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Plant genomics MCP server — 32 tools across 11 backends (Ensembl Plants, Phytozome, UniProt, Europe PMC, QuickGO, NCBI B
32 tools for plant-genomics locus lookup over the Model Context Protocol — 16 single-locus + 12 parallel-batch + 4 cross-source synthesis variants. Free, public sources: Ensembl Plants, Phytozome BioMart, UniProtKB, Europe PMC, QuickGO, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, and BAR (Bio-Analytic Resource for Plant Biology).
pipx install plant-genomics-mcp
claude mcp add plant-genomics --scope local -- plant-genomics-mcp
# GHCR Docker image
docker pull ghcr.io/musharna/plant-genomics-mcp:latest
claude mcp add plant-genomics --scope local -- \
docker run --rm -i ghcr.io/musharna/plant-genomics-mcp:latest
# From source
git clone https://github.com/musharna/plant-genomics-mcp.git
cd plant-genomics-mcp
python -m venv .venv && .venv/bin/pip install -e .
claude mcp add plant-genomics --scope local -- "$(pwd)/.venv/bin/plant-genomics-mcp"
32 tools across 11 backends — Ensembl Plants, Phytozome BioMart,
UniProtKB, Europe PMC, QuickGO, NCBI BLAST, Gramene, KEGG, STRING-DB,
ATTED-II, BAR. 16 single-locus + 12 parallel-batch + 4 cross-source
synthesis. All take a TAIR-style locus (e.g. AT1G01010) plus
optional organism= (slug / scientific name / common name / NCBI taxid
— 12-plant curated coverage matrix at the pgmcp://organisms/coverage
MCP resource). All publish JSON outputSchema and EDAM ontology tags.
| # | Category | Tool | What it does |
|---|---|---|---|
| 1 | Gene metadata (live) | ensembl_plants_lookup_locus | Fetches gene record from Ensembl Plants REST (any plant species). |
| 2 | Cross-references (live) | get_gene_xrefs | Fetches cross-DB references (UniProt, NCBI Gene, TAIR, GO, …) from Ensembl. |
| 3 | Gene metadata (live) | phytozome_lookup_locus | Fetches gene record from Phytozome BioMart (any Phytozome proteome). |
| 4 | Protein (live) | resolve_locus_to_uniprot | Resolves a locus to its UniProtKB record (Swiss-Prot preferred, TrEMBL OK). |
| 5 | Literature (live) | locus_literature | Searches Europe PMC for papers mentioning the locus (free, no API key). |
| 6 | GO annotations (live) | locus_go_annotations | Fetches QuickGO GO annotations (locus → UniProt → QuickGO). |
| 7 | Sequence search (live) | blast_sequence | NCBI BLAST URLAPI — async Put/Get polling with progress notifications. |
| 8 | Homology (live) | gramene_homologs | Fetches Gramene v69 homology entries (ortholog / paralog) with gene_tree_id. |
| 9 | Pathways (live) | kegg_pathways | Fetches KEGG pathway memberships. 7 organisms: Arabidopsis (ath:, native AGI), + rice (osa:), maize (zma:), soybean (gmx:), barley (hvg:), poplar (pop:), brachypodium (bdi:) bridged via Ensembl → Entrez ID. |
| 10 | Interactions (live) | string_interactions | Fetches STRING-DB first-neighbor interaction partners with per-channel score. |
| 11 | Coexpression (live) | atted_coexpression | Fetches ATTED-II Ath-u.c4-0 top-N coexpression neighbors with z-scores. |
| 12 | Curator summary (live) | bar_gene_summary | Fetches BAR ThaleMine + GAIA-aliases curator summary for an Arabidopsis locus. |
| 13 | Expression (live) | bar_efp_expression | Fetches BAR eFP-Browser expression profile (mean ± SD per tissue) for a locus. |
| 14 | Interactions (live) | bar_aiv_interactions | Fetches BAR AIV interaction partners (Arabidopsis + rice) with confidence + papers. |
| 15 | Curator summary (live) | tair_locus_info | Silent upgrade — alias of bar_gene_summary. MCP tool name preserved for clients. |
| 16 | Subscription redirect | plantcyc_locus_info | Returns subscription notice + redirect to live backends. No upstream call. |
| 17 | Batch (live) | batch_* (twelve variants) | Parallel per-locus fanout for tools 1–6, 8–12, 14. Up to 50 loci per call. |
| 18 | Synthesis (live) | *_synth / consensus_homologs (four) | Compose 2–5 backends in parallel, return a SynthesisEnvelope with per-step status. |
After install, the simplest call returns the Ensembl Plants record for
NAC001 — the canonical worked example used throughout examples/:
// arguments
{ "locus": "AT1G01010" }
// result (truncated)
{
"id": "AT1G01010",
"organism": "arabidopsis_thaliana",
"display_name": "NAC001",
"biotype": "protein_coding",
"seq_region_name": "1",
"start": 3631,
"end": 5899,
"strand": 1,
"assembly_name": "TAIR10",
"description": "NAC domain containing protein 1 ..."
