plant-genomics-mcp 1.0.3

Plant genomics MCP — 32 tools across 10 live backends (Ensembl Plants, Phytozome, UniProt, Europe PMC, QuickGO, BLAST, Gramene, KEGG, STRING, ATTED-II, BAR) for Claude Code

plant-genomics-mcp

32 tools for plant-genomics locus lookup via 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

• BAR (Bio-Analytic Resource for Plant Biology, U Toronto — Global Core Biodata Resource 2023). PlantCyc is an informational stub that redirects to the free alternatives (BioCyc PLANT orgid is paid-subscription-gated, probed 2026-05-21).

Tools at a glance

#	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 ath: pathway memberships for an Arabidopsis locus.
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.
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	Subscription redirect	plantcyc_locus_info	Returns subscription notice + redirect to live backends. No upstream call.
17	Batch (live)	batch_* (twelve variants)	Parallel per-locus fanout for tools 1–6, 8–12, 14. Up to 50 loci per call.
18	Synthesis (live)	*_synth / consensus_homologs (four)	Compose 2–5 backends in parallel, return a SynthesisEnvelope with per-step status.

Live tools take a TAIR-style locus (e.g. AT1G01010) plus an optional unified organism= parameter (default arabidopsis_thaliana) and return a structured record. organism= accepts a canonical slug (oryza_sativa), scientific name (Oryza sativa), common name (rice), or NCBI taxonomy ID (39947) — all resolve to the same 12-plant curated coverage matrix (see pgmcp://organisms/coverage). Subscription tools take a locus and return a structured redirect record — they do not call the gated upstream.

Batch variants (batch_ensembl_plants_lookup_locus, batch_get_gene_xrefs, batch_phytozome_lookup_locus, batch_resolve_locus_to_uniprot, batch_locus_literature, batch_locus_go_annotations, batch_gramene_homologs, batch_kegg_pathways, batch_string_interactions, batch_atted_coexpression, batch_bar_gene_summary, batch_bar_aiv_interactions) take a loci: string[] (1–50 items) plus the same optional organism= argument. They return {tool, count, results, errors} where results[locus] is the same shape as the single-locus tool and errors[locus] is a [ClassName] message string for PlantGenomicsError failures ([NotFoundError], [RateLimitError], …). Ensembl's batch uses the native POST /lookup/id endpoint (one HTTP round-trip); everything else fans out via asyncio.gather.

All thirty-two tools publish JSON outputSchema for client-side validation and EDAM ontology tags (operation_2422 Data retrieval; topic topic_0780 Plant biology + topic_0114 Gene structure) on _meta for registry indexers.

Resources

The server advertises four read-only MCP resources (resources/list + resources/read); JSON unless otherwise noted:

URI	MIME	What
pgmcp://cache/stats	application/json	Per-backend TTLCache rollup — {hits, misses, size} for each of the ten live backends
pgmcp://organisms/phytozome	application/json	Slug → Phytozome organism_id map, derived from the curated v0.9 organisms.ORGANISMS registry
pgmcp://backends/status	application/json	Per-backend liveness rollup — name, base_url, kind (live or stub), subscription_gated, probed_at
pgmcp://organisms/coverage	text/markdown	Markdown table of all 12 supported plants × 5 ID slots (ncbi_taxid, ensembl, phytozome, string, europe_pmc)

Useful for an operator to confirm caching is doing work without shelling into the process, and for clients that want to enumerate supported organisms / backends programmatically. The coverage matrix lets a client introspect supported organism coverage in one read instead of probing resolve_organism per organism.

Prompts

The server exposes three parameterized prompts (prompts/list + prompts/get) for one-click multi-tool workflows:

Name	Required args	Optional args	What it chains
analyze_locus	locus	organism (default arabidopsis_thaliana)	Ensembl annotation → xrefs → UniProt → Europe PMC literature → QuickGO annotations
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 homologs → KEGG pathways → UniProt → STRING interactions → ATTED-II coexpression

Clients populate their slash-command menu from prompts/list, so the workflow is one user selection deep instead of requiring the user to remember the tool ordering.

Real-execution proof transcripts of all three chains (against the live upstream APIs) live in examples/ — one JSON + Markdown pair per prompt. v0.8 adds a 4-tool synthesis walkthrough at examples/v0.8_synthesis_walkthrough.md, captured by examples/_run_synthesis_chain.py.

