@cyanheads/pubchem-mcp-server 0.4.1 → 0.4.3

package/Dockerfile

@@ -4,15 +4,17 @@
 # This stage installs all dependencies (including dev), builds the TypeScript
 # source code into JavaScript, and prepares the production assets.
 # ==============================================================================
-FROM oven/bun:1.3 AS build
+FROM oven/bun:1.3.14 AS build
 
 WORKDIR /usr/src/app
 
 # Copy dependency manifests for optimized layer caching
 COPY package.json bun.lock ./
 
-# Install all dependencies (including dev dependencies for building)
-RUN bun install --frozen-lockfile
+# Install all dependencies (including dev dependencies for building).
+# The BuildKit cache mount persists Bun's global package cache across builds.
+RUN --mount=type=cache,target=/root/.bun/install/cache \
+    bun install --frozen-lockfile --ignore-scripts
 
 # Copy the rest of the source code
 COPY . .
@@ -28,7 +30,7 @@ RUN bun run build
 # application. It uses a slim base image and only includes production
 # dependencies and build artifacts.
 # ==============================================================================
-FROM oven/bun:1.3-slim AS production
+FROM oven/bun:1.3.14-slim AS production
 
 WORKDIR /usr/src/app
 
@@ -51,15 +53,17 @@ COPY package.json bun.lock ./
 # that are not needed in the final production image.
 # Remove platform-specific bun/rollup binaries pulled as optionalDependencies
 # by @modelcontextprotocol/ext-apps — only needed for its build toolchain, not runtime.
-RUN bun install --production --frozen-lockfile --ignore-scripts \
+RUN --mount=type=cache,target=/root/.bun/install/cache \
+    bun install --production --frozen-lockfile --ignore-scripts \
     && rm -rf node_modules/@oven node_modules/@rollup
 
 # Conditionally install OpenTelemetry optional peer dependencies (Tier 3).
 # These are not bundled by default to keep the base image lean. Enable at build time
 # with: docker build --build-arg OTEL_ENABLED=true
 ARG OTEL_ENABLED=true
-RUN if [ "$OTEL_ENABLED" = "true" ]; then \
-      bun add @hono/otel \
+RUN --mount=type=cache,target=/root/.bun/install/cache \
+    if [ "$OTEL_ENABLED" = "true" ]; then \
+      bun add --omit=dev --ignore-scripts @hono/otel \
         @opentelemetry/instrumentation-http \
         @opentelemetry/exporter-metrics-otlp-http \
         @opentelemetry/exporter-trace-otlp-http \

package/LICENSE

@@ -175,7 +175,7 @@
 
    END OF TERMS AND CONDITIONS
 
-   Copyright 2025 Casey Hand (cyanheads)
+   Copyright 2025 Casey Hand @cyanheads
 
    Licensed under the Apache License, Version 2.0 (the "License");
    you may not use this file except in compliance with the License.

package/README.md

@@ -7,7 +7,7 @@
 
 <div align="center">
 
-[![Version](https://img.shields.io/badge/Version-0.4.1-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-0.4.3-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-^7.0.2-3178C6.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>
 

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

@@ -1 +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"}
+{"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;;wCAiBxB,CAAC"}

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

@@ -7,7 +7,7 @@ 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).',
+    description: 'Summary for a PubChem BioAssay by AID — name, description, source, protocol, and substance counts.',
     mimeType: 'application/json',
     params: z.object({
         aid: z.coerce.number().int().positive().describe('PubChem Assay ID.'),

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

@@ -1 +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"}
+{"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,EACT,oGAAoG;IACtG,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.js

@@ -8,7 +8,7 @@ import { getPubChemClient } from '../../../services/pubchem/pubchem-client.js';
 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.',
+    description: 'Bioassay activity profile for a PubChem compound by CID. Returns up to 25 assays; use pubchem_get_bioactivity to filter by outcome or molecular target and to raise the cap.',
     mimeType: 'application/json',
     params: z.object({
         cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),

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

@@ -1 +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"}
+{"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,8KAA8K;IAChL,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.js

@@ -6,7 +6,7 @@ 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).',
+    description: 'A 2D structure diagram (PNG, 300x300) for a PubChem compound by CID. Use pubchem_get_compound_image to choose the image size.',
     mimeType: 'image/png',
     params: z.object({
         cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),

