plant-genomics-mcp
by musharna
README.md
# 🌱 plant-genomics-mcp
> **56 tools** for plant-genomics locus lookup over the Model Context Protocol —
> 29 single-locus + 1 motif lookup + 1 region query + 1 assembly listing + 1 release report + 1 variant annotator + 1 gene-set enrichment + 1 BLAST search + 2 member lists (family entry, gene tree) + 13 parallel-batch + 5 cross-source synthesis variants.
> 23 free, public sources: 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, 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)
<p align="center">
<img src="examples/assets/cc-answer.png" alt="Claude Code with plant-genomics-mcp answering a prompt about Arabidopsis NAC001 (AT1G01010): the Ensembl Plants record (chr1:3,631-5,899, protein-coding) and UniProtKB entry Q0WV96 (NAC1_ARATH, 429 aa). Real output, trimmed" 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."**
The server supplies the tools (here: Ensembl Plants, UniProt, QuickGO, KEGG,
STRING-DB and Europe PMC lookups); which ones get called, in what order and in
how many turns is up to the client. In the recording at the top of this page
(a narrower prompt), Claude Code picked the calls itself and returned one
combined answer. Swap in any locus and pass `organism=` for cross-species —
e.g. rice `Os01g0100100` (`oryza_sativa`) — and each tool maps the organism to
that backend's own identifier.
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`](examples/arf_family/PAGE.md).
## 🛠️ Tools
**56 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.
29 single-locus + 1 motif lookup + 1 region query + 1 assembly listing + 1 release report + 1 variant annotator + 1 gene-set
enrichment + 1 BLAST search + 2 member lists + 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 top-N coexpression neighbors with a score: z-score for Arabidopsis, logit score (LSmr) for the other releases. |
| 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 ± 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 — alias of `bar_gene_summary`. MCP tool name preserved for clients. |
| 16 | Metabolism (live) | `plantcyc_locus_info` | Walks gene → enzyme → reactions → 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` — the fetch half of lookup → fetch → 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` — "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 — "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) — 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 → UniProt → 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 → 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 → 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 → UniProt → 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 — 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 — 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 — 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` — 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) — most-severe consequence + per-transcript SO terms, IMPACT, SIFT. 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 unmapped. 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 — score, MAF, SNP effect, phenotype/study. Arabidopsis-only. |
| 33 | Diversity (live) | `arabidopsis_natural_variation` | 1001 Genomes natural-variation SNP effects across 1135 accessions — chr, position, effect, impact, amino-acid change, transcript + gene span. Arabidopsis-only. |
| 34 | Batch (live) | `batch_*` (twelve dedicated variants) | Parallel per-locus fanout for tools 1–6, 8–12, 14. Up to 50 loci per call. |
| 35 | Batch (live) | `batch_locus_call` | Runs any tool whose only required argument is `locus` (33 tools, including `gene_report` and the synthesis tools) over up to 50 loci; the shared `args` are checked against that tool's schema once, before any call. |
| 36 | Synthesis (live) | `*_synth` / `consensus_homologs` (four) | Compose 2–5 backends in parallel, return a `SynthesisEnvelope` with per-step status. |
| 37 | Synthesis (live) | `gene_report` | One-shot "tell me about this gene" dossier — annotation + xrefs + protein + domains + GO + KEGG + STRING + literature composed into a rendered Markdown `result.markdown` (+ structured `result.sections`). |
| 38 | Families (live) | `entry_members` | Every protein in one organism carrying an InterPro / Pfam / PANTHER entry, with the locus each maps to (entry → genes; the reverse of tools 23 and 30). UniProt `total` + cursor paging; reviewed-only by default. |
