UniBind API

This API provides an easy-to-use REST web interface to query/retrieve data from the UniBind database. The API comes with a human browsable interface and also a programmatic interface which return the results in different formats, including json, jsonp, yaml, bed, and also api for a browsable interface.

# 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

celltypes

list

GET /api/v1/celltypes/

List all the cell-lines/tissue names available in UniBind.

Query Parameters

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

Parameter	Description
`search`	A search term.

# Load the schema document
$ coreapi get https://unibind2018.uio.no/api/v1/docs/

# Interact with the API endpoint
$ coreapi action celltypes list -p search=...

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 = ["celltypes", "list"]
var params = {
    search: ...,
}
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("https://unibind2018.uio.no/api/v1/docs/")

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

collections

list

GET /api/v1/collections/

List all the collections available in UniBind.

Query Parameters

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

Parameter	Description
`search`	A search term.

# Load the schema document
$ coreapi get https://unibind2018.uio.no/api/v1/docs/

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

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: ...,
}
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("https://unibind2018.uio.no/api/v1/docs/")

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

datasets

list

GET /api/v1/datasets/

REST API endpoint that returns a list of all the datasets used.

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.
`biological_condition`	Biological condition or source (e.g. dht).
`cell_line`	Cell line or tissue name. For example: MCF7
`collection`	Collection membership of the data, such as Permissive or Robust.
`data_source`	Source of the data, such as ENCODE, GEO, AE(Array Express)
`has_pvalue`	Select datasets meeting a p-value threshold.
`identifier`	The dataset identifier, such ENCODE or GEO dataset ID. For example: GSE60130
`jaspar_id`	JASPAR database profile matrix ID. For example: MA0492.1
`model`	Prediction model involved in the production of datasets.
`species`	Species name associated with a TF
`summary`	Obtain summary of TF and related data
`tf_name`	Search by TF name (case-insensitive). For example: SMAD3
`threshold_pvalue`	Threshold applying to p-value filtering: log(p-value); maximum 0.

# Load the schema document
$ coreapi get https://unibind2018.uio.no/api/v1/docs/

# Interact with the API endpoint
$ coreapi action datasets list -p page=... -p page_size=... -p search=... -p order=... -p biological_condition=... -p cell_line=... -p collection=... -p data_source=... -p has_pvalue=... -p identifier=... -p jaspar_id=... -p model=... -p species=... -p summary=... -p tf_name=... -p threshold_pvalue=...

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 = ["datasets", "list"]
var params = {
    page: ...,
    page_size: ...,
    search: ...,
    order: ...,
    biological_condition: ...,
    cell_line: ...,
    collection: ...,
    data_source: ...,
    has_pvalue: ...,
    identifier: ...,
    jaspar_id: ...,
    model: ...,
    species: ...,
    summary: ...,
    tf_name: ...,
    threshold_pvalue: ...,
}
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("https://unibind2018.uio.no/api/v1/docs/")

# Interact with the API endpoint
action = ["datasets", "list"]
params = {
    "page": ...,
    "page_size": ...,
    "search": ...,
    "order": ...,
    "biological_condition": ...,
    "cell_line": ...,
    "collection": ...,
    "data_source": ...,
    "has_pvalue": ...,
    "identifier": ...,
    "jaspar_id": ...,
    "model": ...,
    "species": ...,
    "summary": ...,
    "tf_name": ...,
    "threshold_pvalue": ...,
}
result = client.action(schema, action, params=params)

create

POST /api/v1/datasets/

Support POST requests for search result downloads. This requires the FormParser and MultiPartParser classes to be enabled.

Request Body

The request body should be a "application/x-www-form-urlencoded" encoded object, containing the following items.

Parameter	Description
`tf_name` required
`total_peaks`

# Load the schema document
$ coreapi get https://unibind2018.uio.no/api/v1/docs/

# Interact with the API endpoint
$ coreapi action datasets create -p tf_name=... -p total_peaks=...

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 = ["datasets", "create"]
var params = {
    tf_name: ...,
    total_peaks: ...,
}
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("https://unibind2018.uio.no/api/v1/docs/")

# Interact with the API endpoint
action = ["datasets", "create"]
params = {
    "tf_name": ...,
    "total_peaks": ...,
}
result = client.action(schema, action, params=params)

read

GET /api/v1/datasets/{tf_id}/

Return TFBS detail (dataset) information.

Path Parameters

The following parameters should be included in the URL path.