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

@@ -1 +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"}
+{"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,+HAA+H;IACjI,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.map

@@ -1 +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"}
+{"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;;wCA8BjC,CAAC"}

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

@@ -6,26 +6,30 @@ 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).',
+    description: 'GHS hazard classification for a PubChem compound by CID — signal word, pictograms, hazard (H) and precautionary (P) statements. Not every compound carries a deposited classification.',
     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 };
+        const lookup = await client.getSafetyData(params.cid);
+        // A resource returns raw JSON with no notice surface, so `status` is the only way a reader
+        // can tell a mistyped CID from a compound that genuinely carries no GHS classification.
+        if (lookup.status !== 'ok') {
+            return { cid: params.cid, hasData: false, status: lookup.status };
+        }
         return {
             cid: params.cid,
             hasData: true,
+            status: lookup.status,
             ghs: {
-                signalWord: data.signalWord,
-                pictograms: data.pictograms,
-                hazardStatements: data.hazardStatements,
-                precautionaryStatements: data.precautionaryStatements,
+                signalWord: lookup.ghs.signalWord,
+                pictograms: lookup.ghs.pictograms,
+                hazardStatements: lookup.ghs.hazardStatements,
+                precautionaryStatements: lookup.ghs.precautionaryStatements,
             },
-            source: data.source,
+            source: lookup.ghs.source,
         };
     },
 });

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

@@ -1 +1 @@
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+{"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,wLAAwL;IAC1L,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,MAAM,GAAG,MAAM,MAAM,CAAC,aAAa,CAAC,MAAM,CAAC,GAAG,CAAC,CAAC;QACtD,2FAA2F;QAC3F,wFAAwF;QACxF,IAAI,MAAM,CAAC,MAAM,KAAK,IAAI,EAAE,CAAC;YAC3B,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,GAAG,EAAE,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC;QACpE,CAAC;QACD,OAAO;YACL,GAAG,EAAE,MAAM,CAAC,GAAG;YACf,OAAO,EAAE,IAAI;YACb,MAAM,EAAE,MAAM,CAAC,MAAM;YACrB,GAAG,EAAE;gBACH,UAAU,EAAE,MAAM,CAAC,GAAG,CAAC,UAAU;gBACjC,UAAU,EAAE,MAAM,CAAC,GAAG,CAAC,UAAU;gBACjC,gBAAgB,EAAE,MAAM,CAAC,GAAG,CAAC,gBAAgB;gBAC7C,uBAAuB,EAAE,MAAM,CAAC,GAAG,CAAC,uBAAuB;aAC5D;YACD,MAAM,EAAE,MAAM,CAAC,GAAG,CAAC,MAAM;SAC1B,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}

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

@@ -9,7 +9,7 @@ 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.',
+    description: 'External cross-references (CAS RN, registry IDs, PubMed) for a PubChem compound by CID, up to 25 per type. Use pubchem_get_compound_xrefs for the full set of xref types and a higher per-type cap.',
     mimeType: 'application/json',
     params: z.object({
         cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),

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

@@ -1 +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"}
+{"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,qMAAqM;IACvM,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.js

@@ -8,7 +8,7 @@ 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).',
+    description: 'Core physicochemical properties for a PubChem compound by CID. Use pubchem_get_compound_details to select properties or add descriptions, synonyms, drug-likeness, and classification.',
     mimeType: 'application/json',
     params: z.object({
         cid: z.coerce.number().int().positive().describe('PubChem Compound ID.'),

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

@@ -1 +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"}
+{"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,wLAAwL;IAC1L,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

@@ -3,12 +3,12 @@
  * @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>)[];
+}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ResourceDefinition<import("zod").ZodObject<{
+    aid: import("zod").ZodCoercedNumber<unknown>;
+}, import("zod/v4/core").$strip>, undefined, undefined>)[];
 //# sourceMappingURL=index.d.ts.map

