JASPAR API

This API provides easy-to-use REST web interface to query/retrieve matrix profile data from the latest version of JASPAR database. The API comes with a human browsable interface and also programmatic interface, which return the results in eight different formats, including json, jsonp, jaspar, meme, transfac, pfm, yaml and bed

# Install the command line client
$ pip install coreapi-cli

<!-- Load the JavaScript client library -->
<script src="/static/rest_framework/js/coreapi-0.1.1.js"></script>
<script src="/api/v1/docs/schema.js"></script>

# Install the Python client library
$ pip install coreapi

collections

list

GET /api/v1/collections/

List all the collections are available in JASPAR.

Query Parameters

The following parameters should be included as part of a URL query string.

Parameter	Description
`search`	A search term.
`order`	Which field to use when ordering the results.
`release`	Access a specific release of JASPAR. Available releases are: 2014, 2016, 2018 and 2020. If blank it will pull data from latest release seven (JASPAR 2020).

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action collections list -p search=... -p order=... -p release=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["collections", "list"]
var params = {
    search: ...,
    order: ...,
    release: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["collections", "list"]
params = {
    "search": ...,
    "order": ...,
    "release": ...,
}
result = client.action(schema, action, params=params)

read

GET /api/v1/collections/{collection}/

API endpoint that returns a list of all matrix profiles based on collection name.

Collection names are: 'CORE', 'CNE', 'PHYLOFACTS', 'SPLICE', 'POLII', 'FAM','PBM','PBM_HOMEO','PBM_HLH', 'UNVALIDATED'

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`collection` required

Query Parameters

The following parameters should be included as part of a URL query string.

Parameter	Description
`search`	A search term.
`order`	Which field to use when ordering the results.
`version`	If set to latest, return latest version
`release`	Access a specific release of JASPAR. Available releases are: 2014, 2016, 2018 and 2020. If blank it will pull data from latest release seven (JASPAR 2020).

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action collections read -p collection=... -p search=... -p order=... -p version=... -p release=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["collections", "read"]
var params = {
    collection: ...,
    search: ...,
    order: ...,
    version: ...,
    release: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["collections", "read"]
params = {
    "collection": ...,
    "search": ...,
    "order": ...,
    "version": ...,
    "release": ...,
}
result = client.action(schema, action, params=params)

infer

read

GET /api/v1/infer/{sequence}/

Infer matrix profiles, given protien sequence

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`sequence` required

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action infer read -p sequence=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["infer", "read"]
var params = {
    sequence: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["infer", "read"]
params = {
    "sequence": ...,
}
result = client.action(schema, action, params=params)

live

list

GET /api/v1/live/

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action live list

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["live", "list"]
client.action(schema, action).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["live", "list"]
result = client.action(schema, action)

matrix

list

GET /api/v1/matrix/

REST API endpoint that returns a list of all matrix profiles.

Query Parameters

The following parameters should be included as part of a URL query string.

Parameter	Description
`page`	A page number within the paginated result set.
`page_size`	Number of results to return per page.
`search`	A search term.
`order`	Which field to use when ordering the results.
`collection`	JASPAR Collection name. For example: CORE or CNE.
`name`	Search by TF name (case-sensitive). For example: SMAD3
`tax_group`	Taxonomic group. For example: Vertebrates
`tax_id`	Taxa ID. For example: 9606 for Human & 10090 for Mus musculus. Multiple IDs can be added separated by commas (e.g. tax_id=9606,10090).
`tf_class`	Transcription factor class. For example: Zipper-Type
`tf_family`	Transcription factor family. For example: SMAD factors
`data_type`	Type of data/experiment. For example: ChIP-seq, PBM, SELEX etc.
`version`	If set to latest, return latest version
`release`	Access a specific release of JASPAR. Available releases are: 2014, 2016, 2018 and 2020. If blank it will pull data from latest release seven (JASPAR 2020).

