pubchem-mcp-server

Search Compounds

pubchem_search_compounds

Read-onlyIdempotent

Search PubChem for chemical compounds by identifier (name, SMILES, InChI, or InChIKey, up to 25 per call), molecular formula in Hill notation, substructure or superstructure containment, 2D Tanimoto similarity, or the compounds a bioassay (AID) found active or tested. Returns a page of CIDs — reach matches past maxResults with offset. Optionally hydrate results with properties to avoid a follow-up pubchem_get_compound_details call.

Input Schema

Name	Required	Description
`aid`	No	Required for assay search. PubChem Assay ID (AID) whose compounds to list, from 1 to 2147483647, e.g. 1000. Find AIDs for a biological target with pubchem_search_assays.
`query`	No	Required for substructure/superstructure/similarity searches. A SMILES string (e.g. "CC(=O)O") or PubChem CID as a string from 1 to 2147483647 (e.g. "2244").
`offset`	No	Zero-based index of the first CID to return. Pass the nextOffset from a previous call to read the following page. Identifier lookups resolve every match up front, so paging them is free, and assay searches fetch only the requested page, so both page to the end of their matches. Formula, substructure, superstructure, and similarity searches have to ask PubChem for offset + maxResults records to reach a page, so deep pages cost progressively more upstream: those four accept an offset up to 10000. Default: 0.
`formula`	No	Required for formula search. Molecular formula in Hill notation (e.g. "C6H12O6", "CaH2O2").
`queryType`	No	Required for structure/similarity searches. Format of the query: "smiles" or "cid".
`threshold`	No	Similarity search only. Minimum Tanimoto similarity (70-100). 90+ for close analogs, 70-80 for scaffold hops. Default: 90.
`activeOnly`	No	Assay search only. When true (default), lists only the compounds the assay marked active; false lists every compound it tested.
`maxResults`	No	Maximum CIDs to return per page. The per-call cap is 200: a larger value (up to 1000) returns a page of 200 and is reported in cappedInputs. Use offset to reach matches past this page. Default: 20.
`properties`	No	Optional: fetch these properties for each result, avoiding a follow-up details call. E.g. ["MolecularFormula", "MolecularWeight", "CanonicalSMILES"].
`searchType`	Yes	Search strategy; each mode needs its own fields. "identifier": name/SMILES/InChI/InChIKey lookup — requires identifierType and identifiers. "formula": molecular formula — requires formula. "substructure": find compounds containing the query as a substructure. "superstructure": find compounds that are themselves substructures of the query. "similarity": 2D Tanimoto similarity to the query. substructure, superstructure, and similarity require query and queryType. "assay": compounds tested in a PubChem bioassay — requires aid; activeOnly (default true) keeps only the compounds the assay marked active.
`identifiers`	No	Required for identifier search. Array of identifiers to resolve. The per-call cap is 25: the first 25 are looked up, and any past that (up to 1000 in all) are returned in unprocessed, in input order, and reported in cappedInputs. Examples: ["aspirin", "ibuprofen"] for name, ["CC(=O)OC1=CC=CC=C1C(=O)O"] for SMILES, ["InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)"] for inchi (sent exactly as written, case kept), ["BSYNRYMUTXBXSQ-UHFFFAOYSA-N"] for inchikey (27-char block format; uppercased before lookup, any case accepted).
`identifierType`	No	Required for identifier search. Type of chemical identifier: "name", "smiles", "inchi" (a full InChI string, case-sensitive), or "inchikey".
`allowOtherElements`	No	Formula search only. When true, includes compounds with additional elements beyond the formula.

