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73/100
2 months ago

plant-genomics-mcp

▎ Provides 32 tools for plant-genomics locus lookup across 11 free public backends (Ensembl Plants, Phytozome, UniProtKB, Europe PMC, QuickGO, NCBI BLAST, Gramene, KEGG, STRING-DB, ATTED-II, BAR). Takes a TAIR-style locus plus optional organism and returns gene metadata, functional/pathway annotation, interactions, co-expression, and literature — in single-locus, batch, and cross-source synthesis.

→ musharna/plant-genomics-mcp· listed on glama

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Limited view: static analysis for Python is partially covered.

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Who stands behind it

musharna

Source: Glama · also listed on github_code

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Install from

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// key findings
✅
No credential exfiltration, no sensitive file access, no obfuscation
Static analysis found nothing flowing your secrets to unexpected places.
✅
Open source with a license and README
Anyone can audit the code, the license is declared, and the publisher documents what it does.
🔐
You'll be asked for 1 credential: PLANT_GENOMICS_MCP_HTTP_TOKEN
These are read from process.env at runtime. Make sure you trust where they’ll be sent.
// environment variables
To run this server yourself, you supply these values. They go in your own MCP client configuration and stay on your machine. The secret label means the value is sensitive, not that the server mishandles it.
configPLANT_GENOMICS_MCP_LIVE1 .venv/bin/pytest -q # adds live network probes
configPLANT_GENOMICS_MCP_NCBI_EMAILIf you use BLAST NCBI etiquette contact. Unset → placeholder + per-call warning; NCBI may throttle.
configPLANT_GENOMICS_MCP_CACHE_DISABLEDunset Any non-empty value makes every cache a no-op.
🔐 secretPLANT_GENOMICS_MCP_HTTP_TOKENbearer-token gate (), and NCBI BLAST
configPLANT_GENOMICS_MCP_HTTP_MAX_BODY2097152 (2 MiB) Reject POSTs with Content-Length larger than this.
configPLANT_GENOMICS_MCP_HTTP_HOST127.0.0.1 HTTP bind address.
configPLANT_GENOMICS_MCP_HTTP_PORT8765 HTTP TCP port.
// quality suggestions

Tool annotations

No tools have read-only/destructive annotations

Add readOnlyHint or destructiveHint annotations to every tool so hosts can warn users before invoking.

All four hints declared on every tool

32/32 tools missing one or more hints — ensembl_plants_lookup_locus (missing: readOnlyHint, destructiveHint, idempotentHint, openWorldHint); get_gene_xrefs (missing: readOnlyHint, destructiveHint, idempotentHint, openWorldHint); phytozome_lookup_locus (missing: readOnlyHint, destructiveHint, idempotentHint, openWorldHint), +29 more. OpenAI's directory rejects tools where any of the four hints are missing or non-boolean.

For every tool, set all four hints (readOnlyHint, destructiveHint, idempotentHint, openWorldHint) to explicit true/false values that match the handler’s actual behaviour.

Tests exist

No test files found

Add tests that exercise each declared tool.

Claim the listing to review these findings one by one and send us a correction where you disagree, straight to the team. Claiming also means we tell you when the grade moves, and reach you first if we find anything urgent.

// full audit trail
The findings above are the summary. The full trail, every check we ran, each deduction, the network hosts observed and the dependency advisories, goes to verified publishers, along with an alert whenever a new one lands. Verified publishers can also review each finding and dispute it in one click. Publisher corrections have sharpened several of our checks this month, because the maintainer knows the codebase better than any scanner.
// improvement guidance — verified publishers only
We have 3 concrete improvements we can share with the publisher of this MCP. Each comes with specific guidance to raise the trust score.
// embed badge in your README
[![M8ven Score](https://m8ven.ai/badge/mcp/musharna-plant-genomics-mcp-1ebes1)](https://m8ven.ai/mcp/musharna-plant-genomics-mcp-1ebes1)
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commit: d968da55db4482ca52f583e286721068a421e433
code hash: 8af945d2cfd2f129d3370c7f61353637a4e12af123b8cc4b78a41f24533be438
verified: 6/18/2026, 10:45:55 AM
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