plant-genomics-mcp

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PlantCyc: Metabolic Pathways

plantcyc_locus_info

Read-onlyIdempotent

Retrieve metabolic pathway annotations for a plant locus by mapping gene to enzyme, reactions, and PlantCyc pathways, filling gaps left by KEGG and GO. Supports 11 plant genomes; returns pathway details or confirms non-enzymatic genes.

Instructions

Fetch metabolic annotation for a locus from PlantCyc / the Plant Metabolic Network (pmn.plantcyc.org; free BioCyc web-services API, no key). Walks gene → enzyme → catalyzed reactions → PlantCyc pathways in the organism's PGDB, returning enzymes[] + reactions[] (id/name) + pathways[] (id/name) — the metabolic-pathway view KEGG and GO don't provide. A non-enzymatic gene (e.g. a transcription factor) returns found=false with empty lists, not an error. reaction_count is the true total even when the lists are capped; pathway_count is too, or null (unknown) when the gene catalyzes more reactions than are walked for pathways. 11 organisms have a PGDB (arabidopsis, rice, maize, soybean, grape, poplar, tomato, barley, sorghum, medicago, brachypodium); wheat is not yet mapped. Defaults to arabidopsis_thaliana (AraCyc, the best-curated); pass organism= for other species.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`locus`	Yes	e.g. AT3G51240 (Arabidopsis), Os11g0530600 (rice RAP-DB)
`organism`	No	Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid	arabidopsis_thaliana

Output Schema

TableJSON Schema

Name	Required	Description
`found`	Yes	True if the locus resolved to a metabolic gene
`locus`	Yes
`orgid`	Yes	PlantCyc PGDB org id, e.g. ARA (AraCyc)
`enzymes`	Yes	Product monomer (enzyme) frame ids
`organism`	Yes	Canonical organism slug
`pathways`	Yes
`reactions`	Yes
`gene_frame`	No	Resolved PGDB gene frame id
`pathway_count`	Yes	Total distinct pathways (pre-cap); null (unknown) when the gene catalyzes more reactions than are walked for pathways
`reaction_count`	Yes	Total distinct reactions (pre-cap)
`gene_common_name`	No	Gene common name in the PGDB

Schema Changelog

Changes observed during successful MCP inspections.

Changed4 schema fields changedv1.22.0Sep 24, 2026

changedOutput schema / description

Previous value: -"PlantCyc / PMN metabolic annotation for a locus.\n\nWalks gene → enzyme → reactions → pathways in the organism's PGDB via the\nfree BioCyc web-services API. ``found=False`` with empty lists when the\nlocus has no metabolic annotation (e.g. a non-enzymatic gene like a\ntranscription factor) — this is a normal result, not an error.\n``reaction_count`` / ``pathway_count`` are the true totals even when the\nreturned lists are capped (see ``plantcyc.MAX_REACTIONS`` / ``MAX_PATHWAYS``)."New value: +"PlantCyc / PMN metabolic annotation for a locus.\n\nWalks gene → enzyme → reactions → pathways in the organism's PGDB via the\nfree BioCyc web-services API. ``found=False`` with empty lists when the\nlocus has no metabolic annotation (e.g. a non-enzymatic gene like a\ntranscription factor) — this is a normal result, not an error.\n``reaction_count`` is the true total even when the returned lists are\ncapped (see ``plantcyc.MAX_REACTIONS`` / ``MAX_PATHWAYS``). ``pathway_count``\nis too, except that pathways are read from the first ``MAX_REACTIONS``\nreactions only, so past that cap it is null: unknown, never a subset's count."

addedOutput schema / properties / pathway_count / anyOf

Added value: +[
+  {
+    "type": "integer"
+  },
+  {
+    "type": "null"
+  }
+]

changedOutput schema / properties / pathway_count / description

Previous value: -"Total distinct pathways (pre-cap)"New value: +"Total distinct pathways (pre-cap); null (unknown) when the gene catalyzes more reactions than are walked for pathways"

removedOutput schema / properties / pathway_count / type
```
Removed value: -"integer"
```