}
Cross-species — pass organism=:
{ "locus": "Os01g0100100", "organism": "oryza_sativa" }
In Claude Code, the same prompt fans out across Ensembl, UniProtKB, and Europe PMC in a single turn (animated demo):
Full per-tool walkthroughs (with real upstream-API transcripts) live in
examples/:
| Walkthrough | Coverage |
|---|---|
analyze_locus_AT1G01010.md | Ensembl → xrefs → UniProt → Europe PMC → QuickGO chain (5 tools). |
find_homologs_AT1G01010_NAC_domain.md | BLAST + per-hit UniProt enrichment. |
biological_context_AT1G01010.md | Gramene + KEGG + UniProt + STRING + ATTED-II (5 tools). |
v0.8_synthesis_walkthrough.md | All 4 v0.8 synthesis tools (*_synth + consensus_homologs) on the same locus. |
cross_organism_walkthrough.md | v0.9 multi-organism resolver against rice + maize — per-backend routing on PyPI v1.0.4. |
Clients discover them via resources/list and prompts/list.
Resources (resources/read):
| URI | What |
|---|---|
pgmcp://cache/stats | Per-backend TTLCache rollup — {hits, misses, size} for each live backend. |
pgmcp://organisms/phytozome | Slug → Phytozome organism_id map. |
pgmcp://backends/status | Per-backend liveness rollup — name, base_url, kind, subscription_gated, probed_at. |
pgmcp://organisms/coverage | Markdown table of all 12 supported plants × 5 ID slots (ncbi_taxid / ensembl / phytozome / …). |
Prompts (prompts/get):
| Name | Required | Optional | Chains |
|---|---|---|---|
analyze_locus | locus | organism (default arabidopsis_thaliana) | Ensembl → xrefs → UniProt → Europe PMC → QuickGO. |
find_homologs | sequence | program (default blastp) | blast_sequence → per-hit resolve_locus_to_uniprot for UniProt-shaped accessions. |
biological_context | locus | top_n (default 10) | Gramene → KEGG → UniProt → STRING → ATTED-II. |
| Transport | How to launch |
|---|---|
| stdio (default) | plant-genomics-mcp (after install) or via Docker above |
| streamable-HTTP | plant-genomics-mcp-http — POST JSON-RPC at http://host:port/mcp |
The HTTP transport is stateless and emits JSON responses by default — the right shape for registry indexers and remote hosting.
A small personal demo runs at:
https://mjarnoldgt76.tail86d19d.ts.net/mcp
Intended for registry indexers, one-off evaluation, and quick interactive testing — not for production workloads. No SLA, no uptime commitment, URL may change without notice (single laptop on a residential connection).
# liveness probe
curl https://mjarnoldgt76.tail86d19d.ts.net/healthz
# {"status":"ok"}
# connect from Claude Code
claude mcp add --transport http plant-genomics-mcp \
https://mjarnoldgt76.tail86d19d.ts.net/mcp
For anything beyond casual evaluation, self-host. The HTTP transport
is the same binary; self-hosting buys deterministic uptime, your own
bearer-token gate (PLANT_GENOMICS_MCP_HTTP_TOKEN), and NCBI BLAST
etiquette under your own contact email.
