@cyanheads/pubchem-mcp-server 0.1.23 → 0.2.0

package/README.md

@@ -1,13 +1,13 @@
 <div align="center">
   <h1>@cyanheads/pubchem-mcp-server</h1>
   <p><b>MCP server for the PubChem chemical database. Search compounds, fetch properties, safety data, bioactivity, cross-references, and entity summaries. STDIO & Streamable HTTP.</b>
-  <div>8 Tools</div>
+  <div>10 Tools • 6 Resources</div>
   </p>
 </div>
 
 <div align="center">
 
-[![Version](https://img.shields.io/badge/Version-0.1.23-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubchem-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubchem-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubchem-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.3.0-f472b6.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-0.2.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubchem-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubchem-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubchem-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-^1.3.0-f472b6.svg?style=flat-square)](https://bun.sh/)
 
 </div>
 
@@ -29,16 +29,18 @@
 
 ## Tools
 
-Eight tools for querying PubChem's chemical information database:
+Ten tools for querying PubChem's chemical information database:
 
 | Tool Name | Description |
 |:----------|:------------|
 | `pubchem_search_compounds` | Search for compounds by name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity. |
 | `pubchem_get_compound_details` | Get physicochemical properties, descriptions, synonyms, drug-likeness, and classification for compounds by CID. |
 | `pubchem_get_compound_image` | Fetch a 2D structure diagram (PNG) for a compound by CID. |
-| `pubchem_get_compound_safety` | Get GHS hazard classification and safety data for a compound. |
+| `pubchem_get_compound_3d_structure` | Fetch a 3D conformer (atomic coordinates and bonds) for a compound by CID, as parsed JSON or raw SDF. |
 | `pubchem_get_compound_xrefs` | Get external database cross-references (PubMed, patents, genes, proteins, etc.). |
-| `pubchem_get_bioactivity` | Get a compound's bioactivity profile: assay results, targets, and activity values. |
+| `pubchem_get_compound_safety` | Get GHS hazard classification and safety data for one or more compounds by CID (batch). |
+| `pubchem_get_bioactivity` | Get a compound's bioactivity profile: assay results, targets, and activity values; filter by outcome or molecular target. |
+| `pubchem_get_compound_interactions` | Get drug-drug, drug-food, and chemical-target interactions for a compound by CID. |
 | `pubchem_search_assays` | Find bioassays by biological target (gene symbol, protein, Gene ID, UniProt accession). |
 | `pubchem_get_summary` | Get summaries for PubChem entities: assays, genes, proteins, taxonomy. |
 
@@ -72,7 +74,7 @@ Get detailed compound information by CID.
 Get a compound's bioactivity profile from PubChem BioAssay.
 
 - Returns assay outcomes (Active/Inactive/Inconclusive), target info (protein accessions, NCBI Gene IDs), and quantitative values (IC50, EC50, Ki)
-- Filter by outcome to focus on active results
+- Filter by outcome and/or a specific molecular target (NCBI Gene ID or protein accession)
 - Caps at 100 results per request (well-studied compounds may have thousands)
 
 ---
@@ -85,6 +87,39 @@ Get descriptive summaries for four PubChem entity types.
 - Up to 10 entities per call
 - Type-specific field extraction for clean, structured output
 
+---
+
+### `pubchem_get_compound_interactions`
+
+Get a compound's interaction data by CID.
+
+- Drug-drug interactions (DrugBank), drug-food interactions, and chemical-target binding/activity (BindingDB, ChEMBL, and others)
+- Select which interaction kinds to fetch and cap entries per kind
+- Each entry carries its originating source — coverage is richest for approved drugs
+
+---
+
+### `pubchem_get_compound_3d_structure`
+
+Get a compound's default 3D conformer by CID.
+
+- `format="json"` returns parsed atoms (element + x/y/z) and bonds for direct reasoning; `format="sdf"` returns raw V2000 SDF for passthrough to docking or rendering
+- Optionally lists alternate conformer IDs
+- Returns a typed not-found when PubChem has no computed 3D coordinates (large molecules, mixtures, some salts)
+
+## Resources
+
+Compound and assay records are also exposed as URI-templated MCP resources, backed by the same client methods as the tools:
+
+| URI Template | Returns |
+|:-------------|:--------|
+| `pubchem://compound/{cid}` | Core physicochemical properties (JSON). |
+| `pubchem://compound/{cid}/safety` | GHS hazard classification (JSON). |
+| `pubchem://compound/{cid}/image` | 2D structure diagram (PNG). |
+| `pubchem://compound/{cid}/xrefs` | External cross-references (JSON). |
+| `pubchem://compound/{cid}/bioactivity` | Bioassay activity profile (JSON). |
+| `pubchem://assay/{aid}` | BioAssay summary (JSON). |
+
 ## Features
 
