drug-discovery-prompts/upstream/K-Dense-AI-scientific-agent-skills/skills/database-lookup/references/ena.md

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European Nucleotide Archive (ENA) API Reference		import	https://github.com/K-Dense-AI/scientific-agent-skills/blob/9c9bd2e9/skills/database-lookup/references/ena.md	9c9bd2e9	2026-06-26	prompt	accepted	upstream	false

European Nucleotide Archive (ENA) API Reference

Overview

The ENA is Europe's primary nucleotide sequence repository, part of the International Nucleotide Sequence Database Collaboration (INSDC) alongside NCBI GenBank and DDBJ. It stores raw sequencing reads, assembled sequences, genome assemblies, and associated metadata. ENA provides five complementary APIs for different access patterns.

1. ENA Portal API (Advanced Search)

Base URL

https://www.ebi.ac.uk/ena/portal/api

No authentication required. All endpoints are public.

Key Endpoints

Search records

GET /search?result={result_type}&query={query}&fields={fields}&limit={N}&format={format}

Parameter	Type	Description
result	string	Required. Data type to search. See Result Types below.
query	string	Search query using ENA query syntax.
fields	string	Comma-separated list of fields to return. Use /returnFields to see available fields per result type.
limit	int	Max results to return (default 100000).
offset	int	Pagination offset.
format	string	json (default), tsv.

Query syntax:

tax_id=9606 AND description="*hemoglobin*"
tax_id=9606 AND library_strategy="RNA-Seq"
accession="PRJEB40665"
scientific_name="Escherichia coli" AND dataclass="STD"
country="United Kingdom" AND first_public>2024-01-01

Operators: =, !=, >, <, >=, <=. Use AND, OR, NOT. Wildcards: *. Enclose values with spaces in double quotes.

Example -- search human RNA-Seq runs:

https://www.ebi.ac.uk/ena/portal/api/search?result=read_run&query=tax_id%3D9606%20AND%20library_strategy%3D%22RNA-Seq%22&fields=run_accession,experiment_accession,sample_accession,study_accession,instrument_platform,library_strategy,read_count,base_count&limit=5&format=json

Example -- search nucleotide sequences by organism:

https://www.ebi.ac.uk/ena/portal/api/search?result=sequence&query=tax_id%3D9606%20AND%20description%3D%22*hemoglobin*%22&fields=accession,description,tax_id,scientific_name,base_count&limit=5&format=json

Response:

[
  {
    "accession": "AA126503",
    "description": "zk94h05.s1 Soares_pregnant_uterus_NbHPU Homo sapiens cDNA clone ...",
    "tax_id": "9606"
  }
]

Count records

GET /count?result={result_type}&query={query}

Returns a plain integer count.

Example:

https://www.ebi.ac.uk/ena/portal/api/count?result=read_run&query=tax_id%3D9606%20AND%20library_strategy%3D%22RNA-Seq%22

List available result types

GET /results?format=json

List searchable fields for a result type

GET /searchFields?result={result_type}

List returnable fields for a result type

GET /returnFields?result={result_type}

Result Types

Result Type	Description
sequence	Nucleotide sequences
coding	Coding sequences (CDS)
noncoding	Non-coding sequences
read_run	Raw sequencing reads (runs)
read_experiment	Sequencing experiments
read_study	Studies for raw reads
analysis	Analyses
analysis_study	Studies for analyses
assembly	Genome assemblies
sample	Samples
study	Studies
taxon	Taxonomic classification
wgs_set	Genome assembly contig sets (WGS)
tsa_set	Transcriptome assembly contig sets (TSA)
tls_set	Targeted locus study contig sets (TLS)

---

2. ENA Browser API (Record Retrieval)

Base URL

https://www.ebi.ac.uk/ena/browser/api

Use this for direct retrieval of records by accession number.

Key Endpoints

Retrieve record in XML format

GET /xml/{accession}

Example:

https://www.ebi.ac.uk/ena/browser/api/xml/PRJEB40665
https://www.ebi.ac.uk/ena/browser/api/xml/SRR12345678
https://www.ebi.ac.uk/ena/browser/api/xml/ERS1234567

Retrieve record in EMBL flat file format

GET /embl/{accession}

Example:

https://www.ebi.ac.uk/ena/browser/api/embl/AY585947

Supports ?lineLimit=N to truncate long records.

