# ๐ฑ plant-genomics-mcp
> **50 tools** for plant-genomics locus lookup over the Model Context Protocol โ
> 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).
[](https://pypi.org/project/plant-genomics-mcp/)
[](https://github.com/musharna/plant-genomics-mcp/actions/workflows/test.yml)
[](https://github.com/musharna/plant-genomics-mcp/actions/workflows/docker.yml)
[](https://glama.ai/mcp/servers/musharna/plant-genomics-mcp)
[](https://doi.org/10.5281/zenodo.21636352)
## ๐ฆ Install
```bash
# Zero-install โ uv fetches and runs it on demand
claude mcp add plant-genomics --scope local -- uvx plant-genomics-mcp
```
Other install paths (pipx, Docker, from source)
```bash
# pipx โ 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"
```
## ๐ฌ Try it
Once connected, ask Claude a plain-language question โ you don't have to
name any tool or remember the chain:
> **"Tell me everything about the Arabidopsis gene AT1G01010 โ 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 โ e.g. rice
`Os01g0100100` (`oryza_sativa`) โ and it routes to the right backends
automatically.
## ๐ ๏ธ Tools
**50 tools across 23 backends** โ 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
โ 12-plant curated coverage matrix at the `pgmcp://organisms/coverage`
MCP resource). All publish JSON `outputSchema`, EDAM ontology tags, and
behaviour annotations โ every tool is `readOnlyHint` + `openWorldHint`, so
hosts can surface them without a destructive-action confirmation prompt.
Full tool matrix
| # | 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, โฆ) 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 โ UniProt โ QuickGO). |
| 7 | Sequence search (live) | `blast_sequence` | NCBI BLAST URLAPI โ 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 โ 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 ยฑ 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 โ alias of `bar_gene_summary`. MCP tool name preserved for clients. |
| 16 | Metabolism (live) | `plantcyc_locus_info` | Walks gene โ enzyme โ reactions โ 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` โ the fetch half of lookup โ fetch โ 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` โ "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 โ "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) โ 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 โ UniProt โ 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 โ 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 โ 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 โ UniProt โ 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 โ 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 โ 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 โ 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` โ 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) โ 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 โ score, MAF, SNP effect, phenotype/study. Arabidopsis-only. |
| 33 | Diversity (live) | `arabidopsis_natural_variation` | 1001 Genomes natural-variation SNP effects across 1135 accessions โ chr, position, effect, impact, amino-acid change, transcript + gene span. Arabidopsis-only. |
| 34 | Batch (live) | `batch_*` (twelve variants) | Parallel per-locus fanout for tools 1โ6, 8โ12, 14. Up to 50 loci per call. |
| 35 | Synthesis (live) | `*_synth` / `consensus_homologs` (four) | Compose 2โ5 backends in parallel, return a `SynthesisEnvelope` with per-step status. |
| 36 | Synthesis (live) | `gene_report` | One-shot "tell me about this gene" dossier โ annotation + xrefs + protein + domains + GO + KEGG + STRING + literature composed into a rendered Markdown `result.markdown` (+ structured `result.sections`). |
## โก Quickstart
After install, the simplest call returns the Ensembl Plants record for
NAC001 โ the canonical worked example used throughout `examples/`:
```jsonc
// 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 โ pass `organism=`:
```jsonc
{ "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](examples/assets/cc-demo.gif)):
Full per-tool walkthroughs (with real upstream-API transcripts) live in
[`examples/`](examples/):
| Walkthrough | Coverage |
| ----------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------- |
| [`gene_report_AT1G01010.md`](examples/gene_report_AT1G01010.md) | One-shot Markdown gene dossier โ 7 backends composed, with graceful KEGG degradation. |
| [`analyze_locus_AT1G01010.md`](examples/analyze_locus_AT1G01010.md) | Ensembl โ xrefs โ UniProt โ Europe PMC โ QuickGO chain (5 tools). |
| [`find_homologs_AT1G01010_NAC_domain.md`](examples/find_homologs_AT1G01010_NAC_domain.md) | BLAST + per-hit UniProt enrichment. |
| [`biological_context_AT1G01010.md`](examples/biological_context_AT1G01010.md) | Gramene + KEGG + UniProt + STRING + ATTED-II (5 tools). |
| [`v0.8_synthesis_walkthrough.md`](examples/v0.8_synthesis_walkthrough.md) | All 4 v0.8 synthesis tools (`*_synth` + `consensus_homologs`) on the same locus. |
| [`cross_organism_walkthrough.md`](examples/cross_organism_walkthrough.md) | v0.9 multi-organism resolver against rice + maize โ per-backend routing on PyPI v1.0.4. |
## ๐ Resources & prompts
Four read-only MCP resources + three parameterized prompts
Clients discover them via `resources/list` and `prompts/list`.