Output Schema

Name	Required	Description
`cap`	No	The page size applied: maxResults, or the per-call cap when maxResults exceeds it.
`error`	No	Present when the call failed. Absent on success.
`shown`	No	CIDs returned on this page.
`notice`	No	Recovery guidance when no compounds matched (for an assay search, when the assay recorded none of the requested kind), when the offset runs past the matches observed, when identifiers had no match or could not be interpreted, when identifiers collided on one CID, when further pages remain, or when a bounded search reached the offset ceiling. Absent when this page is complete and every identifier resolved to its own CID.
`offset`	No	Zero-based index of the first CID returned.
`results`	No	Matching compounds.
`truncated`	No	True when matching CIDs remain past this page.
`activeOnly`	No	Assay search only: true when the list holds only the compounds the assay marked active, false when it holds every compound tested.
`nextOffset`	No	Offset to pass on the next call to continue past this page. Omitted when no further matches remain, and when a formula, substructure, superstructure, or similarity page would continue past the 10000 offset ceiling (truncated stays true, and the notice says how to narrow the search and names the page at offset 10000 when it still reaches further matches).
`searchType`	No	Search strategy used: identifier, formula, substructure, superstructure, similarity, or assay.
`totalFound`	No	Exact number of matching CIDs across all pages. Omitted when a formula, substructure, superstructure, or similarity search saturated the records it requested — PubChem returns no match count for those, so totalFoundAtLeast reports a floor instead.
`unprocessed`	No	Identifier-mode only: identifiers past the per-call cap of 25, in input order, not looked up. Pass them in a follow-up call. Omitted when every identifier was looked up.
`cappedInputs`	No	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.
`totalFoundAtLeast`	No	Lower bound on matching CIDs, reported in place of totalFound when the exact count is unavailable. At least this many match, and the true total may be higher; page further with offset to observe more.
`unresolvedIdentifiers`	No	Identifier-mode only: input identifiers that resolved to no CID — PubChem had no match, or could not interpret the input as identifierType (the notice says which). Omitted when every identifier resolved and for non-identifier searches.

Schema Changelog

Changes observed during successful MCP inspections.

Changed10 schema fields changedOct 24, 2026

changedInput schema / properties / identifierType / description

Previous value: -"Required for identifier search. Type of chemical identifier: \"name\", \"smiles\", or \"inchikey\"."New value: +"Required for identifier search. Type of chemical identifier: \"name\", \"smiles\", \"inchi\" (a full InChI string, case-sensitive), or \"inchikey\"."

changedInput schema / properties / identifierType / enum

Previous value: -[
-  "name",
-  "smiles",
-  "inchikey"
-]New value: +[
+  "name",
+  "smiles",
+  "inchi",
+  "inchikey"
+]

changedInput schema / properties / identifiers / description

Previous value: -"Required for identifier search. Array of identifiers to resolve. The per-call cap is 25: the first 25 are looked up, and any past that (up to 1000 in all) are returned in unprocessed, in input order, and reported in cappedInputs. Examples: [\"aspirin\", \"ibuprofen\"] for name, [\"CC(=O)OC1=CC=CC=C1C(=O)O\"] for SMILES, [\"BSYNRYMUTXBXSQ-UHFFFAOYSA-N\"] for inchikey (27-char block format; uppercased before lookup, any case accepted)."New value: +"Required for identifier search. Array of identifiers to resolve. The per-call cap is 25: the first 25 are looked up, and any past that (up to 1000 in all) are returned in unprocessed, in input order, and reported in cappedInputs. Examples: [\"aspirin\", \"ibuprofen\"] for name, [\"CC(=O)OC1=CC=CC=C1C(=O)O\"] for SMILES, [\"InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)\"] for inchi (sent exactly as written, case kept), [\"BSYNRYMUTXBXSQ-UHFFFAOYSA-N\"] for inchikey (27-char block format; uppercased before lookup, any case accepted)."

changedInput schema / properties / offset / description

Previous value: -"Zero-based index of the first CID to return. Pass the nextOffset from a previous call to read the following page. Identifier lookups resolve every match up front, so paging them is free, and assay searches fetch only the requested page; formula, substructure, superstructure, and similarity searches have to ask PubChem for offset + maxResults records to reach a page, so deep pages cost progressively more upstream — hence the 10000 ceiling. Default: 0."New value: +"Zero-based index of the first CID to return. Pass the nextOffset from a previous call to read the following page. Identifier lookups resolve every match up front, so paging them is free, and assay searches fetch only the requested page, so both page to the end of their matches. Formula, substructure, superstructure, and similarity searches have to ask PubChem for offset + maxResults records to reach a page, so deep pages cost progressively more upstream: those four accept an offset up to 10000. Default: 0."

changedInput schema / properties / offset / maximum

Previous value: -10000New value: +9007199254740991

changedInput schema / properties / searchType / description

Previous value: -"Search strategy; each mode needs its own fields. \"identifier\": name/SMILES/InChIKey lookup — requires identifierType and identifiers. \"formula\": molecular formula — requires formula. \"substructure\": find compounds containing the query as a substructure. \"superstructure\": find compounds that are themselves substructures of the query. \"similarity\": 2D Tanimoto similarity to the query. substructure, superstructure, and similarity require query and queryType. \"assay\": compounds tested in a PubChem bioassay — requires aid; activeOnly (default true) keeps only the compounds the assay marked active."New value: +"Search strategy; each mode needs its own fields. \"identifier\": name/SMILES/InChI/InChIKey lookup — requires identifierType and identifiers. \"formula\": molecular formula — requires formula. \"substructure\": find compounds containing the query as a substructure. \"superstructure\": find compounds that are themselves substructures of the query. \"similarity\": 2D Tanimoto similarity to the query. substructure, superstructure, and similarity require query and queryType. \"assay\": compounds tested in a PubChem bioassay — requires aid; activeOnly (default true) keeps only the compounds the assay marked active."