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action matrix list -p page=... -p page_size=... -p search=... -p order=... -p collection=... -p name=... -p tax_group=... -p tax_id=... -p tf_class=... -p tf_family=... -p data_type=... -p version=... -p release=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["matrix", "list"]
var params = {
    page: ...,
    page_size: ...,
    search: ...,
    order: ...,
    collection: ...,
    name: ...,
    tax_group: ...,
    tax_id: ...,
    tf_class: ...,
    tf_family: ...,
    data_type: ...,
    version: ...,
    release: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["matrix", "list"]
params = {
    "page": ...,
    "page_size": ...,
    "search": ...,
    "order": ...,
    "collection": ...,
    "name": ...,
    "tax_group": ...,
    "tax_id": ...,
    "tf_class": ...,
    "tf_family": ...,
    "data_type": ...,
    "version": ...,
    "release": ...,
}
result = client.action(schema, action, params=params)

read

GET /api/v1/matrix/{matrix_id}/

Gets profile detail information

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`matrix_id` required

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action matrix read -p matrix_id=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["matrix", "read"]
var params = {
    matrix_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["matrix", "read"]
params = {
    "matrix_id": ...,
}
result = client.action(schema, action, params=params)

versions > list

GET /api/v1/matrix/{base_id}/versions/

List matrix profile versions based on base_id

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`base_id` required

Query Parameters

The following parameters should be included as part of a URL query string.

Parameter	Description
`order`	Which field to use when ordering the results.

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action matrix versions &gt; list -p base_id=... -p order=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["matrix", "versions &gt; list"]
var params = {
    base_id: ...,
    order: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["matrix", "versions &gt; list"]
params = {
    "base_id": ...,
    "order": ...,
}
result = client.action(schema, action, params=params)

releases

list

GET /api/v1/releases/

REST API endpoint that returns all releases of JASPAR database.

Query Parameters

The following parameters should be included as part of a URL query string.

Parameter	Description
`page`	A page number within the paginated result set.
`page_size`	Number of results to return per page.
`order`	Which field to use when ordering the results.

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action releases list -p page=... -p page_size=... -p order=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["releases", "list"]
var params = {
    page: ...,
    page_size: ...,
    order: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["releases", "list"]
params = {
    "page": ...,
    "page_size": ...,
    "order": ...,
}
result = client.action(schema, action, params=params)

read

GET /api/v1/releases/{release_number}/

Gets JASPAR release information based on release number

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`release_number` required

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action releases read -p release_number=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["releases", "read"]
var params = {
    release_number: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["releases", "read"]
params = {
    "release_number": ...,
}
result = client.action(schema, action, params=params)

sites

read

GET /api/v1/sites/{matrix_id}/

List matrix profile sites based on matrix_id

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`matrix_id` required

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action sites read -p matrix_id=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["sites", "read"]
var params = {
    matrix_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["sites", "read"]
params = {
    "matrix_id": ...,
}
result = client.action(schema, action, params=params)

species

list

GET /api/v1/species/

API endpoint that returns a list of all species.

Query Parameters

The following parameters should be included as part of a URL query string.

Parameter	Description
`page`	A page number within the paginated result set.
`page_size`	Number of results to return per page.
`search`	A search term.
`order`	Which field to use when ordering the results.
`release`	Access a specific release of JASPAR. Available releases are: 2014, 2016, 2018 and 2020. If blank it will pull data from latest release seven (JASPAR 2020).

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action species list -p page=... -p page_size=... -p search=... -p order=... -p release=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["species", "list"]
var params = {
    page: ...,
    page_size: ...,
    search: ...,
    order: ...,
    release: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["species", "list"]
params = {
    "page": ...,
    "page_size": ...,
    "search": ...,
    "order": ...,
    "release": ...,
}
result = client.action(schema, action, params=params)

read

GET /api/v1/species/{tax_id}/

API endpoint that returns a list of all matrix profiles based on species.

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`tax_id` required

Query Parameters

The following parameters should be included as part of a URL query string.

Parameter	Description
`search`	A search term.
`order`	Which field to use when ordering the results.
`version`	If set to latest, return latest version
`release`	Access a specific release of JASPAR. Available releases are: 2014, 2016, 2018 and 2020. If blank it will pull data from latest release seven (JASPAR 2020).