**Resources** (`resources/read`):
| URI | What |
| ----------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------ |
| `pgmcp://cache/stats` | Per-backend `TTLCache` rollup โ `{hits, misses, size}` for each live backend. |
| `pgmcp://organisms/phytozome` | Slug โ Phytozome `organism_id` map. |
| `pgmcp://backends/status` | Per-backend liveness rollup โ `name`, `base_url`, `kind`, `subscription_gated`. |
| `pgmcp://organisms/coverage` | Markdown table of all 12 supported plants ร 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 โ xrefs โ UniProt โ Europe PMC โ QuickGO. |
| `find_homologs` | `sequence` | `program` (default `blastp`) | `blast_sequence` โ per-hit `resolve_locus_to_uniprot` for UniProt-shaped accessions. |
| `biological_context` | `locus` | `top_n` (default 10) | Gramene โ KEGG โ UniProt โ STRING โ ATTED-II. |
## ๐ Transports
| Transport | How to launch |
| --------------- | ------------------------------------------------------------------- |
| stdio (default) | `plant-genomics-mcp` (after install) or via Docker above |
| streamable-HTTP | `plant-genomics-mcp-http` โ POST JSON-RPC at `http://host:port/mcp` |
The HTTP transport is stateless and emits JSON responses by default โ
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 โ **not for production workloads**. No SLA, no
uptime commitment, URL may change without notice (single laptop on a
residential connection).
```bash
# 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.
## โ๏ธ 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 โฅ32 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 โ placeholder + per-call warning; NCBI may throttle. |
All env vars (HTTP bind, body cap, cache, BLAST concurrency)
| 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 โ 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`.
## โ ๏ธ Error model
Wire-prefix taxonomy + batch result shape
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 โ back off and retry |
| `[UpstreamUnavailableError]` | 5xx past retry budget โ 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`.
## ๐งช Development
```bash
.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` โ a bare `uv sync` omits (and removes) the test
dependencies. See [CONTRIBUTING.md](CONTRIBUTING.md#dev-setup).
CI runs the unit suite + the stdio smoke on every push/PR (matrix:
Python 3.11, 3.12, 3.13, 3.14 โ 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`](docs/benchmarking.md).
```bash
.venv/bin/python scripts/benchmark_annotations.py # full live sweep (~3-5 min)
```
See [`CHANGELOG.md`](CHANGELOG.md) for release notes, including the
v0.8 โ v0.9 `species=`/`organism_id=` โ `organism=` migration and the
v1.0.1 HTTP-token enforcement change.
## MCP registry
Listed in the [official MCP registry](https://registry.modelcontextprotocol.io)
under the namespace below (ownership-verification token for `mcp-publisher`):
```
mcp-name: io.github.musharna/plant-genomics-mcp
```
## License
MIT โ see [`LICENSE`](LICENSE). Underlying services (Ensembl Plants,
Phytozome, TAIR, PlantCyc, BAR) have their own terms of use; consult
each before bulk querying.