chembl-mcp-server

chembl-get-bioactivities

chembl_get_bioactivities

Read-onlyIdempotent

The flagship compound↔target bioactivity bridge: measurements for a molecule (target deconvolution / selectivity), a target (lead finding), or both together (how potently one compound hits one target). Supply at least one of molecule_chembl_id (from chembl_search_molecules) or target_chembl_id (from chembl_search_targets) — supplying both narrows to that compound–target pair, supplying neither is an error. Filter by standard_type (IC50/Ki/EC50/…), minimum potency pchembl_value_min, assay_type, and organism. Not every measurement has a derivable pchembl_value, so potency_view picks which side of that split you get: the default "potency_ranked" returns the measurements that have one, most potent first (ChEMBL sorts the rest first otherwise, which is why they are not merged), and "null_potency" returns exactly the measurements that have none. totalCount is the honest full match count across both views either way. Mixing measurement types (IC50 vs Ki) is a scientific error — set standard_type to compare like with like. A popular target carries tens of thousands of rows: results spill to a DataCanvas table (call chembl_dataframe_describe for its columns, then chembl_dataframe_query for honest aggregates across the staged set), while an inline preview answers the immediate question. Each view stages its own table (bioactivities / bioactivities_null_potency), so running both against one canvas_id lets a UNION ALL rebuild the full set. The staged table is capped at CHEMBL_MAX_SPILL_ROWS; when the cap is hit, truncated is true and the table is a bounded slice, not the complete view. The inline rows are always capped at limit, so compare that against totalCount before treating them as the whole answer. Spilling the rest requires CANVAS_PROVIDER_TYPE=duckdb; without it the inline preview is all there is.

Input Schema

TableJSON Schema

Name	Required	Description	Default
`limit`	No	Maximum rows in the inline preview. Defaults to the server default (25). The full set still spills to the canvas.
`organism`	No	Restrict to a target organism, e.g. "Homo sapiens" (case-insensitive exact match).
`canvas_id`	No	Optional canvas ID from a prior call to reuse the same canvas. Each potency_view re-stages its own table, so a second query of the SAME view REPLACES (overwrites) its prior rows — it does not append — while the other view's table is left intact, which is what lets both coexist on one canvas. Omit to mint a fresh canvas.
`assay_type`	No	Restrict to an assay type code: "B" (binding), "F" (functional), "A" (ADMET), "T" (toxicity).
`potency_view`	No	Which side of the pchembl_value presence split to retrieve. "potency_ranked" (default) returns the measurements that have a derivable pchembl_value, most potent first. "null_potency" returns exactly the measurements that have none — the rows the ranked view excludes, otherwise unreachable. The two partition the match set and stage to separate canvas tables.	potency_ranked
`standard_type`	No	Restrict to one measurement type, e.g. "IC50", "Ki", "EC50". Set this to compare potencies validly.
`target_chembl_id`	No	ChEMBL target ID (from chembl_search_targets), e.g. "CHEMBL203". Supply this, molecule_chembl_id, or both — both narrows to that compound–target pair.
`pchembl_value_min`	No	Minimum pchembl_value (−log10 molar potency), e.g. 7 keeps sub-100 nM activities. Only valid on the potency_ranked view — the null_potency rows have no pchembl_value to compare against.
`molecule_chembl_id`	No	ChEMBL molecule ID (from chembl_search_molecules), e.g. "CHEMBL941". Supply this, target_chembl_id, or both — both narrows to that compound–target pair.

Output Schema

TableJSON Schema

Name	Required	Description
`error`	No	Present when the call failed. Absent on success.
`notice`	No	Guidance when no measurements matched, or how to SQL the spilled set.
`spilled`	No	True when the view exceeded the preview and was staged on the canvas.
`canvas_id`	No	Canvas ID holding the staged table — pass to chembl_dataframe_describe to list its columns, then to chembl_dataframe_query to run SQL over them. Null when canvas is disabled or nothing spilled.
`truncated`	No	True when the CHEMBL_MAX_SPILL_ROWS cap was hit before the upstream view was exhausted — the staged table is a bounded slice, NOT the complete view, so aggregates over it are a sample. Narrow the filters to bring the view under the cap.
`activities`	No	Bioactivity rows for the selected potency_view — the inline preview, or the full view when it fit without spilling.
`table_name`	No	Canvas table name holding the staged rowset, and the FROM target for chembl_dataframe_query SQL — "bioactivities" for potency_ranked, "bioactivities_null_potency" for null_potency. Null when not spilled.
`totalCount`	No	Total matching measurements upstream — the honest full count spanning BOTH potency views, before any preview cap. The staged/preview rows are the selected view of this.
`potency_view`	No	Which view these rows came from: "potency_ranked" = measurements with a derivable pchembl_value; "null_potency" = measurements with none. Re-call with the other value to reach the rest of totalCount.
`appliedFilters`	No	Filters as the server parsed them.
`canvasDisabled`	No	True when CANVAS_PROVIDER_TYPE is not duckdb, so large sets could not spill — the inline rows are a capped preview, not the full set.
`staged_row_count`	No	Rows actually registered on the canvas table. Null when nothing spilled. Below the view total when truncated is true.

