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.

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 declare readOnly, idempotent, and open-world behavior; the description adds useful pagination behavior via nextCursor/cursor and explains the result contents (type, organism, component accessions and 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 is compact, front-loaded with purpose, then input requirements, return contents, precision guidance, and pagination. Every sentence adds useful information 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?

Given a complete input schema, an output schema, and annotations covering read-only/idempotent behavior, the description covers everything needed to invoke the tool correctly: purpose, required input modes, optional filters, precision ordering, and pagination handling.

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 baseline is 3. The description adds meaningful semantic guidance beyond the schema: at least one of three inputs is required, UniProt accession is the most precise resolver, and the cursor must be reused with the same filters. This elevates it above baseline.

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 opens with a specific verb and resource: 'Resolve a protein/gene/UniProt accession to the ChEMBL target ID'. It also names the downstream consumer, chembl_get_bioactivities, which clearly differentiates this resolver from its siblings.

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 states the workflow context ('target→leads workflow') and gives concrete input guidance: supply at least one of accession, gene_symbol, or query, and optionally filter by organism and target_type. It does not explicitly list when-not-to-use alternatives, but the purpose is clear enough to make selection unambiguous.

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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