Transports

Transport	Status	How to launch
stdio	default	plant-genomics-mcp (after install) or via Docker below
streamable-HTTP	added	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. Env knobs:

Variable	Default	Effect
PLANT_GENOMICS_MCP_HTTP_HOST	127.0.0.1	Bind address
PLANT_GENOMICS_MCP_HTTP_PORT	8765	TCP port
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

Hosted endpoint

A small personal demo of this server runs at:

https://mjarnoldgt76.tail86d19d.ts.net/mcp

This is intended for registry indexers, one-off evaluation, and quick interactive testing — not for production workloads. No SLA, no uptime commitment, and the URL may change or disappear without notice. The host is a single laptop on a residential connection.

Liveness probe:

curl https://mjarnoldgt76.tail86d19d.ts.net/healthz
# {"status":"ok"}

Connect from Claude Code:

claude mcp add --transport http plant-genomics-mcp \
  https://mjarnoldgt76.tail86d19d.ts.net/mcp

For anything beyond casual evaluation — self-host. The HTTP transport is the same binary (see Install). Self-hosting buys you (a) deterministic uptime, (b) the required bearer-token gate via PLANT_GENOMICS_MCP_HTTP_TOKEN, and (c) NCBI BLAST etiquette under your own PLANT_GENOMICS_MCP_NCBI_EMAIL.

v1.0.1 breaking change: plant-genomics-mcp-http now requires PLANT_GENOMICS_MCP_HTTP_TOKEN to be set to a value of at least 32 characters. The container aborts at startup with a clear error if the env var is missing or too short. Generate one with openssl rand -hex 32 and pass it via env_file: or the compose environment: block. v1.0.0 documented this as fail-closed but the code shipped fail-open-on-absent — v1.0.1 closes that gap. Stdio transport is unaffected.

Install

pipx (recommended)

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

Docker (GHCR)

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"

Usage examples

1. ensembl_plants_lookup_locus

Fetch a gene record from Ensembl Plants. Default organism is arabidopsis_thaliana; pass organism= for any other supported plant (oryza_sativa, zea_mays, solanum_lycopersicum, ...).

// 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:

{ "locus": "Os01g0100100", "organism": "oryza_sativa" }

2. get_gene_xrefs

Fetch cross-database references from Ensembl Plants. Same host / organism conventions as ensembl_plants_lookup_locus. The response wraps Ensembl's top-level array (so it validates against the MCP outputSchema's required type=object root) and adds a by_db rollup keyed on Ensembl's dbname — so a chain consumer can lift out a single foreign accession without walking the list.

{ "locus": "AT1G01010" }

// result (xrefs[] truncated)
{
  "locus": "AT1G01010",
  "organism": "arabidopsis_thaliana",
  "count": 8,
  "xrefs": [
    { "dbname": "Uniprot_gn", "primary_id": "Q0WV96", "info_type": "DEPENDENT" },
    { "dbname": "EntrezGene", "primary_id": "839580", "display_id": "NAC001" },
    { "dbname": "TAIR_LOCUS", "primary_id": "AT1G01010", "info_type": "DIRECT" },
  ],
  "by_db": {
    "Uniprot_gn": ["Q0WV96"],
    "EntrezGene": ["839580"],
    "TAIR_LOCUS": ["AT1G01010"],
  },
}

Typical chain pattern — pull the UniProt accession out of by_db without parsing xrefs[]:

xrefs = await call("get_gene_xrefs", {"locus": "AT1G01010"})
uniprot_id = xrefs["by_db"].get("Uniprot_gn", [None])[0]  # "Q0WV96"

This is the cross-database pivot — pair with resolve_locus_to_uniprot for the canonical UniProt entry, or hand by_db["EntrezGene"] to an NCBI sibling MCP.

3. phytozome_lookup_locus

Fetch a gene record from Phytozome BioMart. Default organism is arabidopsis_thaliana (Phytozome organism_id=167, controller-verified live). Pass organism= for any other Phytozome proteome covered by the curated registry — see pgmcp://organisms/phytozome for the slug → organism_id map, or pgmcp://organisms/coverage for the full per-backend coverage matrix.

{ "locus": "AT1G01010" }

// result
{
  "organism_name": "Athaliana_TAIR10",
  "gene_name": "AT1G01010",
  "chromosome": "Chr1",
  "gene_start": "3631",
  "gene_end": "5899",
  "strand": "1",
  "description": "NAC domain containing protein 1 ..."
}

4. resolve_locus_to_uniprot

Resolve a plant locus to its canonical UniProtKB record. Prefers reviewed (Swiss-Prot) entries; falls back to unreviewed (TrEMBL) when no curated record exists — the common case for non-Arabidopsis plants. organism= defaults to arabidopsis_thaliana; pass a canonical slug, scientific name, common name, or NCBI taxid for any of the 12 supported plants.