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

Previous value: -"Machine-readable failure mode. Declared by this tool: `missing_identifier_args`: searchType is \"identifier\" but identifierType or identifiers were omitted. `missing_formula`: searchType is \"formula\" but the formula field was omitted or blank. `missing_structure_args`: substructure/superstructure/similarity search with query or queryType omitted, or a blank query. `invalid_cid_query`: structure/similarity search with queryType \"cid\" but query is not an integer CID from 1 to 2147483647. `missing_aid`: searchType is \"assay\" but aid was omitted. `aid_not_found`: assay search where PubChem has no live assay with the given AID. `identifier_rejected`: identifier search where PubChem rejected every identifier in the batch as unreadable (HTTP 400) — for SMILES, a string it could not standardize into a structure. A batch with any other outcome lists rejected inputs in unresolvedIdentifiers instead. `search_query_rejected`: PubChem failed a formula, substructure, superstructure, or similarity search with HTTP 500 \"Search status indicates failure\" — its answer for a malformed SMILES or formula, a SMILES with a \"*\" wildcard atom, or a CID with no record. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `missing_identifier_args`: searchType is \"identifier\" but identifierType or identifiers were omitted. `missing_formula`: searchType is \"formula\" but the formula field was omitted or blank. `missing_structure_args`: substructure/superstructure/similarity search with query or queryType omitted, or a blank query. `invalid_cid_query`: structure/similarity search with queryType \"cid\" but query is not an integer CID from 1 to 2147483647. `offset_ceiling_exceeded`: formula, substructure, superstructure, or similarity search with offset above 10000. `missing_aid`: searchType is \"assay\" but aid was omitted. `aid_not_found`: assay search where PubChem has no live assay with the given AID. `identifier_rejected`: identifier search where PubChem rejected every identifier in the batch as unreadable (HTTP 400) — for SMILES or InChI, a string it could not standardize into a structure. A batch with any other outcome lists rejected inputs in unresolvedIdentifiers instead. `search_query_rejected`: PubChem failed a formula, substructure, superstructure, or similarity search with HTTP 500 \"Search status indicates failure\" — its answer for a malformed SMILES or formula, a SMILES with a \"*\" wildcard atom, or a CID with no record. Other values are possible when a failure originates below the handler."

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

Previous value: -[
-  "missing_identifier_args",
-  "missing_formula",
-  "missing_structure_args",
-  "invalid_cid_query",
-  "missing_aid",
-  "aid_not_found",
-  "identifier_rejected",
-  "search_query_rejected"
-]New value: +[
+  "missing_identifier_args",
+  "missing_formula",
+  "missing_structure_args",
+  "invalid_cid_query",
+  "offset_ceiling_exceeded",
+  "missing_aid",
+  "aid_not_found",
+  "identifier_rejected",
+  "search_query_rejected"
+]

changedOutput schema / properties / nextOffset / description

Previous value: -"Offset to pass on the next call to continue past this page. Omitted when no further matches remain."New value: +"Offset to pass on the next call to continue past this page. Omitted when no further matches remain, and when a formula, substructure, superstructure, or similarity page would continue past the 10000 offset ceiling (truncated stays true, and the notice says how to narrow the search and names the page at offset 10000 when it still reaches further matches)."

changedOutput schema / properties / notice / description

Previous value: -"Recovery guidance when no compounds matched (for an assay search, when the assay recorded none of the requested kind), when the offset runs past the matches observed, when identifiers had no match or could not be interpreted, when identifiers collided on one CID, or when further pages remain. Absent when this page is complete and every identifier resolved to its own CID."New value: +"Recovery guidance when no compounds matched (for an assay search, when the assay recorded none of the requested kind), when the offset runs past the matches observed, when identifiers had no match or could not be interpreted, when identifiers collided on one CID, when further pages remain, or when a bounded search reached the offset ceiling. Absent when this page is complete and every identifier resolved to its own CID."