Schema Changelog

Changes observed during successful MCP inspections.

Changed43 schema fields changedSep 19, 2026
- addedInput schema / properties / canvas_id / pattern
```
Added value: +"^[A-Za-z0-9_-]{10}$"
```
- removedOutput schema / properties / activities / items / properties / assay_description / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / assay_description / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / activities / items / properties / assay_type / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / assay_type / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / activities / items / properties / molecule_pref_name / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / molecule_pref_name / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / activities / items / properties / pchembl_value / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / pchembl_value / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / activities / items / properties / relation / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / relation / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / activities / items / properties / standard_relation / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / standard_relation / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / activities / items / properties / standard_type / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / standard_type / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / activities / items / properties / standard_units / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / standard_units / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / activities / items / properties / standard_value / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / standard_value / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / activities / items / properties / target_organism / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / target_organism / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / activities / items / properties / target_pref_name / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / target_pref_name / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / activities / items / properties / type / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / type / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / activities / items / properties / units / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / units / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / activities / items / properties / value / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / activities / items / properties / value / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / appliedFilters / properties / assay_type / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / appliedFilters / properties / assay_type / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / appliedFilters / properties / organism / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / appliedFilters / properties / organism / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / appliedFilters / properties / pchembl_value_min / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / appliedFilters / properties / pchembl_value_min / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / appliedFilters / properties / standard_type / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / appliedFilters / properties / standard_type / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / canvas_id / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / canvas_id / type
```
Added value: +[
+  "string",
+  "null"
+]
```
- removedOutput schema / properties / staged_row_count / anyOf
```
Removed value: -[
-  {
-    "type": "number"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / staged_row_count / type
```
Added value: +[
+  "number",
+  "null"
+]
```
- removedOutput schema / properties / table_name / anyOf
```
Removed value: -[
-  {
-    "type": "string"
-  },
-  {
-    "type": "null"
-  }
-]
```
- addedOutput schema / properties / table_name / 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": [
+      "activities",
+      "totalCount",
+      "potency_view",
+      "spilled",
+      "canvas_id",
+      "table_name",
+      "staged_row_count",
+      "truncated",
+      "canvasDisabled",
+      "appliedFilters"
+    ]
+  },
+  {
+    "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_filter`: Neither molecule_chembl_id nor target_chembl_id was supplied, so the query had nothing to scope to. `contradictory_potency_filter`: pchembl_value_min was supplied alongside potency_view \"null_potency\", whose rows have no pchembl_value for the floor to compare against — the combination can only ever match zero measurements. Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "missing_filter",
+            "contradictory_potency_filter"
+          ],
+          "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: -[
-  "activities",
-  "totalCount",
-  "potency_view",
-  "spilled",
-  "canvas_id",
-  "table_name",
-  "staged_row_count",
-  "truncated",
-  "canvasDisabled",
-  "appliedFilters"
-]

First observedAug 13, 2026

TDQS

A5/5.0

Behavior5/5

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

The description discloses substantial behavior beyond the readOnly/idempotent annotations: the potency_ranked vs null_potency split, spill-to-canvas behavior, CHEMBL_MAX_SPILL_ROWS cap and truncated flag, inline limit caveat, per-view table overwrite semantics, and the CANVAS_PROVIDER_TYPE=duckdb requirement. None of this is implied by the annotations alone, and it does not contradict them.

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 long but every sentence earns its place, covering usage, error conditions, scientific caveats, paging, and spill behavior. Key scoping information is front-loaded in the first sentence, and the density is justified by the tool's nine parameters and complex data-partitioning semantics.

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 tool with this complexity, the description is remarkably complete: it explains the full match count, the split views, inline vs staged results, truncation semantics, the duckdb prerequisite, and how to reconstruct the full set via a UNION ALL. The presence of an output schema means return-value specifics are covered structurally, so no critical guidance is missing.

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 schema coverage is 100%, the description adds critical meaning: at least one of molecule_chembl_id or target_chembl_id must be supplied, pchembl_value_min is only valid on potency_ranked, canvas_id re-stages and overwrites the same view, and potency_view maps to the presence/absence of a derivable pchembl_value. It also clarifies that both view tables can coexist on one canvas for a UNION ALL reconstruction.

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 by naming the tool a 'compound↔target bioactivity bridge' and then states exactly what it returns: measurements for a molecule, a target, or both together. It immediately distinguishes this from sibling tools by framing the molecule/target relationship and by referencing the sibling search tools as the source of valid IDs.

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 explicit when-to-use guidance: supply molecule_chembl_id for target deconvolution/selectivity, target_chembl_id for lead finding, or both to narrow to a pair. It also gives an explicit exclusion—supplying neither is an error—and warns against mixing measurement types, telling the agent to set standard_type to compare like with like.

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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