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pubchem-mcp-server

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Get Compound Interactions

pubchem_get_compound_interactions
Read-onlyIdempotent

Retrieve a compound's drug-drug, drug-food, and target interaction records from PubChem, with source labels and paging offsets for each interaction kind.

Instructions

Get a compound's interaction data: drug-drug interactions (DrugBank), drug-food interactions, and chemical-target interactions (binding/activity from BindingDB, ChEMBL, and others). Each entry carries its originating source. Results are paged per kind, with the source-record total and the next offset reported for each. Richest for approved drugs; many compounds have no deposited interaction records. Drug-drug and target interactions come from PubChem's SDQ service, which can refuse automated requests — a refused kind is reported in failedKinds while the others still return; per-target activity is also available from pubchem_get_bioactivity.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidYesPubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.
kindsNoInteraction kinds to fetch. "drug-drug" (interactions with other drugs), "drug-food" (dietary interactions), "target" (binding/activity against molecular targets). "drug-drug" and "target" come from PubChem's SDQ service, which can refuse automated requests; "drug-food" comes from PUG View. Per-target activity is also available from pubchem_get_bioactivity. Default: ["drug-drug"].
offsetNoZero-based start position within each requested kind, counted in source records rather than returned entries. The same offset applies to every kind in the call, and the kinds advance at different rates — when paging past the first page, request one kind per call and pass that kind's nextOffset. Default: 0.
maxEntriesNoMax entries per kind per page. The per-call cap is 50: a larger value (up to 1000) reads a page of 50 per kind and is reported in cappedInputs. Well-studied drugs have a long tail of interactions; use offset to reach the ones past this page. Default: 10.

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidNoPubChem Compound ID.
errorNoPresent when the call failed. Absent on success.
noticeNoGuidance when a kind failed, when no interaction data was found, when the offset runs past every requested kind, or when further pages remain. Absent when this page is complete and every kind resolved.
offsetNoZero-based start position read within each requested kind.
pagingNoPer-kind page position, one entry per requested kind that was retrieved. A kind listed in failedKinds is absent — its position is unknown, not exhausted.
entriesNoInteraction entries across the requested kinds.
truncatedNoTrue when at least one requested kind has source records remaining past this page. Which kinds, and how many records each holds, is in paging[].truncated / paging[].totalRecords.
nextOffsetNoOffset to pass on the next call, reported when exactly one requested kind has records remaining. Omitted when none do, and when several do — those advance to different positions, so read paging[].nextOffset instead.
failedKindsNoInteraction kinds that could not be retrieved (comma-separated). The returned entries cover the kinds that succeeded. The notice says, per failed kind, whether a retry can help: a timeout or upstream error can clear, while a refusal from PubChem's SDQ service (drug-drug, target) does not.
cappedInputsNoInputs that asked for more than their per-call cap, with the value requested and the value served. An ID batch lists the IDs past the cap in unprocessed. Omitted when every input was within its cap.
returnedCountNoTotal interaction entries returned across all kinds.
requestedKindsNoInteraction kinds requested (comma-separated).