Changed18 schema fields changedOct 15, 2026

addedInput schema / properties / activeOnly

Added value: +{
+  "default": true,
+  "description": "Assay search only. When true (default), lists only the compounds the assay marked active; false lists every compound it tested.",
+  "type": "boolean"
+}

addedInput schema / properties / aid

Added value: +{
+  "description": "Required for assay search. PubChem Assay ID (AID) whose compounds to list, from 1 to 2147483647, e.g. 1000. Find AIDs for a biological target with pubchem_search_assays.",
+  "maximum": 2147483647,
+  "minimum": 1,
+  "type": "integer"
+}

changedInput schema / properties / identifiers / description

Previous value: -"Required for identifier search. Array of identifiers to resolve (1-25). Examples: [\"aspirin\", \"ibuprofen\"] for name, [\"CC(=O)OC1=CC=CC=C1C(=O)O\"] for SMILES, [\"BSYNRYMUTXBXSQ-UHFFFAOYSA-N\"] for inchikey (27-char block format)."New value: +"Required for identifier search. Array of identifiers to resolve. The per-call cap is 25: the first 25 are looked up, and any past that (up to 1000 in all) are returned in unprocessed, in input order, and reported in cappedInputs. Examples: [\"aspirin\", \"ibuprofen\"] for name, [\"CC(=O)OC1=CC=CC=C1C(=O)O\"] for SMILES, [\"BSYNRYMUTXBXSQ-UHFFFAOYSA-N\"] for inchikey (27-char block format; uppercased before lookup, any case accepted)."

changedInput schema / properties / identifiers / maxItems
```
Previous value: -25New value: +1000
```

changedInput schema / properties / maxResults / description

Previous value: -"Maximum CIDs to return per page (1-200). Use offset to reach matches past this page. Default: 20."New value: +"Maximum CIDs to return per page. The per-call cap is 200: a larger value (up to 1000) returns a page of 200 and is reported in cappedInputs. Use offset to reach matches past this page. Default: 20."

changedInput schema / properties / maxResults / maximum
```
Previous value: -200New value: +1000
```

changedInput schema / properties / offset / description

Previous value: -"Zero-based index of the first CID to return. Pass the nextOffset from a previous call to read the following page. Identifier lookups resolve every match up front, so paging them is free; formula, substructure, superstructure, and similarity searches have to ask PubChem for offset + maxResults records to reach a page, so deep pages cost progressively more upstream — hence the 10000 ceiling. Default: 0."New value: +"Zero-based index of the first CID to return. Pass the nextOffset from a previous call to read the following page. Identifier lookups resolve every match up front, so paging them is free, and assay searches fetch only the requested page; formula, substructure, superstructure, and similarity searches have to ask PubChem for offset + maxResults records to reach a page, so deep pages cost progressively more upstream — hence the 10000 ceiling. Default: 0."

changedInput schema / properties / query / description

Previous value: -"Required for substructure/superstructure/similarity searches. A SMILES string (e.g. \"CC(=O)O\") or PubChem CID as a string (e.g. \"2244\")."New value: +"Required for substructure/superstructure/similarity searches. A SMILES string (e.g. \"CC(=O)O\") or PubChem CID as a string from 1 to 2147483647 (e.g. \"2244\")."

changedInput schema / properties / searchType / description

Previous value: -"Search strategy; each mode needs its own fields. \"identifier\": name/SMILES/InChIKey lookup — requires identifierType and identifiers. \"formula\": molecular formula — requires formula. \"substructure\": find compounds containing the query as a substructure. \"superstructure\": find compounds that are themselves substructures of the query. \"similarity\": 2D Tanimoto similarity to the query. substructure, superstructure, and similarity require query and queryType."New value: +"Search strategy; each mode needs its own fields. \"identifier\": name/SMILES/InChIKey lookup — requires identifierType and identifiers. \"formula\": molecular formula — requires formula. \"substructure\": find compounds containing the query as a substructure. \"superstructure\": find compounds that are themselves substructures of the query. \"similarity\": 2D Tanimoto similarity to the query. substructure, superstructure, and similarity require query and queryType. \"assay\": compounds tested in a PubChem bioassay — requires aid; activeOnly (default true) keeps only the compounds the assay marked active."

changedInput schema / properties / searchType / enum

Previous value: -[
-  "identifier",
-  "formula",
-  "substructure",
-  "superstructure",
-  "similarity"
-]New value: +[
+  "identifier",
+  "formula",
+  "substructure",
+  "superstructure",
+  "similarity",
+  "assay"
+]

addedOutput schema / properties / activeOnly

Added value: +{
+  "description": "Assay search only: true when the list holds only the compounds the assay marked active, false when it holds every compound tested.",
+  "type": "boolean"
+}

changedOutput schema / properties / cap / description

Previous value: -"The maxResults cap that was applied."New value: +"The page size applied: maxResults, or the per-call cap when maxResults exceeds it."