| 39 | Families (live) | `gene_tree_members` | Every gene in an Ensembl Compara gene tree — the `gene_tree_id` that `gramene_homologs` returns — with locus, protein id, species and organism; `target_organism` keeps one organism's members. `total` + `limit`. |
| 40 | Homology (live) | `ensembl_plants_paralogs` | Paralogues Ensembl Compara records for a locus — `within_species_paralog` and the `other_paralog` ("ancient paralogues") that `gramene_homologs` drops — closest first, with perc_id, taxonomy level and protein id. Not a family list: test membership with `interpro_domains`. `total` + `limit`. |
| 41 | Region query (live) | `ensembl_plants_assembly` | An organism's Ensembl assembly — name, GCA accession, karyotype — and every top-level seq-region with its length: the `region` names `ensembl_region_query` takes, chromosomes first, so a region walk is planned before its first call. `total` + `limit`. |
| 42 | Provenance (live) | `upstream_release` | The release a backend's own endpoint calls current (Ensembl, STRING, QuickGO, JASPAR, KEGG), for the backends whose answers state none; PDBe, AraGWAS and Europe PMC publish none and say why. A separate request, so read it before and after a run: equal values mean no release changed. |
</details>
## ⚡ Quickstart
After install, the simplest call returns the Ensembl Plants record for
NAC001 — 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 — pass `organism=`:
```jsonc
{ "locus": "Os01g0100100", "organism": "oryza_sativa" }
```
A recorded Claude Code session (2026-05-24) with a narrower prompt — the
Ensembl record, UniProtKB entry and top three Europe PMC papers for
AT1G01010 — answered it in one turn:
<p align="center">
<img src="examples/assets/cc-demo.png" alt="Claude Code (Opus 4.7) calling plant-genomics-mcp 3 times to return the AT1G01010 / NAC1_ARATH record with Ensembl, UniProt Q0WV96, and the top-3 Europe PMC papers" width="820">
</p>
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 — 7 backends composed, with graceful KEGG degradation. |
| [`analyze_locus_AT1G01010.md`](examples/analyze_locus_AT1G01010.md) | Ensembl → xrefs → UniProt → Europe PMC → 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) | The four v0.8 synthesis tools (`*_synth` + `consensus_homologs`) on one locus. Captured 2026-05-22 at v0.8. |
| [`cross_organism_walkthrough.md`](examples/cross_organism_walkthrough.md) | v0.9 multi-organism resolver against rice + maize — per-backend routing. Captured 2026-05-24 against PyPI v1.0.4. |
## 📚 Resources & prompts
<details>
<summary>Four read-only MCP resources + three parameterized prompts</summary>
Clients discover them via `resources/list` and `prompts/list`.
**Resources** (`resources/read`):
| URI | What |
| ----------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------ |
| `pgmcp://cache/stats` | Per-backend `TTLCache` rollup — `{hits, misses, size}` for each live backend. |
| `pgmcp://organisms/phytozome` | Slug → Phytozome `organism_id` map. |
| `pgmcp://backends/status` | Static per-backend roster — `name`, `base_url`, citation DOI, `subscription_gated`, `kind`. Nothing is probed: `kind` is always `"live"` and says nothing about whether the backend is up right now. |
| `pgmcp://organisms/coverage` | Markdown table of all 12 supported plants × 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 → xrefs → UniProt → Europe PMC → QuickGO. |
| `find_homologs` | `sequence` | `program` (default `blastp`) | `blast_sequence` → per-hit `resolve_locus_to_uniprot` for UniProt-shaped accessions. |
| `biological_context` | `locus` | `top_n` (default 10) | Gramene → KEGG → UniProt → STRING → ATTED-II. |
</details>
## 🔌 Transports
| Transport | How to launch |
| --------------- | ------------------------------------------------------------------- |
| stdio (default) | `plant-genomics-mcp` (after install) or via Docker above |
| streamable-HTTP | `plant-genomics-mcp-http` — POST JSON-RPC at `http://host:port/mcp` |
The HTTP transport is stateless and emits JSON responses by default —
the right shape for registry indexers and remote hosting.
### Self-hosting
There is no public hosted endpoint. To use the HTTP transport, run it
yourself: it is the same binary, gated by your own bearer token
(`PLANT_GENOMICS_MCP_HTTP_TOKEN`), with NCBI BLAST requests sent under your
own contact email.
## ⚙️ 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 ≥32 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 → placeholder + per-call warning; NCBI may throttle. |
<details>
<summary>All env vars (HTTP bind, body cap, cache, BLAST concurrency)</summary>
| 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 — 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`.