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

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

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

@@ -8,8 +8,8 @@ export declare const getBioactivity: import("@cyanheads/mcp-ts-core").ToolDefini
     cid: z.ZodNumber;
     outcomeFilter: z.ZodDefault<z.ZodEnum<{
         active: "active";
-        inactive: "inactive";
         all: "all";
+        inactive: "inactive";
     }>>;
     targetGeneId: z.ZodOptional<z.ZodNumber>;
     targetAccession: z.ZodOptional<z.ZodString>;

package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.d.ts

@@ -7,8 +7,8 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const getCompound3dStructure: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     cid: z.ZodNumber;
     format: z.ZodDefault<z.ZodEnum<{
-        sdf: "sdf";
         json: "json";
+        sdf: "sdf";
     }>>;
     includeAlternateConformerIds: z.ZodDefault<z.ZodBoolean>;
     maxAtoms: z.ZodOptional<z.ZodNumber>;

package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js

@@ -17,7 +17,7 @@ const DEFAULT_BOND_CAP = 200;
 const DEFAULT_SDF_LINE_CAP = 500;
 export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure', {
     title: 'Get Compound 3D Structure',
-    description: 'Get a compound\'s default 3D conformer — atomic coordinates and bonds — for one CID. format="json" (default) returns parsed atoms and bonds the model can reason over directly; 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).',
+    description: '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).',
     annotations: {
         readOnlyHint: true,
         idempotentHint: true,
@@ -36,7 +36,7 @@ export const getCompound3dStructure = tool('pubchem_get_compound_3d_structure',
         includeAlternateConformerIds: z
             .boolean()
             .default(false)
-            .describe('List the IDs of additional computed conformers beyond the default. Adds one extra API call. Default: false.'),
+            .describe('List the IDs of additional computed conformers beyond the default. Slower than the default response. Default: false.'),
         maxAtoms: z
             .number()
             .int()

package/dist/mcp-server/tools/definitions/get-compound-3d-structure.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/get-compound-details.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"get-compound-details.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-details.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA4GjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;wCA2Y7B,CAAC"}
+{"version":3,"file":"get-compound-details.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-details.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA4GjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;wCAuZ7B,CAAC"}

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

@@ -96,7 +96,7 @@ function computeDrugLikeness(properties) {
 // ── Tool definition ────────────────────────────────────────────────────
 export const getCompoundDetails = tool('pubchem_get_compound_details', {
     title: 'Get Compound Details',
-    description: '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), all known synonyms, drug-likeness assessment (Lipinski/Veber rules), and/or pharmacological classification (FDA classes, MeSH classes, ATC codes). Efficiently batches up to 100 CIDs.',
+    description: '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), all 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.',
     annotations: {
         readOnlyHint: true,
         idempotentHint: true,
@@ -107,7 +107,7 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             .array(z.number().int().positive())
             .min(1)
             .max(100)
-            .describe('PubChem Compound IDs to fetch (1-100). Batched efficiently. Resolve from names/SMILES with pubchem_search_compounds.'),
+            .describe('PubChem Compound IDs to fetch (1-100). Resolve from names/SMILES with pubchem_search_compounds.'),
         properties: z
             .array(propertyEnum)
             .optional()
@@ -122,11 +122,11 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
             .min(1)
             .max(20)
             .default(3)
-            .describe('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.'),
+            .describe('Max number of distinct description entries per compound (1-20). PubChem returns near-duplicate summaries from many depositors; duplicates are collapsed before this cap applies. Default: 3.'),
         includeSynonyms: z
             .boolean()
             .default(false)
-            .describe('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.'),
+            .describe('Fetch all known names and synonyms (trade names, systematic names, registry numbers). Slower for large CID lists.'),
         maxSynonyms: z
             .number()
             .int()
@@ -137,7 +137,7 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
         includeDrugLikeness: z
             .boolean()
             .default(false)
-            .describe('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.'),
+            .describe('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: z
             .boolean()
             .default(false)
@@ -371,11 +371,17 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                     lines.push(`  FDA: ${cls.fdaClasses.join(', ')}`);
                 if (cls.fdaMechanisms.length > 0)
                     lines.push(`  MoA: ${cls.fdaMechanisms.join(', ')}`);
+                /**
+                 * MeSH classes render in full — structuredContent carries the whole list uncapped.
+                 * Each value is a multi-sentence scope note that routinely contains both "; " and
+                 * ", ", so no inline separator can mark an entry boundary unambiguously. One entry
+                 * per line instead: inlineData collapses embedded newlines, so a value cannot forge
+                 * a bullet of its own and the line break is an unforgeable entry boundary.
+                 */
                 if (cls.meshClasses.length > 0) {
-                    const meshDisplay = cls.meshClasses.length > 3
-                        ? `${cls.meshClasses.slice(0, 3).join('; ')} (+${cls.meshClasses.length - 3} more)`
-                        : cls.meshClasses.join('; ');
-                    lines.push(`  MeSH: ${meshDisplay}`);
+                    lines.push('  MeSH:');
+                    for (const meshClass of cls.meshClasses)
+                        lines.push(`    - ${inlineData(meshClass)}`);
                 }
                 if (cls.atcCodes.length > 0) {
                     const atcDisplay = cls.atcCodes
@@ -412,7 +418,15 @@ export const getCompoundDetails = tool('pubchem_get_compound_details', {
                 const total = c.synonymsTotal ?? c.synonyms.length;
                 const more = total - c.synonyms.length;
                 const suffix = more > 0 ? ` (+${more} more)` : '';
-                const syns = c.synonyms.map(inlineData).join(', ');
+                /**
+                 * Pipe-separated: CAS-style inverted names ("Benzoic acid, 2-(acetyloxy)-") carry
+                 * their own ", ", which would split one synonym into two. " | " is this formatter's
+                 * existing inline multi-value separator. A bare "|" does turn up in depositor
+                 * synonyms as mangled Greek letters ("17|A-Oestradiol"), so the delimiter is the
+                 * space-padded form; that exact sequence was absent from every synonym sampled,
+                 * but unlike the MeSH line break it is a rare-collision separator, not a proof.
+                 */
+                const syns = c.synonyms.map(inlineData).join(' | ');
                 blocks.push(`\n**Synonyms** (${total} total): ${syns}${suffix}`);
             }
             blocks.push('');

