This server provides read-only access to PubChem chemical and bioassay data via MCP tools and resources.
Search compounds by name, SMILES, InChIKey, molecular formula, substructure/superstructure, or 2D similarity (Tanimoto).
Get compound details: physicochemical properties, descriptions, synonyms, drug-likeness (Lipinski/Veber), and pharmacological classification (FDA, MeSH, ATC).
Fetch compound images: 2D structure diagrams as PNG (small or large).
Fetch 3D structures: parsed atoms/bonds or raw SDF, with alternate conformer IDs.
Get cross-references: PubMed, patents, CAS/registry numbers, genes, proteins, taxonomy IDs.
Get safety data: GHS signal word, pictograms, H-codes, P-codes with source attribution.
Get bioactivity profiles: assay outcomes, targets, activity values; filter by outcome or target.
Get interactions: drug-drug, drug-food, and chemical-target interactions.
Search assays by biological target (gene symbol, protein name, Gene ID, UniProt accession).
Get entity summaries for assays, genes, proteins, and taxonomy.
Resources expose compound properties, safety, image, xrefs, bioactivity, and assay summaries via URI templates.
Provides access to PubChem's chemical information database, enabling searches for chemical compounds by identifier, structure, similarity, and molecular formula. Retrieves compound properties, structural images, substance details, bioassay summaries, and cross-references to external databases including PubMed.
Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@pubchem-mcp-server search for aspirin and get its molecular weight"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
Public Hosted Server: https://pubchem.caseyjhand.com/mcp
Chemical compound and bioassay data from PubChem's PUG REST and PUG View APIs. Search compounds by identifier, formula, or structure; fetch physicochemical properties, safety data, bioactivity, interactions, cross-references, and 3D structures; find bioassays by biological target. Runs as a stdio process, a local Streamable HTTP server, or the public hosted endpoint above.
Tool | Description |
| Search for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity. |
| Get physicochemical properties, descriptions, synonyms, drug-likeness, and classification for compounds by CID. |
| Fetch a 2D structure diagram (PNG) for a compound by CID. |
| Fetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF. |
| Get external database cross-references (PubMed, patents, genes, proteins, etc.). |
| Get GHS hazard classification and safety data for one or more compounds by CID (batch). |
| Get a compound's bioactivity profile: assay results, targets, and activity values; filter by outcome or molecular target. |
| Get drug-drug, drug-food, and chemical-target interactions for a compound by CID. |
| Find bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession). |
| Get summaries for PubChem entities: assays, genes, proteins, taxonomy. |
Compound and assay records are also exposed as URI-templated resources, backed by the same client methods as the tools; many MCP clients are tool-only and never surface resources.
Resource | Description |
| Core physicochemical properties (JSON). |
| GHS hazard classification (JSON). |
| 2D structure diagram (PNG). |
| External cross-references (JSON). |
| Bioassay activity profile (JSON). |
| BioAssay summary (JSON). |
Related MCP server: PubChem Chemical Safety MCP Server
pubchem_search_compounds toolFive search strategies: identifier (name/SMILES/InChIKey, batched 1-25), formula (Hill notation, optional allowOtherElements), substructure/superstructure containment, or 2D Tanimoto similarity (threshold 70-100, default 90)
Each strategy needs its own fields — identifier: identifierType + identifiers; formula: formula; substructure/superstructure/similarity: query + queryType — and a missing or blank one is rejected before the upstream call
Caps at 200 CIDs per page (default 20); offset pages to a ceiling of 10,000 — identifier lookups resolve every match up front so paging is free, while formula/structure/similarity searches cost more upstream per deep page
Optional properties hydration avoids a follow-up pubchem_get_compound_details call
Identifier mode reports unresolvedIdentifiers for inputs that resolved to no CID — no PubChem match, or a SMILES PubChem cannot interpret — while the rest of the batch still resolves, plus notices when multiple inputs collide on one CID
A query PubChem cannot search on (malformed SMILES or formula, a * wildcard atom, a CID with no record) fails fast with a search_query_rejected hint naming what to fix
Reports an exact totalFound when the full match set was observed, or a totalFoundAtLeast floor when a bounded upstream search saturated
pubchem_get_compound_details toolUp to 100 CIDs per call; 27 available properties, defaulting to a core set of 14 (formula, weight, IUPAC name, SMILES forms, InChIKey, XLogP, TPSA, H-bond/rotatable-bond counts, heavy atom count, charge, complexity)
Optional textual descriptions, paged via descriptionOffset/maxDescriptions (default 3, up to 20) — fetched only for the first 10 CIDs in the batch, remaining CIDs listed in skippedCids
Optional synonyms for every found CID, paged via synonymOffset/maxSynonyms (default 20, up to 100)
Optional drug-likeness assessment (Lipinski Rule of Five + Veber rules), computed from the returned properties at no extra latency
Optional pharmacological classification (FDA classes/mechanisms, MeSH classes, ATC codes) — same 10-CID fan-out cap as descriptions
Per-CID found: false distinguishes a nonexistent CID from a real compound PubChem simply has no data for
pubchem_get_compound_image toolSingle CID; size is "small" (100x100) or "large" (300x300, default)
Returns base64-encoded PNG plus width/height
Typed cid_not_found error when PubChem has no record for the CID
pubchem_get_compound_3d_structure toolSingle CID; format="json" (default) returns parsed atoms (element + x/y/z) and bonds, format="sdf" returns the raw V2000 SDF text
maxAtoms/maxBonds cap the JSON preview (default 200 each); atomCount/bondCount always report the full totals, with any capping disclosed via enrichment
includeRawSdf bypasses the default 500-line cap on the raw SDF text
Optional includeAlternateConformerIds lists conformer IDs beyond the default
Typed no_3d_structure error when PubChem has no computed 3D coordinates (large molecules, mixtures, some salts)
pubchem_get_compound_xrefs toolSingle CID; one or more xrefTypes — string IDs (RegistryID, RN for CAS numbers, PatentID) and numeric IDs (PubMedID, GeneID, ProteinGI, TaxonomyID)
Paged per type: maxPerType up to 500 (default 50), with the same offset applied across every requested type
Each type reports its own totalAvailable and truncated flag
Empty-result notice distinguishes "this compound has none of the requested types" from a possibly-mistyped CID
pubchem_get_compound_safety toolBatch of 1-25 CIDs
Returns GHS signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes), with source attribution
Per-CID status: ok, no_ghs_data (compound exists, no deposited classification), or cid_not_found (no PubChem record at all) — kept distinct so a bad CID never reads as "no hazards on file"
Precautionary statements carry a decoded flag — false for codes needing label-specific fill text or outside the decoder table; the code itself is still authoritative
pubchem_get_bioactivity toolSingle CID; filter by outcomeFilter (active/inactive/all, default all) and/or targetGeneId/targetAccession
Caps at 100 results per page (default 20); offset reaches the rest
Reports totalAssays/activeCount/inactiveCount for the whole compound, plus filteredCount/returnedCount for the current page
Notices distinguish "no bioactivity data at all" from "the filter excluded everything" from "offset past the end"
pubchem_get_compound_interactions toolSingle CID; one or more kinds — drug-drug (DrugBank), drug-food, target (binding/activity from BindingDB, ChEMBL, and others); default ["drug-drug"]
maxEntries per kind per page (1-50, default 10); offset counts source records rather than returned entries, capped at 2,147,483,646
Each kind pages independently — paging[] reports per-kind totalRecords/nextOffset/truncated; the top-level nextOffset is populated only when exactly one requested kind still has records left
A kind that fails to retrieve is named in failedKinds without failing the kinds that succeeded
pubchem_search_assays toolSearch by targetType: genesymbol/proteinname (text), geneid (NCBI Gene ID), proteinaccession (UniProt)
Caps at 200 AIDs per page (default 50); offset pages to the total found
Rejects a blank targetQuery and a non-numeric geneid query before the upstream call
Reports totalFound across all pages and distinguishes "no match" from "offset past the end"
pubchem_get_summary toolentityType: assay (AID), gene (NCBI Gene ID), protein (UniProt accession), or taxonomy (Tax ID); up to 10 identifiers per call
Per-identifier found flag; populated fields depend on entityType (taxonomy includes an ordered lineage, gene includes symbol/taxonomy)
Notice reports how many identifiers were not found and which ID type entityType expects
pubchem://compound/{cid} resourceCore physicochemical properties (the same default 14-property set as pubchem_get_compound_details), as application/json
Throws a typed not-found when the CID doesn't exist in PubChem
Use pubchem_get_compound_details to select specific properties or add descriptions, synonyms, drug-likeness, and classification
pubchem://compound/{cid}/safety resourceGHS hazard classification as application/json
status (ok/no_ghs_data/cid_not_found) is the only signal distinguishing a bad CID from a compound with no deposited classification — a resource read has no notice surface
pubchem://compound/{cid}/image resource2D structure diagram, 300x300 PNG, returned as a base64 blob
Use pubchem_get_compound_image for the 100x100 size option
pubchem://compound/{cid}/xrefs resourceFocused default set — RN (CAS), RegistryID, PubMedID — up to 25 IDs per type, as application/json
Use pubchem_get_compound_xrefs for the full set of xref types, a higher per-type cap, and offset paging
pubchem://compound/{cid}/bioactivity resourceUp to 25 assays as application/json, plus totalAssays/activeCount for the whole compound
Use pubchem_get_bioactivity to filter by outcome or target, raise the cap, or page with offset
pubchem://assay/{aid} resourceBioAssay summary as application/json — name, description, source, protocol, substance counts
Throws a typed not-found when the AID doesn't exist
Built on @cyanheads/mcp-ts-core: stdio and Streamable HTTP transports, pluggable auth (none / jwt / oauth), swappable storage (in-memory, filesystem, Supabase, Cloudflare KV/R2/D1), structured logging with optional OpenTelemetry tracing.
PubChem-specific:
Covers both PUG REST (search, properties, cross-references, safety, bioactivity, interactions) and PUG View (textual descriptions, pharmacological classification) endpoints
Rate-limited client (5 req/s) with automatic request queuing, and retry with exponential backoff on 5xx errors and network failures
A cancelled tool call or resource read stops its PubChem work — queued requests, in-flight fetches, retry backoffs, and async-search polling — and fails with RequestCancelled
Hand-rolled V2000 SDF parser for 3D conformer atoms and bonds; drug-likeness (Lipinski/Veber) computed from already-fetched properties, adding no extra latency
All tools are read-only and idempotent — no API keys required, PubChem's API is freely accessible
Agent-friendly output:
Discriminated output contracts — per-CID status (ok / no_ghs_data / cid_not_found) and found flags let callers branch on data instead of matching an error string
Graceful partial failure — batch tools return per-item results alongside unresolvedIdentifiers, skippedCids, and failedKinds rather than failing the whole call
Response shaping — truncation disclosure (truncated, shown/cap, nextOffset) on every capped list, plus a totalFoundAtLeast floor in place of a count when an upstream search saturates
Typed error reasons — validation and not-found failures declare a reason (e.g. cid_not_found, missing_identifier_args, invalid_cid_query) with actionable recovery text, not generic messages
A public instance is available at https://pubchem.caseyjhand.com/mcp — no installation required. Point any MCP client at it via Streamable HTTP:
{
"mcpServers": {
"pubchem-mcp-server": {
"type": "streamable-http",
"url": "https://pubchem.caseyjhand.com/mcp"
}
}
}Add the following to your MCP client configuration file.
{
"mcpServers": {
"pubchem-mcp-server": {
"type": "stdio",
"command": "bunx",
"args": ["@cyanheads/pubchem-mcp-server@latest"],
"env": {
"MCP_TRANSPORT_TYPE": "stdio"
}
}
}
}Or with npx (no Bun required):
{
"mcpServers": {
"pubchem-mcp-server": {
"type": "stdio",
"command": "npx",
"args": ["-y", "@cyanheads/pubchem-mcp-server@latest"],
"env": {
"MCP_TRANSPORT_TYPE": "stdio"
}
}
}
}Or with Docker:
{
"mcpServers": {
"pubchem-mcp-server": {
"type": "stdio",
"command": "docker",
"args": ["run", "-i", "--rm", "-e", "MCP_TRANSPORT_TYPE=stdio", "ghcr.io/cyanheads/pubchem-mcp-server:latest"]
}
}
}For Streamable HTTP, set the transport and start the server:
MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
# Server listens at http://localhost:3010/mcpBun v1.4.0 or higher (or Node.js v24+).
No API keys required — PubChem's API is freely accessible.
