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

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

Output Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`organism`	No	Organism ChEMBL records for the assay itself, not its target's organism. Null when the assay records none, even when the target is a human protein.
`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.

Changed1 schema field changedOct 29, 2026

changedOutput schema / properties / organism / description

Previous value: -"Assay organism. Null when unspecified."New value: +"Organism ChEMBL records for the assay itself, not its target's organism. Null when the assay records none, even when the target is a human protein."

Changed2 schema fields changedOct 24, 2026
- removedInput schema / properties / assay_chembl_id / minLength
```
Removed value: -1
```
- addedInput schema / properties / assay_chembl_id / pattern
```
Added value: +"^\\s*[Cc][Hh][Ee][Mm][Bb][Ll]\\d+\\s*$"
```

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 does not need to restate safety traits. It adds useful domain transparency by explaining the 1–9 confidence score and what lower scores imply about directness of the assay.

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 three dense sentences with no wasted text. It front-loads the returned provenance, then the confidence-score meaning, then the input source and use case.

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?

With annotations covering safety behavior and an output schema covering return structure, the description supplies the remaining domain context: what assay provenance includes, how to interpret confidence, and when to call it. Nothing essential for correct selection or invocation is missing.

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?

Schema coverage is 100%, and the schema already says the parameter is a ChEMBL assay ID from a bioactivity row with an example. The description reinforces the source as chembl_get_bioactivities, but it does not add format or validation semantics beyond the schema.

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 resource and tells the agent exactly what provenance fields are returned: description, type, target, organism, and confidence score. It also distinguishes this lookup from the sibling bioactivity tool by explaining that this is the assay-level context behind a bioactivity row.

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 source for the required ID (assay_chembl_id from a chembl_get_bioactivities row) and an explicit use case: call this before ranking measurements together to judge comparability. That is clear when-to-use guidance tied to the sibling tool.

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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