</details>
## ⚠️ Error model
<details>
<summary>Wire-prefix taxonomy + batch result shape</summary>
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 — back off and retry |
| `[UpstreamUnavailableError]` | 5xx past retry budget — 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`.
</details>
## 🧪 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` — 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 — the full `requires-python` range), with a
dead proxy set so an ungated network call fails. A separate `live-smoke` job
runs two live test files (`tests/test_verify_genes.py`,
`tests/test_arf_mcp_client.py`, InterPro and PANTHER) on Python 3.12 on the
same pushes and PRs; it reports a result but is not a required check, because its result depends on
third-party services. The rest of the live suite (`PLANT_GENOMICS_MCP_LIVE=1`)
is not run in CI.
**Drift detection.** `scripts/benchmark_annotations.py` runs a curated corpus
of 27 loci (spanning all 12 organisms) through 12 functions — the organism
resolver plus 11 lookups across 9 of the 23 backends (ATTED-II, BAR, Ensembl
Plants, Europe PMC, Gramene, KEGG, Phytozome, STRING-DB, UniProt) — and
compares the results to a frozen snapshot of earlier results
(`scripts/benchmark_annotations.expected.json`), emitting PASS / DRIFT / FAIL
plus two cross-source consistency invariants. A change is detected relative to
that snapshot, not checked against an independent truth. BLAST and the
synthesis pipelines are registered in the script, but no corpus locus
exercises them. A scheduled GitHub Actions workflow
(`.github/workflows/benchmark.yml`) runs it weekly and pages when the same loci
fail on a re-run. Operator guide: [`docs/benchmarking.md`](docs/benchmarking.md).
```bash
.venv/bin/python scripts/benchmark_annotations.py # full live sweep
```
See [`CHANGELOG.md`](CHANGELOG.md) for release notes, including the
v0.8 → v0.9 `species=`/`organism_id=` → `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 — see [`LICENSE`](LICENSE). Underlying services (Ensembl Plants,
Phytozome, TAIR, PlantCyc, BAR) have their own terms of use; consult
each before bulk querying.
TDQS
A3.7/5.0
Scored across 56 tools
Disambiguation3/5
The descriptions are unusually thorough and often explicitly contrast sibling tools (e.g., string_interactions vs experimental_interactions, alphafold_structure vs experimental_structures). However, the set contains several genuinely overlapping clusters: the tair_locus_info/bar_gene_summary alias, multiple synthesis dossiers (gene_report, analyze_locus_synth, biological_context_synth, consensus_homologs), many homology/orthology tools, and the generic batch_locus_call alongside dedicated batch_* variants. An agent could still misselect among these, especially when choosing between a one-shot dossier and its component tools.
Naming Consistency4/5
Most tools use snake_case with recognizable patterns: batch_* for batch variants, resource_action or locus_attribute for single-source tools, and _synth for prompt-equivalent syntheses. Minor deviations exist, such as verb-first names (get_sequence, resolve_locus_to_uniprot, find_homologs_synth) mixed with noun-first names (locus_go_annotations, interpro_domains, blast_sequence), but the convention remains readable and largely predictable. This is not chaotic, just slightly mixed.
Tool Count2/5
56 tools is far beyond the typical 3-15 range and is inflated by many dedicated batch variants plus synthesis wrappers, even though a generic batch_locus_call already exists. While the server integrates many plant-genomics data sources, the surface feels heavy and contains redundancy that could be consolidated. This is too many tools for an agent to navigate comfortably, despite the breadth of the domain.
Completeness4/5
The surface covers a wide range of plant-genomics needs: locus resolution, sequences, BLAST, GO and plant ontology, pathways, homology, interactions, coexpression, expression, variation, GWAS, structure, domains, literature, and TF motifs. Minor gaps remain, such as no arbitrary genomic-region sequence retrieval, no multiple sequence alignment or phylogenetic tree tool, and several tools restricted to Arabidopsis or a 12-organism list. Still, the read-only research surface is robust overall.
Maintenance
ActivityActive
ResponsivenessResponsive