Clone the repository:
git clone https://github.com/cyanheads/pubchem-mcp-server.gitNavigate into the directory:
cd pubchem-mcp-serverInstall dependencies:
bun installConfigure environment (optional):
cp .env.example .env
# edit .env to override transport, session mode, storage, or logging defaultsVariable | Description | Default |
| Transport: |
|
| Port for HTTP server. |
|
| Host for HTTP server. |
|
|
|
|
| Auth mode: |
|
| Log level (RFC 5424). |
|
| Storage backend. |
|
| Enable OpenTelemetry. |
|
See .env.example for the full list of optional overrides.
Build and run:
# One-time build
bun run rebuild
# Run the built server
bun run start:stdio
# or
bun run start:httpRun checks and tests:
bun run devcheck # Lint, format, typecheck, security
bun run test # Vitest test suite
bun run lint:mcp # Validate MCP definitions against specdocker build -t pubchem-mcp-server .
docker run --rm -p 3010:3010 pubchem-mcp-serverThe Dockerfile defaults to HTTP transport, stateless session mode, and logs to /var/log/pubchem-mcp-server. OpenTelemetry peer dependencies are installed by default — build with --build-arg OTEL_ENABLED=false to omit them.
Directory | Purpose |
|
|
| Tool definitions ( |
| Resource definitions ( |
| PubChem API client — rate limiting, retry, and response/SDF parsing. |
| Build, clean, devcheck, and tree generation scripts. |
| Unit and integration tests. |
See CLAUDE.md for development guidelines and architectural rules. The short version:
Handlers throw, framework catches — no try/catch in tool logic
Use ctx.log for request-scoped logging
Wrap external API calls: validate the raw PubChem response → normalize to a domain type → return the output schema; never fabricate missing fields
Register new tools and resources in the index.ts barrel files
Issues are welcome. Run checks before submitting:
bun run devcheck
bun run testApache-2.0 — see LICENSE for details.
Get a compound's bioactivity profile: which assays tested it, activity outcomes (Active/Inactive/Inconclusive), target identifiers (NCBI Gene ID, UniProt/GenBank accession), and quantitative values (IC50, EC50, Ki, etc.). Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein accession) to focus the profile — e.g. "is this compound active against target T?".
| Name | Required | Description | Default |
|---|---|---|---|
| cid | Yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. | |
| offset | No | Zero-based index of the first assay to return, applied after the outcome and target filters. Pass the nextOffset from a previous call to read the following page. Default: 0. | |
| maxResults | No | Max assay results to return per page (1-100). Well-studied compounds have thousands of records; use offset to reach the ones past this page. Default: 20. | |
| targetGeneId | No | Filter to assays against this NCBI Gene ID. Obtain Gene IDs from pubchem_search_assays or the targetGeneId field of an unfiltered result here. Combine with outcomeFilter="active" to answer "is this compound active against target T?". | |
| outcomeFilter | No | Filter by activity outcome. "active" shows only assays where the compound showed activity — most useful for understanding biological profile. Default: "all". | all |
| targetAccession | No | Filter to assays against this target protein accession (UniProt/GenBank), e.g. "P35354". Obtain accessions from pubchem_search_assays or the targetAccession field of an unfiltered result here. |
| Name | Required | Description |
|---|---|---|
| cap | No | The maxResults cap that was applied. |
| cid | No | PubChem Compound ID. |
| error | No | Present when the call failed. Absent on success. |
| shown | No | Assays returned on this page. |
| notice | No | Recovery guidance when the filter yields no results or the compound has no bioactivity data. |
| offset | No | Zero-based index of the first assay returned. |
| results | No | Assay results matching the filter. |
| truncated | No | True when matching assays remain past this page. |
| nextOffset | No | Offset to pass on the next call to continue past this page. Omitted when no further assays match. |
| activeCount | No | Assays with "Active" outcome. |
| totalAssays | No | Total unique assays for this compound. |
| targetFilter | No | Target filter applied (gene ID and/or protein accession), when set. |
| filteredCount | No | Exact number of assays matching the outcome and target filters, across all pages. |
| inactiveCount | No | Assays with "Inactive" outcome. |
| outcomeFilter | No | Outcome filter applied: active, inactive, or all. |
| returnedCount | No | Assays returned on this page. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, openWorldHint, and idempotentHint, so the safety profile is covered. The description adds meaningful behavioral context beyond annotations by specifying the composition of the bioactivity profile and the filtering behavior, without contradicting the annotations.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is two dense, purposeful sentences. The main resource and result contents are front-loaded, and the filtering use case earns its place with a concrete example. There is no filler or redundancy.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the rich input schema, output schema, and readOnly/openWorld/idempotent annotations, the description provides the missing orientation an agent needs: what a bioactivity profile contains and how to answer a target-specific question. Nothing essential to selecting and invoking the tool is absent.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%, and the schema already documents every parameter in detail, including offset pagination and the targetGeneId/outcomeFilter combination. The description reinforces the intended query pattern but does not meaningfully add new parameter-level semantics, so the baseline 3 applies.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description starts with a specific verb and resource ('Get a compound's bioactivity profile') and enumerates exactly what is returned: assays, activity outcomes, target identifiers, and quantitative values. The detail is specific enough to distinguish this from sibling tools like pubchem_get_compound_interactions and pubchem_get_compound_xrefs.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description gives clear context for when to use the tool, including a concrete example ('is this compound active against target T?') and how to focus results by outcome or target. It does not explicitly state when not to use it or name alternatives, so it falls just short of a 5.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns atoms and bonds parsed into structured fields; format="sdf" returns the raw V2000 SDF text for passthrough to docking, rendering, or conformer tools. Optionally lists alternate conformer IDs. Not every compound has computed 3D coordinates (large molecules, mixtures, and some salts do not).
| Name | Required | Description | Default |
|---|---|---|---|
| cid | Yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. | |
| format | No | Output format. "json" (default) returns parsed atoms and bonds. "sdf" returns the raw V2000 SDF text for passthrough to other tools. | json |
| maxAtoms | No | Cap the atoms returned in the format="json" preview. atomCount always reports the full total; omitted rows are disclosed via the truncated/shownAtoms enrichment. Defaults to the first 200 atoms. | |
| maxBonds | No | Cap the bonds returned in the format="json" preview. bondCount always reports the full total; omitted rows are disclosed via the truncated/shownBonds enrichment. Defaults to the first 200 bonds. | |
| includeRawSdf | No | For format="sdf", return the complete raw V2000 SDF even when it exceeds the safe line cap. Default false: an SDF longer than 500 lines is line-capped with disclosure. No effect when format="json". | |
| includeAlternateConformerIds | No | List the IDs of additional computed conformers beyond the default. Slower than the default response. Default: false. |
| Name | Required | Description |
|---|---|---|
| cid | No | PubChem Compound ID. |
| sdf | No | Raw V2000 SDF text. Populated when format="sdf". |
| atoms | No | Parsed atoms. Populated when format="json". |
| bonds | No | Parsed bonds. Populated when format="json". |
| error | No | Present when the call failed. Absent on success. |
| notice | No | Guidance naming which lists were capped and how to widen them. |
| atomCap | No | The atom cap applied (explicit maxAtoms or the safe default), when the atom list was capped. |
| bondCap | No | The bond cap applied (explicit maxBonds or the safe default), when the bond list was capped. |
| atomCount | No | Number of atoms in the conformer. |
| bondCount | No | Number of bonds in the conformer. |
| truncated | No | True when the atom list, bond list, or raw SDF was capped below its total. atomCount/bondCount always report the full totals. |
| shownAtoms | No | Atoms returned after the cap, when fewer than atomCount. Raise maxAtoms for more. |
| shownBonds | No | Bonds returned after the cap, when fewer than bondCount. Raise maxBonds for more. |
| conformerId | No | Default (primary) conformer ID. Present when includeAlternateConformerIds is set. |
| shownSdfLines | No | SDF lines returned when format="sdf" and the raw text was line-capped. Set includeRawSdf for the full record. |
| alternateConformerIds | No | Conformer IDs beyond the default. Present when includeAlternateConformerIds is set and alternates exist. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnly, idempotent, and openWorld hints. The description adds useful behavioral context beyond these: format differences (parsed JSON vs. raw SDF), the caveat that not every compound has 3D coordinates, and performance notes (alternate conformer listing is slower). It also discloses truncation behavior in the parameter descriptions, which is behaviorally relevant. No contradictions 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.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is two sentences that front-load the core purpose and then add important qualifications (format options, missing-coordinate caveat). It is efficient without being terse, and every sentence adds value. Some redundancy with the schema exists, but the description remains appropriately sized.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the output schema exists, the description does not need to explain return values. It covers the main behavior, both format options, and a key failure mode (missing 3D coordinates). It doesn't explicitly state what happens on a missing conformer, but that could be in the output schema. Overall, it is complete for the tool's complexity.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100% – every parameter already has a clear description in the schema. The tool's description does not add meaning beyond what the schema provides (e.g., it recaps format behavior but that's also in the schema). Therefore, baseline 3 is appropriate; the schema does the heavy lifting.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description states a specific verb and resource: 'Get a compound's default 3D conformer — atomic coordinates and bonds — for one CID.' This clearly distinguishes it from sibling tools like pubchem_get_compound_details or pubchem_get_compound_image, which focus on other aspects. The scope ('for one CID') adds precision.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides clear context about what the tool does and its format options, but it does not explicitly name alternatives or state when to use this tool versus a sibling. However, it implies usage by its specificity (3D structure) and includes a caveat about missing coordinates, which helps set expectations. The lack of explicit exclusions prevents a score of 5.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Get detailed compound information by CID. Returns physicochemical properties (molecular weight, SMILES, InChIKey, XLogP, TPSA, etc.), optionally with a textual description (pharmacology, mechanism, therapeutic use), known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Accepts up to 100 CIDs per call.
| Name | Required | Description | Default |
|---|---|---|---|
| cids | Yes | PubChem Compound IDs to fetch (1-100). Resolve from names/SMILES with pubchem_search_compounds. | |
| properties | No | Properties to retrieve. Defaults to a core set: MolecularFormula, MolecularWeight, IUPACName, CanonicalSMILES, IsomericSMILES, InChIKey, XLogP, TPSA, HBondDonorCount, HBondAcceptorCount, RotatableBondCount, HeavyAtomCount, Charge, Complexity. | |
| maxSynonyms | No | Max synonyms returned per compound per page (1-100). PubChem lists hundreds for common drugs; use synonymOffset to reach the ones past this page. Default: 20. | |
| synonymOffset | No | Zero-based index of the first synonym to return within each compound's synonym list. The same offset is applied to every compound in the batch. Pass the nextSynonymOffset from a previous call to read the following page. Default: 0. | |
| includeSynonyms | No | Fetch known names and synonyms (trade names, systematic names, registry numbers), paged via synonymOffset/maxSynonyms. Fetched for every found CID in the batch. Slower for large CID lists. | |
| maxDescriptions | No | Max number of distinct description entries per compound per page (1-20). PubChem returns near-duplicate summaries from many depositors; duplicates are collapsed before this cap applies. Default: 3. | |
| descriptionOffset | No | Zero-based index of the first description to return within each compound's description list. The same offset is applied to every compound in the batch. Pass the nextDescriptionOffset from a previous call to read the following page. Default: 0. | |
| includeDescription | No | Include textual descriptions (pharmacology, mechanism, therapeutic use) attributed by source. Well-studied compounds have many overlapping summaries — paged via descriptionOffset/maxDescriptions. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without descriptions and are listed in the response's skippedCids. | |
| includeDrugLikeness | No | Compute drug-likeness assessment: Lipinski Rule of Five (MW, XLogP, HBD, HBA) and Veber rules (TPSA, rotatable bonds). Computed from the returned properties, so it adds no latency. | |
| includeClassification | No | Include pharmacological classification: FDA Established Pharmacologic Classes, mechanisms of action, MeSH classes, and ATC codes. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without classification and are listed in the response's skippedCids. |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| notice | No | Recovery guidance covering the skipped CIDs, an offset that runs past every compound, and pages that remain. Absent when nothing was skipped or truncated. |
| compounds | No | Compound detail records. |
| truncated | No | True when this response is not the whole picture: a compound has further synonyms or descriptions past this page, or CIDs were skipped by the per-call fan-out limit. Per-compound totals are in compounds[].synonymsTotal / compounds[].descriptionsTotal; the skipped CIDs are in skippedCids. |
| skippedCids | No | CIDs found in PubChem whose descriptions and classification were NOT fetched because the batch exceeded the per-call fan-out limit. Their absence from a record means "not requested", not "PubChem has none" — re-request these CIDs in a follow-up call. Present only when CIDs were skipped. |
| enrichedCids | No | CIDs whose descriptions and classification were fetched. Present only when the batch exceeded the per-call fan-out limit and other CIDs were skipped. |
| synonymOffset | No | Zero-based index of the first synonym returned within each compound's list. Present when includeSynonyms is true. |
| descriptionOffset | No | Zero-based index of the first description returned within each compound's list. Present when includeDescription is true. |
| nextSynonymOffset | No | synonymOffset to pass on the next call to continue past this page. Omitted when no compound in the batch has further synonyms. |
| nextDescriptionOffset | No | descriptionOffset to pass on the next call to continue past this page. Omitted when no compound in the batch has further descriptions. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint and idempotentHint, so safety is covered. The description adds the batch capacity limit ('up to 100 CIDs per call') and the optionality of descriptions, synonyms, drug-likeness, and classification. The surprising 'first 10 CIDs only' limitation is not in the top-level description, but it is documented in the parameter descriptions, so an agent reading the schema will still discover it.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is two sentences with no filler: the first sentence states the core action and return types, the second covers optional content and the batch limit. Every clause earns its place.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the rich schema, output schema presence, and annotations, the top-level description is complete enough for an agent to select and call the tool correctly. It provides a compact overview while the schema carries parameter-level details like pagination and the first-10-CID caveat.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%, and each parameter already has a detailed description explaining defaults, pagination, and effects like skippedCids. The top-level description adds thematic grouping but no parameter syntax or semantics beyond what the schema already provides, so the baseline of 3 is appropriate.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
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: 'Get detailed compound information by CID.' It then enumerates the actual content categories — physicochemical properties, descriptions, synonyms, drug-likeness, and pharmacological classification — which clearly distinguishes this tool from siblings like bioactivity, safety, xrefs, and 3D structure.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
Usage is implied rather than explicit: the tool should be used when detailed compound data by CID is needed. There is no direct comparison with sibling tools or a when-not-to-use statement, though the schema does point users to pubchem_search_compounds for resolving names/SMILES to CIDs.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Fetch a 2D structure diagram (PNG image) for a compound by CID.
