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.

Changed2 schema fields changedSep 26, 2026

changedOutput schema / properties / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode."New value: +"Machine-readable failure mode. Declared by this tool: `not_found`: ChEMBL has no record for the requested identifier or structure. `rate_limited`: ChEMBL rate-limits the upstream request. Other values are possible when a failure originates below the handler."

addedOutput schema / properties / error / properties / data / properties / reason / examples
```
Added value: +[
+  "not_found",
+  "rate_limited"
+]
```

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 establish read-only, idempotent, open-world behavior, so the description is not required to repeat those. It adds real behavioral context by explaining the confidence score semantics (9 = direct assay, lower = homologous or indirect), which is not visible in the annotations and matters when comparing assays.

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 and front-loaded: it defines the resource and its content, then states the input dependency and the intended use case. Every sentence earns its place, with 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 a rich output schema and annotations already set, the description tells the agent what the tool returns, how to source its ID, and why it matters. Nothing material is missing for correct selection and invocation.

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 input schema already covers assay_chembl_id fully with format and an example, and schema coverage is 100%. The description repeats the dependency on bioactivity rows but does not add new semantic depth beyond the schema, so the baseline score of 3 is appropriate.

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 purpose: exposing assay provenance for a bioactivity row, and enumerates meaningful fields (description, type, target, organism, confidence score). It clearly distinguishes itself from siblings by sourcing its ID from chembl_get_bioactivities rather than searching or querying dataframes.

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

Usage Guidelines5/5

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

It gives an explicit trigger ('Supply assay_chembl_id from a chembl_get_bioactivities row') and a clear decision context ('Call this to judge whether two measurements are comparable before ranking them together'). This tells an agent exactly when this tool is the right step in a workflow.

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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