claude-scientific-skills/scientific-skills/jaspar-database/references/api_reference.md

JASPAR API v1 Reference

Base URL

https://jaspar.elixir.no/api/v1/

No authentication required. Responses are JSON.

Core Endpoints

GET /matrix/

Search and list TF binding profiles.

Parameters:

Parameter	Type	Description	Example
name	string	TF name (partial match)	CTCF
matrix_id	string	Exact matrix ID	MA0139.1
collection	string	Collection name	CORE
tax_group	string	Taxonomic group	vertebrates
species	string	Species name or tax ID	9606, Homo sapiens
tf_class	string	TF structural class	C2H2 zinc finger factors
tf_family	string	TF family	BEN domain factors
type	string	Experimental method	ChIP-seq, SELEX
version	string	latest or specific version	latest
page	int	Page number	1
page_size	int	Results per page (max 500)	25

Response:

{
  "count": 1210,
  "next": "https://jaspar.elixir.no/api/v1/matrix/?page=2",
  "previous": null,
  "results": [
    {
      "matrix_id": "MA0139.1",
      "name": "CTCF",
      "collection": "CORE",
      "tax_group": "vertebrates"
    }
  ]
}

GET /matrix/{id}/

Fetch a specific matrix with full details.

Response:

{
  "matrix_id": "MA0139.1",
  "name": "CTCF",
  "collection": "CORE",
  "tax_group": "vertebrates",
  "pfm": {
    "A": [87, 167, 281, ...],
    "C": [291, 145, 49, ...],
    "G": [76, 414, 504, ...],
    "T": [205, 114, 27, ...]
  },
  "consensus": "CCGCGNGGNGGCAG",
  "length": 19,
  "species": [{"tax_id": 9606, "name": "Homo sapiens"}],
  "class": ["C2H2 zinc finger factors"],
  "family": ["BEN domain factors"],
  "type": "ChIP-seq",
  "uniprot_ids": ["P49711"],
  "pubmed_ids": ["19172222"],
  "version": 1,
  "latest": true
}

GET /matrix/{id}/logo/

Returns SVG/PNG logo for the matrix.

Parameters: format = svg (default) or png

GET /taxon/

List available species/taxa.

GET /tf_class/

List available TF structural classes.

GET /tf_family/

List available TF families.

GET /collection/

List available collections.

Matrix ID Format

MA{number}.{version}

• MA prefix = Manual curation
• PB prefix = Published (automatic)
• UN prefix = Unvalidated
• Version increments when profile is updated

Common Matrix IDs

Matrix ID	TF	Species	Method
MA0139.1	CTCF	Human	ChIP-seq
MA0098.3	ETS1	Human	SELEX
MA0107.1	RELA (NF-kB p65)	Human	SELEX
MA0048.2	NHLH1	Human	SELEX
MA0079.4	SP1	Human	SELEX
MA0080.4	SPI1 (PU.1)	Human	ChIP-seq
MA0025.2	NFIL3	Human	SELEX
MA0002.2	RUNX1	Human	SELEX
MA0004.1	Arnt	Mouse	SELEX
MA0009.2	TAL1::GATA1	Human	SELEX

TF Classes (partial list)

• C2H2 zinc finger factors
• Basic leucine zipper factors (bZIP)
• Basic helix-loop-helix factors (bHLH)
• Homeodomain factors
• Forkhead box (FOX) factors
• ETS-domain factors
• Nuclear hormone receptors
• Tryptophan cluster factors
• p53-like transcription factors
• STAT factors
• MADS box factors
• T-box factors

Python Example: Batch Download

import requests, json, time

def download_all_human_profiles(output_file="jaspar_human_profiles.json"):
    """Download all human TF profiles from JASPAR CORE collection."""
    url = "https://jaspar.elixir.no/api/v1/matrix/"
    params = {
        "collection": "CORE",
        "species": "9606",
        "version": "latest",
        "page_size": 500,
        "page": 1
    }

    profiles = []
    while True:
        response = requests.get(url, params=params)
        data = response.json()
        profiles.extend(data["results"])

        if not data["next"]:
            break
        params["page"] += 1
        time.sleep(0.5)

    # Fetch full details for each profile
    full_profiles = []
    for p in profiles:
        detail_url = f"https://jaspar.elixir.no/api/v1/matrix/{p['matrix_id']}/"
        detail = requests.get(detail_url).json()
        full_profiles.append(detail)
        time.sleep(0.1)  # Be respectful

    with open(output_file, "w") as f:
        json.dump(full_profiles, f)

    return full_profiles