chembl-mcp-server

chembl-get-assay

chembl_get_assay

Read-onlyIdempotent

Assay provenance behind a bioactivity row: description, type (binding / functional / ADMET / toxicity), the target it measures, organism, and ChEMBL's 1–9 confidence score (9 = direct assay on the protein target, lower = homologous or indirect). Supply assay_chembl_id from a chembl_get_bioactivities row. Call this to judge whether two measurements are comparable before ranking them together.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`assay_chembl_id`	Yes	ChEMBL assay ID from a bioactivity row's assay_chembl_id, e.g. "CHEMBL674637".

Output Schema

TableJSON Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`organism`	No	Assay organism. Null when unspecified.
`assay_type`	No	Assay type code: B=binding, F=functional, A=ADMET, T=toxicity, P=physicochemical, U=unclassified. Null when absent.
`description`	No	Assay description text. Null when absent.
`assay_chembl_id`	No	The ChEMBL assay ID queried.
`confidence_score`	No	ChEMBL confidence score, 1–9 (9 = direct single-protein assay; lower = homologous/indirect). Null when unscored.
`target_chembl_id`	No	ChEMBL target ID the assay measures — chain to chembl_search_targets/chembl_get_bioactivities. Null when unassigned.
`assay_type_description`	No	Human-readable assay type, e.g. "Binding". Null when absent.
`confidence_description`	No	Human-readable confidence description, e.g. "Direct single protein target assigned". Null when absent.

Schema Changelog

Changes observed during successful MCP inspections.

Changed14 schema fields changedSep 19, 2026

removedOutput schema / properties / assay_type / anyOf

Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]

addedOutput schema / properties / assay_type / type
```
Added value: +[
+  "string",
+  "null"
+]
```

removedOutput schema / properties / assay_type_description / anyOf

Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]

addedOutput schema / properties / assay_type_description / type
```
Added value: +[
+  "string",
+  "null"
+]
```

removedOutput schema / properties / confidence_description / anyOf

Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]

addedOutput schema / properties / confidence_description / type
```
Added value: +[
+  "string",
+  "null"
+]
```

removedOutput schema / properties / confidence_score / anyOf

Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]

addedOutput schema / properties / confidence_score / type
```
Added value: +[
+  "number",
+  "null"
+]
```

removedOutput schema / properties / description / anyOf

Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]

addedOutput schema / properties / description / type
```
Added value: +[
+  "string",
+  "null"
+]
```

removedOutput schema / properties / organism / anyOf

Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]

addedOutput schema / properties / organism / type
```
Added value: +[
+  "string",
+  "null"
+]
```

removedOutput schema / properties / target_chembl_id / anyOf

Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]

addedOutput schema / properties / target_chembl_id / type
```
Added value: +[
+  "string",
+  "null"
+]
```

Changed6 schema fields changedAug 25, 2026

changedInput schema / $schema

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

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

changedOutput schema / $schema

Previous value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"

addedOutput schema / anyOf

Added value: +[
+  {
+    "not": {
+      "required": [
+        "error"
+      ]
+    },
+    "required": [
+      "assay_chembl_id",
+      "description",
+      "assay_type",
+      "assay_type_description",
+      "target_chembl_id",
+      "organism",
+      "confidence_score",
+      "confidence_description"
+    ]
+  },
+  {
+    "required": [
+      "error"
+    ]
+  }
+]

addedOutput schema / properties / error

Added value: +{
+  "additionalProperties": {},
+  "description": "Present when the call failed. Absent on success.",
+  "properties": {
+    "code": {
+      "description": "JSON-RPC error code for this failure.",
+      "maximum": 9007199254740991,
+      "minimum": -9007199254740991,
+      "type": "integer"
+    },
+    "data": {
+      "additionalProperties": {},
+      "properties": {
+        "reason": {
+          "description": "Machine-readable failure mode.",
+          "type": "string"
+        },
+        "recovery": {
+          "additionalProperties": {},
+          "description": "Actionable next step for the caller.",
+          "properties": {
+            "hint": {
+              "type": "string"
+            }
+          },
+          "required": [
+            "hint"
+          ],
+          "type": "object"
+        },
+        "retryable": {
+          "description": "Whether retrying may succeed.",
+          "type": "boolean"
+        }
+      },
+      "type": "object"
+    },
+    "message": {
+      "description": "Human-readable description of what went wrong.",
+      "type": "string"
+    }
+  },
+  "required": [
+    "code",
+    "message"
+  ],
+  "type": "object"
+}

removedOutput schema / required

Removed value: -[
-  "assay_chembl_id",
-  "description",
-  "assay_type",
-  "assay_type_description",
-  "target_chembl_id",
-  "organism",
-  "confidence_score",
-  "confidence_description"
-]

First observedAug 13, 2026

TDQS

A4.5/5.0

Behavior4/5

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

Annotations already cover readOnly, idempotent, and open-world behavior. The description adds valuable behavioral context by explaining the 1-9 confidence score meaning, including the 9 = direct assay distinction, which helps agents interpret results correctly.

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 compact, front-loaded with the core resource and fields, and every sentence earns its place: what is returned, where the input comes from, and when to use the tool. No filler or redundant restatement.

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?

For a single-parameter read-only lookup with an output schema present, the description is complete. It explains the return content, the input provenance, and the intended decision-making use case, leaving no critical gap for an agent 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?

Schema coverage is 100% with a clear example, so the baseline is 3. The description adds extra semantic value by explicitly directing the agent to obtain the parameter from chembl_get_bioactivities, tying the input to a specific upstream sibling tool.

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 resource ('assay provenance behind a bioactivity row') and the specific fields returned: description, type, target, organism, and confidence score. It is clearly distinct from siblings like chembl_get_bioactivities because it operates on an assay_chembl_id rather than returning bioactivity rows.

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 explicitly says to call this 'to judge whether two measurements are comparable before ranking them together' and tells the agent to supply the assay_chembl_id from a chembl_get_bioactivities row. It does not explicitly name alternatives or exclusions, but the usage context is clear.

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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