PlantCyc: Metabolic Pathways

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

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

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"
+  }
+}

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``)."

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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"
+]