annotation(s) or sequence of given md5sum (M5NR ID)
This is a synchronous GET request.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
maximum number of items requested
This is an optional parameter and may be passed in the query string.
zero based index of the first data object to be returned
This is an optional parameter and may be passed in the query string.
name of the attribute the returned data is ordered by
This is an optional parameter and may be passed in the query string.
if true return sequence output, else return annotation output, default is false
This is an optional parameter and may be passed in the query string.
source name to restrict search by
This is an optional parameter and may be passed in the query string.
M5NR version, default 1
This is an optional parameter and may be passed in the query string.
unique identifier in form of md5 checksum
This is a required parameter and must be passed as a REST parameter.
This attribute has an object structure:
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
link to the next set or null if this is the last set
total number of available data items
resource location of this object instance
version of M5NR
Return annotations for function names containing the given text
This is a synchronous GET request.
if true return only those annotations that exactly match input text, default is false
This is an optional parameter and may be passed in the query string.
if true return map of { 'function_id' : 'function_text' } only
This is an optional parameter and may be passed in the query string.
if true return only those annotations that do not match input text, default is false
This is an optional parameter and may be passed in the query string.
maximum number of items requested
This is an optional parameter and may be passed in the query string.
zero based index of the first data object to be returned
This is an optional parameter and may be passed in the query string.
name of the attribute the returned data is ordered by
This is an optional parameter and may be passed in the query string.
source name to restrict search by
This is an optional parameter and may be passed in the query string.
M5NR version, default 1
This is an optional parameter and may be passed in the query string.
text string of partial function name
This is a required parameter and must be passed as a REST parameter.
This attribute has an object structure:
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
link to the next set or null if this is the last set
total number of available data items
resource location of this object instance
version of M5NR
Return annotations for organism names containing the given text
This is a synchronous GET request.
if true return only those annotations that exactly match input text, default is false
This is an optional parameter and may be passed in the query string.
if true return only those annotations that do not match input text, default is false
This is an optional parameter and may be passed in the query string.
maximum number of items requested
This is an optional parameter and may be passed in the query string.
zero based index of the first data object to be returned
This is an optional parameter and may be passed in the query string.
name of the attribute the returned data is ordered by
This is an optional parameter and may be passed in the query string.
source name to restrict search by
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
M5NR version, default 1
This is an optional parameter and may be passed in the query string.
text string of partial organism name
This is a required parameter and must be passed as a REST parameter.
This attribute has an object structure:
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
link to the next set or null if this is the last set
total number of available data items
resource location of this object instance
version of M5NR
Return annotation(s) for md5sum (M5NR ID) of given sequence
This is a synchronous GET request.
maximum number of items requested
This is an optional parameter and may be passed in the query string.
zero based index of the first data object to be returned
This is an optional parameter and may be passed in the query string.
name of the attribute the returned data is ordered by
This is an optional parameter and may be passed in the query string.
source name to restrict search by
This is an optional parameter and may be passed in the query string.
M5NR version, default 1
This is an optional parameter and may be passed in the query string.
text string of protein sequence
This is a required parameter and must be passed as a REST parameter.
This attribute has an object structure:
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
link to the next set or null if this is the last set
total number of available data items
resource location of this object instance
version of M5NR
Return annotations of given source protein IDs
This is a synchronous POST request.
unique identifier from source DB
This parameter must be passed in the message body.
maximum number of items requested
This parameter must be passed in the message body.
zero based index of the first data object to be returned
This parameter must be passed in the message body.
name of the attribute the returned data is ordered by
This parameter must be passed in the message body.
M5NR version, default 1
This parameter must be passed in the message body.
This attribute has an object structure:
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
link to the next set or null if this is the last set
total number of available data items
resource location of this object instance
version of M5NR
Return annotations or sequences of given md5sums (M5NR ID)
This is a synchronous POST request.
unique identifier in form of md5 checksum
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
maximum number of items requested
This parameter must be passed in the message body.
zero based index of the first data object to be returned
This parameter must be passed in the message body.
name of the attribute the returned data is ordered by
This parameter must be passed in the message body.
if true return sequence output, else return annotation output, default is false
This parameter must be passed in the message body.
source name to restrict search by
This parameter must be passed in the message body.
M5NR version, default 1
This parameter must be passed in the message body.