 Built on [`@cyanheads/mcp-ts-core`](https://github.com/cyanheads/mcp-ts-core):
@@ -111,7 +146,7 @@ A public instance is available at `https://pubchem.caseyjhand.com/mcp` — no in
 ```json
 {
   "mcpServers": {
-    "pubchem": {
+    "pubchem-mcp-server": {
       "type": "streamable-http",
       "url": "https://pubchem.caseyjhand.com/mcp"
     }
@@ -126,7 +161,7 @@ Add to your MCP client config (e.g., `claude_desktop_config.json`):
 ```json
 {
   "mcpServers": {
-    "pubchem": {
+    "pubchem-mcp-server": {
       "type": "stdio",
       "command": "bunx",
       "args": ["@cyanheads/pubchem-mcp-server@latest"],

package/dist/index.js

@@ -5,11 +5,13 @@
  * @module index
  */
 import { createApp } from '@cyanheads/mcp-ts-core';
+import { allResourceDefinitions } from './mcp-server/resources/definitions/index.js';
 import { allToolDefinitions } from './mcp-server/tools/definitions/index.js';
 import { initPubChemClient } from './services/pubchem/pubchem-client.js';
 await createApp({
     tools: allToolDefinitions,
-    instructions: "Use the pubchem_* tools to query PubChem's chemical database. Compounds are addressed by CID, assays by AID. Most flows start at `pubchem_search_compounds` (name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity → CIDs), then call per-CID tools for details, safety, image, cross-references, or bioactivity. For bioassays by biological target, chain `pubchem_search_assays` (gene/protein → AIDs) into `pubchem_get_bioactivity`. `pubchem_get_summary` covers assay/gene/protein/taxonomy entity lookups.",
+    resources: allResourceDefinitions,
+    instructions: "Use the pubchem_* tools to query PubChem's chemical database. Compounds are addressed by CID, assays by AID. Most flows start at `pubchem_search_compounds` (name, SMILES, InChIKey, formula, substructure, superstructure, or 2D similarity → CIDs), then call per-CID tools for details, safety, image, cross-references, bioactivity, interactions (drug-drug/drug-food/target), or 3D structure. For bioassays by biological target, chain `pubchem_search_assays` (gene/protein → AIDs) into `pubchem_get_bioactivity`. `pubchem_get_summary` covers assay/gene/protein/taxonomy entity lookups. Compound and assay records are also exposed as URI-addressable resources (e.g. `pubchem://compound/{cid}`, `pubchem://assay/{aid}`).",
     landing: {
         tagline: 'Search PubChem for chemical compounds, properties, safety, bioactivity, and cross-references.',
         repoRoot: 'https://github.com/cyanheads/pubchem-mcp-server',

package/dist/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;GAIG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,kBAAkB,EAAE,MAAM,yCAAyC,CAAC;AAC7E,OAAO,EAAE,iBAAiB,EAAE,MAAM,sCAAsC,CAAC;AAEzE,MAAM,SAAS,CAAC;IACd,KAAK,EAAE,kBAAkB;IACzB,YAAY,EACV,8gBAA8gB;IAChhB,OAAO,EAAE;QACP,OAAO,EACL,+FAA+F;QACjG,QAAQ,EAAE,iDAAiD;QAC3D,KAAK,EAAE;YACL,EAAE,KAAK,EAAE,SAAS,EAAE,IAAI,EAAE,mCAAmC,EAAE,QAAQ,EAAE,IAAI,EAAE;YAC/E;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;YACD;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;SACF;KACF;IACD,KAAK;QACH,iBAAiB,EAAE,CAAC;IACtB,CAAC;CACF,CAAC,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;GAIG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,sBAAsB,EAAE,MAAM,6CAA6C,CAAC;AACrF,OAAO,EAAE,kBAAkB,EAAE,MAAM,yCAAyC,CAAC;AAC7E,OAAO,EAAE,iBAAiB,EAAE,MAAM,sCAAsC,CAAC;AAEzE,MAAM,SAAS,CAAC;IACd,KAAK,EAAE,kBAAkB;IACzB,SAAS,EAAE,sBAAsB;IACjC,YAAY,EACV,4sBAA4sB;IAC9sB,OAAO,EAAE;QACP,OAAO,EACL,+FAA+F;QACjG,QAAQ,EAAE,iDAAiD;QAC3D,KAAK,EAAE;YACL,EAAE,KAAK,EAAE,SAAS,EAAE,IAAI,EAAE,mCAAmC,EAAE,QAAQ,EAAE,IAAI,EAAE;YAC/E;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;YACD;gBACE,KAAK,EAAE,eAAe;gBACtB,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;SACF;KACF;IACD,KAAK;QACH,iBAAiB,EAAE,CAAC;IACtB,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/assay.resource.d.ts

