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ena-biosamples-mcp

by Abinesh-T
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Python
Remote

ena-biosamples-mcp

CI

An MCP server that lets researchers ask questions about public genomics data in the European Nucleotide Archive (ENA) and BioSamples in plain English, from any MCP client (Claude, IDE agents, custom agents).

Question in, insight out: "How many domestic cattle samples were collected in the UK, and is their metadata good enough for a livestock project?" becomes a handful of API calls and a checked, explained answer.

Demo

1. Counting records with a country filter

Counting domestic cattle samples in ENA and filtering to the United Kingdom

2. Checking metadata against a livestock project's requirements

Checking three UK cattle samples for sex and breed

The second check found a real data-quality issue: the first UK "cattle" samples are rumen bacteria from an in vitro fermentation study, submitted under a metagenome checklist, so they can never carry sex or breed. Their coordinates are also written in degrees-minutes-seconds while labelled as decimal degrees.

Tools

Tool

Example question

Source

count_records

"How many cattle sequencing runs are in ENA?"

ENA Portal API

search_samples

"Show me cattle samples collected in the United Kingdom"

ENA Portal API

get_biosample

"What tissue and breed is sample SAMEA103957639?"

BioSamples API

check_sample_metadata

"Does this sample have sex and breed for a FAANG-style project?"

BioSamples API

check_sample_metadata always checks the fields ENA requires on every sample (organism, collection date, geographic location) and accepts extra required fields per project. Each field is reported as ok, absent, declared_missing (an INSDC missing-value term such as "not collected") or invalid_format (e.g. a collection date that isn't ISO 8601).

Quick start

Claude desktop app (stdio)

Requires uv. Add to the MCP config and restart the app:

{
  "mcpServers": {
    "ena-biosamples": {
      "command": "/full/path/to/uv",
      "args": ["--directory", "/path/to/ena-biosamples-mcp", "run", "ena-mcp"]
    }
  }
}

Docker (Streamable HTTP)

docker build -t ena-biosamples-mcp .
docker run --rm -p 8000:8000 ena-biosamples-mcp
# MCP endpoint: http://localhost:8000/mcp

Development

uv sync
uv run pytest                          # unit tests, no network
uv run ruff check .
uv run python scripts/smoke_live.py    # live check against ENA and BioSamples

Settings can be overridden with ENA_MCP_* environment variables; see .env.example.

Design notes

  • Service layer. All HTTP calls live in ena_service.py and biosamples_service.py. MCP tools in server.py only delegate, and tests swap in a mock transport.

  • Metadata rules are pure functions (metadata_check.py), so consortium-specific rules can be added and tested without touching the network.

  • Verified against the live APIs, not just the docs. Findings that shaped the code:

    • The ENA count endpoint returns TSV with a header line, not a bare number.

    • country="United Kingdom*" returns 0 results while country="United Kingdom" returns 5,188, so countries are matched exactly (case-insensitive). country="*Kingdom*" returns the same 5,188, so no region-suffixed UK values are missed.

    • "cattle" resolves to the genus Bos, which also covers yak and zebu. Results carry a note telling the client to ask for a species such as Bos taurus.

  • Clear errors. Unknown species, private samples and wrong accession types come back as readable messages the model can relay to the user.

Roadmap

  • Validate coordinates (decimal degrees vs. degrees-minutes-seconds), found during the demo

  • Check samples against full ENA and consortium checklists (e.g. FAANG, ERGA)

  • Aggregate tools, e.g. samples per country or per year for a species

  • Response caching and polite rate limiting for bulk questions

License

MIT