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 / error / properties / data / properties / reason / description

Previous value: -"Machine-readable failure mode. Declared by this tool: `missing_identifier_args`: searchType is \"identifier\" but identifierType or identifiers were omitted. `missing_formula`: searchType is \"formula\" but the formula field was omitted or blank. `missing_structure_args`: substructure/superstructure/similarity search with query or queryType omitted, or a blank query. `invalid_cid_query`: structure/similarity search with queryType \"cid\" but query is not a positive integer CID. `identifier_rejected`: identifier search where PubChem rejected every identifier in the batch as unreadable (HTTP 400) — for SMILES, a string it could not standardize into a structure. A batch with any other outcome lists rejected inputs in unresolvedIdentifiers instead. `search_query_rejected`: PubChem failed a formula, substructure, superstructure, or similarity search with HTTP 500 \"Search status indicates failure\" — its answer for a malformed SMILES or formula, a SMILES with a \"*\" wildcard atom, or a CID with no record. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `missing_identifier_args`: searchType is \"identifier\" but identifierType or identifiers were omitted. `missing_formula`: searchType is \"formula\" but the formula field was omitted or blank. `missing_structure_args`: substructure/superstructure/similarity search with query or queryType omitted, or a blank query. `invalid_cid_query`: structure/similarity search with queryType \"cid\" but query is not an integer CID from 1 to 2147483647. `missing_aid`: searchType is \"assay\" but aid was omitted. `aid_not_found`: assay search where PubChem has no live assay with the given AID. `identifier_rejected`: identifier search where PubChem rejected every identifier in the batch as unreadable (HTTP 400) — for SMILES, a string it could not standardize into a structure. A batch with any other outcome lists rejected inputs in unresolvedIdentifiers instead. `search_query_rejected`: PubChem failed a formula, substructure, superstructure, or similarity search with HTTP 500 \"Search status indicates failure\" — its answer for a malformed SMILES or formula, a SMILES with a \"*\" wildcard atom, or a CID with no record. Other values are possible when a failure originates below the handler."

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

Previous value: -[
-  "missing_identifier_args",
-  "missing_formula",
-  "missing_structure_args",
-  "invalid_cid_query",
-  "identifier_rejected",
-  "search_query_rejected"
-]New value: +[
+  "missing_identifier_args",
+  "missing_formula",
+  "missing_structure_args",
+  "invalid_cid_query",
+  "missing_aid",
+  "aid_not_found",
+  "identifier_rejected",
+  "search_query_rejected"
+]

changedOutput schema / properties / notice / description

Previous value: -"Recovery guidance when no compounds matched, when the offset runs past the matches observed, when identifiers had no match or could not be interpreted, when identifiers collided on one CID, or when further pages remain. Absent when this page is complete and every identifier resolved to its own CID."New value: +"Recovery guidance when no compounds matched (for an assay search, when the assay recorded none of the requested kind), when the offset runs past the matches observed, when identifiers had no match or could not be interpreted, when identifiers collided on one CID, or when further pages remain. Absent when this page is complete and every identifier resolved to its own CID."

changedOutput schema / properties / searchType / description

Previous value: -"Search strategy used: identifier, formula, substructure, superstructure, or similarity."New value: +"Search strategy used: identifier, formula, substructure, superstructure, similarity, or assay."

addedOutput schema / properties / unprocessed

Added value: +{
+  "description": "Identifier-mode only: identifiers past the per-call cap of 25, in input order, not looked up. Pass them in a follow-up call. Omitted when every identifier was looked up.",
+  "items": {
+    "type": "string"
+  },
+  "type": "array"
+}

Changed4 schema fields changedSep 25, 2026

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

Previous value: -"Machine-readable failure mode. Declared by this tool: `missing_identifier_args`: searchType is \"identifier\" but identifierType or identifiers were omitted. `missing_formula`: searchType is \"formula\" but the formula field was omitted or blank. `missing_structure_args`: substructure/superstructure/similarity search with query or queryType omitted, or a blank query. `invalid_cid_query`: structure/similarity search with queryType \"cid\" but query is not a positive integer CID. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `missing_identifier_args`: searchType is \"identifier\" but identifierType or identifiers were omitted. `missing_formula`: searchType is \"formula\" but the formula field was omitted or blank. `missing_structure_args`: substructure/superstructure/similarity search with query or queryType omitted, or a blank query. `invalid_cid_query`: structure/similarity search with queryType \"cid\" but query is not a positive integer CID. `identifier_rejected`: identifier search where PubChem rejected every identifier in the batch as unreadable (HTTP 400) — for SMILES, a string it could not standardize into a structure. A batch with any other outcome lists rejected inputs in unresolvedIdentifiers instead. `search_query_rejected`: PubChem failed a formula, substructure, superstructure, or similarity search with HTTP 500 \"Search status indicates failure\" — its answer for a malformed SMILES or formula, a SMILES with a \"*\" wildcard atom, or a CID with no record. Other values are possible when a failure originates below the handler."