@@ -0,0 +1,9 @@
+/**
+ * @fileoverview Resource — summary for a PubChem BioAssay by AID.
+ * @module mcp-server/resources/definitions/assay.resource
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const assayResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
+    aid: z.ZodCoercedNumber<unknown>;
+}, z.core.$strip>, undefined, undefined>;
+//# sourceMappingURL=assay.resource.d.ts.map

package/dist/mcp-server/resources/definitions/assay.resource.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"assay.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/assay.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIrD,eAAO,MAAM,aAAa;;wCAgBxB,CAAC"}

package/dist/mcp-server/resources/definitions/assay.resource.js

@@ -0,0 +1,24 @@
+/**
+ * @fileoverview Resource — summary for a PubChem BioAssay by AID.
+ * @module mcp-server/resources/definitions/assay.resource
+ */
+import { resource, z } from '@cyanheads/mcp-ts-core';
+import { notFound } from '@cyanheads/mcp-ts-core/errors';
+import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
+export const assayResource = resource('pubchem://assay/{aid}', {
+    name: 'pubchem-assay',
+    description: 'Summary for a PubChem BioAssay by AID (mirrors pubchem_get_summary for assays).',
+    mimeType: 'application/json',
+    params: z.object({
+        aid: z.coerce.number().int().positive().describe('PubChem Assay ID.'),
+    }),
+    async handler(params) {
+        const client = getPubChemClient();
+        const summary = await client.getEntitySummary('assay', params.aid);
+        if (!summary) {
+            throw notFound(`No PubChem assay found for AID ${params.aid}.`, { aid: params.aid });
+        }
+        return { aid: params.aid, summary };
+    },
+});
+//# sourceMappingURL=assay.resource.js.map

package/dist/mcp-server/resources/definitions/assay.resource.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"assay.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/assay.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,aAAa,GAAG,QAAQ,CAAC,uBAAuB,EAAE;IAC7D,IAAI,EAAE,eAAe;IACrB,WAAW,EAAE,iFAAiF;IAC9F,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;KACtE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,OAAO,GAAG,MAAM,MAAM,CAAC,gBAAgB,CAAC,OAAO,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC;QACnE,IAAI,CAAC,OAAO,EAAE,CAAC;YACb,MAAM,QAAQ,CAAC,kCAAkC,MAAM,CAAC,GAAG,GAAG,EAAE,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC;QACvF,CAAC;QACD,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,OAAO,EAAE,CAAC;IACtC,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.d.ts

@@ -0,0 +1,9 @@
+/**
+ * @fileoverview Resource — bioassay activity profile for a compound by CID.
+ * @module mcp-server/resources/definitions/compound-bioactivity.resource
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const compoundBioactivityResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
+    cid: z.ZodCoercedNumber<unknown>;
+}, z.core.$strip>, undefined, undefined>;
+//# sourceMappingURL=compound-bioactivity.resource.d.ts.map

package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"compound-bioactivity.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-bioactivity.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAMrD,eAAO,MAAM,2BAA2B;;wCAoBtC,CAAC"}

package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js

@@ -0,0 +1,28 @@
+/**
+ * @fileoverview Resource — bioassay activity profile for a compound by CID.
+ * @module mcp-server/resources/definitions/compound-bioactivity.resource
+ */
+import { resource, z } from '@cyanheads/mcp-ts-core';
+import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
+/** Well-studied compounds have thousands of assays — the resource read returns a head slice. */
+const MAX_RESULTS = 25;
+export const compoundBioactivityResource = resource('pubchem://compound/{cid}/bioactivity', {
+    name: 'pubchem-compound-bioactivity',
+    description: 'Bioassay activity profile for a PubChem compound by CID (mirrors pubchem_get_bioactivity). Returns up to 25 assays; use the tool to filter and page.',
+    mimeType: 'application/json',
+    params: z.object({
+        cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),
+    }),
+    async handler(params) {
+        const client = getPubChemClient();
+        const rows = await client.getAssaySummary(params.cid);
+        const activeCount = rows.filter((r) => r.outcome === 'Active').length;
+        return {
+            cid: params.cid,
+            totalAssays: rows.length,
+            activeCount,
+            results: rows.slice(0, MAX_RESULTS),
+        };
+    },
+});
+//# sourceMappingURL=compound-bioactivity.resource.js.map