{ "locus": "AT1G01010" }

// result
{
  "locus_query": "AT1G01010",
  "primaryAccession": "Q0WV96",
  "uniProtkbId": "NAC1_ARATH",
  "entryType": "UniProtKB reviewed (Swiss-Prot)",
  "reviewed": true,
  "recommendedName": "NAC domain-containing protein 1",
  "geneNames": ["NAC001"],
  "organism": "Arabidopsis thaliana",
  "taxonId": 3702,
  "sequenceLength": 429,
  "web_url": "https://www.uniprot.org/uniprotkb/Q0WV96"
}

This is the protein-side entry point for any downstream workflow: structure (AlphaFold, RCSB), domains (InterPro, PROSITE), pathways (Reactome, the subscriber path into PlantCyc), variants (ClinVar via the human-orthology bridge).

5. locus_literature

Search Europe PMC for literature mentioning a plant locus. Free, no API key. Returns up to size records (default 10, capped at 25) with title, authors, journal, year, DOI/PMID/PMCID, open-access status, citation count, and abstract. For non-Arabidopsis organisms the species common name is appended to the query (rice, maize, tomato, …) to disambiguate locus IDs that might otherwise collide with unrelated literature.

{ "locus": "AT1G01010", "size": 3 }

// result (hits[] truncated)
{
  "locus": "AT1G01010",
  "organism": "arabidopsis_thaliana",
  "query": "AT1G01010",
  "hitCount": 40,
  "returned": 3,
  "hits": [
    {
      "id": "41152268",
      "source": "MED",
      "pmid": "41152268",
      "pmcid": "PMC12569054",
      "doi": "10.1038/s41526-025-00525-5",
      "title": "GLARE: discovering hidden patterns in spaceflight transcriptome ...",
      "authorString": "Seo D, Strickland HF, Zhou M, ...",
      "journalTitle": "npj Microgravity",
      "pubYear": "2025",
      "citedByCount": 0,
      "isOpenAccess": "Y",
      "hasPDF": "Y",
      "web_url": "https://europepmc.org/article/PMC/PMC12569054",
    },
    // ...
  ],
}

This is the literature entry point — pair it with the protein-side chain (resolve_locus_to_uniprot → AlphaFold) or the cross-DB pivot (get_gene_xrefs → NCBI Gene) to ground a locus first, then fan out to the most-cited or most-recent papers.

6. locus_go_annotations

Fetch Gene Ontology annotations for a plant locus from QuickGO (EBI). Free, no API key. The locus is first resolved to a UniProt accession (same logic as resolve_locus_to_uniprot), then QuickGO is queried by geneProductId. Returns raw annotations[] plus a by_aspect rollup ({molecular_function: [{goId, goName}, ...], biological_process: [...], cellular_component: [...]}) deduped on goId so the high-level term set is one read away.

{ "locus": "AT1G01010", "limit": 5 }

// result
{
  "locus": "AT1G01010",
  "uniprot_accession": "Q0WV96",
  "numberOfHits": 9,
  "returned": 5,
  "annotations": [
    {
      "geneProductId": "UniProtKB:Q0WV96",
      "symbol": "NAC001",
      "qualifier": "enables",
      "goId": "GO:0000976",
      "goName": "transcription cis-regulatory region binding",
      "goAspect": "molecular_function",
      "goEvidence": "IPI",
      "reference": "PMID:30356219",
      "assignedBy": "TAIR",
      "taxonId": 3702,
      "taxonName": "Arabidopsis thaliana",
      // ...
    },
    // ...
  ],
  "by_aspect": {
    "molecular_function": [
      { "goId": "GO:0000976", "goName": "transcription cis-regulatory region binding" },
    ],
    "biological_process": [
      { "goId": "GO:0006355", "goName": "regulation of DNA-templated transcription" },
    ],
    "cellular_component": [{ "goId": "GO:0005634", "goName": "nucleus" }],
  },
}

[NotFoundError] propagates from either step — a locus with no UniProt entry can't be queried in QuickGO, so the caller gets a typed error rather than an empty result that hides the resolution failure.