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

Previous value: -[
-  "missing_identifier_args",
-  "missing_formula",
-  "missing_structure_args",
-  "invalid_cid_query"
-]New value: +[
+  "missing_identifier_args",
+  "missing_formula",
+  "missing_structure_args",
+  "invalid_cid_query",
+  "identifier_rejected",
+  "search_query_rejected"
+]

changedOutput schema / properties / notice / description

Previous value: -"Recovery guidance when no compounds matched, when the offset runs past the matches observed, when identifiers failed to resolve, or when further pages remain. Absent when this page is complete and every identifier resolved."New value: +"Recovery guidance when no compounds matched, when the offset runs past the matches observed, when identifiers had no match or could not be interpreted, when identifiers collided on one CID, or when further pages remain. Absent when this page is complete and every identifier resolved to its own CID."

changedOutput schema / properties / unresolvedIdentifiers / description

Previous value: -"Identifier-mode only: input identifiers that resolved to no CID. Omitted when every identifier resolved and for non-identifier searches."New value: +"Identifier-mode only: input identifiers that resolved to no CID — PubChem had no match, or could not interpret the input as identifierType (the notice says which). Omitted when every identifier resolved and for non-identifier searches."

Changed2 schema fields changedSep 25, 2026

changedInput schema / properties / searchType / description

Previous value: -"Search strategy. \"identifier\": name/SMILES/InChIKey lookup. \"formula\": molecular formula. \"substructure\": find compounds containing the query as a substructure. \"superstructure\": find compounds that are themselves substructures of the query. \"similarity\": 2D Tanimoto similarity to the query."New value: +"Search strategy; each mode needs its own fields. \"identifier\": name/SMILES/InChIKey lookup — requires identifierType and identifiers. \"formula\": molecular formula — requires formula. \"substructure\": find compounds containing the query as a substructure. \"superstructure\": find compounds that are themselves substructures of the query. \"similarity\": 2D Tanimoto similarity to the query. substructure, superstructure, and similarity require query and queryType."

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

Previous value: -"Machine-readable failure mode. Declared by this tool: `missing_identifier_args`: searchType is \"identifier\" but identifierType or identifiers were omitted. `missing_formula`: searchType is \"formula\" but the formula field was omitted. `missing_structure_args`: substructure/superstructure/similarity search missing query or queryType. `invalid_cid_query`: structure/similarity search with queryType \"cid\" but query is not a positive integer CID. Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `missing_identifier_args`: searchType is \"identifier\" but identifierType or identifiers were omitted. `missing_formula`: searchType is \"formula\" but the formula field was omitted or blank. `missing_structure_args`: substructure/superstructure/similarity search with query or queryType omitted, or a blank query. `invalid_cid_query`: structure/similarity search with queryType \"cid\" but query is not a positive integer CID. Other values are possible when a failure originates below the handler."

Changed1 schema field changedSep 19, 2026

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

Previous value: -"Machine-readable failure mode. Declared by this tool: `missing_identifier_args`: searchType is \"identifier\" but identifierType or identifiers were omitted `missing_formula`: searchType is \"formula\" but the formula field was omitted `missing_structure_args`: substructure/superstructure/similarity search missing query or queryType `invalid_cid_query`: structure/similarity search with queryType \"cid\" but query is not a positive integer CID Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `missing_identifier_args`: searchType is \"identifier\" but identifierType or identifiers were omitted. `missing_formula`: searchType is \"formula\" but the formula field was omitted. `missing_structure_args`: substructure/superstructure/similarity search missing query or queryType. `invalid_cid_query`: structure/similarity search with queryType \"cid\" but query is not a positive integer CID. Other values are possible when a failure originates below the handler."