package/dist/mcp-server/resources/definitions/compound-bioactivity.resource.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"compound-bioactivity.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-bioactivity.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,gGAAgG;AAChG,MAAM,WAAW,GAAG,EAAE,CAAC;AAEvB,MAAM,CAAC,MAAM,2BAA2B,GAAG,QAAQ,CAAC,sCAAsC,EAAE;IAC1F,IAAI,EAAE,8BAA8B;IACpC,WAAW,EACT,sJAAsJ;IACxJ,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACzE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,eAAe,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QACtD,MAAM,WAAW,GAAG,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,KAAK,QAAQ,CAAC,CAAC,MAAM,CAAC;QACtE,OAAO;YACL,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,WAAW,EAAE,IAAI,CAAC,MAAM;YACxB,WAAW;YACX,OAAO,EAAE,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,WAAW,CAAC;SACpC,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/compound-image.resource.d.ts

@@ -0,0 +1,11 @@
+/**
+ * @fileoverview Resource — a 2D structure diagram (PNG) for a compound by CID.
+ * @module mcp-server/resources/definitions/compound-image.resource
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const compoundImageResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
+    cid: z.ZodCoercedNumber<unknown>;
+}, z.core.$strip>, z.ZodObject<{
+    base64: z.ZodString;
+}, z.core.$strip>, undefined>;
+//# sourceMappingURL=compound-image.resource.d.ts.map

package/dist/mcp-server/resources/definitions/compound-image.resource.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"compound-image.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-image.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGrD,eAAO,MAAM,qBAAqB;;;;6BAuBhC,CAAC"}

package/dist/mcp-server/resources/definitions/compound-image.resource.js

@@ -0,0 +1,28 @@
+/**
+ * @fileoverview Resource — a 2D structure diagram (PNG) for a compound by CID.
+ * @module mcp-server/resources/definitions/compound-image.resource
+ */
+import { resource, z } from '@cyanheads/mcp-ts-core';
+import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
+export const compoundImageResource = resource('pubchem://compound/{cid}/image', {
+    name: 'pubchem-compound-image',
+    description: 'A 2D structure diagram (PNG) for a PubChem compound by CID (mirrors pubchem_get_compound_image).',
+    mimeType: 'image/png',
+    params: z.object({
+        cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),
+    }),
+    output: z.object({
+        base64: z.string().describe('Base64-encoded PNG image data.'),
+    }),
+    async handler(params) {
+        const client = getPubChemClient();
+        const buffer = await client.getImage(params.cid, 'large');
+        return { base64: Buffer.from(buffer).toString('base64') };
+    },
+    // Binary content: emit the PNG as a base64 blob rather than the default JSON text.
+    format(result, meta) {
+        const { base64 } = result;
+        return [{ uri: meta.uri.href, mimeType: meta.mimeType, blob: base64 }];
+    },
+});
+//# sourceMappingURL=compound-image.resource.js.map

package/dist/mcp-server/resources/definitions/compound-image.resource.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"compound-image.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-image.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,qBAAqB,GAAG,QAAQ,CAAC,gCAAgC,EAAE;IAC9E,IAAI,EAAE,wBAAwB;IAC9B,WAAW,EACT,kGAAkG;IACpG,QAAQ,EAAE,WAAW;IACrB,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACzE,CAAC;IACF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;KAC9D,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,MAAM,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,GAAG,EAAE,OAAO,CAAC,CAAC;QAC1D,OAAO,EAAE,MAAM,EAAE,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,QAAQ,CAAC,EAAE,CAAC;IAC5D,CAAC;IAED,mFAAmF;IACnF,MAAM,CAAC,MAAM,EAAE,IAAI;QACjB,MAAM,EAAE,MAAM,EAAE,GAAG,MAA4B,CAAC;QAChD,OAAO,CAAC,EAAE,GAAG,EAAE,IAAI,CAAC,GAAG,CAAC,IAAI,EAAE,QAAQ,EAAE,IAAI,CAAC,QAAQ,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC;IACzE,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/compound-safety.resource.d.ts