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed6 schema fields changedv0.7.0
    • changedInput schema / properties / cid / maximum
      Previous value: -9007199254740991New value: +2147483647
    • changedInput schema / properties / kinds / description
      Previous value: -"Interaction kinds to fetch. \"drug-drug\" (interactions with other drugs), \"drug-food\" (dietary interactions), \"target\" (binding/activity against molecular targets). Default: [\"drug-drug\"]."New value: +"Interaction kinds to fetch. \"drug-drug\" (interactions with other drugs), \"drug-food\" (dietary interactions), \"target\" (binding/activity against molecular targets). \"drug-drug\" and \"target\" come from PubChem's SDQ service, which can refuse automated requests; \"drug-food\" comes from PUG View. Per-target activity is also available from pubchem_get_bioactivity. Default: [\"drug-drug\"]."
    • changedInput schema / properties / maxEntries / description
      Previous value: -"Max entries per kind per page (1-50). Well-studied drugs have a long tail of interactions; use offset to reach the ones past this page. Default: 10."New value: +"Max entries per kind per page. The per-call cap is 50: a larger value (up to 1000) reads a page of 50 per kind and is reported in cappedInputs. Well-studied drugs have a long tail of interactions; use offset to reach the ones past this page. Default: 10."
    • changedInput schema / properties / maxEntries / maximum
      Previous value: -50New value: +1000
    • addedOutput schema / properties / cappedInputs
      Added value: +{
+  "description": "Inputs that asked for more than their per-call cap, with the value requested and the value served. An ID batch lists the IDs past the cap in unprocessed. Omitted when every input was within its cap.",
+  "items": {
+    "additionalProperties": false,
+    "description": "One input served at its per-call cap.",
+    "properties": {
+      "input": {
+        "description": "Input name, e.g. \"maxResults\" or \"cids\".",
+        "type": "string"
+      },
+      "requested": {
+        "description": "Value requested: the page size, or the number of IDs in the batch.",
+        "type": "number"
+      },
+      "served": {
+        "description": "Value served: the per-call cap.",
+        "type": "number"
+      },
+      "unprocessed": {
+        "description": "ID batches only: IDs past the cap, listed in unprocessed in input order.",
+        "type": "number"
+      }
+    },
+    "required": [
+      "input",
+      "requested",
+      "served"
+    ],
+    "type": "object"
+  },
+  "type": "array"
+}
    • changedOutput schema / properties / failedKinds / description
      Previous value: -"Interaction kinds that could not be retrieved (comma-separated). The returned entries cover the kinds that succeeded; retry to re-attempt the failed ones."New value: +"Interaction kinds that could not be retrieved (comma-separated). The returned entries cover the kinds that succeeded. The notice says, per failed kind, whether a retry can help: a timeout or upstream error can clear, while a refusal from PubChem's SDQ service (drug-drug, target) does not."
  2. Changed2 schema fields changedv0.6.5
    • removedInput schema / properties / cid / exclusiveMinimum
      Removed value: -0
    • addedInput schema / properties / cid / minimum
      Added value: +1
  3. Changed7 schema fields changedv0.6.1
    • 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": [
+      "cid",
+      "entries",
+      "paging",
+      "requestedKinds",
+      "returnedCount",
+      "truncated",
+      "offset"
+    ]
+  },
+  {
+    "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"
+}
    • addedOutput schema / properties / truncated
      Added value: +{
+  "description": "True when at least one requested kind has source records remaining past this page. Which kinds, and how many records each holds, is in paging[].truncated / paging[].totalRecords.",
+  "type": "boolean"
+}
    • removedOutput schema / required
      Removed value: -[
-  "cid",
-  "entries",
-  "paging",
-  "requestedKinds",
-  "returnedCount",
-  "offset"
-]
  4. Changed8 schema fields changedv0.6.0
    • changedInput schema / properties / maxEntries / description
      Previous value: -"Max entries per kind (1-50). Well-studied drugs have a long tail of interactions. Default: 10."New value: +"Max entries per kind per page (1-50). Well-studied drugs have a long tail of interactions; use offset to reach the ones past this page. Default: 10."
    • addedInput schema / properties / offset
      Added value: +{
+  "default": 0,
+  "description": "Zero-based start position within each requested kind, counted in source records rather than returned entries. The same offset applies to every kind in the call, and the kinds advance at different rates — when paging past the first page, request one kind per call and pass that kind's nextOffset. Default: 0.",
+  "maximum": 2147483646,
+  "minimum": 0,
+  "type": "integer"
+}
    • removedOutput schema / properties / entries / items / properties / severity
      Removed value: -{
-  "description": "Raw severity as the source reports it — not normalized across sources, and frequently unset (most sources embed severity in the statement text).",
-  "type": "string"
-}
    • addedOutput schema / properties / nextOffset
      Added value: +{
+  "description": "Offset to pass on the next call, reported when exactly one requested kind has records remaining. Omitted when none do, and when several do — those advance to different positions, so read paging[].nextOffset instead.",
+  "type": "number"
+}
    • changedOutput schema / properties / notice / description
      Previous value: -"Guidance when no interaction data was found for the requested kinds."New value: +"Guidance when a kind failed, when no interaction data was found, when the offset runs past every requested kind, or when further pages remain. Absent when this page is complete and every kind resolved."
    • addedOutput schema / properties / offset
      Added value: +{
+  "description": "Zero-based start position read within each requested kind.",
+  "type": "number"
+}
    • addedOutput schema / properties / paging
      Added value: +{
+  "description": "Per-kind page position, one entry per requested kind that was retrieved. A kind listed in failedKinds is absent — its position is unknown, not exhausted.",
+  "items": {
+    "additionalProperties": false,
+    "description": "Page position for one interaction kind.",
+    "properties": {
+      "kind": {
+        "description": "Interaction category this page covers.",
+        "enum": [
+          "drug-drug",
+          "drug-food",
+          "target"
+        ],
+        "type": "string"
+      },
+      "nextOffset": {
+        "description": "Offset to pass on the next call to continue this kind past the current page. Omitted when no records remain.",
+        "type": "number"
+      },
+      "returnedCount": {
+        "description": "Interaction entries returned for this kind.",
+        "type": "number"
+      },
+      "totalRecords": {
+        "description": "Source records available for this kind, across all pages. Entries are derived from these records and can be fewer: a \"target\" record naming no molecular target and a \"drug-drug\" record carrying no statement both yield nothing, and duplicate measurements collapse within a page. Pages divide the records, not the entries, so a duplicate split across two pages is reported on both.",
+        "type": "number"
+      },
+      "truncated": {
+        "description": "True when source records remain for this kind past the current page.",
+        "type": "boolean"
+      }
+    },
+    "required": [
+      "kind",
+      "returnedCount",
+      "totalRecords",
+      "truncated"
+    ],
+    "type": "object"
+  },
+  "type": "array"
+}
    • changedOutput schema / required
      Previous value: -[
-  "cid",
-  "entries",
-  "requestedKinds",
-  "returnedCount"
-]New value: +[
+  "cid",
+  "entries",
+  "paging",
+  "requestedKinds",
+  "returnedCount",
+  "offset"
+]
  5. Addedv0.2.2

