JASPAR API
This API provides an easy-to-use REST web interface to query/retrieve matrix
profile data from the latest version of the JASPAR database. The API comes
with a human browsable interface and also a 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
collections
list
List all the collections 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, 2020 and 2022. If blank, the query will provide data from the latest release. |
# Load the schema document
$ coreapi get https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action collections list -p search=... -p order=... -p release=...
read
API endpoint that returns a list of all matrix profiles based on collection name.
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, 2020 and 2022. If blank, the query will provide data from the latest release. |
# Load the schema document
$ coreapi get https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action collections read -p collection=... -p search=... -p order=... -p version=... -p release=...
infer
read
Infer matrix profiles, given a protein sequence.
Path Parameters
The following parameters should be included in the URL path.
Parameter | Description |
---|---|
sequence required |
# Load the schema document
$ coreapi get https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action infer read -p sequence=...
live-api
# Load the schema document
$ coreapi get https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action live-api list
matrix
list
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, 2020 and 2022. If blank, the query will provide data from the latest release. |
# Load the schema document
$ coreapi get https://testjaspar.uio.no/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=...
read
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 https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action matrix read -p matrix_id=...
versions > list
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 https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action matrix versions list -p base_id=... -p order=...
releases
list
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 https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action releases list -p page=... -p page_size=... -p order=...
read
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 https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action releases read -p release_number=...
sites
read
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 https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action sites read -p matrix_id=...
species
list
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, 2020 and 2022. If blank, the query will provide data from the latest release. |
# Load the schema document
$ coreapi get https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action species list -p page=... -p page_size=... -p search=... -p order=... -p release=...
read
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, 2020 and 2022. If blank, the query will provide data from the latest release. |
# Load the schema document
$ coreapi get https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action species read -p tax_id=... -p search=... -p order=... -p version=... -p release=...
taxon
list
List all the taxonomic groups that 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, 2020 and 2022. If blank, the query will provide data from the latest release. |
# Load the schema document
$ coreapi get https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action taxon list -p release=...
read
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, 2020 and 2022. If blank, the query will provide data from the latest release. |
# Load the schema document
$ coreapi get https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action taxon read -p tax_group=... -p search=... -p order=... -p version=... -p release=...
tffm
list
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, 2020 and 2022. If blank, the query will provide data from the latest release. |
# Load the schema document
$ coreapi get https://testjaspar.uio.no/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=...
read
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 https://testjaspar.uio.no/api/v1/docs/
# Interact with the API endpoint
$ coreapi action tffm read -p tffm_id=...