| Name | Required | Description | Default |
|---|---|---|---|
| cid | Yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. | |
| size | No | Image size: "small" (100x100) or "large" (300x300). Default: "large". | large |
| Name | Required | Description |
|---|---|---|
| cid | No | PubChem Compound ID. |
| error | No | Present when the call failed. Absent on success. |
| width | No | Image width in pixels. |
| height | No | Image height in pixels. |
| mimeType | No | MIME type — always "image/png". |
| imageBase64 | No | Base64-encoded PNG image data. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint=true and idempotentHint=true, so the safety profile is covered. The description adds that the result is a PNG image, but it does not disclose additional behavioral context such as output size constraints beyond the schema or any limitations of the 2D rendering. This is acceptable but not rich.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is one short sentence with no filler. The core action and output type are front-loaded, making it immediately scannable, and every word contributes to meaning.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
This is a simple read-only tool with one required parameter, a fully documented optional enum, and an output schema present. The description plus schema fully specify how to invoke it correctly. It only misses explicit sibling routing, but that gap is already captured under usage_guidelines.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%, with both cid and size fully documented and size's enum values described. The description adds only the redundant 'by CID' phrase, providing no meaningful parameter semantics beyond what the schema already gives. Baseline 3 is appropriate.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description names a specific verb ('Fetch'), a specific resource ('2D structure diagram (PNG image)'), and the required input ('by CID'). The '2D' qualifier explicitly distinguishes it from the sibling tool pubchem_get_compound_3d_structure, so an agent can identify the correct tool immediately.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description implies the usage context: an agent should call this when a 2D PNG image of a compound is needed. However, it does not explicitly state when to prefer this tool over siblings like pubchem_get_compound_details or pubchem_get_compound_3d_structure. The cid parameter description does provide a useful prerequisite by pointing to pubchem_search_compounds.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
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.
| Name | Required | Description | Default |
|---|---|---|---|
| cid | Yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. | |
| kinds | No | Interaction kinds to fetch. "drug-drug" (interactions with other drugs), "drug-food" (dietary interactions), "target" (binding/activity against molecular targets). Default: ["drug-drug"]. | |
| offset | No | 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. | |
| maxEntries | No | 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. |
| Name | Required | Description |
|---|---|---|
| cid | No | PubChem Compound ID. |
| error | No | Present when the call failed. Absent on success. |
| notice | No | 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. |
| offset | No | Zero-based start position read within each requested kind. |
| paging | No | 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. |
| entries | No | Interaction entries across the requested kinds. |
| truncated | No | 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. |
| nextOffset | No | 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. |
| failedKinds | No | Interaction kinds that could not be retrieved (comma-separated). The returned entries cover the kinds that succeeded; retry to re-attempt the failed ones. |
| returnedCount | No | Total interaction entries returned across all kinds. |
| requestedKinds | No | Interaction kinds requested (comma-separated). |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations declare readOnlyHint, openWorldHint, and idempotentHint, but the description adds valuable context beyond these: results are paged per kind with source-record totals and nextOffset, and that richness varies by drug type. It also discloses that many compounds lack records, which is open-world behavior. This enriches the annotation-driven understanding without contradiction.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is concise, spanning three sentences that each earn their place: the first explains what is fetched, the second explains paging behavior, and the third sets expectations on data richness. It is front-loaded with purpose, and the paging detail is critical for correct usage. No fluff or redundant repetition of schema details.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the complexity of paging logic and multiple interaction kinds, the description fully covers necessary operational details: paging per kind, nextOffset semantics, and the recommendation for one kind per call. The output schema exists, so return format is not needed in the description. The description also notes the open-world nature (many compounds have no records), which is essential context for agents. All critical information is covered.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%, so the description does not need to explain parameters, but it enhances understanding of the `offset` and `maxEntries` interplay by noting that kinds advance at different rates and advising one kind per call when paging. The description of `kinds` in the schema aligns with the description's list of interactions concatenated with sourcesressor. This adds a layer of nuance not present in the schema, though baseline is 3 due to high coverage.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description clearly identifies the tool as fetching compound interaction data, listing specific interaction types (drug-drug, drug-food, chemical-target) and their sources. It distinguishes itself from siblings like pubchem_get_bioactivity, which focuses on bioactivity data, and pubchem_get_compound_details, which covers general details. The specificity of 'interaction data' with enumerated kinds and source mentions leaves no ambiguity about purpose.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides clear context for when to use this tool (to retrieve interaction data) and notes that it is richest for approved drugs, implying alternatives for other cases. It does not explicitly warn against using it for bioactivity assays, but the direct reference to interaction data and the enumerations in the schema differentiate it from siblings like pubchem_get_bioactivity. The mention that many compounds have no deposited records guides expectation setting, which is useful for decision-making.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Get GHS (Globally Harmonized System) hazard classification and safety data for one or more compounds by CID. Returns signal word, pictograms, hazard statements (H-codes), and precautionary statements (P-codes) per compound. Data sourced from PubChem depositors — source attribution included.
| Name | Required | Description | Default |
|---|---|---|---|
| cids | Yes | PubChem Compound IDs to fetch safety data for (1-25). Resolve from names/SMILES with pubchem_search_compounds. |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| notice | No | Recovery guidance when one or more CIDs returned no GHS data, listing the unrecognized CIDs to verify separately from the CIDs that exist but carry no deposited classification. |
| results | No | Safety results, one per requested CID (input order preserved). |
| withDataCount | No | CIDs with GHS safety data available. |
| requestedCount | No | CIDs requested. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint and idempotentHint, so no contradiction exists. The description adds valuable behavioral context by stating the data is sourced from PubChem depositors and that source attribution is included, which informs the agent about data provenance and potential variability without contradicting the openWorldHint.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Three sentences with no filler: the first states the action and resource, the second enumerates the returned data types, and the third notes provenance. The most important scoping information is front-loaded.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
This is a simple one-parameter, read-only, idempotent tool with a full output schema and annotations covering side effects and openness. The description supplies enough operational context—input format, output contents, and data source—so an agent can select and invoke it correctly without missing information.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100% and the schema already explains cids semantics, including the 1-25 range and the resolution workflow via pubchem_search_compounds. The description adds no additional parameter-level meaning beyond 'by CID', so a baseline score of 3 is appropriate.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description uses a specific verb ('Get') and resource ('GHS hazard classification and safety data') and specifies the input mechanism ('by CID'). It clearly distinguishes this tool from siblings like pubchem_get_compound_details and pubchem_get_compound_image by focusing on safety/H-codes/P-codes.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description clearly scopes the tool to GHS safety data, which implies when it should be used, and the input schema reinforces that names/SMILES must be resolved via pubchem_search_compounds first. It does not explicitly name alternatives or exclusions, but the uniqueness of the safety-data purpose makes the intended usage unambiguous.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Get external database cross-references for a compound: PubMed citations, patent IDs, gene/protein associations, registry numbers, and taxonomy IDs. Results are paged per type — capped at maxPerType with the total count reported; reach the IDs past a page with offset.
| Name | Required | Description | Default |
|---|---|---|---|
| cid | Yes | PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds. | |
| offset | No | Zero-based index of the first ID to return within each xref type. The same offset is applied to every requested type. Pass the nextOffset from a previous call to read the following page. Default: 0. | |
| xrefTypes | Yes | Cross-reference types to retrieve. String IDs: RegistryID (DSSTox/EPA registry numbers), RN (CAS numbers), PatentID. Numeric IDs: PubMedID, GeneID (NCBI Gene), ProteinGI (legacy NCBI Protein GI), TaxonomyID. | |
| maxPerType | No | Max IDs to return per xref type per page (1-500). A compound may have thousands of PubMed references; use offset to reach the ones past this page. Total count always reported. Default: 50. |
| Name | Required | Description |
|---|---|---|
| cid | No | PubChem Compound ID. |
| error | No | Present when the call failed. Absent on success. |
| xrefs | No | Cross-references grouped by type. |
| notice | No | Recovery guidance when every requested xref type returned zero IDs, when the offset runs past every type, or when further pages remain. Absent when this page is complete and non-empty. |
| offset | No | Zero-based index of the first ID returned within each type. |
| truncated | No | True when at least one requested type has IDs remaining past this page. Which types, and how many IDs each holds in total, is in xrefs[].truncated / xrefs[].totalAvailable. |
| nextOffset | No | Offset to pass on the next call to continue past this page. Omitted when no requested type has further IDs. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, idempotentHint, and openWorldHint, so the safety profile is covered. The description adds behavioral value by explaining pagination semantics: results are paged per type, capped at maxPerType, total counts are always reported, and offset reaches further IDs. This goes beyond the annotations without contradicting them.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Two sentences with no waste: the first fronts the purpose and lists the xref types, the second packs the pagination behavior. Every clause earns its place, and the most important information appears first.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
Given the presence of a detailed input schema, an output schema, and safety annotations, the description is complete enough for an agent to call the tool correctly. It covers how to page through results and how to resolve the compound ID, with the only gap being explicit routing among sibling tools.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%, so the baseline is 3. The description adds meaning beyond the schema by clarifying that pagination is per xref type and that the total count is reported, which illuminates the behavior of offset and maxPerType. It does not repeat parameter formats but reinforces their usage.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description states a specific verb ('Get') and resource ('external database cross-references for a compound'), and enumerates the types of xrefs it returns (PubMed citations, patent IDs, gene/protein associations, registry numbers, taxonomy IDs). It is clearly distinct from most siblings, but it does not explicitly distinguish itself from the potentially overlapping pubchem_get_compound_details, so it falls short of a 5.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description provides useful context on pagination and the cid schema field directs users to pubchem_search_compounds for resolving names/SMILES. However, it does not state when to use this tool versus alternatives such as pubchem_get_compound_details or pubchem_get_summary, nor does it give any exclusions.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Get descriptive summaries for PubChem entities by ID. Supports assays (AID), genes (Gene ID), proteins (UniProt accession), and taxonomy (Tax ID). Up to 10 per call.
| Name | Required | Description | Default |
|---|---|---|---|
| entityType | Yes | Entity type. Determines ID format and returned fields. | |
| identifiers | Yes | Entity identifiers (1-10). Type depends on entityType: - assay: AID (number), e.g. [1000] - gene: Gene ID (number), e.g. [1956] - protein: UniProt accession (string), e.g. ["P00533"] - taxonomy: Tax ID (number), e.g. [9606] |
| Name | Required | Description |
|---|---|---|
| error | No | Present when the call failed. Absent on success. |
| notice | No | Recovery guidance when one or more identifiers were not found. |
| summaries | No | Summary results. |
| entityType | No | Entity type queried. |
| foundCount | No | Identifiers resolved to a summary. |
| requestedCount | No | Identifiers requested. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, openWorldHint, and idempotentHint, covering the main safety and repeatability traits. The description adds 'Up to 10 per call,' but this repeats the schema maxItems and does not disclose new behavioral context beyond the structured data.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Two sentences with no filler. The main purpose is front-loaded, and the supported entity types are listed compactly without redundancy.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
The description covers the four entity categories and the batch limit, while the schema and output schema supply parameter and return details. It is sufficient for a read-only lookup tool, though it omits alternative-tool guidance entirely.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%, including detailed identifier formats for each entity type. The description's entity-type list is a useful high-level summary but does not add meaning beyond what the input schema already provides.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description states a clear verb and resource: 'Get descriptive summaries for PubChem entities by ID.' It also enumerates four supported entity types, which distinguishes it from compound-specific siblings like pubchem_get_compound_details.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
There is no guidance on when to use this tool versus sibling tools. It does not name alternatives or provide exclusions such as 'for detailed compound data, use pubchem_get_compound_details instead.'