@@ -0,0 +1,9 @@
+/**
+ * @fileoverview Resource — GHS hazard classification for a compound by CID.
+ * @module mcp-server/resources/definitions/compound-safety.resource
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const compoundSafetyResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
+    cid: z.ZodCoercedNumber<unknown>;
+}, z.core.$strip>, undefined, undefined>;
+//# sourceMappingURL=compound-safety.resource.d.ts.map

package/dist/mcp-server/resources/definitions/compound-safety.resource.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"compound-safety.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-safety.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGrD,eAAO,MAAM,sBAAsB;;wCAyBjC,CAAC"}

package/dist/mcp-server/resources/definitions/compound-safety.resource.js

@@ -0,0 +1,32 @@
+/**
+ * @fileoverview Resource — GHS hazard classification for a compound by CID.
+ * @module mcp-server/resources/definitions/compound-safety.resource
+ */
+import { resource, z } from '@cyanheads/mcp-ts-core';
+import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
+export const compoundSafetyResource = resource('pubchem://compound/{cid}/safety', {
+    name: 'pubchem-compound-safety',
+    description: 'GHS hazard classification for a PubChem compound by CID (mirrors pubchem_get_compound_safety).',
+    mimeType: 'application/json',
+    params: z.object({
+        cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),
+    }),
+    async handler(params) {
+        const client = getPubChemClient();
+        const data = await client.getSafetyData(params.cid);
+        if (!data)
+            return { cid: params.cid, hasData: false };
+        return {
+            cid: params.cid,
+            hasData: true,
+            ghs: {
+                signalWord: data.signalWord,
+                pictograms: data.pictograms,
+                hazardStatements: data.hazardStatements,
+                precautionaryStatements: data.precautionaryStatements,
+            },
+            source: data.source,
+        };
+    },
+});
+//# sourceMappingURL=compound-safety.resource.js.map

package/dist/mcp-server/resources/definitions/compound-safety.resource.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"compound-safety.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-safety.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,MAAM,CAAC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,iCAAiC,EAAE;IAChF,IAAI,EAAE,yBAAyB;IAC/B,WAAW,EACT,gGAAgG;IAClG,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACzE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QACpD,IAAI,CAAC,IAAI;YAAE,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC;QACtD,OAAO;YACL,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,OAAO,EAAE,IAAI;YACb,GAAG,EAAE;gBACH,UAAU,EAAE,IAAI,CAAC,UAAU;gBAC3B,UAAU,EAAE,IAAI,CAAC,UAAU;gBAC3B,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,uBAAuB,EAAE,IAAI,CAAC,uBAAuB;aACtD;YACD,MAAM,EAAE,IAAI,CAAC,MAAM;SACpB,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/compound-xrefs.resource.d.ts

@@ -0,0 +1,9 @@
+/**
+ * @fileoverview Resource — external cross-references for a compound by CID.
+ * @module mcp-server/resources/definitions/compound-xrefs.resource
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const compoundXrefsResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
+    cid: z.ZodCoercedNumber<unknown>;
+}, z.core.$strip>, undefined, undefined>;
+//# sourceMappingURL=compound-xrefs.resource.d.ts.map

package/dist/mcp-server/resources/definitions/compound-xrefs.resource.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"compound-xrefs.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-xrefs.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAOrD,eAAO,MAAM,qBAAqB;;wCAoBhC,CAAC"}

package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js

@@ -0,0 +1,29 @@
+/**
+ * @fileoverview Resource — external cross-references for a compound by CID.
+ * @module mcp-server/resources/definitions/compound-xrefs.resource
+ */
+import { resource, z } from '@cyanheads/mcp-ts-core';
+import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
+/** A focused default set for the resource read — the full tool exposes all xref types. */
+const RESOURCE_XREF_TYPES = ['RN', 'RegistryID', 'PubMedID'];
+const MAX_PER_TYPE = 25;
+export const compoundXrefsResource = resource('pubchem://compound/{cid}/xrefs', {
+    name: 'pubchem-compound-xrefs',
+    description: 'External cross-references (CAS RN, registry IDs, PubMed) for a PubChem compound by CID (mirrors pubchem_get_compound_xrefs). Use the tool for the full set of xref types.',
+    mimeType: 'application/json',
+    params: z.object({
+        cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),
+    }),
+    async handler(params) {
+        const client = getPubChemClient();
+        const xrefs = [];
+        for (const type of RESOURCE_XREF_TYPES) {
+            const ids = await client.getXrefs(params.cid, type);
+            if (ids.length > 0) {
+                xrefs.push({ type, ids: ids.slice(0, MAX_PER_TYPE), totalAvailable: ids.length });
+            }
+        }
+        return { cid: params.cid, xrefs };
+    },
+});
+//# sourceMappingURL=compound-xrefs.resource.js.map