Retrieve sequence in FASTA format

GET /fasta/{accession}

Example:

https://www.ebi.ac.uk/ena/browser/api/fasta/AY585947

Response Formats

Endpoint	Format	Use case
/xml/{accession}	XML	Full structured metadata for studies, samples, experiments, runs
/embl/{accession}	EMBL flat file	Annotated sequences with features
/fasta/{accession}	FASTA	Raw nucleotide/protein sequences

Accession Types

Prefix	Entity	Example
PRJEB / PRJNA / PRJDB	Study/Project	PRJEB40665
ERX / SRX / DRX	Experiment	ERX1234567
ERS / SRS / DRS	Sample	ERS1234567
ERR / SRR / DRR	Run	ERR1234567
GCA	Genome assembly	GCA_000001405.29
Standard INSDC	Sequence	AY585947, M10051

---

3. ENA Taxonomy REST API

Base URL

https://www.ebi.ac.uk/ena/taxonomy/rest

Key Endpoints

Lookup by taxonomy ID

GET /tax-id/{taxId}

Example:

https://www.ebi.ac.uk/ena/taxonomy/rest/tax-id/9606

Response:

{
  "taxId": 9606,
  "scientificName": "Homo sapiens",
  "commonName": "human",
  "formalName": true,
  "rank": "species",
  "division": "HUM",
  "lineage": "Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; ...; Homo; ",
  "geneticCode": "1",
  "mitochondrialGeneticCode": "2",
  "submittable": true,
  "binomial": true,
  "metagenome": false,
  "otherNames": [
    {"nameClass": "authority", "name": "Linnaeus, 1758"},
    {"nameClass": "genbank common name", "name": "human"}
  ]
}

Search by scientific name

GET /scientific-name/{name}

Example:

https://www.ebi.ac.uk/ena/taxonomy/rest/scientific-name/Homo%20sapiens

Returns an array of matching taxonomy records.

Search by common name

GET /any-name/{name}

Example:

https://www.ebi.ac.uk/ena/taxonomy/rest/any-name/human

Suggest names (autocomplete)

GET /suggest-for-submission/{partialName}

Example:

https://www.ebi.ac.uk/ena/taxonomy/rest/suggest-for-submission/Homo%20sap

---

4. ENA Cross Reference Service

Base URL

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

Retrieves links between ENA records and external databases (UniProt, PDB, PubMed, etc.).

Key Endpoints

Search cross-references by accession

GET /json/search?accession={accession}

Parameter	Type	Description
accession	string	ENA accession to look up cross-references for.
source	string	Filter by source database (e.g., UniProtKB).
target	string	Filter by target type.
limit	int	Max results.
offset	int	Pagination offset.

Example:

https://www.ebi.ac.uk/ena/xref/rest/json/search?accession=A00145

Response:

[
  {
    "Source": "EuropePMC",
    "Source Primary Accession": "PMC12345",
    "Source Secondary Accession": "",
    "Source URL": "https://europepmc.org/...",
    "Source Secondary URL": "",
    "Target": "sequence",
    "Target Primary Accession": "A00145",
    "Target Secondary Accession": "",
    "Target URL": "https://www.ebi.ac.uk/ena/...",
    "Has Inferred": "N",
    "Inferred From": ""
  }
]

---

5. CRAM Reference Registry

Base URL

https://www.ebi.ac.uk/ena/cram

Retrieves reference sequences used in CRAM file compression.

Key Endpoints

Lookup by MD5 checksum

GET /md5/{md5}

Example:

https://www.ebi.ac.uk/ena/cram/md5/b1eba5b6e4440e22e1e02f7e0febd2da

Lookup by SHA1 checksum

GET /sha1/{sha1}

Returns the reference sequence in FASTA format.

---

Common Search Patterns

# All RNA-Seq runs for a species
result=read_run&query=tax_id=9606 AND library_strategy="RNA-Seq"

# WGS assemblies for an organism
result=assembly&query=tax_id=562 AND assembly_type="primary metagenome"

# Sequences by study accession
result=sequence&query=study_accession="PRJEB40665"

# Samples from a country with collection date
result=sample&query=country="Germany" AND collection_date>=2024-01-01

# Coding sequences for a gene keyword
result=coding&query=description="*BRCA1*" AND tax_id=9606

# Count available datasets
/count?result=read_run&query=tax_id=9606

# Get metadata fields available for a result type
/returnFields?result=read_run
/searchFields?result=read_run

Rate Limits

• No authentication required
• No formal published rate limit, but be courteous: avoid more than ~5 concurrent requests
• Large result sets: use limit and offset for pagination
• For bulk downloads of sequence data (FASTQ, etc.), use ENA's FTP/Aspera services rather than the REST API

Tips

• ENA vs SRA: ENA and NCBI SRA mirror each other's data (both are INSDC members). ENA accessions (ERR/ERX/ERS/PRJEB) and NCBI accessions (SRR/SRX/SRS/PRJNA) are cross-referenced. Use whichever API has the query features you need.
• Portal API for search, Browser API for retrieval: Use the Portal API when you need to search across many records with filters. Use the Browser API when you have a specific accession and want the full record.
• JSON vs XML: The Portal API returns JSON or TSV. The Browser API primarily returns XML, EMBL, or FASTA.
• Field discovery: Always check /returnFields?result={type} and /searchFields?result={type} to see what's available for each result type -- fields differ between result types.
• Cross-references: Use the xref service to find links from ENA records to UniProt, PDB, PubMed, and other databases.