43-wentorai-research-plugins-skills-domains-biomedical-ena-sequence-api

brycewang-stanford/Auto-Empirical-Research-SkillsBiology Medicine and BioinformaticsAudit pendingSnapshot 89fc75dfc5a5

Summary

This source did not publish a separate summary. Review SKILL.md before using the skill.

SKILL.md

European Nucleotide Archive (ENA) API

Overview

The European Nucleotide Archive (ENA) at EMBL-EBI is one of the three global nucleotide sequence databases (with NCBI GenBank and DDBJ). It provides access to raw sequencing reads, assembled sequences, and functional annotations from all organisms. The API supports accession lookup, text search, and bulk data retrieval. Free, no authentication required.

API Endpoints

Portal API (Search)

# Search for studies
curl "https://www.ebi.ac.uk/ena/portal/api/search?query=CRISPR+cas9&result=study&limit=20&format=json"

# Search for samples
curl "https://www.ebi.ac.uk/ena/portal/api/search?query=human+gut+microbiome&result=sample&limit=20&format=json"

# Search for runs (sequencing data)
curl "https://www.ebi.ac.uk/ena/portal/api/search?query=RNA-seq+cancer&result=read_run&limit=20&format=json"

Browser API (Accession Lookup)

# Get record by accession
curl "https://www.ebi.ac.uk/ena/browser/api/xml/PRJEB12345"

# Get in JSON format
curl "https://www.ebi.ac.uk/ena/browser/api/summary/PRJEB12345"

# Get sequence in FASTA
curl "https://www.ebi.ac.uk/ena/browser/api/fasta/AF123456"

# Get in EMBL flat file format
curl "https://www.ebi.ac.uk/ena/browser/api/embl/AF123456"

Taxonomy Search

# Search by organism
curl "https://www.ebi.ac.uk/ena/portal/api/search?query=tax_tree(9606)&result=study&limit=20&format=json"

# Get taxonomy details
curl "https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/9606"

Result Types

Type	Description	Example accession
`study`	Research project	PRJEB12345
`sample`	Biological sample	SAMEA12345
`experiment`	Library/protocol

Parameter	Description	Example
`query`	Search text or taxonomy	`query=SARS-CoV-2`
`result`	Result type	`result=study`
`limit`	Max results (default 100K)	`limit=50`
`offset`	Pagination offset	`offset=100`
`format`	Response format	`json`, `tsv`, `xml`
`fields`	Specific fields	`fields=accession,description`

import requests

PORTAL_URL = "https://www.ebi.ac.uk/ena/portal/api"
BROWSER_URL = "https://www.ebi.ac.uk/ena/browser/api"


def search_studies(query: str, limit: int = 20) -> list:
    """Search ENA for research studies."""
    params = {
        "query": query,
        "result": "study",
        "limit": limit,
        "format": "json",
        "fields": "study_accession,study_title,study_description,"
                  "tax_id,scientific_name,center_name",
    }
    resp = requests.get(f"{PORTAL_URL}/search", params=params)
    resp.raise_for_status()
    return resp.json()


def search_runs(query: str, limit: int = 20) -> list:
    """Search for sequencing runs."""
    params = {
        "query": query,
        "result": "read_run",
        "limit": limit,
        "format": "json",
        "fields": "run_accession,experiment_title,instrument_platform,"
                  "library_strategy,read_count,base_count",
    }
    resp = requests.get(f"{PORTAL_URL}/search", params=params)
    resp.raise_for_status()
    return resp.json()


def get_fasta(accession: str) -> str:
    """Retrieve sequence in FASTA format."""
    resp = requests.get(f"{BROWSER_URL}/fasta/{accession}")
    resp.raise_for_status()
    return resp.text


def get_study_runs(study_accession: str) -> list:
    """Get all sequencing runs for a study."""
    params = {
        "query": f'study_accession="{study_accession}"',
        "result": "read_run",
        "format": "json",
        "fields": "run_accession,fastq_ftp,read_count,base_count",
        "limit": 1000,
    }
    resp = requests.get(f"{PORTAL_URL}/search", params=params)
    resp.raise_for_status()
    return resp.json()


# Example: find COVID-19 sequencing studies
studies = search_studies("SARS-CoV-2 whole genome", limit=5)
for s in studies:
    print(f"{s['study_accession']}: {s['study_title']}")
    print(f"  Organism: {s.get('scientific_name')}")

# Example: find RNA-seq runs
runs = search_runs("RNA-seq breast cancer", limit=5)
for r in runs:
    reads = int(r.get("read_count", 0))
    print(f"{r['run_accession']}: {r.get('experiment_title', '')}")
    print(f"  Platform: {r.get('instrument_platform')} | "
          f"Reads: {reads:,}")

# Download FASTQ files (from run metadata)
# The fastq_ftp field provides FTP paths:
wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/ERR123/ERR123456/ERR123456_1.fastq.gz

# Bulk download via Aspera (faster)
ascp -QT -l 300m -P33001 \
  [email protected]:/vol1/fastq/ERR123/ERR123456/ ./

43-wentorai-research-plugins-skills-domains-biomedical-ena-sequence-api

Summary

SKILL.md

European Nucleotide Archive (ENA) API

Overview

API Endpoints

Portal API (Search)

Browser API (Accession Lookup)

Taxonomy Search

Result Types

Query Parameters

Python Usage

Data Access

References

Related skills