package/dist/mcp-server/resources/definitions/compound-xrefs.resource.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"compound-xrefs.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound-xrefs.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AAExE,0FAA0F;AAC1F,MAAM,mBAAmB,GAAG,CAAC,IAAI,EAAE,YAAY,EAAE,UAAU,CAAU,CAAC;AACtE,MAAM,YAAY,GAAG,EAAE,CAAC;AAExB,MAAM,CAAC,MAAM,qBAAqB,GAAG,QAAQ,CAAC,gCAAgC,EAAE;IAC9E,IAAI,EAAE,wBAAwB;IAC9B,WAAW,EACT,2KAA2K;IAC7K,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACzE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,KAAK,GAA8E,EAAE,CAAC;QAC5F,KAAK,MAAM,IAAI,IAAI,mBAAmB,EAAE,CAAC;YACvC,MAAM,GAAG,GAAG,MAAM,MAAM,CAAC,QAAQ,CAAC,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,CAAC;YACpD,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,YAAY,CAAC,EAAE,cAAc,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;YACpF,CAAC;QACH,CAAC;QACD,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,KAAK,EAAE,CAAC;IACpC,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/compound.resource.d.ts

@@ -0,0 +1,9 @@
+/**
+ * @fileoverview Resource — a compound's core physicochemical properties by CID.
+ * @module mcp-server/resources/definitions/compound.resource
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const compoundResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
+    cid: z.ZodCoercedNumber<unknown>;
+}, z.core.$strip>, undefined, undefined>;
+//# sourceMappingURL=compound.resource.d.ts.map

package/dist/mcp-server/resources/definitions/compound.resource.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"compound.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAKrD,eAAO,MAAM,gBAAgB;;wCAoB3B,CAAC"}

package/dist/mcp-server/resources/definitions/compound.resource.js

@@ -0,0 +1,28 @@
+/**
+ * @fileoverview Resource — a compound's core physicochemical properties by CID.
+ * @module mcp-server/resources/definitions/compound.resource
+ */
+import { resource, z } from '@cyanheads/mcp-ts-core';
+import { notFound } from '@cyanheads/mcp-ts-core/errors';
+import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
+import { DEFAULT_PROPERTIES } from '../../../services/pubchem/types.js';
+export const compoundResource = resource('pubchem://compound/{cid}', {
+    name: 'pubchem-compound',
+    description: 'Core physicochemical properties for a PubChem compound by CID (mirrors pubchem_get_compound_details).',
+    mimeType: 'application/json',
+    params: z.object({
+        cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),
+    }),
+    async handler(params) {
+        const client = getPubChemClient();
+        const rows = await client.getProperties([params.cid], [...DEFAULT_PROPERTIES]);
+        const row = rows[0];
+        // PubChem returns HTTP 200 with a {CID}-only row for a nonexistent CID — treat as not-found.
+        if (!row || !Object.keys(row).some((k) => k !== 'CID')) {
+            throw notFound(`No PubChem compound found for CID ${params.cid}.`, { cid: params.cid });
+        }
+        const { CID: _CID, ...properties } = row;
+        return { cid: params.cid, properties };
+    },
+});
+//# sourceMappingURL=compound.resource.js.map

package/dist/mcp-server/resources/definitions/compound.resource.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"compound.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/compound.resource.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EAAE,gBAAgB,EAAE,MAAM,sCAAsC,CAAC;AACxE,OAAO,EAAE,kBAAkB,EAAE,MAAM,6BAA6B,CAAC;AAEjE,MAAM,CAAC,MAAM,gBAAgB,GAAG,QAAQ,CAAC,0BAA0B,EAAE;IACnE,IAAI,EAAE,kBAAkB;IACxB,WAAW,EACT,uGAAuG;IACzG,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,GAAG,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;KACzE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,MAAM;QAClB,MAAM,MAAM,GAAG,gBAAgB,EAAE,CAAC;QAClC,MAAM,IAAI,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,kBAAkB,CAAC,CAAC,CAAC;QAC/E,MAAM,GAAG,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;QACpB,6FAA6F;QAC7F,IAAI,CAAC,GAAG,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,KAAK,KAAK,CAAC,EAAE,CAAC;YACvD,MAAM,QAAQ,CAAC,qCAAqC,MAAM,CAAC,GAAG,GAAG,EAAE,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,CAAC,CAAC;QAC1F,CAAC;QACD,MAAM,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,UAAU,EAAE,GAAG,GAAG,CAAC;QACzC,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,UAAU,EAAE,CAAC;IACzC,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/index.d.ts