This attribute has an object structure:
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
link to the next set or null if this is the last set
total number of available data items
resource location of this object instance
version of M5NR
Return annotations for function names containing the given texts
This is a synchronous POST request.
text string of partial function name
This parameter must be passed in the message body.
if true return only those annotations that exactly match input text, default is false
This parameter must be passed in the message body.
if true return only [{ 'function_id' :
This parameter must be passed in the message body.
if true return only those annotations that do not match input text, default is false
This parameter must be passed in the message body.
maximum number of items requested
This parameter must be passed in the message body.
md5 to constrain search by
This parameter must be passed in the message body.
zero based index of the first data object to be returned
This parameter must be passed in the message body.
name of the attribute the returned data is ordered by
This parameter must be passed in the message body.
source name to restrict search by
This parameter must be passed in the message body.
M5NR version, default 1
This parameter must be passed in the message body.
This attribute has an object structure:
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
link to the next set or null if this is the last set
total number of available data items
resource location of this object instance
version of M5NR
Return annotations for given function IDs
This is a synchronous POST request.
if true return map of {
This parameter must be passed in the message body.
function index ID
This parameter must be passed in the message body.
M5NR version, default 1
This parameter must be passed in the message body.
This attribute has an object structure:
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
link to the next set or null if this is the last set
total number of available data items
resource location of this object instance
version of M5NR
Return annotations for organism names containing the given texts
This is a synchronous POST request.
text string of partial organism name
This parameter must be passed in the message body.
if true return only those annotations that exactly match input text, default is false
This parameter must be passed in the message body.
if true return only those annotations that do not match input text, default is false
This parameter must be passed in the message body.
maximum number of items requested
This parameter must be passed in the message body.
md5 to constrain search by
This parameter must be passed in the message body.
zero based index of the first data object to be returned
This parameter must be passed in the message body.
name of the attribute the returned data is ordered by
This parameter must be passed in the message body.
source name to restrict search by
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
M5NR version, default 1
This parameter must be passed in the message body.
This attribute has an object structure:
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
link to the next set or null if this is the last set
total number of available data items
resource location of this object instance
version of M5NR
Return annotations for md5s (M5NR ID) of given sequences
This is a synchronous POST request.
text string of protein sequence
This parameter must be passed in the message body.
maximum number of items requested
This parameter must be passed in the message body.
zero based index of the first data object to be returned
This parameter must be passed in the message body.
name of the attribute the returned data is ordered by
This parameter must be passed in the message body.
source name to restrict search by
This parameter must be passed in the message body.
M5NR version, default 1
This parameter must be passed in the message body.
This attribute has an object structure:
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
link to the next set or null if this is the last set
total number of available data items
resource location of this object instance
version of M5NR
Create cassandra keyspace for new M5NR version, requires admin auth token
This is a synchronous POST request.
M5NR version
This parameter must be passed in the message body.
error message if any
status of action
time action was completed
Insert data into given cassandra table for new M5NR version, requires admin auth token
This is a synchronous POST request.
variable types for column insert
This parameter must be passed in the message body.
table to insert into
This parameter must be passed in the message body.
M5NR version
This parameter must be passed in the message body.
error message if any
status of action
time action was completed
A profile in biom format that contains abundance counts
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Returns a BIOM v1.0 object as described here: http://biom-format.org/documentation/format_versions/biom-1.0.html
This is a asynchronous GET request.
negative exponent value for maximum e-value cutoff: default is 5
This is an optional parameter and may be passed in the query string.
filter the return results to only include abundances based on genes with this function
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
filter the return results to only include annotations that contain this text
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
if true do not return metagenome metadata in 'columns' object, default is false
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
one or more metagenome or project unique identifier
This is an optional parameter and may be passed in the query string.
percent value for minimum % identity cutoff: default is 60
This is an optional parameter and may be passed in the query string.
value for minimum alignment length cutoff: default is 15
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
M5NR version, default 1
This is an optional parameter and may be passed in the query string.
This attribute has an object structure:
the matrix values
time the output data was generated
format specification name
url to the format specification
identifier of the data generator
unique object identifier
data type of the elements in the return matrix
result_type of the elements in the return matrix
type of the data encoding matrix (dense or sparse)
This attribute has an object structure:
list of the dimension sizes of the return matrix
type of the data in the return table (taxon, function or gene)
resource location of this object instance
Returns a BIOM v1.0 object as described here: http://biom-format.org/documentation/format_versions/biom-1.0.html.
