Plant Genomics

🌱 plant-genomics-mcp

50 tools for plant-genomics locus lookup over the Model Context Protocol — 28 single-locus + 1 motif lookup + 1 region query + 1 variant annotator + 1 gene-set enrichment + 1 BLAST search + 12 parallel-batch + 5 cross-source synthesis variants. Free, public sources: Ensembl Plants, Phytozome BioMart, UniProtKB, Europe PMC, QuickGO, Planteome, PlantCyc/PMN, g:Profiler, NCBI BLAST, Gramene, JASPAR, KEGG, STRING-DB, ATTED-II, ThaleMine, and BAR (Bio-Analytic Resource for Plant Biology).

📦 Install

# Zero-install — uv fetches and runs it on demand
claude mcp add plant-genomics --scope local -- uvx plant-genomics-mcp

# pipx — installs the CLI onto your PATH
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"

💬 Try it

Once connected, ask Claude a plain-language question — you don't have to name any tool or remember the chain:

"Tell me everything about the Arabidopsis gene AT1G01010 — its function, GO terms, KEGG pathways, protein-interaction partners, and recent papers."

Claude fans out across Ensembl Plants, UniProt, QuickGO, KEGG, STRING-DB, and Europe PMC in a single turn and hands back one synthesized answer. Swap in any locus and pass organism= for cross-species — e.g. rice Os01g0100100 (oryza_sativa) — and it routes to the right backends automatically.

🛠️ Tools

50 tools across 23 backends — Ensembl Plants, Phytozome BioMart, UniProtKB, Europe PMC, QuickGO, Planteome, PlantCyc/PMN, g:Profiler, AlphaFold DB, PDBe, InterPro, JASPAR, PANTHER, OrthoDB, AraGWAS, 1001 Genomes, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, ThaleMine, BAR. 28 single-locus + 1 motif lookup + 1 region query + 1 variant annotator + 1 gene-set enrichment + 1 BLAST search + 12 parallel-batch + 5 cross-source synthesis. Most 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, EDAM ontology tags, and behaviour annotations — every tool is readOnlyHint + openWorldHint, so hosts can surface them without a destructive-action confirmation prompt.