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Find PubChem bioassays associated with a biological target. Search by gene symbol (e.g. "EGFR"), protein name, NCBI Gene ID, or UniProt accession. Returns a page of assay IDs (AIDs) — page past maxResults with offset — which can be explored further with pubchem_get_summary.
| Name | Required | Description | Default |
|---|---|---|---|
| offset | No | Zero-based index of the first AID to return. Pass the nextOffset from a previous call to read the following page. Default: 0. | |
| maxResults | No | Max AIDs to return per page (1-200). Popular targets may have thousands of assays; use offset to reach the ones past this page. Default: 50. | |
| targetType | Yes | Target identifier type. "genesymbol" and "proteinname" accept text names. "geneid" accepts NCBI Gene IDs. "proteinaccession" accepts UniProt accessions. | |
| targetQuery | Yes | Target identifier. Examples: "EGFR" (genesymbol), "Epidermal growth factor receptor" (proteinname), "1956" (geneid), "P00533" (proteinaccession). |
| Name | Required | Description |
|---|---|---|
| cap | No | The maxResults cap that was applied. |
| aids | No | PubChem Assay IDs. |
| error | No | Present when the call failed. Absent on success. |
| shown | No | AIDs returned on this page. |
| notice | No | Recovery guidance when no assays matched, when the offset runs past the result set, or when further pages remain. Absent when this page is complete and non-empty. |
| offset | No | Zero-based index of the first AID returned. |
| truncated | No | True when matching AIDs remain past this page. |
| nextOffset | No | Offset to pass on the next call to continue past this page. Omitted when no further AIDs match. |
| targetType | No | Target identifier type used: genesymbol, proteinname, geneid, or proteinaccession. |
| totalFound | No | Total AIDs found for this target, across all pages. |
| targetQuery | No | Target identifier searched. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, openWorldHint, and idempotentHint, covering safety and idempotency. The description adds value by disclosing the paginated return ('page of assay IDs'), how to page with offset, and the maxResults limit, which are behavioral details not present in the annotations. No contradictions exist.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
Two sentences with no redundancy. The purpose is front-loaded, the identifier types are listed, and the pagination/next-step info is concise. Every sentence earns its place.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
The description covers the tool's purpose, the input identifier types, the output (AIDs), pagination behavior, and the natural next step. An output schema exists, so detailed return fields are not needed. No critical gap remains for an agent to call it correctly.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema description coverage is 100%, so the schema already documents all four parameters with examples and ranges. The description reinforces the accepted target types but does not add substantive meaning beyond the schema. Baseline 3 is appropriate.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description states a specific verb ('Find'), a clear resource ('PubChem bioassays'), and the criteria ('associated with a biological target'), distinguishing it from sibling compound search tools. It also lists the accepted identifier types, making the tool's scope unambiguous.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description gives workflow context by noting returned AIDs 'can be explored further with pubchem_get_summary', implicitly indicating when to use this tool versus that one. However, it does not explicitly contrast it with sibling search tools like pubchem_search_compounds, so it falls just short of full exclusion guidance.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Search PubChem for chemical compounds by identifier (name, SMILES, or InChIKey, batched up to 25), molecular formula in Hill notation, substructure or superstructure containment, or 2D Tanimoto similarity. 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.
| Name | Required | Description | Default |
|---|---|---|---|
| query | No | Required for substructure/superstructure/similarity searches. A SMILES string (e.g. "CC(=O)O") or PubChem CID as a string (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; 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. | |
| 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. | |
| maxResults | No | Maximum CIDs to return per page (1-200). 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/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. | |
| identifiers | No | 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). | |
| identifierType | No | Required for identifier search. Type of chemical identifier: "name", "smiles", or "inchikey". | |
| allowOtherElements | No | Formula search only. When true, includes compounds with additional elements beyond the formula. |
| Name | Required | Description |
|---|---|---|
| cap | No | The maxResults cap that was applied. |
| 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, 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. |
| offset | No | Zero-based index of the first CID returned. |
| results | No | Matching compounds. |
| truncated | No | True when matching CIDs remain past this page. |
| nextOffset | No | Offset to pass on the next call to continue past this page. Omitted when no further matches remain. |
| searchType | No | Search strategy used: identifier, formula, substructure, superstructure, or similarity. |
| 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. |
| 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. |
Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?
Annotations already declare readOnlyHint, openWorldHint, and idempotentHint, so the description need not restate these. It adds behavioral context by mentioning pagination via offset and the option to hydrate properties to avoid a follow-up call. No contradictions with annotations exist. It does not discuss rate limits or error conditions, but these are not essential given the read-only, idempotent nature.
Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.
Is the description appropriately sized, front-loaded, and free of redundancy?
The description is exactly two sentences with no filler. It front-loads the core purpose and search types in the first sentence, then adds pagination and property hydration details in the second. Every phrase contributes to understanding the tool, and there is no redundancy or tangential information.
Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.
Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?
For a tool with five search modes and 11 parameters, the description provides a high-level overview of all major capabilities, including pagination and optional property hydration. The presence of an output schema and a fully descriptive input schema means the description does not need to repeat parameter details. It covers the essential aspects an agent needs to know to decide when and how to invoke the tool, though it does not delve into edge cases or error scenarios.
Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.
Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?
Schema coverage is 100%, so all parameters are already fully documented in the input schema. The description adds high-level context like 'batched up to 25' and 'Hill notation' and '2D Tanimoto similarity', but these details are also present in the schema's parameter descriptions. The description adds minimal additional meaning beyond what the schema provides, so a baseline of 3 is appropriate.
Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.
Does the description clearly state what the tool does and how it differs from similar tools?
The description explicitly states it searches PubChem for chemical compounds and enumerates all five search modes (identifier, formula, substructure, superstructure, similarity). It clearly distinguishes itself from sibling tools like pubchem_get_compound_details by noting it returns CIDs and can optionally hydrate properties to avoid a follow-up call. The verb 'search' plus resource 'PubChem' and specific search types make the purpose unmistakable.
Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.
Does the description explain when to use this tool, when not to, or what alternatives exist?
The description explicitly mentions that hydrating properties avoids a follow-up pubchem_get_compound_details call, which provides clear guidance on when to use this tool over that sibling. It also implies usage scenarios for each search type through its enumeration, though it does not explicitly state exclusions or when not to use it. The schema further details each search mode's requirements, so the guidance is largely sufficient.
Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
v0.6.5pubchem_get_bioactivity4 fields changedInput schema / properties / cid / exclusiveMinimumRemoved value: -0Input schema / properties / cid / minimumAdded value: +1Input schema / properties / targetGeneId / exclusiveMinimumRemoved value: -0Input schema / properties / targetGeneId / minimumAdded value: +1pubchem_get_compound_3d_structure6 fields changedInput schema / properties / cid / exclusiveMinimumRemoved value: -0Input schema / properties / cid / minimumAdded value: +1Input schema / properties / maxAtoms / exclusiveMinimumRemoved value: -0Input schema / properties / maxAtoms / minimumAdded value: +1Input schema / properties / maxBonds / exclusiveMinimumRemoved value: -0Input schema / properties / maxBonds / minimumAdded value: +1pubchem_get_compound_details2 fields changedInput schema / properties / cids / items / exclusiveMinimumRemoved value: -0Input schema / properties / cids / items / minimumAdded value: +1pubchem_get_compound_image2 fields changedInput schema / properties / cid / exclusiveMinimumRemoved value: -0Input schema / properties / cid / minimumAdded value: +1pubchem_get_compound_interactions2 fields changedInput schema / properties / cid / exclusiveMinimumRemoved value: -0Input schema / properties / cid / minimumAdded value: +1pubchem_get_compound_safety2 fields changedInput schema / properties / cids / items / exclusiveMinimumRemoved value: -0Input schema / properties / cids / items / minimumAdded value: +1pubchem_get_compound_xrefs2 fields changedInput schema / properties / cid / exclusiveMinimumRemoved value: -0Input schema / properties / cid / minimumAdded value: +1pubchem_search_compounds5 fields changedInput schema / properties / searchType / descriptionPrevious 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."Output schema / properties / error / properties / data / properties / reason / descriptionPrevious 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. `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."Output schema / properties / error / properties / data / properties / reason / examplesPrevious 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"
+]Output schema / properties / notice / descriptionPrevious 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."Output schema / properties / unresolvedIdentifiers / descriptionPrevious 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."v0.6.3pubchem_get_compound_3d_structure1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `no_3d_structure`: PubChem has no computed 3D conformer for the requested CID Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `no_3d_structure`: PubChem has no computed 3D conformer for the requested CID. Other values are possible when a failure originates below the handler."pubchem_get_compound_image1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `cid_not_found`: PubChem returned 404 for the requested CID Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `cid_not_found`: PubChem returned 404 for the requested CID. Other values are possible when a failure originates below the handler."pubchem_search_assays1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious value: -"Machine-readable failure mode. Declared by this tool: `blank_target_query`: targetQuery is empty or whitespace-only `invalid_geneid_query`: targetType is \"geneid\" but targetQuery is not a positive integer Other values are possible when a failure originates below the handler."New value: +"Machine-readable failure mode. Declared by this tool: `blank_target_query`: targetQuery is empty or whitespace-only. `invalid_geneid_query`: targetType is \"geneid\" but targetQuery is not a positive integer. Other values are possible when a failure originates below the handler."pubchem_search_compounds1 field changedOutput schema / properties / error / properties / data / properties / reason / descriptionPrevious 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."v0.6.2pubchem_get_compound_details26 fields changedOutput schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / hba / properties / pass / anyOfRemoved value: -[
- {
- "type": "boolean"
- },
- {
- "type": "null"
- }
-]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / hba / properties / pass / typeAdded value: +[
+ "boolean",
+ "null"
+]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / hba / properties / value / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / hba / properties / value / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / hbd / properties / pass / anyOfRemoved value: -[
- {
- "type": "boolean"
- },
- {
- "type": "null"
- }
-]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / hbd / properties / pass / typeAdded value: +[
+ "boolean",
+ "null"
+]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / hbd / properties / value / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / hbd / properties / value / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / mw / properties / pass / anyOfRemoved value: -[
- {
- "type": "boolean"
- },
- {
- "type": "null"
- }
-]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / mw / properties / pass / typeAdded value: +[
+ "boolean",
+ "null"