@@ -0,0 +1,14 @@
+/**
+ * @fileoverview Resource definition barrel — all PubChem MCP resources.
+ * @module mcp-server/resources/definitions
+ */
+export declare const allResourceDefinitions: (import("@cyanheads/mcp-ts-core").ResourceDefinition<import("zod").ZodObject<{
+    aid: import("zod").ZodCoercedNumber<unknown>;
+}, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ResourceDefinition<import("zod").ZodObject<{
+    cid: import("zod").ZodCoercedNumber<unknown>;
+}, import("zod/v4/core").$strip>, undefined, undefined> | import("@cyanheads/mcp-ts-core").ResourceDefinition<import("zod").ZodObject<{
+    cid: import("zod").ZodCoercedNumber<unknown>;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    base64: import("zod").ZodString;
+}, import("zod/v4/core").$strip>, undefined>)[];
+//# sourceMappingURL=index.d.ts.map

package/dist/mcp-server/resources/definitions/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AASH,eAAO,MAAM,sBAAsB;;;;;;;;+CAOlC,CAAC"}

package/dist/mcp-server/resources/definitions/index.js

@@ -0,0 +1,19 @@
+/**
+ * @fileoverview Resource definition barrel — all PubChem MCP resources.
+ * @module mcp-server/resources/definitions
+ */
+import { assayResource } from './assay.resource.js';
+import { compoundResource } from './compound.resource.js';
+import { compoundBioactivityResource } from './compound-bioactivity.resource.js';
+import { compoundImageResource } from './compound-image.resource.js';
+import { compoundSafetyResource } from './compound-safety.resource.js';
+import { compoundXrefsResource } from './compound-xrefs.resource.js';
+export const allResourceDefinitions = [
+    compoundResource,
+    compoundSafetyResource,
+    compoundImageResource,
+    compoundXrefsResource,
+    compoundBioactivityResource,
+    assayResource,
+];
+//# sourceMappingURL=index.js.map

package/dist/mcp-server/resources/definitions/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/index.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAE,aAAa,EAAE,MAAM,qBAAqB,CAAC;AACpD,OAAO,EAAE,gBAAgB,EAAE,MAAM,wBAAwB,CAAC;AAC1D,OAAO,EAAE,2BAA2B,EAAE,MAAM,oCAAoC,CAAC;AACjF,OAAO,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AACrE,OAAO,EAAE,sBAAsB,EAAE,MAAM,+BAA+B,CAAC;AACvE,OAAO,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAErE,MAAM,CAAC,MAAM,sBAAsB,GAAG;IACpC,gBAAgB;IAChB,sBAAsB;IACtB,qBAAqB;IACrB,qBAAqB;IACrB,2BAA2B;IAC3B,aAAa;CACd,CAAC"}

package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts

@@ -11,6 +11,8 @@ export declare const getBioactivity: import("@cyanheads/mcp-ts-core").ToolDefini
         inactive: "inactive";
         all: "all";
     }>>;
+    targetGeneId: z.ZodOptional<z.ZodNumber>;
+    targetAccession: z.ZodOptional<z.ZodString>;
     maxResults: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     cid: z.ZodNumber;
@@ -31,6 +33,7 @@ export declare const getBioactivity: import("@cyanheads/mcp-ts-core").ToolDefini
     }, z.core.$strip>>;
 }, z.core.$strip>, undefined, {
     readonly outcomeFilter: z.ZodString;
+    readonly targetFilter: z.ZodOptional<z.ZodString>;
     readonly filteredCount: z.ZodNumber;
     readonly returnedCount: z.ZodNumber;
     readonly notice: z.ZodOptional<z.ZodString>;

package/dist/mcp-server/tools/definitions/get-bioactivity.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsKzB,CAAC"}
+{"version":3,"file":"get-bioactivity.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-bioactivity.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA0MzB,CAAC"}