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action species read -p tax_id=... -p search=... -p order=... -p version=... -p release=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["species", "read"]
var params = {
    tax_id: ...,
    search: ...,
    order: ...,
    version: ...,
    release: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["species", "read"]
params = {
    "tax_id": ...,
    "search": ...,
    "order": ...,
    "version": ...,
    "release": ...,
}
result = client.action(schema, action, params=params)

taxon

list

GET /api/v1/taxon/

List all the collections are available in JASPAR.

Query Parameters

The following parameters should be included as part of a URL query string.

Parameter	Description
`release`	Access a specific release of JASPAR. Available releases are: 2014, 2016, 2018 and 2020. If blank it will pull data from latest release seven (JASPAR 2020).

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action taxon list -p release=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["taxon", "list"]
var params = {
    release: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["taxon", "list"]
params = {
    "release": ...,
}
result = client.action(schema, action, params=params)

read

GET /api/v1/taxon/{tax_group}/

API endpoint that returns a list of all matrix profiles based on taxonomic group.

Available taxonomic groups are: vertebrates, plants, insects, nematodes, fungi, urochordates

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`tax_group` required

Query Parameters

The following parameters should be included as part of a URL query string.

Parameter	Description
`search`	A search term.
`order`	Which field to use when ordering the results.
`version`	If set to latest, return latest version
`release`	Access a specific release of JASPAR. Available releases are: 2014, 2016, 2018 and 2020. If blank it will pull data from latest release seven (JASPAR 2020).

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action taxon read -p tax_group=... -p search=... -p order=... -p version=... -p release=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["taxon", "read"]
var params = {
    tax_group: ...,
    search: ...,
    order: ...,
    version: ...,
    release: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["taxon", "read"]
params = {
    "tax_group": ...,
    "search": ...,
    "order": ...,
    "version": ...,
    "release": ...,
}
result = client.action(schema, action, params=params)

tffm

list

GET /api/v1/tffm/

REST API endpoint that returns a list of all TFFM profiles.

Query Parameters

The following parameters should be included as part of a URL query string.

Parameter	Description
`page`	A page number within the paginated result set.
`page_size`	Number of results to return per page.
`search`	A search term.
`order`	Which field to use when ordering the results.
`tax_group`	Taxonomic group. For example: Vertebrates or Plants
`release`	Access a specific release of JASPAR. Available releases are: 2014, 2016, 2018 and 2020. If blank it will pull data from latest release seven (JASPAR 2020).

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action tffm list -p page=... -p page_size=... -p search=... -p order=... -p tax_group=... -p release=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["tffm", "list"]
var params = {
    page: ...,
    page_size: ...,
    search: ...,
    order: ...,
    tax_group: ...,
    release: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["tffm", "list"]
params = {
    "page": ...,
    "page_size": ...,
    "search": ...,
    "order": ...,
    "tax_group": ...,
    "release": ...,
}
result = client.action(schema, action, params=params)

read

GET /api/v1/tffm/{tffm_id}/

Gets TFFM detail information

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`tffm_id` required

# Load the schema document
$ coreapi get http://jaspar2020.genereg.net/api/v1/docs/

# Interact with the API endpoint
$ coreapi action tffm read -p tffm_id=...

var coreapi = window.coreapi  // Loaded by `coreapi.js`
var schema = window.schema    // Loaded by `schema.js`

// Initialize a client
var client = new coreapi.Client()

// Interact with the API endpoint
var action = ["tffm", "read"]
var params = {
    tffm_id: ...,
}
client.action(schema, action, params).then(function(result) {
    // Return value is in 'result'
})

import coreapi

# Initialize a client & load the schema document
client = coreapi.Client()
schema = client.get("http://jaspar2020.genereg.net/api/v1/docs/")

# Interact with the API endpoint
action = ["tffm", "read"]
params = {
    "tffm_id": ...,
}
result = client.action(schema, action, params=params)