This is a asynchronous GET request.
negative exponent value for maximum e-value cutoff: default is 5
This is an optional parameter and may be passed in the query string.
filter the return results to only include abundances based on genes with this organism
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
filter the return results to only include annotations that contain this text
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
if true do not return metagenome metadata in 'columns' object, default is false
This is an optional parameter and may be passed in the query string.
one or more metagenome or project unique identifier
This is an optional parameter and may be passed in the query string.
percent value for minimum % identity cutoff: default is 60
This is an optional parameter and may be passed in the query string.
value for minimum alignment length cutoff: default is 15
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
M5NR version, default 1
This is an optional parameter and may be passed in the query string.
This attribute has an object structure:
the matrix values
time the output data was generated
format specification name
url to the format specification
identifier of the data generator
unique object identifier
data type of the elements in the return matrix
result_type of the elements in the return matrix
type of the data encoding matrix (dense or sparse)
This attribute has an object structure:
list of the dimension sizes of the return matrix
type of the data in the return table (taxon, function or gene)
resource location of this object instance
Metagenomic metadata is data providing information about one or more aspects of a set sequences from a sample of some environment
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
This is a synchronous GET request.
the metadata sheet is valid
if not valid, reason why
valid metadata object for project and its samples and libraries
Returns static template for metadata object relationships and types
This is a synchronous GET request.
This attribute has a hash structure:
This attribute has a hash structure:
This attribute has a hash structure:
This attribute has a hash structure:
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.
metadata label
This is an optional parameter and may be passed in the query string.
version of CV ontology to use
This is an optional parameter and may be passed in the query string.
This attribute has a hash structure:
This attribute has a hash structure:
Returns static ontology used in metadata for the given name and version.
This is a synchronous GET request.
ontology name
This is a required parameter and must be passed as a REST parameter.
version of ontology to use
This is a required parameter and must be passed as a REST parameter.
ontology name
This attribute has a hash structure:
ontology ID of root
option to show root when displaying
this type
version of this ontology
Update metadata CV ontology with new version, requires admin auth token
This is a synchronous POST request.
ontology name
This parameter must be passed in the message body.
root ID for lookup
This parameter must be passed in the message body.
file with data
This parameter must be passed in the message body.
version of ontology to add
This parameter must be passed in the message body.
status of update
time of completion
Returns all versions available for given ontology.
This is a synchronous GET request.
ontology metadata label
This is an optional parameter and may be passed in the query string.
version number
version number
version number
Returns list of unique metadata values submitted by users for given label
This is a synchronous GET request.
valid metadata label
This is a required parameter and must be passed as a REST parameter.
metadata label
count of unique values
metadata value
Returns full nested metadata for a project in same format as template, or metadata for a single metagenome.
This is a synchronous GET request.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
unique object identifier
This is a required parameter and must be passed as a REST parameter.
This attribute has a hash structure:
unique object identifier
human readable identifier
number of samples in project
sample object containing sample metadata, sample libraries, sample envPackage
Create project with given metadata spreadsheet and metagenome IDs, either upload or shock node
This is a synchronous POST request.
unique metagenome ID
This parameter must be passed in the message body.
shock node ID of metadata spreadsheet
This parameter must be passed in the message body.
xlsx or xls format spreadsheet with metadata
This parameter must be passed in the message body.
ID of metagenome with metadata added
error message that may have occurred
unique object identifier
Update project with given metadata spreadsheet and metagenome IDs, either upload or shock node
This is a synchronous POST request.
option to map metadata from spreadsheet to metagenomes using ID, default is name
This parameter must be passed in the message body.
unique metagenome ID
This parameter must be passed in the message body.
shock node ID of metadata spreadsheet
This parameter must be passed in the message body.
unique project identifier
This parameter must be passed in the message body.
xlsx or xls format spreadsheet with metadata
This parameter must be passed in the message body.
ID of metagenome with metadata added
error message that may have occurred
unique object identifier
Validate given metadata spreadsheet, either upload or shock node
This is a synchronous POST request.
shock node ID of metadata spreadsheet
This parameter must be passed in the message body.
xlsx or xls format spreadsheet with metadata
This parameter must be passed in the message body.
the metadata sheet is valid
if not valid, reason why
valid metadata object for project and its samples and libraries
Validate given metadata value
This is a synchronous GET request.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
metadata label
This is an optional parameter and may be passed in the query string.
metadata value
This is an optional parameter and may be passed in the query string.
version of CV ontology to use
This is an optional parameter and may be passed in the query string.
the inputted value is valid for the given category and label
if not valid, reason why
A metagenome is an analyzed set sequences from a sample of some environment
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Returns a set of data matching the query criteria.
