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Plant Genomics

السجل الرسمي أخرى

Plant genomics MCP — 58 tools across 24 backends with cross-source synthesis.

الشيفرة المصدرية الموقع التوثيق

التثبيت

أضف هذا إلى إعدادات MCP في عميلك (Claude Desktop: claude_desktop_config.json، وCursor: ‏.cursor/mcp.json، ويستخدم VS Code وغيره الصيغة نفسها «mcpServers»).

PYPI package plant-genomics-mcp
Claude Code 
claude mcp add plant-genomics -- uvx plant-genomics-mcp==1.30.0
إعداد JSON (Claude Desktop وCursor وVS Code) 
{
    "mcpServers": {
        "plant-genomics": {
            "command": "uvx",
            "args": [
                "plant-genomics-mcp==1.30.0"
            ]
        }
    }
}

التوثيق

مأخوذ من ملف README للمشروع على GitHub ويُحدَّث أسبوعيًا. تفتح الروابط على GitHub.

المحتويات
  1. plant-genomics-mcp
  2. Does it help?
  3. Install
  4. Try it
  5. Tools
  6. Configuration
  7. Development
  8. License

plant-genomics-mcp

plant-genomics-mcp is an MCP server that lets AI agents look up plant genes in 23 free public databases, from Ensembl Plants and UniProt to KEGG, STRING and AlphaFold, with curated coverage of 12 plants.

Does it help?

Yes, over Claude alone, which declined most lookups. Against web search it is not measurably more accurate, on single lookups or on harder multi-step ones.

Claude Opus 5.5, in Claude Code, answered 52 plant gene-lookup questions three times each: 151 of 156 right with web search, 156 of 156 with the server, not separated (4 questions against 0, McNemar p = 0.125). On 36 harder questions (orthologs then coordinates, ID mapping, genes in an interval; re-run 2026-10-18) both got all 108 right; the server was faster at the median (0.77×, 95% CI 0.64 to 0.96) and dearer (1.72×, 1.46 to 2.24). The key comes from the databases the server reads, so this tests the lookups, not whether those databases are right.

Method, controls and limitations: benchmarks/agent_qa.

Install

# 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)

# 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

Ask in plain language; the client picks the tools:

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

For another species, name it or pass organism= (e.g. rice Os01g0100100, oryza_sativa). A recorded ortholog run, where Claude checked three sources and said which one does not back the rice match:

Prompts and full answers for both screenshots: examples/assets/cards/RUN.md.

A worked 64-call run over 114 genes in three organisms, with the 51 gaps it logged (39 since closed), is in examples/arf_family/PAGE.md. Per-tool walkthroughs, including the one-call gene dossier gene_report_AT1G01010.md, are in examples/.

Tools

56 tools across 23 backends:

AreaTools
Gene recordsensembl_plants_lookup_locus, phytozome_lookup_locus, get_gene_xrefs, bar_gene_summary, tair_locus_info
Sequenceget_sequence, blast_sequence
Protein and structureresolve_locus_to_uniprot, interpro_domains, alphafold_structure, experimental_structures
Functionlocus_go_annotations, locus_plant_ontology, locus_gene_rifs, go_enrichment, locus_literature
Pathwayskegg_pathways, plantcyc_locus_info
Interactions and expressionstring_interactions, experimental_interactions, bar_aiv_interactions, atted_coexpression, bar_efp_expression
Homology and familiesgramene_homologs, ensembl_plants_paralogs, orthodb_orthologs, panther_family, gene_tree_members, entry_members
TF motifstf_binding_motifs, jaspar_motif
Variationlocus_variants, vep_annotate, aragwas_associations, arabidopsis_natural_variation
Regions and assembliesensembl_region_query, ensembl_plants_assembly
Provenanceupstream_release
Batch and synthesisbatch_* (12), batch_locus_call, *_synth (3), consensus_homologs, gene_report

Most take a locus (e.g. AT1G01010) and an optional organism=. Every tool is marked read-only. What each tool does, the list of backends, the MCP resources and prompts, all environment variables and the error model: docs/reference.md.

Configuration

stdio (plant-genomics-mcp, the default) needs no configuration. plant-genomics-mcp-http serves streamable HTTP at http://host:port/mcp; there is no public endpoint, so you run it yourself, behind your own token.

VariableWhenEffect
PLANT_GENOMICS_MCP_HTTP_TOKENHTTP transport onlyBearer token for /mcp; must be ≥32 chars or the HTTP server aborts at startup. Generate openssl rand -hex 32.
PLANT_GENOMICS_MCP_NCBI_EMAILIf you use BLASTNCBI etiquette contact. Unset → placeholder + per-call warning; NCBI may throttle.

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 .

A bare uv sync omits the test dependencies. CI runs the unit suite and the stdio smoke on Python 3.11–3.14 with the network blocked. A weekly job checks 27 loci against a frozen snapshot and pages on drift (docs/benchmarking.md). Setup: CONTRIBUTING.md. Release notes: CHANGELOG.md.

License

MIT, see LICENSE. The underlying services (Ensembl Plants, Phytozome, TAIR, PlantCyc, BAR) have their own terms of use; check them before bulk querying.

الأسئلة الشائعة

ما هو Plant Genomics؟

Plant genomics MCP — 58 tools across 24 backends with cross-source synthesis.

كيف أثبّت Plant Genomics؟

يعمل على جهازك. في Claude Code: claude mcp add plant-genomics -- uvx plant-genomics-mcp==1.30.0. وفي العملاء الآخرين، الصق إعداد JSON من هذه الصفحة في إعدادات MCP الخاصة بهم.

هل يحتاج Plant Genomics إلى مفتاح API؟

لا يذكر إدراجه في السجل أي مفتاح أو سر إلزامي. قد تتطلب بعض الميزات حسابًا لدى الخدمة التي يتصل بها.

هل Plant Genomics مفتوح المصدر؟

نعم. شيفرته متاحة على GitHub بترخيص MIT.

من يصون Plant Genomics؟

ينشره musharna. يدرجه AI.tn لكنه لا يصونه ولا يوصي به.

من سجل MCP الرسمي. الإدراج ليس توصية: راجع شيفرة الخادم وصلاحياته قبل منحه الوصول إلى بياناتك.