Parameter	Description
`tf_id` required

# Load the schema document
$ coreapi get https://unibind2018.uio.no/api/v1/docs/

# Interact with the API endpoint
$ coreapi action datasets read -p tf_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 = ["datasets", "read"]
var params = {
    tf_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("https://unibind2018.uio.no/api/v1/docs/")

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

live-api

list

GET /api/v1/live-api/

# Load the schema document
$ coreapi get https://unibind2018.uio.no/api/v1/docs/

# Interact with the API endpoint
$ coreapi action live-api 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-api", "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("https://unibind2018.uio.no/api/v1/docs/")

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

species

list

GET /api/v1/species/

List all the species names available in UniBind.

Query Parameters

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

Parameter	Description
`search`	A search term.

# Load the schema document
$ coreapi get https://unibind2018.uio.no/api/v1/docs/

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

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 = {
    search: ...,
}
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("https://unibind2018.uio.no/api/v1/docs/")

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

specific

list

GET /api/v1/specific/

REST API endpoint that returns a list of profile-specific datasets.

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.
`biological_condition`	Biological condition or source (e.g. dht).
`cell_line`	Cell line or tissue name. For example: MCF7
`collection`	Collection membership of the data, such as Permissive or Robust.
`data_source`	Source of the data, such as ENCODE, GEO, AE(Array Express)
`has_pvalue`	Select datasets meeting a p-value threshold.
`identifier`	The dataset identifier, such ENCODE or GEO dataset ID. For example: GSE60130
`jaspar_id`	JASPAR database profile matrix ID. For example: MA0492.1
`model`	Prediction model involved in the production of datasets.
`species`	Species name associated with a TF
`summary`	Obtain summary of TF and related data
`tf_name`	Search by TF name (case-insensitive). For example: SMAD3
`threshold_pvalue`	Threshold applying to p-value filtering: log(p-value); maximum 0.

# Load the schema document
$ coreapi get https://unibind2018.uio.no/api/v1/docs/

# Interact with the API endpoint
$ coreapi action specific list -p page=... -p page_size=... -p search=... -p order=... -p biological_condition=... -p cell_line=... -p collection=... -p data_source=... -p has_pvalue=... -p identifier=... -p jaspar_id=... -p model=... -p species=... -p summary=... -p tf_name=... -p threshold_pvalue=...

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 = ["specific", "list"]
var params = {
    page: ...,
    page_size: ...,
    search: ...,
    order: ...,
    biological_condition: ...,
    cell_line: ...,
    collection: ...,
    data_source: ...,
    has_pvalue: ...,
    identifier: ...,
    jaspar_id: ...,
    model: ...,
    species: ...,
    summary: ...,
    tf_name: ...,
    threshold_pvalue: ...,
}
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("https://unibind2018.uio.no/api/v1/docs/")

# Interact with the API endpoint
action = ["specific", "list"]
params = {
    "page": ...,
    "page_size": ...,
    "search": ...,
    "order": ...,
    "biological_condition": ...,
    "cell_line": ...,
    "collection": ...,
    "data_source": ...,
    "has_pvalue": ...,
    "identifier": ...,
    "jaspar_id": ...,
    "model": ...,
    "species": ...,
    "summary": ...,
    "tf_name": ...,
    "threshold_pvalue": ...,
}
result = client.action(schema, action, params=params)

create

POST /api/v1/specific/

Support POST requests for search result downloads. This requires the FormParser and MultiPartParser classes to be enabled.

Request Body

The request body should be a "application/x-www-form-urlencoded" encoded object, containing the following items.

Parameter	Description
`folder` required
`peak_caller` required
`distance_threshold` required
`score_threshold` required
`adj_centrimo_pvalue` required
`total_tfbs`

# Load the schema document
$ coreapi get https://unibind2018.uio.no/api/v1/docs/

# Interact with the API endpoint
$ coreapi action specific create -p folder=... -p peak_caller=... -p distance_threshold=... -p score_threshold=... -p adj_centrimo_pvalue=... -p total_tfbs=...

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 = ["specific", "create"]
var params = {
    folder: ...,
    peak_caller: ...,
    distance_threshold: ...,
    score_threshold: ...,
    adj_centrimo_pvalue: ...,
    total_tfbs: ...,
}
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("https://unibind2018.uio.no/api/v1/docs/")

# Interact with the API endpoint
action = ["specific", "create"]
params = {
    "folder": ...,
    "peak_caller": ...,
    "distance_threshold": ...,
    "score_threshold": ...,
    "adj_centrimo_pvalue": ...,
    "total_tfbs": ...,
}
result = client.action(schema, action, params=params)

tfs

list

GET /api/v1/tfs/

List all the transcription factors available in UniBind.

# Load the schema document
$ coreapi get https://unibind2018.uio.no/api/v1/docs/

# Interact with the API endpoint
$ coreapi action tfs 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 = ["tfs", "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("https://unibind2018.uio.no/api/v1/docs/")

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