This is a synchronous GET request.
principal investigator's first name
This is an optional parameter and may be passed in the query string.
principal investigator's last name
This is an optional parameter and may be passed in the query string.
environmental biome, EnvO term
This is an optional parameter and may be passed in the query string.
date sample collected
This is an optional parameter and may be passed in the query string.
country where sample taken
This is an optional parameter and may be passed in the query string.
time the metagenome was first created
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
search parameter: query string for an env_package metadata field
This is an optional parameter and may be passed in the query string.
environmental package of sample, GSC term
This is an optional parameter and may be passed in the query string.
environmental feature, EnvO term
This is an optional parameter and may be passed in the query string.
search parameter: query string for function
This is an optional parameter and may be passed in the query string.
unique metagenome identifier
This is an optional parameter and may be passed in the query string.
latitude where sample taken
This is an optional parameter and may be passed in the query string.
search parameter: query string for a library metadata field
This is an optional parameter and may be passed in the query string.
maximum number of items requested
This is an optional parameter and may be passed in the query string.
location where sample taken
This is an optional parameter and may be passed in the query string.
longitude where sample taken
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
environmental material, EnvO term
This is an optional parameter and may be passed in the query string.
search parameter: md5 checksum of feature sequence
This is an optional parameter and may be passed in the query string.
search parameter: query string for any metadata field
This is an optional parameter and may be passed in the query string.
name of metagenome
This is an optional parameter and may be passed in the query string.
zero based index of the first data object to be returned
This is an optional parameter and may be passed in the query string.
metagenome object field to sort by (default is id)
This is an optional parameter and may be passed in the query string.
search parameter: query string for organism
This is an optional parameter and may be passed in the query string.
search parameter: query string for a project metadata field
This is an optional parameter and may be passed in the query string.
id of project containing metagenome
This is an optional parameter and may be passed in the query string.
name of project containing metagenome
This is an optional parameter and may be passed in the query string.
search parameter: query string for a sample metadata field
This is an optional parameter and may be passed in the query string.
sequencing method
This is an optional parameter and may be passed in the query string.
sequencing type
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This attribute has an object structure:
This parameter value can be chosen from the following (the first being default):
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
name of the attribute the returned data is ordered by
link to the next set or null if this is the last set
total number of available data items
resource location of this object instance
version of the object
Returns a single data object.
This is a synchronous GET request.
if true do not use cache
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
unique object identifier
This is a required parameter and must be passed as a REST parameter.
time the metagenome was first created
unique metagenome identifier
reference to the related library object
key value pairs describing all metadata
key value pairs describing MIxS metadata
name of metagenome
key value pairs describing pipeline parameters
reference to the project object
reference to the related sample object
sequencing type
key value pairs describing statistics
This parameter value can be chosen from the following (the first being default):
resource location of this object instance
version of the metagenome
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Retrieve MiXS Profile object for given ID
This is a synchronous GET request.
unique MiXS Profile identifier
This is a required parameter and must be passed as a REST parameter.
This attribute has an object structure:
profile description
required field name
unique MiXS Profile identifier
profile name
package name with required field
Listing of avaiable MiXS Profiles in MG-RAST
This is a synchronous GET request.
This attribute has an object structure:
total number of available data items
resource location of this object instance
Validate a MiXS Profile against current schema
This is a synchronous POST request.
profile in json format file
This parameter must be passed in the message body.
version of schema to validate against
This parameter must be passed in the message body.
the inputted profile is valid with the current schema
if not valid, reason why
version of schema profile was validated against
Upload a new MiXS Profile to MG-RAST
This is a synchronous POST request.
profile in json format file
This parameter must be passed in the message body.
version of schema to validate against
This parameter must be passed in the message body.
if valid, unique identifier for uploaded profile
the inputted profile is valid with the current schema
if not valid, reason why
version of schema profile was validated against
Update an existing MiXS Profile in MG-RAST
This is a synchronous POST request.
profile in json format file
This parameter must be passed in the message body.
unique MiXS Profile identifier
This is a required parameter and must be passed as a REST parameter.
unique identifier for updated profile
the inputted profile is valid with the current schema
if not valid, reason why
version of schema profile was validated against
Retrieve current MiXS Schema
This is a synchronous GET request.
version of schema to retrieve, default is most current
This is an optional parameter and may be passed in the query string.