Changed21 schema fields changedv1.18.2Jul 24, 2026

changedInput schema / properties / locus / description

Previous value: -"TAIR-canonical locus, e.g. AT1G01010"New value: +"e.g. AT3G51240 (Arabidopsis), Os11g0530600 (rice RAP-DB)"

addedInput schema / properties / organism

Added value: +{
+  "default": "arabidopsis_thaliana",
+  "description": "Plant organism — accepts canonical slug (arabidopsis_thaliana), scientific or common name, or NCBI taxid",
+  "type": [
+    "string",
+    "integer"
+  ]
+}

addedOutput schema / $defs

Added value: +{
+  "PlantCycPathway": {
+    "additionalProperties": true,
+    "description": "One PlantCyc/PMN pathway the locus participates in.",
+    "properties": {
+      "id": {
+        "anyOf": [
+          {
+            "type": "string"
+          },
+          {
+            "type": "null"
+          }
+        ],
+        "default": null,
+        "description": "Pathway frame id, e.g. PWY-6787",
+        "title": "Id"
+      },
+      "name": {
+        "anyOf": [
+          {
+            "type": "string"
+          },
+          {
+            "type": "null"
+          }
+        ],
+        "default": null,
+        "description": "Pathway common name, e.g. flavonoid biosynthesis",
+        "title": "Name"
+      }
+    },
+    "title": "PlantCycPathway",
+    "type": "object"
+  },
+  "PlantCycReaction": {
+    "additionalProperties": true,
+    "description": "One reaction catalyzed by a locus's gene product (PlantCyc/PMN).",
+    "properties": {
+      "id": {
+        "anyOf": [
+          {
+            "type": "string"
+          },
+          {
+            "type": "null"
+          }
+        ],
+        "default": null,
+        "description": "Reaction frame id, e.g. RXN-7775",
+        "title": "Id"
+      },
+      "name": {
+        "anyOf": [
+          {
+            "type": "string"
+          },
+          {
+            "type": "null"
+          }
+        ],
+        "default": null,
+        "description": "Reaction common name, if the frame has one",
+        "title": "Name"
+      }
+    },
+    "title": "PlantCycReaction",
+    "type": "object"
+  }
+}

changedOutput schema / description

Previous value: -"PlantCyc stub response — adds ``plantcyc_web_url`` to the shared shape."New value: +"PlantCyc / PMN metabolic annotation for a locus.\n\nWalks gene → enzyme → reactions → pathways in the organism's PGDB via the\nfree BioCyc web-services API. ``found=False`` with empty lists when the\nlocus has no metabolic annotation (e.g. a non-enzymatic gene like a\ntranscription factor) — this is a normal result, not an error.\n``reaction_count`` / ``pathway_count`` are the true totals even when the\nreturned lists are capped (see ``plantcyc.MAX_REACTIONS`` / ``MAX_PATHWAYS``)."

removedOutput schema / properties / alternatives

Removed value: -{
-  "description": "Tool names users should call instead",
-  "items": {
-    "type": "string"
-  },
-  "title": "Alternatives",
-  "type": "array"
-}

removedOutput schema / properties / alternatives_note

Removed value: -{
-  "description": "What the alternatives do and do NOT cover",
-  "title": "Alternatives Note",
-  "type": "string"
-}

addedOutput schema / properties / enzymes

Added value: +{
+  "description": "Product monomer (enzyme) frame ids",
+  "items": {
+    "type": "string"
+  },
+  "title": "Enzymes",
+  "type": "array"
+}

addedOutput schema / properties / found

Added value: +{
+  "description": "True if the locus resolved to a metabolic gene",
+  "title": "Found",
+  "type": "boolean"
+}

addedOutput schema / properties / gene_common_name

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Gene common name in the PGDB",
+  "title": "Gene Common Name"
+}

addedOutput schema / properties / gene_frame

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "description": "Resolved PGDB gene frame id",
+  "title": "Gene Frame"
+}

addedOutput schema / properties / organism

Added value: +{
+  "description": "Canonical organism slug",
+  "title": "Organism",
+  "type": "string"
+}

