🌱 plant-genomics-mcp

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).

PyPI Docker codecov Python License

📦 Install

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"

🛠️ Tools

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.

⚡ Quickstart

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.

📚 Resources & prompts

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.

🔌 Transports

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.

Hosted endpoint

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.

⚙️ Configuration

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.

⚠️ Error model

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.

🧪 Development

.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.

MCP registry

Listed in the official MCP registry under the namespace below (ownership-verification token for mcp-publisher):

mcp-name: io.github.musharna/plant-genomics-mcp

License

MIT — see LICENSE. Underlying services (Ensembl Plants, Phytozome, TAIR, PlantCyc, BAR) have their own terms of use; consult each before bulk querying.

plant-genomics-mcp