This attribute has an object structure:
profile description
required field name
unique MiXS Profile identifier
profile name
package name with required field
Update current MiXS Schema
This is a synchronous POST request.
schema in json format file
This parameter must be passed in the message body.
version of schema to upload
This parameter must be passed in the message body.
This attribute has an object structure:
profile description
required field name
unique MiXS Profile identifier
profile name
package name with required field
A feature profile in json format that contains abundance and similarity values along with annotations
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Submits profile creation
This is a asynchronous GET request.
if true, return condensed profile (integer ids for annotations, non-lca only)
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
force rerun and set retry number, default is zero - no retry
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
M5NR version, default is 1
This is an optional parameter and may be passed in the query string.
unique object identifier
This is a required parameter and must be passed as a REST parameter.
unique status identifier
cv
resource location of this object instance
Return profile status and/or results
This is a synchronous GET request.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
RFC 4122 UUID for process
This is a required parameter and must be passed as a REST parameter.
time the profile was completed
unique profile status identifier
md5sum of profile
number of rows in profile data
size of profile in bytes
source name used in profile
cv
resource location of this object instance
A project is a composition of samples, libraries and metagenomes being analyzed in a global context.
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Returns a set of data matching the query criteria.
This is a synchronous GET request.
maximum number of items requested
This is an optional parameter and may be passed in the query string.
zero based index of the first data object to be returned
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This attribute has an object structure:
This parameter value can be chosen from the following (the first being default):
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
name of the attribute the returned data is ordered by
link to the next set or null if this is the last set
total number of available data items
Returns a single data object.
This is a synchronous GET request.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
unique object identifier
This is a required parameter and must be passed as a REST parameter.
time the object was first created
a short, comprehensive description of the project
the official name of the source of funding of this project
unique object identifier
a list of references to the related library objects
key value pairs describing metadata
a list of references to the related metagenome objects
human readable identifier
the first and last name of the principal investigator of the project
a list of references to the related sample objects
This parameter value can be chosen from the following (the first being default):
resource location of this object instance
version of the object
Research Object Manifest for MG-RAST Metagenome
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Returns a single manifest object.
This is a synchronous GET request.
unique object identifier
This is a required parameter and must be passed as a REST parameter.
This attribute has an object structure:
This attribute has an object structure:
time this manifest was created
unique metagenome identifier
name of this file
A metagenomic sample from some environment.
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Returns a set of data matching the query criteria.
This is a synchronous GET request.
maximum number of items requested
This is an optional parameter and may be passed in the query string.
zero based index of the first data object to be returned
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
This attribute has an object structure:
maximum number of data items returned, default is 10
link to the previous set or null if this is the first set
zero based index of the first returned data item
name of the attribute the returned data is ordered by
link to the next set or null if this is the last set
total number of available data items
Returns a single data object.
This is a synchronous GET request.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
unique object identifier
This is a required parameter and must be passed as a REST parameter.
time the object was first created
This attribute has an object structure:
unique object identifier
a list of references to the related library objects
key value pairs describing metadata
a list of references to the related metagenome objects
human readable identifier
reference to the project of this sample
resource location of this object instance
version of the object
Elastic search for Metagenomes
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Elastic Upsert
This is a synchronous POST request.
if true return ES docuemnt to upsert without POSTing it
This parameter must be passed in the message body.
tuple of function name (string) and abundance (int)
This parameter must be passed in the message body.
index name, default: metagenome_index
This parameter must be passed in the message body.
mapping of taxa level name (string) to list of tuples: taxa name (string) and abundace (int)
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
unique object identifier
This is a required parameter and must be passed as a REST parameter.
unique MG-RAST metagenome identifier
status of action
Elastic search
This is a synchronous GET request.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
sort field value to return results after
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
if true return ES search query
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
percent abundance cutoff for function name
This is an optional parameter and may be passed in the query string.
function name to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
index name, default: metagenome_index
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
maximum number of datasets returned
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
This parameter value can be chosen from the following (the first being default):
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
if true do not use _score for first level ordering
This is an optional parameter and may be passed in the query string.
fieldname to sort by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
if true include public data in query
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
taxonomic level the name belongs to, required with percent cutoff
This is an optional parameter and may be passed in the query string.
percent abundance cutoff for taxonomy name
This is an optional parameter and may be passed in the query string.
taxonomy name to filter results by
This is an optional parameter and may be passed in the query string.
metadata to filter results by
This is an optional parameter and may be passed in the query string.
submission runs input through a series of validation and pre-processing steps, then submits the results to the MG-RAST anaylsis pipeline. this requires authentication
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
list all submissions by user
This is a synchronous GET request.
if true and user is admin, list all submissions, default is off
This is an optional parameter and may be passed in the query string.
