ChatSpatial

analyze_enrichment

DestructiveIdempotent

Identify enriched gene sets and pathways in spatial transcriptomics data using GSEA, ORA, or spatial enrichment mapping to reveal underlying biological processes.

Instructions

Perform gene set enrichment analysis.

Args:
    data_id: Dataset ID
    params: Required - species must be specified. See EnrichmentParameters for methods and gene_set_database options.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`params`	Yes
`data_id`	Yes

Output Schema

TableJSON Schema

Name	Required	Description
`method`	Yes
`warnings`	No	Non-fatal conditions that may affect result interpretation.
`n_gene_sets`	Yes
`n_significant`	No
`top_gene_sets`	Yes
`top_depleted_sets`	Yes
`spatial_scores_key`	No
`n_successful_signatures`	No

Schema Changelog

Changes observed during successful MCP inspections.

Changed4 schema fields changedv1.5.3Aug 19, 2026

addedOutput schema / properties / n_significant / anyOf

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

addedOutput schema / properties / n_significant / default
```
Added value: +null
```
removedOutput schema / properties / n_significant / type
```
Removed value: -"integer"
```

changedOutput schema / required

Previous value: -[
-  "method",
-  "n_gene_sets",
-  "n_significant",
-  "top_gene_sets",
-  "top_depleted_sets"
-]New value: +[
+  "method",
+  "n_gene_sets",
+  "top_gene_sets",
+  "top_depleted_sets"
+]

Changed8 schema fields changedv1.3.2Aug 10, 2026

addedInput schema / additionalProperties
```
Added value: +false
```
addedOutput schema / additionalProperties
```
Added value: +false
```

removedOutput schema / properties / adjusted_pvalues

Removed value: -{
-  "anyOf": [
-    {
-      "additionalProperties": {
-        "type": "number"
-      },
-      "type": "object"
-    },
-    {
-      "type": "null"
-    }
-  ],
-  "default": null,
-  "title": "Adjusted Pvalues"
-}

removedOutput schema / properties / enrichment_scores

Removed value: -{
-  "additionalProperties": {
-    "type": "number"
-  },
-  "title": "Enrichment Scores",
-  "type": "object"
-}

removedOutput schema / properties / gene_set_statistics

Removed value: -{
-  "additionalProperties": {
-    "additionalProperties": true,
-    "type": "object"
-  },
-  "title": "Gene Set Statistics",
-  "type": "object"
-}

removedOutput schema / properties / pvalues

Removed value: -{
-  "anyOf": [
-    {
-      "additionalProperties": {
-        "type": "number"
-      },
-      "type": "object"
-    },
-    {
-      "type": "null"
-    }
-  ],
-  "default": null,
-  "title": "Pvalues"
-}

removedOutput schema / properties / spatial_metrics

Removed value: -{
-  "anyOf": [
-    {
-      "additionalProperties": true,
-      "type": "object"
-    },
-    {
-      "type": "null"
-    }
-  ],
-  "default": null,
-  "title": "Spatial Metrics"
-}

addedOutput schema / properties / warnings

Added value: +{
+  "description": "Non-fatal conditions that may affect result interpretation.",
+  "items": {
+    "type": "string"
+  },
+  "title": "Warnings",
+  "type": "array"
+}

Changed4 schema fields changedv1.2.8May 12, 2026

addedInput schema / properties / params / $ref

Added value: +"#/$defs/EnrichmentParameters"

removedInput schema / properties / params / anyOf

Removed value: -[
-  {
-    "$ref": "#/$defs/EnrichmentParameters"
-  },
-  {
-    "type": "null"
-  }
-]

removedInput schema / properties / params / default
```
Removed value: -null
```

changedInput schema / required

Previous value: -[
-  "data_id"
-]New value: +[
+  "data_id",
+  "params"
+]

First observedv1.2.7May 11, 2026

TDQS

C2.9/5.0

Behavior2/5

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

Annotations include destructiveHint=true and idempotentHint=true, but the description provides no additional behavioral context. It does not mention potential side effects, modifications to the dataset, or any safety considerations. While it doesn't contradict annotations, it adds no value beyond what the annotations already convey, leaving the agent uninformed about the tool's actual behavior on data.

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 extremely concise: a single sentence and two argument placeholders. It avoids redundancy and gets straight to the point. Every word earns its place, though it may be too sparse for a complex tool. However, for conciseness, it is exemplary—no fluff, no filler.

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

Completeness2/5

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

Despite having an output schema, the description is minimal and does not explain the overall context of use. It fails to mention the type of data expected, the output interpretation, or any preconditions (e.g., data must be loaded and preprocessed). It also does not relate to the analysis pipeline or when to apply this analysis. For a tool with many configurable parameters and complex behavior, this is incomplete and leaves the agent without sufficient guidance.

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?

The schema provides detailed descriptions for most parameters (e.g., method, species, max_genes), and the description adds only a note that species must be specified and points to EnrichmentParameters for details. Given high schema coverage, the description adds marginal value. However, it does highlight the required nature of species, which is helpful, but does not explain semantics beyond that. Baseline of 3 is appropriate as the description slightly supplements the schema but does not compensate for deeper meaning.

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

Purpose4/5

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

The description states the tool 'Performs gene set enrichment analysis' which is a specific verb and resource. It clearly distinguishes from generic analysis tools but doesn't explicitly differentiate from sibling tools like analyze_spatial_statistics or deconvolve_data, though the enrichment focus is evident. It lacks a clear scope or mention of input/output context, but the core purpose is unambiguous.

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

Usage Guidelines2/5

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

The description gives only a minimal usage hint: 'Required - species must be specified.' It does not explain when to use this tool over alternatives, what scenarios it suits, or when not to use it. There is no reference to the relevant analysis workflow or comparison with sibling tools like find_markers or compute_embeddings. This guidance is insufficient for an agent to make an informed selection.

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