plant-genomics-mcp

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OrthoDB: Orthologs

orthodb_orthologs

Read-onlyIdempotent

Resolve a plant gene locus to its OrthoDB ortholog group and cross-species member genes. Returns group metadata and per-organism gene lists, with optional target_organism filtering.

Instructions

Resolve a locus to its OrthoDB ortholog group and cross-species member genes (data.orthodb.org; free, no key). Searches at the Viridiplantae level, then returns the group metadata (name, evolutionary rate) and member genes grouped by organism (organism, gene id, description). organism_count is the true cluster total; the member list is capped with truncated flagged. found=false when the locus maps to no ortholog group. Works for all 12 organisms. NOTE: unlike the other locus tools, organism= does NOT scope the search — the group is resolved from the locus id alone at the Viridiplantae level, and organism is only validated and echoed back. Passing a mismatched organism therefore still returns the locus's real group. target_organism= DOES filter: it keeps only that organism's members, before the cap, so a 2,000-member group cannot hide rice or wheat behind 'limit'.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`limit`	No	Max ortholog member rows to return. 'member_count' always reports the true pre-cap total and 'truncated' says whether the cap bit.
`locus`	Yes	e.g. AT1G01060 (Arabidopsis), Os01g0100100 (rice RAP-DB)
`cursor`	No	next_cursor from the previous page; omit for the first (#123)
`organism`	No	Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid. Validated and echoed only: it does NOT scope the OrthoDB search, which keys on the locus id at the Viridiplantae level	arabidopsis_thaliana
`target_organism`	No	Keep only this organism's members (slug, scientific/common name, or NCBI taxid), filtered BEFORE the cap. Adds 'member_count_all_organisms' for the whole group.

Output Schema

TableJSON Schema

Name	Required	Description
`found`	Yes	True if the locus maps to an ortholog group
`group`	No	Group metadata {id, name, evolutionary_rate, level_name, …}
`locus`	Yes
`total`	Yes	How many members (all organisms, or target_organism when given) exist upstream for this query, all pages (pre-cap) (#123)
`members`	No	Per-gene {organism, gene_id, xref, description}
`organism`	Yes	Canonical organism as requested — echoed, not inferred from the hit. Does not scope the search (see class docstring)
`returned`	Yes	Rows in this payload (#123)
`truncated`	Yes	True if the member list was capped
`next_cursor`	No	Pass back as cursor= to get the rows after this page; null on the last page. Opaque, and bound to this tool and query (#123)
`member_count`	Yes	Member genes before the cap (pre-cap; = total)
`organism_count`	Yes	Number of member organisms in the whole ortholog group (pre-cap) — the true cluster total, unaffected by the member cap below
`target_organism`	No	Canonical organism the members were filtered to, when target_organism was passed
`upstream_version`	No	OrthoDB release that produced THIS response, as stated by the release pinned in every request path (/v12/). null means OrthoDB did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered.
`member_count_all_organisms`	No	Whole-group member total (pre-filter, pre-cap); present only when filtered

Schema Changelog

Changes observed during successful MCP inspections.

Changed1 schema field changedv1.27.0Sep 27, 2026

changedOutput schema / properties / upstream_version / description

Previous value: -"OrthoDB release that produced THIS response, — always null today: this backend states no release on its responses. null means OrthoDB did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered."New value: +"OrthoDB release that produced THIS response, as stated by the release pinned in every request path (/v12/). null means OrthoDB did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered."

Changed10 schema fields changedv1.22.0Sep 24, 2026

addedInput schema / properties / cursor

Added value: +{
+  "description": "next_cursor from the previous page; omit for the first (#123)",
+  "type": "string"
+}

addedInput schema / properties / target_organism

Added value: +{
+  "description": "Keep only this organism's members (slug, scientific/common name, or NCBI taxid), filtered BEFORE the cap. Adds 'member_count_all_organisms' for the whole group.",
+  "type": [
+    "string",
+    "integer"
+  ]
+}

changedOutput schema / properties / member_count / description

Previous value: -"Member genes returned (post-cap)"New value: +"Member genes before the cap (pre-cap; = total)"

addedOutput schema / properties / member_count_all_organisms

Added value: +{
+  "anyOf": [
+    {
+      "type": "integer"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Whole-group member total (pre-filter, pre-cap); present only when filtered",
+  "title": "Member Count All Organisms"
+}