+]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / mw / properties / value / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / mw / properties / value / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / xLogP / properties / pass / anyOfRemoved value: -[
- {
- "type": "boolean"
- },
- {
- "type": "null"
- }
-]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / xLogP / properties / pass / typeAdded value: +[
+ "boolean",
+ "null"
+]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / xLogP / properties / value / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / xLogP / properties / value / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / compounds / items / properties / drugLikeness / properties / pass / anyOfRemoved value: -[
- {
- "type": "boolean"
- },
- {
- "type": "null"
- }
-]Output schema / properties / compounds / items / properties / drugLikeness / properties / pass / typeAdded value: +[
+ "boolean",
+ "null"
+]Output schema / properties / compounds / items / properties / drugLikeness / properties / veber / properties / rotatableBonds / properties / pass / anyOfRemoved value: -[
- {
- "type": "boolean"
- },
- {
- "type": "null"
- }
-]Output schema / properties / compounds / items / properties / drugLikeness / properties / veber / properties / rotatableBonds / properties / pass / typeAdded value: +[
+ "boolean",
+ "null"
+]Output schema / properties / compounds / items / properties / drugLikeness / properties / veber / properties / rotatableBonds / properties / value / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / compounds / items / properties / drugLikeness / properties / veber / properties / rotatableBonds / properties / value / typeAdded value: +[
+ "number",
+ "null"
+]Output schema / properties / compounds / items / properties / drugLikeness / properties / veber / properties / tpsa / properties / pass / anyOfRemoved value: -[
- {
- "type": "boolean"
- },
- {
- "type": "null"
- }
-]Output schema / properties / compounds / items / properties / drugLikeness / properties / veber / properties / tpsa / properties / pass / typeAdded value: +[
+ "boolean",
+ "null"
+]Output schema / properties / compounds / items / properties / drugLikeness / properties / veber / properties / tpsa / properties / value / anyOfRemoved value: -[
- {
- "type": "number"
- },
- {
- "type": "null"
- }
-]Output schema / properties / compounds / items / properties / drugLikeness / properties / veber / properties / tpsa / properties / value / typeAdded value: +[
+ "number",
+ "null"
+]v0.6.1pubchem_get_bioactivity6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "cid",
+ "totalAssays",
+ "activeCount",
+ "inactiveCount",
+ "results",
+ "outcomeFilter",
+ "filteredCount",
+ "returnedCount",
+ "offset"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded 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"
+}Output schema / requiredRemoved value: -[
- "cid",
- "totalAssays",
- "activeCount",
- "inactiveCount",
- "results",
- "outcomeFilter",
- "filteredCount",
- "returnedCount",
- "offset"
-]pubchem_get_compound_3d_structure6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "cid",
+ "atomCount",
+ "bondCount"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded 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: `no_3d_structure`: PubChem has no computed 3D conformer for the requested CID Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "no_3d_structure"
+ ],
+ "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"
+}Output schema / requiredRemoved value: -[
- "cid",
- "atomCount",
- "bondCount"
-]pubchem_get_compound_details7 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "compounds",
+ "truncated"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded 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"
+}Output schema / properties / truncatedAdded value: +{
+ "description": "True when this response is not the whole picture: a compound has further synonyms or descriptions past this page, or CIDs were skipped by the per-call fan-out limit. Per-compound totals are in compounds[].synonymsTotal / compounds[].descriptionsTotal; the skipped CIDs are in skippedCids.",
+ "type": "boolean"
+}Output schema / requiredRemoved value: -[
- "compounds"
-]pubchem_get_compound_image6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "cid",
+ "imageBase64",
+ "mimeType",
+ "width",
+ "height"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded 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: `cid_not_found`: PubChem returned 404 for the requested CID Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "cid_not_found"
+ ],
+ "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"
+}Output schema / requiredRemoved value: -[
- "cid",
- "imageBase64",
- "mimeType",
- "width",
- "height"
-]pubchem_get_compound_interactions7 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "cid",
+ "entries",
+ "paging",
+ "requestedKinds",
+ "returnedCount",
+ "truncated",
+ "offset"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded 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"
+}Output schema / properties / truncatedAdded 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"
+}Output schema / requiredRemoved value: -[
- "cid",
- "entries",
- "paging",
- "requestedKinds",
- "returnedCount",
- "offset"
-]pubchem_get_compound_safety6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "results",
+ "requestedCount",
+ "withDataCount"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded 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"
+}Output schema / requiredRemoved value: -[
- "results",
- "requestedCount",
- "withDataCount"
-]pubchem_get_compound_xrefs7 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "cid",
+ "xrefs",
+ "offset",
+ "truncated"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded 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"
+}Output schema / properties / truncatedAdded value: +{
+ "description": "True when at least one requested type has IDs remaining past this page. Which types, and how many IDs each holds in total, is in xrefs[].truncated / xrefs[].totalAvailable.",
+ "type": "boolean"
+}Output schema / requiredRemoved value: -[
- "cid",
- "xrefs",
- "offset"
-]pubchem_get_summary6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "entityType",
+ "summaries",
+ "requestedCount",
+ "foundCount"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded 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"
+}Output schema / requiredRemoved value: -[
- "entityType",
- "summaries",
- "requestedCount",
- "foundCount"
-]pubchem_search_assays6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "aids",
+ "targetType",
+ "targetQuery",
+ "totalFound",
+ "offset"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded 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: `blank_target_query`: targetQuery is empty or whitespace-only `invalid_geneid_query`: targetType is \"geneid\" but targetQuery is not a positive integer Other values are possible when a failure originates below the handler.",
+ "examples": [
+ "blank_target_query",
+ "invalid_geneid_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"
+}Output schema / requiredRemoved value: -[
- "aids",
- "targetType",
- "targetQuery",
- "totalFound",
- "offset"
-]pubchem_search_compounds6 fields changedInput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Input schema / additionalPropertiesAdded value: +falseOutput schema / $schemaPrevious value: -"http://json-schema.org/draft-07/schema#"New value: +"https://json-schema.org/draft/2020-12/schema"Output schema / anyOfAdded value: +[
+ {
+ "not": {
+ "required": [
+ "error"
+ ]
+ },
+ "required": [
+ "results",
+ "searchType",
+ "offset"
+ ]
+ },
+ {
+ "required": [
+ "error"
+ ]
+ }
+]Output schema / properties / errorAdded 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"
+}Output schema / requiredRemoved value: -[
- "results",
- "searchType",
- "offset"
-]v0.6.0pubchem_get_bioactivity10 fields changedInput schema / properties / maxResults / descriptionPrevious value: -"Max assay results to return (1-100). Well-studied compounds have thousands of records. Default: 20."New value: +"Max assay results to return per page (1-100). Well-studied compounds have thousands of records; use offset to reach the ones past this page. Default: 20."Input schema / properties / maxResults / typePrevious value: -"number"New value: +"integer"Input schema / properties / offsetAdded value: +{
+ "default": 0,
+ "description": "Zero-based index of the first assay to return, applied after the outcome and target filters. Pass the nextOffset from a previous call to read the following page. Default: 0.",
+ "maximum": 9007199254740991,
+ "minimum": 0,
+ "type": "integer"
+}Output schema / properties / filteredCount / descriptionPrevious value: -"Assays matching the outcome and target filters, before the maxResults cap."New value: +"Exact number of assays matching the outcome and target filters, across all pages."Output schema / properties / nextOffsetAdded value: +{
+ "description": "Offset to pass on the next call to continue past this page. Omitted when no further assays match.",
+ "type": "number"
+}Output schema / properties / offsetAdded value: +{
+ "description": "Zero-based index of the first assay returned.",
+ "type": "number"
+}Output schema / properties / returnedCount / descriptionPrevious value: -"Assays returned after the maxResults cap."New value: +"Assays returned on this page."Output schema / properties / shown / descriptionPrevious value: -"Assays returned after the maxResults cap."New value: +"Assays returned on this page."Output schema / properties / truncated / descriptionPrevious value: -"True when results were capped at maxResults — more matching assays exist."New value: +"True when matching assays remain past this page."Output schema / requiredPrevious value: -[
- "cid",
- "totalAssays",
- "activeCount",
- "inactiveCount",
- "results",
- "outcomeFilter",
- "filteredCount",
- "returnedCount"
-]New value: +[
+ "cid",
+ "totalAssays",
+ "activeCount",
+ "inactiveCount",
+ "results",
+ "outcomeFilter",
+ "filteredCount",
+ "returnedCount",
+ "offset"
+]pubchem_get_compound_3d_structure1 field changedInput schema / properties / includeAlternateConformerIds / descriptionPrevious value: -"List the IDs of additional computed conformers beyond the default. Adds one extra API call. Default: false."New value: +"List the IDs of additional computed conformers beyond the default. Slower than the default response. Default: false."pubchem_get_compound_details20 fields changedInput schema / properties / cids / descriptionPrevious value: -"PubChem Compound IDs to fetch (1-100). Batched efficiently. Resolve from names/SMILES with pubchem_search_compounds."New value: +"PubChem Compound IDs to fetch (1-100). Resolve from names/SMILES with pubchem_search_compounds."Input schema / properties / descriptionOffsetAdded value: +{
+ "default": 0,
+ "description": "Zero-based index of the first description to return within each compound's description list. The same offset is applied to every compound in the batch. Pass the nextDescriptionOffset from a previous call to read the following page. Default: 0.",
+ "maximum": 9007199254740991,
+ "minimum": 0,
+ "type": "integer"
+}Input schema / properties / includeClassification / descriptionPrevious value: -"Include pharmacological classification: FDA Established Pharmacologic Classes, mechanisms of action, MeSH classes, and ATC codes. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without classification."New value: +"Include pharmacological classification: FDA Established Pharmacologic Classes, mechanisms of action, MeSH classes, and ATC codes. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without classification and are listed in the response's skippedCids."Input schema / properties / includeDescription / descriptionPrevious value: -"Include textual descriptions (pharmacology, mechanism, therapeutic use) attributed by source. Well-studied compounds have many overlapping summaries — capped via maxDescriptions. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without descriptions."New value: +"Include textual descriptions (pharmacology, mechanism, therapeutic use) attributed by source. Well-studied compounds have many overlapping summaries — paged via descriptionOffset/maxDescriptions. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without descriptions and are listed in the response's skippedCids."Input schema / properties / includeDrugLikeness / descriptionPrevious value: -"Compute drug-likeness assessment: Lipinski Rule of Five (MW, XLogP, HBD, HBA) and Veber rules (TPSA, rotatable bonds). No extra API calls — computed from properties."New value: +"Compute drug-likeness assessment: Lipinski Rule of Five (MW, XLogP, HBD, HBA) and Veber rules (TPSA, rotatable bonds). Computed from the returned properties, so it adds no latency."Input schema / properties / includeSynonyms / descriptionPrevious value: -"Fetch all known names and synonyms (trade names, systematic names, registry numbers). One API call per CID — slower than the property batch for large CID lists."New value: +"Fetch known names and synonyms (trade names, systematic names, registry numbers), paged via synonymOffset/maxSynonyms. Fetched for every found CID in the batch. Slower for large CID lists."Input schema / properties / maxDescriptions / descriptionPrevious value: -"Max number of distinct description entries per compound (1-20). PubChem returns near-duplicate summaries from many depositors; we dedup and cap to keep responses focused. Default: 3."New value: +"Max number of distinct description entries per compound per page (1-20). PubChem returns near-duplicate summaries from many depositors; duplicates are collapsed before this cap applies. Default: 3."Input schema / properties / maxSynonyms / descriptionPrevious value: -"Max synonyms returned per compound (1-100). PubChem lists hundreds for common drugs; capped to keep the response focused. Default: 20."New value: +"Max synonyms returned per compound per page (1-100). PubChem lists hundreds for common drugs; use synonymOffset to reach the ones past this page. Default: 20."Input schema / properties / synonymOffsetAdded value: +{