Changed6 schema fields changedAug 21, 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": [
+      "results",
+      "searchType",
+      "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. Declared by this tool: `missing_identifier_args`: searchType is \"identifier\" but identifierType or identifiers were omitted `missing_formula`: searchType is \"formula\" but the formula field was omitted `missing_structure_args`: substructure/superstructure/similarity search missing query or queryType `invalid_cid_query`: structure/similarity search with queryType \"cid\" but query is not a positive integer CID Other values are possible when a failure originates below the handler.",
+          "examples": [
+            "missing_identifier_args",
+            "missing_formula",
+            "missing_structure_args",
+            "invalid_cid_query"
+          ],
+          "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: -[
-  "results",
-  "searchType",
-  "offset"
-]

Changed11 schema fields changedJul 28, 2026

changedInput schema / properties / maxResults / description

Previous value: -"Maximum CIDs to return (1-200). Default: 20."New value: +"Maximum CIDs to return per page (1-200). Use offset to reach matches past this page. Default: 20."

changedInput schema / properties / maxResults / type
```
Previous value: -"number"New value: +"integer"
```

addedInput schema / properties / offset

Added value: +{
+  "default": 0,
+  "description": "Zero-based index of the first CID to return. Pass the nextOffset from a previous call to read the following page. Identifier lookups resolve every match up front, so paging them is free; formula, substructure, superstructure, and similarity searches have to ask PubChem for offset + maxResults records to reach a page, so deep pages cost progressively more upstream — hence the 10000 ceiling. Default: 0.",
+  "maximum": 10000,
+  "minimum": 0,
+  "type": "integer"
+}

addedOutput schema / properties / nextOffset

Added value: +{
+  "description": "Offset to pass on the next call to continue past this page. Omitted when no further matches remain.",
+  "type": "number"
+}

changedOutput schema / properties / notice / description

Previous value: -"Recovery guidance when no compounds matched — echoes search strategy and suggests how to broaden. Absent when results were returned."New value: +"Recovery guidance when no compounds matched, when the offset runs past the matches observed, when identifiers failed to resolve, or when further pages remain. Absent when this page is complete and every identifier resolved."

addedOutput schema / properties / offset

Added value: +{
+  "description": "Zero-based index of the first CID returned.",
+  "type": "number"
+}

changedOutput schema / properties / shown / description

Previous value: -"CIDs returned after the maxResults cap."New value: +"CIDs returned on this page."

changedOutput schema / properties / totalFound / description

Previous value: -"Exact number of matching CIDs, before the maxResults cap. Omitted when a formula, substructure, superstructure, or similarity search filled its page — PubChem returns no match count for those, so totalFoundAtLeast reports a floor instead."New value: +"Exact number of matching CIDs across all pages. Omitted when a formula, substructure, superstructure, or similarity search saturated the records it requested — PubChem returns no match count for those, so totalFoundAtLeast reports a floor instead."

changedOutput schema / properties / totalFoundAtLeast / description

Previous value: -"Lower bound on matching CIDs, reported in place of totalFound when the exact count is unavailable. At least this many match, and the true total may be higher; raise maxResults to retrieve more."New value: +"Lower bound on matching CIDs, reported in place of totalFound when the exact count is unavailable. At least this many match, and the true total may be higher; page further with offset to observe more."

changedOutput schema / properties / truncated / description

Previous value: -"True when CIDs were capped at maxResults — more matches exist than returned."New value: +"True when matching CIDs remain past this page."

changedOutput schema / required

Previous value: -[
-  "results",
-  "searchType"
-]New value: +[
+  "results",
+  "searchType",
+  "offset"
+]

Changed3 schema fields changedJul 28, 2026

changedOutput schema / properties / totalFound / description

Previous value: -"Total CIDs found before the maxResults cap."New value: +"Exact number of matching CIDs, before the maxResults cap. Omitted when a formula, substructure, superstructure, or similarity search filled its page — PubChem returns no match count for those, so totalFoundAtLeast reports a floor instead."

addedOutput schema / properties / totalFoundAtLeast

Added value: +{
+  "description": "Lower bound on matching CIDs, reported in place of totalFound when the exact count is unavailable. At least this many match, and the true total may be higher; raise maxResults to retrieve more.",
+  "type": "number"
+}

changedOutput schema / required

Previous value: -[
-  "results",
-  "searchType",
-  "totalFound"
-]New value: +[
+  "results",
+  "searchType"
+]

Changed1 schema field changedJul 3, 2026

addedOutput schema / properties / unresolvedIdentifiers

Added value: +{
+  "description": "Identifier-mode only: input identifiers that resolved to no CID. Omitted when every identifier resolved and for non-identifier searches.",
+  "items": {
+    "type": "string"
+  },
+  "type": "array"
+}