addedOutput schema / properties / next_cursor

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Pass back as cursor= to get the rows after this page; null on the last page. Opaque, and bound to this tool and query (#123)",
+  "title": "Next Cursor"
+}

addedOutput schema / properties / returned

Added value: +{
+  "description": "Rows in this payload (#123)",
+  "title": "Returned",
+  "type": "integer"
+}

addedOutput schema / properties / target_organism

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Canonical organism the members were filtered to, when target_organism was passed",
+  "title": "Target Organism"
+}

addedOutput schema / properties / total

Added value: +{
+  "description": "How many members (all organisms, or target_organism when given) exist upstream for this query, all pages (pre-cap) (#123)",
+  "title": "Total",
+  "type": "integer"
+}

addedOutput schema / properties / upstream_version

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "OrthoDB release that produced THIS response, — always null today: this backend states no release on its responses. null means OrthoDB did not state one — never that no release exists, and never inferred from a separate metadata call, which can describe a different release than the one that answered.",
+  "title": "Upstream Version"
+}

changedOutput schema / required

Previous value: -[
-  "locus",
-  "organism",
-  "found",
-  "organism_count",
-  "member_count",
-  "truncated"
-]New value: +[
+  "total",
+  "returned",
+  "locus",
+  "organism",
+  "found",
+  "organism_count",
+  "member_count",
+  "truncated"
+]

Changed1 schema field changedv1.20.0Jul 28, 2026

addedInput schema / properties / limit

Added value: +{
+  "default": 100,
+  "description": "Max ortholog member rows to return. 'member_count' always reports the true pre-cap total and 'truncated' says whether the cap bit.",
+  "maximum": 100,
+  "minimum": 1,
+  "type": "integer"
+}

Changed4 schema fields changedv1.19.4Jul 28, 2026

changedInput schema / properties / organism / description

Previous value: -"Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid"New value: +"Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid. Validated and echoed only: it does NOT scope the OrthoDB search, which keys on the locus id at the Viridiplantae level"

changedOutput schema / description

Previous value: -"OrthoDB ortholog group + cross-species member genes for a locus.\n\n``found=False`` means the locus maps to no Viridiplantae ortholog group.\n``organism_count`` is the true cluster total even when members are capped."New value: +"OrthoDB ortholog group + cross-species member genes for a locus.\n\n``found=False`` means the locus maps to no Viridiplantae ortholog group.\n``organism_count`` is the true cluster total even when members are capped.\n\n``organism`` is an echo of the request, NOT a property of the result: the\nsearch keys on the locus id at the Viridiplantae level, so the group comes\nback the same whichever organism was declared."

changedOutput schema / properties / organism / description

Previous value: -"Resolved canonical organism"New value: +"Canonical organism as requested — echoed, not inferred from the hit. Does not scope the search (see class docstring)"

changedOutput schema / properties / organism_count / description

Previous value: -"Number of member organisms (clusters)"New value: +"Number of member organisms in the whole ortholog group (pre-cap) — the true cluster total, unaffected by the member cap below"

Addedv1.18.2Jul 24, 2026

TDQS

A4.4/5.0

Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Beyond the annotations (readOnly, idempotent), the description adds valuable behavioral detail: the cap behavior with truncated flag, the found=false case, the exact role of organism (validated only) vs target_organism (filters before cap), and the true cluster total. This goes well beyond what annotations provide.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is fairly long but every sentence adds value—covering scoping, cap behavior, and the organism distinction. It is front-loaded with the core purpose. It could be trimmed slightly, but the detail is justified given the tool's complexity.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With an output schema present, the description doesn't need to detail return values. It covers the essential behavioral nuances: the cap with truncation, the found flag, the scoping semantics, and the target_organism filtering. Nothing an agent needs to call it correctly is missing.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the schema already documents each parameter's meaning. The description largely repeats that information (e.g., the cap semantics, organism not scoping, target_organism filtering before cap). It adds little new meaning beyond the schema, so the baseline 3 applies.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description states a specific verb ('Resolve'), a resource (OrthoDB ortholog group), and the result (cross-species member genes). It also distinguishes itself from sibling locus tools by noting that organism= does NOT scope the search, making its unique behavior explicit.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

It clearly explains the tool's purpose (ortholog resolution) and highlights the key difference from other locus tools: 'unlike the other locus tools, organism= does NOT scope the search'. This gives agents context for when to choose this tool, though it doesn't explicitly name alternative tools or list when-not-to-use conditions.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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