+ "default": 0,
+ "description": "Zero-based index of the first synonym to return within each compound's synonym list. The same offset is applied to every compound in the batch. Pass the nextSynonymOffset from a previous call to read the following page. Default: 0.",
+ "maximum": 9007199254740991,
+ "minimum": 0,
+ "type": "integer"
+}Output schema / properties / compounds / items / properties / descriptions / descriptionPrevious value: -"Textual descriptions, deduplicated and capped at maxDescriptions. Each entry carries optional source attribution."New value: +"Textual descriptions on this page, deduplicated then windowed by descriptionOffset/maxDescriptions. Each entry carries optional source attribution. Empty when descriptionOffset runs past descriptionsTotal."Output schema / properties / compounds / items / properties / descriptionsTotal / descriptionPrevious value: -"Total distinct descriptions available before truncation. Larger than descriptions.length when more sources exist — increase maxDescriptions to see them."New value: +"Total distinct descriptions available for this compound, across all pages. Larger than descriptions.length when more sources exist — raise maxDescriptions or page with descriptionOffset to see them."Output schema / properties / compounds / items / properties / synonyms / descriptionPrevious value: -"Known names and synonyms."New value: +"Known names and synonyms on this page, windowed by synonymOffset/maxSynonyms. Empty when synonymOffset runs past synonymsTotal."Output schema / properties / compounds / items / properties / synonymsTotal / descriptionPrevious value: -"Total synonyms available before truncation. Larger than synonyms.length when more exist — increase maxSynonyms to see them."New value: +"Total synonyms available for this compound, across all pages. Larger than synonyms.length when more exist — raise maxSynonyms or page with synonymOffset to see them."Output schema / properties / descriptionOffsetAdded value: +{
+ "description": "Zero-based index of the first description returned within each compound's list. Present when includeDescription is true.",
+ "type": "number"
+}Output schema / properties / enrichedCidsAdded value: +{
+ "description": "CIDs whose descriptions and classification were fetched. Present only when the batch exceeded the per-call fan-out limit and other CIDs were skipped.",
+ "items": {
+ "type": "number"
+ },
+ "type": "array"
+}Output schema / properties / nextDescriptionOffsetAdded value: +{
+ "description": "descriptionOffset to pass on the next call to continue past this page. Omitted when no compound in the batch has further descriptions.",
+ "type": "number"
+}Output schema / properties / nextSynonymOffsetAdded value: +{
+ "description": "synonymOffset to pass on the next call to continue past this page. Omitted when no compound in the batch has further synonyms.",
+ "type": "number"
+}Output schema / properties / noticeAdded value: +{
+ "description": "Recovery guidance covering the skipped CIDs, an offset that runs past every compound, and pages that remain. Absent when nothing was skipped or truncated.",
+ "type": "string"
+}Output schema / properties / skippedCidsAdded value: +{
+ "description": "CIDs found in PubChem whose descriptions and classification were NOT fetched because the batch exceeded the per-call fan-out limit. Their absence from a record means \"not requested\", not \"PubChem has none\" — re-request these CIDs in a follow-up call. Present only when CIDs were skipped.",
+ "items": {
+ "type": "number"
+ },
+ "type": "array"
+}Output schema / properties / synonymOffsetAdded value: +{
+ "description": "Zero-based index of the first synonym returned within each compound's list. Present when includeSynonyms is true.",
+ "type": "number"
+}pubchem_get_compound_interactions8 fields changedInput schema / properties / maxEntries / descriptionPrevious 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."Input schema / properties / offsetAdded 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"
+}Output schema / properties / entries / items / properties / severityRemoved 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"
-}Output schema / properties / nextOffsetAdded 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"
+}Output schema / properties / notice / descriptionPrevious 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."Output schema / properties / offsetAdded value: +{
+ "description": "Zero-based start position read within each requested kind.",
+ "type": "number"
+}Output schema / properties / pagingAdded 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"
+}Output schema / requiredPrevious value: -[
- "cid",
- "entries",
- "requestedKinds",
- "returnedCount"
-]New value: +[
+ "cid",
+ "entries",
+ "paging",
+ "requestedKinds",
+ "returnedCount",
+ "offset"
+]pubchem_get_compound_safety6 fields changedOutput schema / properties / notice / descriptionPrevious value: -"Cross-tool guidance when one or more CIDs have no GHS data, pointing to an alternative source."New value: +"Recovery guidance when one or more CIDs returned no GHS data, listing the unrecognized CIDs to verify separately from the CIDs that exist but carry no deposited classification."Output schema / properties / results / items / properties / ghs / properties / precautionaryStatements / items / properties / decodedAdded value: +{
+ "description": "Whether \"statement\" carries the standard text. False for codes needing label-specific fill text the depositor must supply (disposal method, firefighting agent, first-aid reference) and for codes outside the decoder table; the code itself is still authoritative.",
+ "type": "boolean"
+}Output schema / properties / results / items / properties / ghs / properties / precautionaryStatements / items / properties / statement / descriptionPrevious value: -"Precautionary statement text."New value: +"Standard precautionary statement text for the code. Empty string when \"decoded\" is false — PubChem deposits P-codes without text, so a blank statement means the code was not decoded, never that the depositor supplied an empty statement."Output schema / properties / results / items / properties / ghs / properties / precautionaryStatements / items / requiredPrevious value: -[
- "code",
- "statement"
-]New value: +[
+ "code",
+ "statement",
+ "decoded"
+]Output schema / properties / results / items / properties / statusAdded value: +{
+ "description": "Outcome for this CID. \"ok\": GHS data returned. \"no_ghs_data\": the compound exists in PubChem but has no deposited GHS classification. \"cid_not_found\": PubChem has no record for this CID at all — the identifier is wrong, so verify it with pubchem_search_compounds rather than concluding the compound is unclassified.",
+ "enum": [
+ "ok",
+ "no_ghs_data",
+ "cid_not_found"
+ ],
+ "type": "string"
+}Output schema / properties / results / items / requiredPrevious value: -[
- "cid",
- "hasData"
-]New value: +[
+ "cid",
+ "hasData",
+ "status"
+]pubchem_get_compound_xrefs10 fields changedInput schema / properties / maxPerType / descriptionPrevious value: -"Max IDs to return per xref type (1-500). A compound may have thousands of PubMed references. Total count always reported. Default: 50."New value: +"Max IDs to return per xref type per page (1-500). A compound may have thousands of PubMed references; use offset to reach the ones past this page. Total count always reported. Default: 50."Input schema / properties / maxPerType / typePrevious value: -"number"New value: +"integer"Input schema / properties / offsetAdded value: +{
+ "default": 0,
+ "description": "Zero-based index of the first ID to return within each xref type. The same offset is applied to every requested type. Pass the nextOffset from a previous call to read the following page. Default: 0.",
+ "maximum": 9007199254740991,
+ "minimum": 0,
+ "type": "integer"
+}Output schema / properties / nextOffsetAdded value: +{
+ "description": "Offset to pass on the next call to continue past this page. Omitted when no requested type has further IDs.",
+ "type": "number"
+}Output schema / properties / notice / descriptionPrevious value: -"Recovery guidance when every requested xref type returned zero IDs — hints to verify the CID. Absent when any cross-references were found."New value: +"Recovery guidance when every requested xref type returned zero IDs, when the offset runs past every type, or when further pages remain. Absent when this page is complete and non-empty."Output schema / properties / offsetAdded value: +{
+ "description": "Zero-based index of the first ID returned within each type.",
+ "type": "number"
+}Output schema / properties / xrefs / items / properties / ids / descriptionPrevious value: -"Cross-reference IDs (capped by maxPerType)."New value: +"Cross-reference IDs on this page (window of offset + maxPerType)."Output schema / properties / xrefs / items / properties / totalAvailable / descriptionPrevious value: -"Total IDs available before truncation."New value: +"Total IDs available for this type, across all pages."Output schema / properties / xrefs / items / properties / truncated / descriptionPrevious value: -"Whether results were truncated."New value: +"True when IDs for this type remain past the current page."Output schema / requiredPrevious value: -[
- "cid",
- "xrefs"
-]New value: +[
+ "cid",
+ "xrefs",
+ "offset"
+]pubchem_get_summary1 field changedOutput schema / properties / summaries / items / properties / data / properties / lineage / descriptionPrevious value: -"Parent taxonomy lineage (taxonomy summaries)."New value: +"Taxonomic lineage ordered from the most inclusive rank to the most specific, e.g. [\"Eukaryota\", \"Metazoa\", \"Chordata\"] (taxonomy summaries). Ranks that do not apply to the entity are omitted."pubchem_search_assays10 fields changedInput schema / properties / maxResults / descriptionPrevious value: -"Max AIDs to return (1-200). Popular targets may have thousands of assays. Default: 50."New value: +"Max AIDs to return per page (1-200). Popular targets may have thousands of assays; use offset to reach the ones past this page. Default: 50."Input schema / properties / maxResults / typePrevious value: -"number"New value: +"integer"Input schema / properties / offsetAdded value: +{
+ "default": 0,
+ "description": "Zero-based index of the first AID to return. Pass the nextOffset from a previous call to read the following page. Default: 0.",
+ "maximum": 9007199254740991,
+ "minimum": 0,
+ "type": "integer"
+}Output schema / properties / nextOffsetAdded value: +{
+ "description": "Offset to pass on the next call to continue past this page. Omitted when no further AIDs match.",
+ "type": "number"
+}Output schema / properties / notice / descriptionPrevious value: -"Recovery guidance when no assays matched — echoes the target and suggests alternative search types. Absent when assays were returned."New value: +"Recovery guidance when no assays matched, when the offset runs past the result set, or when further pages remain. Absent when this page is complete and non-empty."Output schema / properties / offsetAdded value: +{
+ "description": "Zero-based index of the first AID returned.",
+ "type": "number"
+}Output schema / properties / shown / descriptionPrevious value: -"AIDs returned after the maxResults cap."New value: +"AIDs returned on this page."Output schema / properties / totalFound / descriptionPrevious value: -"Total AIDs found before the maxResults cap."New value: +"Total AIDs found for this target, across all pages."Output schema / properties / truncated / descriptionPrevious value: -"True when AIDs were capped at maxResults — more assays exist than returned."New value: +"True when matching AIDs remain past this page."Output schema / requiredPrevious value: -[
- "aids",
- "targetType",
- "targetQuery",
- "totalFound"
-]New value: +[
+ "aids",
+ "targetType",
+ "targetQuery",
+ "totalFound",
+ "offset"
+]pubchem_search_compounds11 fields changedInput schema / properties / maxResults / descriptionPrevious 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."Input schema / properties / maxResults / typePrevious value: -"number"New value: +"integer"Input schema / properties / offsetAdded 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"
+}Output schema / properties / nextOffsetAdded value: +{
+ "description": "Offset to pass on the next call to continue past this page. Omitted when no further matches remain.",
+ "type": "number"
+}Output schema / properties / notice / descriptionPrevious 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."Output schema / properties / offsetAdded value: +{
+ "description": "Zero-based index of the first CID returned.",
+ "type": "number"
+}Output schema / properties / shown / descriptionPrevious value: -"CIDs returned after the maxResults cap."New value: +"CIDs returned on this page."Output schema / properties / totalFound / descriptionPrevious value: -"Total CIDs found before the maxResults cap."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."Output schema / properties / totalFoundAtLeastAdded 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; page further with offset to observe more.",
+ "type": "number"
+}Output schema / properties / truncated / descriptionPrevious value: -"True when CIDs were capped at maxResults — more matches exist than returned."New value: +"True when matching CIDs remain past this page."Output schema / requiredPrevious value: -[
- "results",
- "searchType",
- "totalFound"
-]New value: +[
+ "results",
+ "searchType",
+ "offset"
+]v0.2.5pubchem_get_compound_3d_structure10 fields changedInput schema / properties / includeRawSdfAdded value: +{
+ "default": false,
+ "description": "For format=\"sdf\", return the complete raw V2000 SDF even when it exceeds the safe line cap. Default false: an SDF longer than 500 lines is line-capped with disclosure. No effect when format=\"json\".",
+ "type": "boolean"
+}Input schema / properties / maxAtomsAdded value: +{