7. tair_locus_info (BAR alias) / 8. plantcyc_locus_info

tair_locus_info is a silent upgrade (v0.10.0) — the MCP tool name is preserved for client compatibility, but the body now delegates to bar_gene_summary instead of returning a subscription-required redirect. BAR (Bio-Analytic Resource for Plant Biology, U Toronto — Global Core Biodata Resource 2023) mirrors the TAIR curator data through ThaleMine + GAIA aliases without the Phoenix Bioinformatics paid subscription. Returned shape is BarGeneSummary (same as bar_gene_summary).

plantcyc_locus_info remains a pure-data redirect — BioCyc PLANT orgid gates its free per-locus REST behind a paid subscription (SRI/Phoenix) and no free mirror covers the metabolic-pathway membership data:

// plantcyc_locus_info { "locus": "AT1G01010" }
{
  "locus": "AT1G01010",
  "plantcyc_web_url": "https://pmn.plantcyc.org/gene?orgid=ARA&id=AT1G01010",
  "status": "subscription_required",
  "probed_at": "2026-05-21",
  "rationale": "PlantCyc per-locus REST endpoints require a paid BioCyc subscription. This MCP does not ship a live PlantCyc client — use the alternatives below for partial coverage.",
  "alternatives": ["kegg_pathways", "ensembl_plants_lookup_locus"],
  "alternatives_note": "kegg_pathways covers pathway membership (no metabolic-network depth); ensembl_plants_lookup_locus covers gene annotation.",
}

plantcyc_locus_info exists for discoverability — a caller who knows of PlantCyc gets a structured pointer to the closest free backends rather than a 404. PlantCyc's metabolic-network value-add is not currently substituted by the alternatives.

9. Batch variants

Each of tools 1–6 has a batch_* variant that takes loci: string[] (1–50) and the same optional arguments, returning a unified envelope:

// batch_ensembl_plants_lookup_locus { "loci": ["AT1G01010", "AT1G01020", "AT9G99999"] }
{
  "tool": "ensembl_plants_lookup_locus",
  "count": 3,
  "results": {
    "AT1G01010": { "id": "AT1G01010", "display_name": "NAC001", "biotype": "protein_coding", ... },
    "AT1G01020": { "id": "AT1G01020", "display_name": "ARV1", ... }
  },
  "errors": {
    "AT9G99999": "[NotFoundError] Ensembl Plants /lookup/id: no record for AT9G99999"
  }
}

batch_ensembl_plants_lookup_locus uses Ensembl's native POST /lookup/id endpoint — one HTTP round-trip handles all loci. The other five batch tools fan out single-locus calls via asyncio.gather, so the wall-clock time is ~max(per_locus_latency) + gather overhead rather than N × per_locus_latency. The wire shape is the same for both implementations.

Error model

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.)

Chain recipes

Annotation fallback chain — TAIR locus to canonical record, with graceful degradation:

1. Call tair_locus_info { locus } (alias of bar_gene_summary) for the curator-vetted summary + alias set.
2. On [UpstreamUnavailableError] (BAR ThaleMine outage), fall back to ensembl_plants_lookup_locus { locus } for the Ensembl Plants record.
3. On a second [UpstreamUnavailableError], fall back to phytozome_lookup_locus { locus } for the Phytozome BioMart record.

Cross-species ortholog probe (manual today, candidate for a built-in chain in a future release):

1. ensembl_plants_lookup_locus { locus, organism: "arabidopsis_thaliana" } → save the display_name.
2. ensembl_plants_lookup_locus { locus: <ortholog_id>, organism: "oryza_sativa" } → compare biotype + description.

Locus → protein → structure (gene to AlphaFold model in two MCP hops, expecting an external AlphaFold / RCSB tool downstream):

1. resolve_locus_to_uniprot { locus: "AT1G01010" } → save primaryAccession (e.g. Q0WV96).
2. Hand the accession to AlphaFold (https://alphafold.ebi.ac.uk/api/prediction/{accession}) or RCSB (https://search.rcsb.org/) via a sibling MCP.
3. On [NotFoundError], the locus has no UniProt entry — usually a non-coding or recently-annotated gene; fall back to ensembl_plants_lookup_locus for the biotype to confirm.

Biological context — homology + pathways + interactions + coexpression for one locus, cross-referenced into a high-confidence functional-partner shortlist:

homologs = await gramene_homologs(locus="AT1G01010")
pathways = await kegg_pathways(locus="AT1G01010")
uniprot = await resolve_locus_to_uniprot(locus="AT1G01010")
interactions = await string_interactions(
    locus_or_accession=uniprot["primaryAccession"], limit=10
)
coex = await atted_coexpression(locus="AT1G01010", top_n=10)
# Cross-reference: interactors ∩ coex_neighbors = high-confidence functional partners.

