io.github.musharna/plant-genomics-mcp

Plant genomics MCP — 32 tools across 11 backends with cross-source synthesis.

16 tools GitHub

No known CVEs

No license

Actively maintained

Last commit 25d ago

Works with most clients

Transport: stdio, sse, http

16 tools · ~1.6k tok

Grade C · 0.8% of 200K ctx

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Health

Step 1

Install in your client

Config is the same across clients — only the file and path differ.

Supported in Claude Desktopstdio, sse, http · Node 18+

Paste into ~/Library/Application Support/Claude/claude_desktop_config.json

{
  "mcpServers": {
    "io-github-musharna-plant-genomics-mcp": {
      "command": "<see-readme>",
      "args": []
    }
  }
}

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Read me

What io.github.musharna/plant-genomics-mcp does

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).

Test This Server

No automated test available for this server. Check the GitHub README for setup instructions.

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Scored, not listed

Why this score

Five weighted categories — click any category to see the underlying evidence.

Score breakdown

58/100across 5 weighted dimensions

How we score →

0255075100

−42

Security

Maintenance

Efficiency

Documentation

Compatibility

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Security

OSV.dev

No known CVEs.

No package registry to scan.

Inventory

Tools (16)

Click any tool to inspect its schema.

~1.6k tokens total

Inventory

Resources (1)

coverage

12-plant curated coverage matrix showing organism support across all tools

pgmcp://organisms/coverage

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Frequently Asked Questions

Is io.github.musharna/plant-genomics-mcp safe to use?: io.github.musharna/plant-genomics-mcp has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.
How do I install io.github.musharna/plant-genomics-mcp?: io.github.musharna/plant-genomics-mcp can be installed by cloning its GitHub repository and following the setup instructions in the README.
What can io.github.musharna/plant-genomics-mcp do?: io.github.musharna/plant-genomics-mcp provides 16 tools: ensembl_plants_lookup_locus, get_gene_xrefs, phytozome_lookup_locus, resolve_locus_to_uniprot, locus_literature and 11 more. See the full tools list on the server page for descriptions and parameters.
What AI clients work with io.github.musharna/plant-genomics-mcp?: io.github.musharna/plant-genomics-mcp is compatible with claude-desktop, cursor, claude-code. It uses stdio and sse and http transport.
Is io.github.musharna/plant-genomics-mcp actively maintained?: io.github.musharna/plant-genomics-mcp is actively maintained — last commit was 25 days ago.

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Discussion

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Has anyone used this with Cursor?How do you handle auth?Any alternatives?

🌱 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).

📦 Install

pipx install plant-genomics-mcp claude mcp add plant-genomics --scope local -- plant-genomics-mcp

Other install paths (Docker, from source)

# 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.

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, …) from Ensembl.
3	Gene metadata (live)	`phytozome_lookup_locus`	Fetches gene record from Phytozome BioMart (any Phytozome proteome).
4	Protein (live)	`resolve_lo

... View full README on GitHub

Frequently Asked Questions

Is io.github.musharna/plant-genomics-mcp safe to use?

io.github.musharna/plant-genomics-mcp has no known CVEs as of the latest MCPpedia security scan. It does not require authentication, so any local process can connect — keep this in mind in shared environments.

How do I install io.github.musharna/plant-genomics-mcp?

io.github.musharna/plant-genomics-mcp can be installed by cloning its GitHub repository and following the setup instructions in the README.

What can io.github.musharna/plant-genomics-mcp do?

io.github.musharna/plant-genomics-mcp provides 16 tools: ensembl_plants_lookup_locus, get_gene_xrefs, phytozome_lookup_locus, resolve_locus_to_uniprot, locus_literature and 11 more. See the full tools list on the server page for descriptions and parameters.

What AI clients work with io.github.musharna/plant-genomics-mcp?

io.github.musharna/plant-genomics-mcp is compatible with claude-desktop, cursor, claude-code. It uses stdio and sse and http transport.

Is io.github.musharna/plant-genomics-mcp actively maintained?

io.github.musharna/plant-genomics-mcp is actively maintained — last commit was 25 days ago.