package/dist/mcp-server/tools/definitions/get-bioactivity.tool.js

@@ -7,7 +7,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
 export const getBioactivity = tool('pubchem_get_bioactivity', {
     title: 'Get Bioactivity',
-    description: "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 to focus on active results.",
+    description: '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?".',
     annotations: {
         readOnlyHint: true,
         idempotentHint: true,
@@ -23,6 +23,16 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
             .enum(['active', 'inactive', 'all'])
             .default('all')
             .describe('Filter by activity outcome. "active" shows only assays where the compound showed activity — most useful for understanding biological profile. Default: "all".'),
+        targetGeneId: z
+            .number()
+            .int()
+            .positive()
+            .optional()
+            .describe('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?".'),
+        targetAccession: z
+            .string()
+            .optional()
+            .describe('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.'),
         maxResults: z
             .number()
             .min(1)
@@ -72,9 +82,13 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
     // and content[]; keys disjoint from output (cid/totalAssays live there).
     enrichment: {
         outcomeFilter: z.string().describe('Outcome filter applied: active, inactive, or all.'),
+        targetFilter: z
+            .string()
+            .optional()
+            .describe('Target filter applied (gene ID and/or protein accession), when set.'),
         filteredCount: z
             .number()
-            .describe('Assays matching the outcome filter, before the maxResults cap.'),
+            .describe('Assays matching the outcome and target filters, before the maxResults cap.'),
         returnedCount: z.number().describe('Assays returned after the maxResults cap.'),
         notice: z
             .string()
@@ -86,19 +100,33 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
         const allRows = await client.getAssaySummary(input.cid);
         const activeCount = allRows.filter((r) => r.outcome === 'Active').length;
         const inactiveCount = allRows.filter((r) => r.outcome === 'Inactive').length;
-        // Filter by outcome
+        // Filter by outcome, then by target — pure filters on rows already in hand
+        // (targetGeneId/targetAccession are populated on every row by the assay summary parser).
         let filtered = allRows;
         if (input.outcomeFilter === 'active') {
-            filtered = allRows.filter((r) => r.outcome === 'Active');
+            filtered = filtered.filter((r) => r.outcome === 'Active');
         }
         else if (input.outcomeFilter === 'inactive') {
-            filtered = allRows.filter((r) => r.outcome === 'Inactive');
+            filtered = filtered.filter((r) => r.outcome === 'Inactive');
+        }
+        const targetLabel = [
+            input.targetGeneId != null ? `GeneID:${input.targetGeneId}` : undefined,
+            input.targetAccession ? `accession:${input.targetAccession}` : undefined,
+        ]
+            .filter(Boolean)
+            .join(' ');
+        if (input.targetGeneId != null) {
+            filtered = filtered.filter((r) => r.targetGeneId === input.targetGeneId);
+        }
+        if (input.targetAccession) {
+            filtered = filtered.filter((r) => r.targetAccession === input.targetAccession);
         }
         const results = filtered.slice(0, input.maxResults);
         ctx.log.info('Bioactivity fetched', {
             cid: input.cid,
             total: allRows.length,
             active: activeCount,
+            filtered: filtered.length,
             returned: results.length,
         });
         ctx.enrich({
@@ -106,11 +134,15 @@ export const getBioactivity = tool('pubchem_get_bioactivity', {
             filteredCount: filtered.length,
             returnedCount: results.length,
         });
+        if (targetLabel)
+            ctx.enrich({ targetFilter: targetLabel });
         if (allRows.length === 0) {
             ctx.enrich.notice(`No bioactivity data found for CID ${input.cid}. The compound may be uncharacterized, or verify the CID with pubchem_search_compounds.`);
         }
         else if (filtered.length === 0) {
-            ctx.enrich.notice(`CID ${input.cid} has ${allRows.length} assay(s) but none match outcomeFilter="${input.outcomeFilter}". Use outcomeFilter="all" to see them.`);
+            ctx.enrich.notice(targetLabel
+                ? `CID ${input.cid} has ${allRows.length} assay(s) but none match the target filter (${targetLabel})${input.outcomeFilter !== 'all' ? ` with outcomeFilter="${input.outcomeFilter}"` : ''}. Verify the target identifier appears in this compound's assays, or widen the filter.`
+                : `CID ${input.cid} has ${allRows.length} assay(s) but none match outcomeFilter="${input.outcomeFilter}". Use outcomeFilter="all" to see them.`);
         }
         return {
             cid: input.cid,