Ena Database

ENA Database

Overview

The European Nucleotide Archive (ENA) is a comprehensive public repository for nucleotide sequence data and associated metadata. Access and query DNA/RNA sequences, raw reads, genome assemblies, and functional annotations through REST APIs and FTP for genomics and bioinformatics pipelines.

When to Use This Skill

This skill should be used when:

• Retrieving nucleotide sequences or raw sequencing reads by accession
• Searching for samples, studies, or assemblies by metadata criteria
• Downloading FASTQ files or genome assemblies for analysis
• Querying taxonomic information for organisms
• Accessing sequence annotations and functional data
• Integrating ENA data into bioinformatics pipelines
• Performing cross-reference searches to related databases
• Bulk downloading datasets via FTP or Aspera

Core Capabilities

1. Data Types and Structure

ENA organizes data into hierarchical object types:

Studies/Projects - Group related data and control release dates. Studies are the primary unit for citing archived data.

Samples - Represent units of biomaterial from which sequencing libraries were produced. Samples must be registered before submitting most data types.

Raw Reads - Consist of:

• Experiments: Metadata about sequencing methods, library preparation, and instrument details
• Runs: References to data files containing raw sequencing reads from a single sequencing run

Assemblies - Genome, transcriptome, metagenome, or metatranscriptome assemblies at various completion levels.

Sequences - Assembled and annotated sequences stored in the EMBL Nucleotide Sequence Database, including coding/non-coding regions and functional annotations.

Analyses - Results from computational analyses of sequence data.

Taxonomy Records - Taxonomic information including lineage and rank.

2. Programmatic Access

ENA provides multiple REST APIs for data access. Consult references/api_reference.md for detailed endpoint documentation.

Key APIs:

ENA Portal API - Advanced search functionality across all ENA data types

• Documentation: https://www.ebi.ac.uk/ena/portal/api/doc
• Use for complex queries and metadata searches

ENA Browser API - Direct retrieval of records and metadata

• Documentation: https://www.ebi.ac.uk/ena/browser/api/doc
• Use for downloading specific records by accession
• Returns data in XML format

ENA Taxonomy REST API - Query taxonomic information

• Access lineage, rank, and related taxonomic data

ENA Cross Reference Service - Access related records from external databases

• Endpoint: https://www.ebi.ac.uk/ena/xref/rest/

CRAM Reference Registry - Retrieve reference sequences

• Endpoint: https://www.ebi.ac.uk/ena/cram/
• Query by MD5 or SHA1 checksums

Rate Limiting: All APIs have a rate limit of 50 requests per second. Exceeding this returns HTTP 429 (Too Many Requests).

3. Searching and Retrieving Data

Browser-Based Search:

• Free text search across all fields
• Sequence similarity search (BLAST integration)
• Cross-reference search to find related records
• Advanced search with Rulespace query builder

Programmatic Queries:

• Use Portal API for advanced searches at scale
• Filter by data type, date range, taxonomy, or metadata fields
• Download results as tabulated metadata summaries or XML records

Example API Query Pattern:

import requests

# Search for samples from a specific study
base_url = "https://www.ebi.ac.uk/ena/portal/api/search"
params = {
    "result": "sample",
    "query": "study_accession=PRJEB1234",
    "format": "json",
    "limit": 100
}

response = requests.get(base_url, params=params)
samples = response.json()