#	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	Metabolism (live)	plantcyc_locus_info	Walks gene → enzyme → reactions → PlantCyc/PMN pathways (free BioCyc web-services API). The metabolic-pathway view KEGG/GO lack; found=false for non-enzymatic genes. 11 species have a PGDB.
17	Sequence (live)	get_sequence	Fetches a locus's sequence (genomic / cds / cdna / protein) from Ensembl /sequence/id — the fetch half of lookup → fetch → BLAST; feed sequence to blast_sequence.
18	Region query (live)	ensembl_region_query	Lists gene/transcript/cds/exon features overlapping a genomic interval (chr:start-end) via Ensembl /overlap/region — "what's in this QTL interval" without a per-locus lookup.
19	Enrichment (live)	go_enrichment	GO + KEGG over-representation for a gene list via g:Profiler g:GOSt — "what is my DE / co-expression set enriched for?" Reports unmapped loci; optional custom background. All 12 organisms.
20	Plant ontology (live)	locus_plant_ontology	Plant Ontology (anatomy / dev-stage) + Trait Ontology annotations for a locus via Planteome (Solr) — the plant-specific ontologies GO doesn't cover. by_ontology rollup; taxon-filtered. Strong for 6 species.
21	Structure (live)	alphafold_structure	AlphaFold DB predicted 3D model for a locus (locus → UniProt → model): global mean pLDDT, per-band confidence, modelled span, and mmCIF / PDB / PAE URLs. found=false when no model is deposited. All 12 organisms.
22	Structure (live)	experimental_structures	PDBe experimentally-solved (X-ray / cryo-EM / NMR) structures for a locus (locus → UniProt): best-first PDB id, chain, method, resolution, coverage, residue span. found=false when none deposited (common for plants). All 12 organisms.
23	Domains (live)	interpro_domains	InterPro domain / family architecture (locus → UniProt): each entry's accession, name, type, source_database (Pfam included), integrated InterPro id, and residue spans, plus a count_by_type rollup. All 12 organisms.
24	TF motifs (live)	tf_binding_motifs	JASPAR curated TF DNA-binding profiles for a locus (locus → UniProt → symbol search, then UniProt-confirmed): matrix id, TF class/family, assay type (SELEX / ChIP-seq / PBM / DAP-seq), IUPAC consensus, PubMed refs, logo URL. Fuzzy name hits for other genes are quarantined in name_only_matches. Arabidopsis-heavy coverage.
25	TF motifs (live)	jaspar_motif	One JASPAR profile by matrix id (e.g. MA0570.1, or MA0570 for the newest version) including the raw position-frequency matrix — the drill-down companion to tf_binding_motifs.
26	Interactions (live)	experimental_interactions	ThaleMine CURATED EXPERIMENTAL interaction partners (BioGRID / IntAct / PSI-MI) for an Arabidopsis locus — per partner: detection method (two hybrid, pull down, ...), PSI-MI relationship type, physical vs genetic, source DB, PubMed IDs, and an evidence count. The experimental counterpart to string_interactions (predicted / text-mined). Arabidopsis only.
27	Function (live)	locus_gene_rifs	ThaleMine curated GeneRIF statements — one-sentence, manually curated descriptions of what the gene does, each tied to a PubMed ID (HY5 has 114). Citable functional context that GO terms and raw abstracts don't provide. Arabidopsis only.
28	Variation (live)	locus_variants	Natural (EVA/dbSNP) variants overlapping a locus's genomic span via Ensembl /overlap/region — id, source, consequence class, alleles, clinical significance. variant_count + truncated. All 12 organisms.
29	Variation (live)	vep_annotate	Ensembl VEP consequence prediction for a variant (region + allele, not locus) — most-severe consequence + per-transcript SO terms, IMPACT, SIFT/PolyPhen. All 12 organisms.
30	Orthology (live)	panther_family	PANTHER protein family + subfamily (id + name), GO terms by aspect, protein class, and pathways. found=false when unclassified. All 12 organisms.
31	Orthology (live)	orthodb_orthologs	OrthoDB ortholog group (name, evolutionary rate) + cross-species member genes at the Viridiplantae level. organism_count + truncated. All 12 organisms.
32	Diversity (live)	aragwas_associations	AraGWAS genome-wide association hits per locus — score, MAF, SNP effect, phenotype/study. Arabidopsis-only.
33	Diversity (live)	arabidopsis_natural_variation	1001 Genomes natural-variation SNP effects across 1135 accessions — chr, position, effect, impact, amino-acid change, transcript + gene span. Arabidopsis-only.
34	Batch (live)	batch_* (twelve variants)	Parallel per-locus fanout for tools 1–6, 8–12, 14. Up to 50 loci per call.
35	Synthesis (live)	*_synth / consensus_homologs (four)	Compose 2–5 backends in parallel, return a SynthesisEnvelope with per-step status.
36	Synthesis (live)	gene_report	One-shot "tell me about this gene" dossier — annotation + xrefs + protein + domains + GO + KEGG + STRING + literature composed into a rendered Markdown result.markdown (+ structured result.sections).

⚡ 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
gene_report_AT1G01010.md	One-shot Markdown gene dossier — 7 backends composed, with graceful KEGG degradation.
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.
pgmcp://organisms/coverage	Markdown table of all 12 supported plants × 9 ID slots (ncbi_taxid / ensembl / phytozome / string / europe_pmc / kegg / atted / gprofiler / plantcyc).

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]'                         # or: uv sync --extra 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 .

With uv, pass --extra dev — a bare uv sync omits (and removes) the test dependencies. See CONTRIBUTING.md.

CI runs the unit suite + the stdio smoke on every push/PR (matrix: Python 3.11, 3.12, 3.13, 3.14 — the full requires-python range). 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.