Changed3 schema fields changedJun 13, 2026

addedOutput schema / properties / cap

Added value: +{
+  "description": "The maxResults cap that was applied.",
+  "type": "number"
+}

addedOutput schema / properties / shown

Added value: +{
+  "description": "CIDs returned after the maxResults cap.",
+  "type": "number"
+}

addedOutput schema / properties / truncated

Added value: +{
+  "description": "True when CIDs were capped at maxResults — more matches exist than returned.",
+  "type": "boolean"
+}

Changed3 schema fields changedMay 30, 2026

addedOutput schema / properties / notice

Added value: +{
+  "description": "Recovery guidance when no compounds matched — echoes search strategy and suggests how to broaden. Absent when results were returned.",
+  "type": "string"
+}

changedOutput schema / properties / totalFound / description

Previous value: -"Total CIDs found (before maxResults cap)."New value: +"Total CIDs found before the maxResults cap."

changedOutput schema / required

Previous value: -[
-  "searchType",
-  "totalFound",
-  "results"
-]New value: +[
+  "results",
+  "searchType",
+  "totalFound"
+]

Changed5 schema fields changedMay 5, 2026

changedInput schema / properties / identifiers / description

Previous value: -"Required for identifier search. Array of identifiers to resolve (1-25). Examples: [\"aspirin\", \"ibuprofen\"] for name, [\"CC(=O)OC1=CC=CC=C1C(=O)O\"] for SMILES."New value: +"Required for identifier search. Array of identifiers to resolve (1-25). Examples: [\"aspirin\", \"ibuprofen\"] for name, [\"CC(=O)OC1=CC=CC=C1C(=O)O\"] for SMILES, [\"BSYNRYMUTXBXSQ-UHFFFAOYSA-N\"] for inchikey (27-char block format)."

changedInput schema / properties / query / description

Previous value: -"Required for substructure/superstructure/similarity searches. A SMILES string or PubChem CID (as string) for the query structure."New value: +"Required for substructure/superstructure/similarity searches. A SMILES string (e.g. \"CC(=O)O\") or PubChem CID as a string (e.g. \"2244\")."

changedInput schema / properties / searchType / description

Previous value: -"Search strategy: \"identifier\" (name/SMILES/InChIKey lookup), \"formula\", \"substructure\", \"superstructure\", or \"similarity\"."New value: +"Search strategy. \"identifier\": name/SMILES/InChIKey lookup. \"formula\": molecular formula. \"substructure\": find compounds containing the query as a substructure. \"superstructure\": find compounds that are themselves substructures of the query. \"similarity\": 2D Tanimoto similarity to the query."

changedOutput schema / properties / results / items / properties / properties / description

Previous value: -"Compound properties when requested."New value: +"Compound properties keyed by name (echoes input.properties; only present when requested)."

changedOutput schema / properties / searchType / description

Previous value: -"The search strategy used."New value: +"Search strategy used: identifier, formula, substructure, superstructure, or similarity."

Changed1 schema field changedApr 24, 2026
- addedOutput schema / properties / results / items / description
```
Added value: +"Matching compound entry."
```
First observedMar 28, 2026

TDQS

A4.6/5.0

Behavior5/5

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

Annotations declare readOnly/idempotent/openWorld, and the description goes well beyond them: it discloses paging via CIDs + offset, that identifier lookups resolve all matches up front, and that formula/structure searches must fetch offset+maxResults upstream so deep pages cost more. Those are non-obvious cost and performance traits an agent needs.

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?

Three dense sentences that front-load the search modes and end on the hydration benefit. The mode enumeration is long but each clause maps to a distinct capability; no wasted framing.

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?

With an output schema present, the description needn't document return fields, and it correctly limits itself to 'returns a page of CIDs' plus offset paging. Combined with annotations and full schema coverage, an agent has everything needed to call it correctly across all six modes.

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, but the description adds real value by tying properties to 'avoid a follow-up details call' and flagging offset-based paging and the 25-identifier/cap semantics. It doesn't restate the per-mode required fields, which is fine given 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?

States a specific verb (search) and resource (PubChem chemical compounds) and enumerates every supported search mode — identifier, formula, substructure, superstructure, similarity, assay. It also names the sibling it can replace (pubchem_get_compound_details) via the hydration option, so an agent can place it among siblings without opening the schema.

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?

Makes the when-to-use explicit for each mode ("up to 25 per call", "reach matches past maxResults with offset", "hydrate results with properties to avoid a follow-up pubchem_get_compound_details call"). It does not, however, state when to prefer a different sibling tool such as pubchem_search_assays for assay discovery — that link only appears in the schema.

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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