+ "description": "Cap the atoms returned in the format=\"json\" preview. atomCount always reports the full total; omitted rows are disclosed via the truncated/shownAtoms enrichment. Defaults to the first 200 atoms.",
+ "exclusiveMinimum": 0,
+ "maximum": 9007199254740991,
+ "type": "integer"
+}Input schema / properties / maxBondsAdded value: +{
+ "description": "Cap the bonds returned in the format=\"json\" preview. bondCount always reports the full total; omitted rows are disclosed via the truncated/shownBonds enrichment. Defaults to the first 200 bonds.",
+ "exclusiveMinimum": 0,
+ "maximum": 9007199254740991,
+ "type": "integer"
+}Output schema / properties / atomCapAdded value: +{
+ "description": "The atom cap applied (explicit maxAtoms or the safe default), when the atom list was capped.",
+ "type": "number"
+}Output schema / properties / bondCapAdded value: +{
+ "description": "The bond cap applied (explicit maxBonds or the safe default), when the bond list was capped.",
+ "type": "number"
+}Output schema / properties / noticeAdded value: +{
+ "description": "Guidance naming which lists were capped and how to widen them.",
+ "type": "string"
+}Output schema / properties / shownAtomsAdded value: +{
+ "description": "Atoms returned after the cap, when fewer than atomCount. Raise maxAtoms for more.",
+ "type": "number"
+}Output schema / properties / shownBondsAdded value: +{
+ "description": "Bonds returned after the cap, when fewer than bondCount. Raise maxBonds for more.",
+ "type": "number"
+}Output schema / properties / shownSdfLinesAdded value: +{
+ "description": "SDF lines returned when format=\"sdf\" and the raw text was line-capped. Set includeRawSdf for the full record.",
+ "type": "number"
+}Output schema / properties / truncatedAdded value: +{
+ "description": "True when the atom list, bond list, or raw SDF was capped below its total. atomCount/bondCount always report the full totals.",
+ "type": "boolean"
+}pubchem_get_compound_details2 fields changedInput schema / properties / maxSynonymsAdded value: +{
+ "default": 20,
+ "description": "Max synonyms returned per compound (1-100). PubChem lists hundreds for common drugs; capped to keep the response focused. Default: 20.",
+ "maximum": 100,
+ "minimum": 1,
+ "type": "integer"
+}Output schema / properties / compounds / items / properties / synonymsTotalAdded value: +{
+ "description": "Total synonyms available before truncation. Larger than synonyms.length when more exist — increase maxSynonyms to see them.",
+ "type": "number"
+}pubchem_get_compound_xrefs1 field changedOutput schema / properties / noticeAdded value: +{
+ "description": "Recovery guidance when every requested xref type returned zero IDs — hints to verify the CID. Absent when any cross-references were found.",
+ "type": "string"
+}pubchem_search_compounds1 field changedOutput schema / properties / unresolvedIdentifiersAdded 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"
+}v0.2.4pubchem_get_bioactivity3 fields changedOutput schema / properties / capAdded value: +{
+ "description": "The maxResults cap that was applied.",
+ "type": "number"
+}Output schema / properties / shownAdded value: +{
+ "description": "Assays returned after the maxResults cap.",
+ "type": "number"
+}Output schema / properties / truncatedAdded value: +{
+ "description": "True when results were capped at maxResults — more matching assays exist.",
+ "type": "boolean"
+}pubchem_search_assays3 fields changedOutput schema / properties / capAdded value: +{
+ "description": "The maxResults cap that was applied.",
+ "type": "number"
+}Output schema / properties / shownAdded value: +{
+ "description": "AIDs returned after the maxResults cap.",
+ "type": "number"
+}Output schema / properties / truncatedAdded value: +{
+ "description": "True when AIDs were capped at maxResults — more assays exist than returned.",
+ "type": "boolean"
+}pubchem_search_compounds3 fields changedOutput schema / properties / capAdded value: +{
+ "description": "The maxResults cap that was applied.",
+ "type": "number"
+}Output schema / properties / shownAdded value: +{
+ "description": "CIDs returned after the maxResults cap.",
+ "type": "number"
+}Output schema / properties / truncatedAdded value: +{
+ "description": "True when CIDs were capped at maxResults — more matches exist than returned.",
+ "type": "boolean"
+}v0.2.2pubchem_get_bioactivity8 fields changedInput schema / properties / targetAccessionAdded value: +{
+ "description": "Filter to assays against this target protein accession (UniProt/GenBank), e.g. \"P35354\". Obtain accessions from pubchem_search_assays or the targetAccession field of an unfiltered result here.",
+ "type": "string"
+}Input schema / properties / targetGeneIdAdded value: +{
+ "description": "Filter to assays against this NCBI Gene ID. Obtain Gene IDs from pubchem_search_assays or the targetGeneId field of an unfiltered result here. Combine with outcomeFilter=\"active\" to answer \"is this compound active against target T?\".",
+ "exclusiveMinimum": 0,
+ "maximum": 9007199254740991,
+ "type": "integer"
+}Output schema / properties / filteredCountAdded value: +{
+ "description": "Assays matching the outcome and target filters, before the maxResults cap.",
+ "type": "number"
+}Output schema / properties / noticeAdded value: +{
+ "description": "Recovery guidance when the filter yields no results or the compound has no bioactivity data.",
+ "type": "string"
+}Output schema / properties / outcomeFilterAdded value: +{
+ "description": "Outcome filter applied: active, inactive, or all.",
+ "type": "string"
+}Output schema / properties / returnedCountAdded value: +{
+ "description": "Assays returned after the maxResults cap.",
+ "type": "number"
+}Output schema / properties / targetFilterAdded value: +{
+ "description": "Target filter applied (gene ID and/or protein accession), when set.",
+ "type": "string"
+}Output schema / requiredPrevious value: -[
- "cid",
- "totalAssays",
- "activeCount",
- "inactiveCount",
- "results"
-]New value: +[
+ "cid",
+ "totalAssays",
+ "activeCount",
+ "inactiveCount",
+ "results",
+ "outcomeFilter",
+ "filteredCount",
+ "returnedCount"
+]pubchem_get_compound_3d_structurepubchem_get_compound_interactionspubchem_get_compound_safety12 fields changedInput schema / properties / cidRemoved value: -{
- "description": "PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds.",
- "exclusiveMinimum": 0,
- "maximum": 9007199254740991,
- "type": "integer"
-}Input schema / properties / cidsAdded value: +{
+ "description": "PubChem Compound IDs to fetch safety data for (1-25). Resolve from names/SMILES with pubchem_search_compounds.",
+ "items": {
+ "exclusiveMinimum": 0,
+ "maximum": 9007199254740991,
+ "type": "integer"
+ },
+ "maxItems": 25,
+ "minItems": 1,
+ "type": "array"
+}Input schema / requiredPrevious value: -[
- "cid"
-]New value: +[
+ "cids"
+]Output schema / properties / cidRemoved value: -{
- "description": "PubChem Compound ID.",
- "type": "number"
-}Output schema / properties / ghsRemoved value: -{
- "additionalProperties": false,
- "description": "GHS classification data.",
- "properties": {
- "hazardStatements": {
- "description": "GHS hazard statements.",
- "items": {
- "additionalProperties": false,
- "description": "GHS hazard statement entry.",
- "properties": {
- "code": {
- "description": "H-code (e.g. \"H225\").",
- "type": "string"
- },
- "statement": {
- "description": "Hazard statement text.",
- "type": "string"
- }
- },
- "required": [
- "code",
- "statement"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "pictograms": {
- "description": "GHS pictogram labels (e.g. \"Flammable\", \"Toxic\").",
- "items": {
- "type": "string"
- },
- "type": "array"
- },
- "precautionaryStatements": {
- "description": "GHS precautionary statements.",
- "items": {
- "additionalProperties": false,
- "description": "GHS precautionary statement entry.",
- "properties": {
- "code": {
- "description": "P-code (e.g. \"P210\").",
- "type": "string"
- },
- "statement": {
- "description": "Precautionary statement text.",
- "type": "string"
- }
- },
- "required": [
- "code",
- "statement"
- ],
- "type": "object"
- },
- "type": "array"
- },
- "signalWord": {
- "description": "GHS signal word: \"Danger\" or \"Warning\".",
- "type": "string"
- }
- },
- "required": [
- "pictograms",
- "hazardStatements",
- "precautionaryStatements"
- ],
- "type": "object"
-}Output schema / properties / hasDataRemoved value: -{
- "description": "Whether GHS safety data is available for this compound.",
- "type": "boolean"
-}Output schema / properties / noticeAdded value: +{
+ "description": "Cross-tool guidance when one or more CIDs have no GHS data, pointing to an alternative source.",
+ "type": "string"
+}Output schema / properties / requestedCountAdded value: +{
+ "description": "CIDs requested.",
+ "type": "number"
+}Output schema / properties / resultsAdded value: +{
+ "description": "Safety results, one per requested CID (input order preserved).",
+ "items": {
+ "additionalProperties": false,
+ "description": "Per-CID safety result.",
+ "properties": {
+ "cid": {
+ "description": "PubChem Compound ID.",
+ "type": "number"
+ },
+ "ghs": {
+ "additionalProperties": false,
+ "description": "GHS classification data.",
+ "properties": {
+ "hazardStatements": {
+ "description": "GHS hazard statements.",
+ "items": {
+ "additionalProperties": false,
+ "description": "GHS hazard statement entry.",
+ "properties": {
+ "code": {
+ "description": "H-code (e.g. \"H225\").",
+ "type": "string"
+ },
+ "statement": {
+ "description": "Hazard statement text.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "statement"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "pictograms": {
+ "description": "GHS pictogram labels (e.g. \"Flammable\", \"Toxic\").",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "precautionaryStatements": {
+ "description": "GHS precautionary statements.",
+ "items": {
+ "additionalProperties": false,
+ "description": "GHS precautionary statement entry.",
+ "properties": {
+ "code": {
+ "description": "P-code (e.g. \"P210\").",
+ "type": "string"
+ },
+ "statement": {
+ "description": "Precautionary statement text.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "code",
+ "statement"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+ },
+ "signalWord": {
+ "description": "GHS signal word: \"Danger\" or \"Warning\".",
+ "type": "string"
+ }
+ },
+ "required": [
+ "pictograms",
+ "hazardStatements",
+ "precautionaryStatements"
+ ],
+ "type": "object"
+ },
+ "hasData": {
+ "description": "Whether GHS safety data is available for this compound.",
+ "type": "boolean"
+ },
+ "source": {
+ "description": "Data source attribution.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "cid",
+ "hasData"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+}Output schema / properties / sourceRemoved value: -{
- "description": "Data source attribution.",
- "type": "string"
-}Output schema / properties / withDataCountAdded value: +{
+ "description": "CIDs with GHS safety data available.",
+ "type": "number"
+}Output schema / requiredPrevious value: -[
- "cid",
- "hasData"
-]New value: +[
+ "results",
+ "requestedCount",
+ "withDataCount"
+]pubchem_get_summary4 fields changedOutput schema / properties / foundCountAdded value: +{
+ "description": "Identifiers resolved to a summary.",
+ "type": "number"
+}Output schema / properties / noticeAdded value: +{
+ "description": "Recovery guidance when one or more identifiers were not found.",
+ "type": "string"
+}Output schema / properties / requestedCountAdded value: +{
+ "description": "Identifiers requested.",
+ "type": "number"
+}Output schema / requiredPrevious value: -[
- "entityType",
- "summaries"
-]New value: +[
+ "entityType",
+ "summaries",
+ "requestedCount",
+ "foundCount"
+]v0.1.22pubchem_get_bioactivity6 fields changedInput schema / properties / cid / descriptionPrevious value: -"PubChem Compound ID."New value: +"PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds."Output schema / properties / results / items / descriptionAdded value: +"Assay result entry."Output schema / properties / results / items / properties / activityValues / items / descriptionAdded value: +"Quantitative activity measurement entry."Output schema / properties / results / items / properties / activityValues / items / properties / name / descriptionPrevious value: -"Measurement name (e.g. IC50, EC50, Ki)."New value: +"Measurement name (e.g. IC50, EC50, Ki). Omitted when not reported."Output schema / properties / results / items / properties / activityValues / items / properties / unit / descriptionPrevious value: -"Unit of measurement (e.g. uM, nM)."New value: +"Unit of measurement (e.g. uM, nM). Omitted when not reported."Output schema / properties / results / items / properties / activityValues / items / requiredPrevious value: -[
- "name",
- "value",
- "unit"
-]New value: +[
+ "value"
+]pubchem_get_compound_details19 fields changedInput schema / properties / cids / descriptionPrevious value: -"PubChem Compound IDs to fetch (1-100). Batched efficiently."New value: +"PubChem Compound IDs to fetch (1-100). Batched efficiently. Resolve from names/SMILES with pubchem_search_compounds."Input schema / properties / includeClassification / descriptionPrevious value: -"Fetch pharmacological classification from PUG View: FDA Established Pharmacologic Classes, mechanisms of action, MeSH classes, and ATC codes. Adds one API call per CID — consider limiting CID count when enabled."New value: +"Include pharmacological classification: FDA Established Pharmacologic Classes, mechanisms of action, MeSH classes, and ATC codes. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without classification."Input schema / properties / includeDescription / descriptionPrevious value: -"Fetch textual description from PUG View (pharmacology, mechanism, therapeutic use). Adds one API call per CID — consider limiting CID count when enabled."New value: +"Include textual descriptions (pharmacology, mechanism, therapeutic use) attributed by source. Well-studied compounds have many overlapping summaries — capped via maxDescriptions. Fetched only for the first 10 CIDs in the batch; remaining CIDs return without descriptions."Input schema / properties / includeSynonyms / descriptionPrevious value: -"Fetch all known names and synonyms (trade names, systematic names, registry numbers)."New value: +"Fetch all known names and synonyms (trade names, systematic names, registry numbers). One API call per CID — slower than the property batch for large CID lists."Input schema / properties / maxDescriptionsAdded value: +{