package/dist/mcp-server/tools/definitions/get-compound-details.tool.js.map

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

@@ -7,8 +7,8 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const getCompoundImage: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     cid: z.ZodNumber;
     size: z.ZodDefault<z.ZodEnum<{
-        small: "small";
         large: "large";
+        small: "small";
     }>>;
 }, z.core.$strip>, z.ZodObject<{
     cid: z.ZodNumber;

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

@@ -21,7 +21,6 @@ export declare const getCompoundInteractions: import("@cyanheads/mcp-ts-core").T
         }>;
         partner: z.ZodOptional<z.ZodString>;
         source: z.ZodString;
-        severity: z.ZodOptional<z.ZodString>;
         text: z.ZodString;
     }, z.core.$strip>>;
 }, z.core.$strip>, undefined, {

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

@@ -1 +1 @@
-{"version":3,"file":"get-compound-interactions.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;EAsIlC,CAAC"}
+{"version":3,"file":"get-compound-interactions.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/get-compound-interactions.tool.ts"],"names":[],"mappings":"AAAA;;;GAGG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;EA+HlC,CAAC"}

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

@@ -43,10 +43,6 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
                 .optional()
                 .describe('Interacting compound, food, or target name as the source reports it.'),
             source: z.string().describe('Originating source (e.g. "DrugBank", "BindingDB").'),
-            severity: z
-                .string()
-                .optional()
-                .describe('Raw severity as the source reports it — not normalized across sources, and frequently unset (most sources embed severity in the statement text).'),
             text: z.string().describe('The interaction statement.'),
         })
             .describe('A single interaction entry.'))
@@ -102,8 +98,7 @@ export const getCompoundInteractions = tool('pubchem_get_compound_interactions',
         }
         for (const e of result.entries) {
             const partner = e.partner ? ` **${inlineData(e.partner)}**` : '';
-            const severity = e.severity ? ` [severity: ${inlineData(e.severity)}]` : '';
-            lines.push(`- (${e.kind})${partner}${severity} _(source: ${inlineData(e.source)})_`);
+            lines.push(`- (${e.kind})${partner} _(source: ${inlineData(e.source)})_`);
             // The interaction statement is upstream free text — render it as an
             // indented blockquote so the data/instruction boundary is explicit.
             for (const q of quoteData(e.text).split('\n'))

package/dist/mcp-server/tools/definitions/get-compound-interactions.tool.js.map

@@ -1 +1 @@
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