addedOutput schema / properties / orgid

Added value: +{
+  "description": "PlantCyc PGDB org id, e.g. ARA (AraCyc)",
+  "title": "Orgid",
+  "type": "string"
+}

addedOutput schema / properties / pathway_count

Added value: +{
+  "description": "Total distinct pathways (pre-cap)",
+  "title": "Pathway Count",
+  "type": "integer"
+}

addedOutput schema / properties / pathways

Added value: +{
+  "items": {
+    "$ref": "#/$defs/PlantCycPathway"
+  },
+  "title": "Pathways",
+  "type": "array"
+}

removedOutput schema / properties / plantcyc_web_url

Removed value: -{
-  "description": "Browser URL for the PlantCyc gene page",
-  "title": "Plantcyc Web Url",
-  "type": "string"
-}

removedOutput schema / properties / probed_at

Removed value: -{
-  "description": "ISO date of the last live access probe (YYYY-MM-DD)",
-  "title": "Probed At",
-  "type": "string"
-}

removedOutput schema / properties / rationale

Removed value: -{
-  "description": "Why this backend is gated",
-  "title": "Rationale",
-  "type": "string"
-}

addedOutput schema / properties / reaction_count

Added value: +{
+  "description": "Total distinct reactions (pre-cap)",
+  "title": "Reaction Count",
+  "type": "integer"
+}

addedOutput schema / properties / reactions

Added value: +{
+  "items": {
+    "$ref": "#/$defs/PlantCycReaction"
+  },
+  "title": "Reactions",
+  "type": "array"
+}

removedOutput schema / properties / status

Removed value: -{
-  "description": "Always \"subscription_required\" — upstream REST is paid-only.",
-  "title": "Status",
-  "type": "string"
-}

changedOutput schema / required

Previous value: -[
-  "locus",
-  "status",
-  "probed_at",
-  "rationale",
-  "alternatives",
-  "alternatives_note",
-  "plantcyc_web_url"
-]New value: +[
+  "locus",
+  "organism",
+  "orgid",
+  "found",
+  "enzymes",
+  "reactions",
+  "pathways",
+  "reaction_count",
+  "pathway_count"
+]

First observedv1.8.0May 30, 2026

TDQS

A4.5/5.0

Behavior4/5

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

Annotations already indicate read-only, open-world, idempotent, and non-destructive, so the safety profile is clear. The description adds valuable behavioral context: non-enzymatic genes return found=false with empty lists (not an error), and reaction_count/pathway_count semantics are explained (true totals even when lists are capped). This goes beyond annotations and clarifies edge cases.

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

Conciseness5/5

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

The description is dense but well-structured: it starts with the purpose, then the data flow, then edge cases, then supported organisms and defaults. Every sentence adds information; there's no fluff. It's longer than typical but justifies the length with rich, useful details.

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?

Given the tool's moderate complexity (walking gene→enzyme→reaction→pathway), the description is complete. It explains the output structure (enzymes, reactions, pathways) and return semantics (found=false for non-enzymatic genes, count meanings). It also covers organism support and default behavior. The output schema exists, so return format is documented. An agent has everything needed to call it correctly.

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

Parameters4/5

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

The schema already documents both parameters (locus and organism) with examples and description. The description adds value by explaining the default organism (arabidopsis_thaliana as AraCyc, best-curated) and that organism accepts canonical slug, scientific name, common name, or taxid. It also lists all 11 supported organisms, which is not in the schema. This goes beyond schema coverage.

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 clearly states the tool fetches metabolic annotation for a locus from PlantCyc, and walks the gene→enzyme→reaction→pathway chain to return metabolic pathways. It specifies a unique resource (PlantCyc/PMN) and distinguishes it from KEGG and GO, and the sibling list shows it's distinct from other locus tools like kegg_pathways and locus_go_annotations.

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?

The description explains when to use this tool: for metabolic pathway information that KEGG and GO don't provide, and it notes that wheat is not supported (an exclusion). It doesn't explicitly say 'use this instead of X' for every sibling, but the context is clear. It also provides defaults and the organism list, which is useful.

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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