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

TableJSON Schema

Name	Required	Description
`limit`	No	Maximum targets to return. 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

TableJSON 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.
`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.

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

A4.8/5.0

Behavior5/5

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

Annotations already mark the call read-only, open-world, and idempotent, and the description adds pagination behavior (capped results with nextCursor/resume rules) and the shape of each returned target (type, organism, component accessions + gene symbols). No contradiction with annotations.

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 front-loads purpose in the first sentence, then packs input requirements, return contents, and pagination into three more sentences with no filler. Every clause earns its place.

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 resolver with an output schema, the description covers input selection, filtering, result content, and pagination, and it names the downstream consumer (chembl_get_bioactivities). There are no missing details an agent would need to call it correctly.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Even though every parameter already has a schema description, the description adds cross-parameter semantics that the schema cannot: at least one of accession/gene_symbol/query is required, accession is the most precise resolver, and cursor must be reused with identical filters. Examples like P00533 and EGFR reinforce the mapping.

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 opening sentence names a specific verb ('Resolve'), a concrete resource (protein/gene/UniProt accession), and the exact output (ChEMBL target ID), and ties it to the target→leads workflow. This makes its role distinct from sibling search tools like chembl_search_molecules.

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?

It states when the tool is needed (before chembl_get_bioactivities in the target→leads workflow) and which inputs to supply, including the preference for UniProt accessions as 'the most precise input.' It does not explicitly list when to choose an alternative, so an agent receives clear context but no formal exclusions.

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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