Or as one parameterized prompt:

prompts/get biological_context locus=AT1G01010 top_n=10

Development

.venv/bin/pip install -e '.[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 .

The _LIVE=1 gate runs additional tests that hit real Ensembl Plants / Phytozome endpoints — useful for catching wire-format drift. The _STDIO_SMOKE=1 gate spawns the MCP server over stdio and round-trips real initialize / list_tools / call_tool requests.

CI runs the unit suite + the stdio smoke on every push/PR (matrix: Python 3.11, 3.12). The live-network gate is not run in CI to avoid flakes from upstream availability.

Cache

Each backend keeps a small in-memory TTL+LRU cache around its HTTP helper (_get / _post). Identical requests within the TTL window return the cached payload without touching the network. Only 200 responses are cached; 4xx/5xx still raise. The cache is process-local — restart the server to drop all entries.

Env knobs (read once at import):

Variable	Default	Purpose
PLANT_GENOMICS_MCP_CACHE_TTL	600	Entry lifetime in seconds.
PLANT_GENOMICS_MCP_CACHE_SIZE	256	Max entries per backend before LRU eviction kicks in.
PLANT_GENOMICS_MCP_CACHE_DISABLED	unset	Any non-empty value makes every cache a no-op.

Progress notifications

For long-running calls (retry storms, the multi-second Phytozome BioMart POST), the server emits MCP notifications/progress messages over the active session. Clients opt in by passing a progressToken in the request _meta; without one, every notification is dropped.

What gets reported:

• Retry sleeps in every backend retry loop (Ensembl Plants /lookup/id/...: HTTP 429, retrying in 1.0s (attempt 2/3)).
• BioMart query bookends — Phytozome BioMart: submitting query before the POST and Phytozome BioMart: query complete after a 200.

progress is a monotonically increasing step counter (not a percentage); total is omitted because retry budgets aren't a useful denominator.

NCBI BLAST contact email

NCBI's BLAST URLAPI policy expects every caller to identify itself with a real contact email so abusive clients can be reached before they get throttled or blocked. blast_sequence reads the operator address from PLANT_GENOMICS_MCP_NCBI_EMAIL and sends it as the email= parameter on every Put/Get. Set this in production — when the variable is unset, the server sends an unmistakable placeholder ([e-mail]) and emits a one-shot progress warning per call, but NCBI may still throttle or block requests that look anonymous.

To prevent the same process from running away with BLAST submissions (NCBI rate-limits per-IP, not per-email), blast_sequence is wrapped in a module-level asyncio.Semaphore capped at 2 in-flight searches. Excess callers wait their turn rather than racing to upstream.

Migrating from v0.8 to v0.9

Every backend tool that previously accepted species= (Ensembl slug) or organism_id= (NCBI taxid) now accepts a single organism= parameter:

# v0.8 (deprecated)
await ensembl_plants.lookup_locus(client, "AT1G01010", species="arabidopsis_thaliana")
await uniprot.lookup_locus(client, "AT1G01010", organism_id=3702)

# v0.9
await ensembl_plants.lookup_locus(client, "AT1G01010", organism="arabidopsis_thaliana")
await uniprot.lookup_locus(client, "AT1G01010", organism="arabidopsis_thaliana")
# All of these also work:
await ensembl_plants.lookup_locus(client, "AT1G01010", organism="Arabidopsis thaliana")
await ensembl_plants.lookup_locus(client, "AT1G01010", organism="thale cress")
await ensembl_plants.lookup_locus(client, "AT1G01010", organism=3702)

sed migration for downstream callers:

sed -i 's/species=/organism=/g; s/organism_id=/organism=/g' your_code.py

The default value (arabidopsis_thaliana) is unchanged, so calls that never passed species= or organism_id= continue to work without code changes.

Output Pydantic models also rename species → organism and organism_taxid → organism (the string slug, not the int). See CHANGELOG.md for the full breaking-change list.

Supported organisms in v0.9

12 plants across the major Ensembl / STRING / Phytozome / Europe PMC backends. See the pgmcp://organisms/coverage MCP resource for the live coverage matrix, or organisms.ORGANISMS in the source.

License

MIT — see LICENSE. Underlying services (Ensembl Plants, Phytozome, TAIR, PlantCyc) have their own terms of use; consult each before bulk querying.