TDQS

A4.6/5.0
Behavior5/5

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

Discloses behavior well beyond the safety annotations: per-kind paging, per-kind record totals and nextOffset, SDQ refusal handling via failedKinds with partial success, and the data-richness caveat ('richest for approved drugs; many compounds have no deposited records'). This is exactly the operational context annotations cannot convey.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Dense but front-loaded: purpose first, then sources, paging, caveats, and the alternative. Every sentence carries operational information, though the description is long and packs several distinct concerns without explicit separation.

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 multi-kind, paged, partially-failing external query with an output schema, it covers purpose, routing, partial-failure semantics, and paging limits. Nothing an agent needs to call it correctly 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 baseline is 3. The description still adds value by explaining the paging model (per-kind offsets, kinds advancing at different rates, capping at 50 with cappedInputs), which reinforces the non-obvious maxEntries/offset interaction described in 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?

Specific verb+resource ('Get a compound's interaction data') with the three kinds enumerated and their distinctive sources named. It clearly distinguishes itself from siblings by scope (interactions vs. bioactivity vs. details) and even names the sibling that overlaps on target activity.

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?

Explicit routing is given for the target-activity alternative ('per-target activity is also available from pubchem_get_bioactivity') and the CID source tool is named in the schema. It stops short of stating when not to use this tool overall or which kinds to prefer, leaving some selection to the agent.

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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