This attribute has an object structure:
timestamp for return of this query
user id
get status of submission from ID
This is a synchronous GET request.
if true show full document of running jobs, default is summary
This is an optional parameter and may be passed in the query string.
RFC 4122 UUID for submission
This is a required parameter and must be passed as a REST parameter.
error message if any
RFC 4122 UUID for submission
submission AWE job info
input file info
output metagenome info
key value pairs of metagenome pipeline parameters
AWE ID of submission
state of submission workflow
timestamp for return of this query
type of submission
user id
delete all files and running processes for given submission ID
This is a synchronous DELETE request.
if true delete all files and metagenomes in mgrast for submission, default just data in inbox
This is an optional parameter and may be passed in the query string.
RFC 4122 UUID for submission
This is a required parameter and must be passed as a REST parameter.
RFC 4122 UUID for submission
status message
timestamp for return of this query
user id
start new submission
This is a asynchronous POST request.
if true sequences are assembeled, default is false
This parameter must be passed in the message body.
RFC 4122 UUID for barcode mapping file
This parameter must be passed in the message body.
if true run bowtie screening, default is true
This parameter must be passed in the message body.
if true return workflow document instead of submitting
This parameter must be passed in the message body.
if true run dereplication, default is true
This parameter must be passed in the message body.
if true run qual score dynamic trimmer, default is true
This parameter must be passed in the message body.
if true run sequence ambiguous bp filtering, default is true
This parameter must be passed in the message body.
if true run sequence length filtering, default is true
This parameter must be passed in the message body.
sequence length filtering multiplier, default is 2.0
This parameter must be passed in the message body.
RFC 4122 UUID for index (barcode) file
This parameter must be passed in the message body.
RFC 4122 UUID for second index file, for double barcodes (optional)
This parameter must be passed in the message body.
maximum ambiguous bps to allow through per sequence, default is 5
This parameter must be passed in the message body.
maximum number of low-quality bases per read, default is 5
This parameter must be passed in the message body.
RFC 4122 UUID for metadata file
This parameter must be passed in the message body.
name of metagenome for pair-join
This parameter must be passed in the message body.
quality threshold for low-quality bases, default is 15
This parameter must be passed in the message body.
RFC 4122 UUID for file to demultiplex
This parameter must be passed in the message body.
RFC 4122 UUID for pair 1 file
This parameter must be passed in the message body.
RFC 4122 UUID for pair 2 file
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
unique MG-RAST project identifier
This parameter must be passed in the message body.
unique MG-RAST project name
This parameter must be passed in the message body.
If true barcodes in mapping file are reverse compliment, default is false
This parameter must be passed in the message body.
If true retain non-overlapping sequences, default is false
This parameter must be passed in the message body.
This parameter value can be chosen from the following (the first being default):
This parameter must be passed in the message body.
RFC 4122 UUID for sequence file
This parameter must be passed in the message body.
error message
RFC 4122 UUID for submission
timestamp for return of this query
user id
start new EBI submission
This is a asynchronous POST request.
if true run debug workflow instead of normal
This parameter must be passed in the message body.
if true overwrite existing metagenome_taxonomy with inputted
This parameter must be passed in the message body.
optional: key value pairs of metagenome_id => taxa_name
This parameter must be passed in the message body.
unique MG-RAST project identifier
This parameter must be passed in the message body.
optional: taxa_name to apply to all metagenomes of project
This parameter must be passed in the message body.
if true only upload files, do not submit XML forms
This parameter must be passed in the message body.
if true return workflow document instead of submitting
This parameter must be passed in the message body.
RFC 4122 UUID for submission
unique MG-RAST project identifier
timestamp for return of this query
user id
validates templates for correct structure and data to fit a valid template
Returns description of parameters and attributes.
This is a synchronous GET request. This request has no parameters.
Checks if the referenced JSON structure is a valid template
This is a synchronous GET request.
SHOCK template id
This is a required parameter and must be passed as a REST parameter.
array of invalid entries
boolean indicating whether the examined template is valid or not
Returns a single data object.
This is a synchronous GET request.
SHOCK template id, default is MG-RAST metagenome metadata template
This is an optional parameter and may be passed in the query string.
SHOCK data id
This is a required parameter and must be passed as a REST parameter.
array of invalid entries
boolean indicating whether the examined template is valid or not