chembl-mcp-server

chembl-search-targets

chembl_search_targets

Read-onlyIdempotent

Resolve a protein/gene/UniProt accession to the ChEMBL target ID that chembl_get_bioactivities needs for the target→leads workflow. Supply at least one of accession (UniProt, e.g. P00533), gene_symbol (e.g. EGFR), or query (free-text name); filter further by organism and target_type. Returns each target with its type, organism, and component UniProt accessions + gene symbols. A UniProt accession from the uniprot/protein server is the most precise input. A capped result carries nextCursor — pass it back as cursor with the same filters to read the next page.

Input Schema

Name	Required	Description
`limit`	No	Maximum targets to return, up to 100 — a larger value is served at 100, with a notice saying so. Defaults to the server default (25) when omitted.
`query`	No	Free-text name match against the target preferred name, e.g. "kinase" or "growth factor receptor".
`cursor`	No	Opaque continuation token from a previous call's nextCursor — resumes where that page ended. Omit for the first page. Re-send the same accession/gene_symbol/query/filters that minted it (only limit may change; it sets this page's size); redeeming it against different filters walks a different result set.
`organism`	No	Restrict to a source organism, e.g. "Homo sapiens" (case-insensitive exact match).
`accession`	No	UniProt accession of a target component, e.g. "P00533". The most precise resolver — from the uniprot/protein server.
`gene_symbol`	No	Gene symbol of a target component, e.g. "EGFR" (case-insensitive exact match).
`target_type`	No	Restrict to a target class, e.g. "SINGLE PROTEIN" or "PROTEIN COMPLEX".

Output Schema

Name	Required	Description
`cap`	No	The limit that was applied.
`error`	No	Present when the call failed. Absent on success.
`shown`	No	Number of targets returned.
`notice`	No	Guidance when no target matched — echoes the filters and suggests how to broaden — and the disclosure that a limit above the maximum was served at the maximum.
`targets`	No	Matching targets (up to the limit).
`truncated`	No	True when the result was capped at the limit.
`nextCursor`	No	Opaque token for the next page — pass it back as cursor with the same filters. Absent when this page is the last one.
`totalCount`	No	Total targets matching the filters before the limit was applied.

Schema Changelog

Changes observed during successful MCP inspections.

Changed3 schema fields changedOct 24, 2026

changedInput schema / properties / limit / description

Previous value: -"Maximum targets to return. Defaults to the server default (25) when omitted."New value: +"Maximum targets to return, up to 100 — a larger value is served at 100, with a notice saying so. Defaults to the server default (25) when omitted."

changedInput schema / properties / limit / maximum
```
Previous value: -100New value: +10000
```

changedOutput schema / properties / notice / description

Previous value: -"Guidance when no target matched — echoes the filters and suggests how to broaden."New value: +"Guidance when no target matched — echoes the filters and suggests how to broaden — and the disclosure that a limit above the maximum was served at the maximum."

Changed2 schema fields changedSep 26, 2026

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

Previous value: -"Machine-readable failure mode. Declared by this tool: `missing_input`: None of query, accession, or gene_symbol was supplied. Other values are possible when a failure originates below the handler."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. `missing_input`: None of query, accession, or gene_symbol was supplied. Other values are possible when a failure originates below the handler."

changedOutput schema / properties / error / properties / data / properties / reason / examples

Previous value: -[
-  "missing_input"
-]New value: +[
+  "not_found",
+  "rate_limited",
+  "missing_input"
+]

Changed8 schema fields changedSep 19, 2026
- removedOutput schema / properties / targets / items / properties / components / items / properties / accession / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / targets / items / properties / components / items / properties / accession / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / targets / items / properties / organism / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / targets / items / properties / organism / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / targets / items / properties / pref_name / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / targets / items / properties / pref_name / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / targets / items / properties / target_type / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / targets / items / properties / target_type / 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": [
+      "targets",
+      "totalCount",
+      "truncated",
+      "shown",
+      "cap"
+    ]
+  },
+  {
+    "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. Declared by this tool: `missing_input`: None of query, accession, or gene_symbol was supplied. Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "missing_input"
+          ],
+          "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: -[
-  "targets",
-  "totalCount",
-  "truncated",
-  "shown",
-  "cap"
-]

Changed2 schema fields changedAug 13, 2026

addedInput schema / properties / cursor

Added value: +{
+  "description": "Opaque continuation token from a previous call's nextCursor — resumes where that page ended. Omit for the first page. Re-send the same accession/gene_symbol/query/filters that minted it (only limit may change; it sets this page's size); redeeming it against different filters walks a different result set.",
+  "type": "string"
+}

addedOutput schema / properties / nextCursor

Added value: +{
+  "description": "Opaque token for the next page — pass it back as cursor with the same filters. Absent when this page is the last one.",
+  "type": "string"
+}

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 the safety profile (readOnly, idempotent, open-world), so the description only needs incremental context — and it supplies the result cap and the nextCursor continuation contract. It does not mention rate limits or failure modes for unmatched accessions, which keeps it off a 5.

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?

Front-loaded with the resolve action and its consumer, then input rules, then return shape, then pagination. Every sentence carries an actionable fact with no filler.

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 7-parameter read-only lookup with full schema coverage, output schema, and annotations, an agent has everything needed: which inputs to prefer, how filtering works, and how to page. Nothing material is missing.

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% so the schema carries most semantics, but the description adds real information the schema cannot: with zero required parameters, the constraint that at least one of accession/gene_symbol/query must be supplied, and which of those resolves most precisely. Cursor re-use guidance largely restates the schema's cursor description.

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?

States a specific verb+resource: resolve a protein/gene/UniProt accession to a ChEMBL target ID. It also ties that output directly to the sibling that consumes it (chembl_get_bioactivities), which lets an agent place this tool in the workflow without inspecting other definitions.

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?

Gives the input selection rule ('supply at least one of accession, gene_symbol, or query') and ranks them ('a UniProt accession … is the most precise input'), plus where the output is needed next. It lacks an explicit when-not-to-use-this statement vs. the other search siblings, so it falls short of a 5.

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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