plant-genomics-mcp

# 🌱 plant-genomics-mcp

> **52 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 + 13 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).

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<p align="center">
  <img src="examples/assets/cc-demo.gif" alt="Claude Code answering a plant-genomics question live — calling plant-genomics-mcp across Ensembl Plants, UniProt, and Europe PMC and synthesizing the AT1G01010 / NAC1_ARATH gene profile in a single turn" width="780">
</p>

## 📦 Install

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

<details>
<summary>Other install paths (pipx, Docker, from source)</summary>

```bash
# 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"
```

</details>

## 💬 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.

A worked 64-call run over 114 genes in three organisms, with the 60 gaps it logged (27 since closed), is in [`examples/arf_family/PAGE.md`](examples/arf_family/PAGE.md).

## 🛠️ Tools

**52 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 + 13 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.

<details>
<summary>Full tool matrix</summary>

| #   | 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.