Stdio needs no configuration. The two env vars that matter:
| Variable | When | Effect |
|---|---|---|
PLANT_GENOMICS_MCP_HTTP_TOKEN | HTTP transport only | Bearer token for /mcp; must be ≥32 chars or the HTTP server aborts at startup. Generate openssl rand -hex 32. |
PLANT_GENOMICS_MCP_NCBI_EMAIL | If you use BLAST | NCBI etiquette contact. Unset → placeholder + per-call warning; NCBI may throttle. |
| Variable | Default | Effect |
|---|---|---|
PLANT_GENOMICS_MCP_HTTP_HOST | 127.0.0.1 | HTTP bind address. |
PLANT_GENOMICS_MCP_HTTP_PORT | 8765 | HTTP TCP port. |
PLANT_GENOMICS_MCP_HTTP_MAX_BODY | 2097152 (2 MiB) | Reject POSTs with Content-Length larger than this. |
PLANT_GENOMICS_MCP_HTTP_STATELESS | 1 | 0 keeps per-client session state (SSE-style). |
PLANT_GENOMICS_MCP_HTTP_JSON | 1 | 0 switches the response shape to streaming SSE events. |
PLANT_GENOMICS_MCP_BLAST_CONCURRENCY | 2 | Max in-flight BLAST searches per process (NCBI per-IP rate limit). |
PLANT_GENOMICS_MCP_CACHE_TTL | 600 | Per-backend TTL+LRU cache entry lifetime, in seconds. 200-only. |
PLANT_GENOMICS_MCP_CACHE_SIZE | 256 | Max entries per backend before LRU eviction. |
PLANT_GENOMICS_MCP_CACHE_DISABLED | unset | Any non-empty value makes every cache a no-op. |
The cache is process-local — restart the server to drop all entries.
Long-running calls (retry storms, multi-second Phytozome BioMart POSTs)
emit MCP notifications/progress over the active session; clients opt
in via progressToken in the request _meta.
All live tools raise PlantGenomicsError subclasses; the MCP SDK
stringifies them into the wire content with a [ClassName] prefix so
clients can route on failure kind without parsing the message:
| Wire prefix | When |
|---|---|
[NotFoundError] | 404 / empty BioMart row / invalid locus identifier |
[RateLimitError] | 429 retry budget exhausted — back off and retry |
[UpstreamUnavailableError] | 5xx past retry budget — service outage, try a peer backend |
[PlantGenomicsError] | Other (BioMart Query ERROR: body, unexpected column count, etc.) |
Batch tools return {tool, count, results, errors} where
results[locus] is the same shape as the single-locus tool and
errors[locus] is the same [ClassName] message string. Ensembl's
batch uses the native POST /lookup/id endpoint (one HTTP round-trip);
everything else fans out via asyncio.gather.
.venv/bin/pip install -e '.[dev]'
.venv/bin/pytest -q # unit tests
PLANT_GENOMICS_MCP_LIVE=1 .venv/bin/pytest -q # adds live network probes
PLANT_GENOMICS_MCP_STDIO_SMOKE=1 .venv/bin/pytest -q # adds stdio smoke
.venv/bin/ruff check .
CI runs the unit suite + the stdio smoke on every push/PR (matrix: Python 3.11, 3.12). The live-network gate is not run in CI to avoid flakes from upstream availability.
Scientific validation / drift detection. scripts/benchmark_annotations.py
drives a curated corpus of canonical loci (27, spanning all 12 organisms)
through every backend + synthesis pipeline and compares results to a frozen
baseline, emitting PASS / DRIFT / FAIL plus cross-source consistency
invariants. It's how upstream data drift is caught. A scheduled GitHub Actions
workflow (.github/workflows/benchmark.yml) runs it weekly and pages on a
confirmed regression. Operator guide: docs/benchmarking.md.
.venv/bin/python scripts/benchmark_annotations.py # full live sweep (~3-5 min)
See CHANGELOG.md for release notes, including the
v0.8 → v0.9 species=/organism_id= → organism= migration and the
v1.0.1 HTTP-token enforcement change.
Listed in the official MCP registry
under the namespace below (ownership-verification token for mcp-publisher):
mcp-name: io.github.musharna/plant-genomics-mcp
MIT — see LICENSE. Underlying services (Ensembl Plants,
Phytozome, TAIR, PlantCyc, BAR) have their own terms of use; consult
each before bulk querying.
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