+ "default": 3,
+ "description": "Max number of distinct description entries per compound (1-20). PubChem returns near-duplicate summaries from many depositors; we dedup and cap to keep responses focused. Default: 3.",
+ "maximum": 20,
+ "minimum": 1,
+ "type": "integer"
+}Output schema / properties / compounds / items / descriptionAdded value: +"Per-CID compound detail record."Output schema / properties / compounds / items / properties / classification / properties / atcCodes / items / descriptionAdded value: +"ATC code entry with hierarchical description."Output schema / properties / compounds / items / properties / descriptionRemoved value: -{
- "description": "Textual description from PUG View.",
- "type": "string"
-}Output schema / properties / compounds / items / properties / descriptionsAdded value: +{
+ "description": "Textual descriptions, deduplicated and capped at maxDescriptions. Each entry carries optional source attribution.",
+ "items": {
+ "additionalProperties": false,
+ "description": "Description entry with optional source attribution.",
+ "properties": {
+ "source": {
+ "description": "Depositor source (e.g. \"DrugBank\", \"Wikipedia\", \"ChEBI\").",
+ "type": "string"
+ },
+ "text": {
+ "description": "Description text.",
+ "type": "string"
+ }
+ },
+ "required": [
+ "text"
+ ],
+ "type": "object"
+ },
+ "type": "array"
+}Output schema / properties / compounds / items / properties / descriptionsTotalAdded value: +{
+ "description": "Total distinct descriptions available before truncation. Larger than descriptions.length when more sources exist — increase maxDescriptions to see them.",
+ "type": "number"
+}Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / mw / descriptionPrevious value: -"Molecular weight rule (≤500)."New value: +"Molecular weight rule (≤500 g/mol)."Output schema / properties / compounds / items / properties / drugLikeness / properties / lipinski / properties / xLogP / descriptionPrevious value: -"XLogP rule (≤5)."New value: +"XLogP rule (≤5; calculated logP)."Output schema / properties / compounds / items / properties / drugLikeness / properties / pass / anyOfAdded value: +[
+ {
+ "type": "boolean"
+ },
+ {
+ "type": "null"
+ }
+]Output schema / properties / compounds / items / properties / drugLikeness / properties / pass / descriptionPrevious value: -"Overall drug-likeness pass."New value: +"Overall drug-likeness pass. Null when insufficient properties were available."Output schema / properties / compounds / items / properties / drugLikeness / properties / pass / typeRemoved value: -"boolean"Output schema / properties / compounds / items / properties / drugLikeness / properties / veber / properties / tpsa / descriptionPrevious value: -"TPSA rule (≤140)."New value: +"Topological polar surface area rule (≤140 Ų)."Output schema / properties / compounds / items / properties / foundAdded value: +{
+ "description": "False when the CID does not exist in PubChem (properties, description, etc. are empty).",
+ "type": "boolean"
+}Output schema / properties / compounds / items / properties / properties / descriptionPrevious value: -"Requested physicochemical properties."New value: +"Physicochemical properties keyed by name (echoes input.properties or the default core set; drug-likeness inputs are appended automatically when includeDrugLikeness is true)."Output schema / properties / compounds / items / requiredPrevious value: -[
- "cid",
- "properties"
-]New value: +[
+ "cid",
+ "found",
+ "properties"
+]pubchem_get_compound_image2 fields changedInput schema / properties / cid / descriptionPrevious value: -"PubChem Compound ID."New value: +"PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds."Output schema / properties / mimeType / descriptionPrevious value: -"Image MIME type."New value: +"MIME type — always \"image/png\"."pubchem_get_compound_safety3 fields changedInput schema / properties / cid / descriptionPrevious value: -"PubChem Compound ID."New value: +"PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds."Output schema / properties / ghs / properties / hazardStatements / items / descriptionAdded value: +"GHS hazard statement entry."Output schema / properties / ghs / properties / precautionaryStatements / items / descriptionAdded value: +"GHS precautionary statement entry."pubchem_get_compound_xrefs7 fields changedInput schema / properties / cid / descriptionPrevious value: -"PubChem Compound ID."New value: +"PubChem Compound ID. Resolve from name/SMILES with pubchem_search_compounds."Input schema / properties / maxPerType / descriptionPrevious value: -"Max IDs to return per xref type (1-500). A compound may have thousands of PubMed references — this cap prevents bloat. Total count always reported. Default: 50."New value: +"Max IDs to return per xref type (1-500). A compound may have thousands of PubMed references. Total count always reported. Default: 50."Input schema / properties / xrefTypes / descriptionPrevious value: -"Cross-reference types to retrieve. Options: RegistryID, RN (CAS numbers), PubMedID, PatentID, GeneID, ProteinGI, TaxonomyID."New value: +"Cross-reference types to retrieve. String IDs: RegistryID (DSSTox/EPA registry numbers), RN (CAS numbers), PatentID. Numeric IDs: PubMedID, GeneID (NCBI Gene), ProteinGI (legacy NCBI Protein GI), TaxonomyID."Output schema / properties / xrefs / items / descriptionAdded value: +"Cross-reference group for one type."Output schema / properties / xrefs / items / properties / ids / items / anyOfPrevious value: -[
- {
- "type": "string"
- },
- {
- "type": "number"
- }
-]New value: +[
+ {
+ "description": "String-form cross-reference ID (e.g. CAS number, patent).",
+ "type": "string"
+ },
+ {
+ "description": "Numeric cross-reference ID (e.g. PubMed ID, Gene ID).",
+ "type": "number"
+ }
+]Output schema / properties / xrefs / items / properties / ids / items / descriptionAdded value: +"Cross-reference identifier — string or number depending on type."Output schema / properties / xrefs / items / properties / type / descriptionPrevious value: -"Cross-reference type."New value: +"Cross-reference type: RegistryID, RN, PubMedID, PatentID, GeneID, ProteinGI, or TaxonomyID."pubchem_get_summary8 fields changedInput schema / properties / identifiers / items / anyOfPrevious value: -[
- {
- "type": "string"
- },
- {
- "type": "number"
- }
-]New value: +[
+ {
+ "description": "String identifier (e.g. UniProt accession).",
+ "type": "string"
+ },
+ {
+ "description": "Numeric identifier (e.g. AID, Gene ID, Tax ID).",
+ "type": "number"
+ }
+]Input schema / properties / identifiers / items / descriptionAdded value: +"Entity identifier — string or number depending on entityType."Output schema / properties / summaries / items / descriptionAdded value: +"Per-identifier summary result."Output schema / properties / summaries / items / properties / data / additionalPropertiesPrevious value: -{}New value: +falseOutput schema / properties / summaries / items / properties / data / descriptionPrevious value: -"Entity summary data (shape varies by type)."New value: +"Entity summary data. Populated fields depend on entityType."Output schema / properties / summaries / items / properties / data / propertiesAdded value: +{
+ "aid": {
+ "description": "Assay ID — present on assay summaries.",
+ "type": "number"
+ },
+ "commonName": {
+ "description": "Common name (taxonomy summaries).",
+ "type": "string"
+ },
+ "description": {
+ "description": "Descriptive text when available.",
+ "type": "string"
+ },
+ "geneId": {
+ "description": "NCBI Gene ID (gene summaries).",
+ "type": "number"
+ },
+ "lineage": {
+ "description": "Parent taxonomy lineage (taxonomy summaries).",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "name": {
+ "description": "Primary display name.",
+ "type": "string"
+ },
+ "numActive": {
+ "description": "Substances marked active (assay summaries).",
+ "type": "number"
+ },
+ "numSubstances": {
+ "description": "Substances tested (assay summaries).",
+ "type": "number"
+ },
+ "proteinAccession": {
+ "description": "Protein accession (protein summaries).",
+ "type": "string"
+ },
+ "rank": {
+ "description": "Taxonomic rank (taxonomy summaries).",
+ "type": "string"
+ },
+ "scientificName": {
+ "description": "Scientific name (taxonomy summaries).",
+ "type": "string"
+ },
+ "sourceName": {
+ "description": "Data source attribution (assay summaries).",
+ "type": "string"
+ },
+ "symbol": {
+ "description": "Gene symbol (gene summaries).",
+ "type": "string"
+ },
+ "synonyms": {
+ "description": "Known synonyms / other names.",
+ "items": {
+ "type": "string"
+ },
+ "type": "array"
+ },
+ "taxonomy": {
+ "description": "Taxonomy scientific name (gene/protein summaries).",
+ "type": "string"
+ },
+ "taxonomyId": {
+ "description": "NCBI Taxonomy ID (gene/protein/taxonomy summaries).",
+ "type": "number"
+ }
+}Output schema / properties / summaries / items / properties / data / propertyNamesRemoved value: -{
- "type": "string"
-}Output schema / properties / summaries / items / properties / identifier / anyOfPrevious value: -[
- {
- "type": "string"
- },
- {
- "type": "number"
- }
-]New value: +[
+ {
+ "description": "String identifier (e.g. UniProt accession).",
+ "type": "string"
+ },
+ {
+ "description": "Numeric identifier (e.g. AID, Gene ID, Tax ID).",
+ "type": "number"
+ }
+]pubchem_search_assays4 fields changedOutput schema / properties / noticeAdded value: +{
+ "description": "Recovery guidance when no assays matched — echoes the target and suggests alternative search types. Absent when assays were returned.",
+ "type": "string"
+}Output schema / properties / targetType / descriptionPrevious value: -"Target identifier type used."New value: +"Target identifier type used: genesymbol, proteinname, geneid, or proteinaccession."Output schema / properties / totalFound / descriptionPrevious value: -"Total AIDs found."New value: +"Total AIDs found before the maxResults cap."Output schema / requiredPrevious value: -[
- "targetType",
- "targetQuery",
- "totalFound",
- "aids"
-]New value: +[
+ "aids",
+ "targetType",
+ "targetQuery",
+ "totalFound"
+]pubchem_search_compounds9 fields changedInput schema / properties / identifiers / descriptionPrevious 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)."Input schema / properties / query / descriptionPrevious 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\")."Input schema / properties / searchType / descriptionPrevious 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."Output schema / properties / noticeAdded value: +{
+ "description": "Recovery guidance when no compounds matched — echoes search strategy and suggests how to broaden. Absent when results were returned.",
+ "type": "string"
+}Output schema / properties / results / items / descriptionAdded value: +"Matching compound entry."Output schema / properties / results / items / properties / properties / descriptionPrevious value: -"Compound properties when requested."New value: +"Compound properties keyed by name (echoes input.properties; only present when requested)."Output schema / properties / searchType / descriptionPrevious value: -"The search strategy used."New value: +"Search strategy used: identifier, formula, substructure, superstructure, or similarity."Output schema / properties / totalFound / descriptionPrevious value: -"Total CIDs found (before maxResults cap)."New value: +"Total CIDs found before the maxResults cap."Output schema / requiredPrevious value: -[
- "searchType",
- "totalFound",
- "results"
-]New value: +[
+ "results",
+ "searchType",
+ "totalFound"
+]v0.1.11pubchem_get_bioactivitypubchem_get_compound_detailspubchem_get_compound_imagepubchem_get_compound_safetypubchem_get_compound_xrefspubchem_get_summarypubchem_search_assayspubchem_search_compoundsScored across 10 tools
Several tools overlap in purpose: 'pubchem_get_bioactivity' and 'pubchem_get_compound_interactions' both return activity/target data, with interactions including bioactivity-like entries. Also, 'pubchem_get_summary' and 'pubchem_get_compound_details' both provide descriptive info for compounds, though summary supports other entities. The distinction between bioactivity and interactions is particularly blurry for agents.
All tools follow a consistent pattern: 'pubchem_' prefix followed by a verb ('get', 'search') and a target object ('compound', 'assays', 'summary'), with specific qualifiers. For example, 'pubchem_get_compound_details', 'pubchem_get_compound_image', 'pubchem_get_bioactivity'. No mixed naming conventions or irregular verbs.
With 10 tools, the count is within the ideal range (3-15) and each tool serves a distinct data retrieval purpose. However, some tools like 'pubchem_get_compound_3d_structure' and 'pubchem_get_compound_image' are narrow utilities, but they still cover necessary compound data. No obvious bloat or excessive specialization.
The tool set is heavily focused on reading/querying compound data, covering search, details, images, structures, safety, bioactivity, interactions, and summaries. Missing operations include any update/delete (not applicable for a database), but more importantly, there's no tool for getting compound synonyms directly (only via details with synonyms flag), and no tool for retrieving patents or other xrefs beyond what's in xrefs. The lack of a direct 'get_compound_by_name' is a gap; search requires a separate step. Also, no support for handling mixtures or salts explicitly. Overall, core lookup is covered but some ancillary data types are missing.
Link compounds to protein targets, rank bioactivity, and look up drug mechanisms and indications.
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