@pharmatools/pubcrawl 2.2.0 → 2.4.0

package/README.md

@@ -1,137 +1,257 @@
-# PubCrawl
+<div align="center">
 
-An [MCP server](https://modelcontextprotocol.io) that gives LLM clients access to PubMed, FDA drug labelling, UK medicines data, and ClinicalTrials.gov. A peer-reviewed pub crawl through the literature — the label — and the trial.
+<img src="./assets/banner.svg" alt="PubCrawl — PubMed, drug labels, and clinical trials for AI assistants" width="100%" />
+
+<h1></h1>
+
+**An [MCP server](https://modelcontextprotocol.io) that gives AI assistants access to PubMed, Europe PMC, FDA & UK drug labelling, and ClinicalTrials.gov.**
+
+_A peer-reviewed pub crawl through the literature — the label — and the trial._
+
+[![ci](https://github.com/nickjlamb/pubcrawl/actions/workflows/build.yml/badge.svg)](https://github.com/nickjlamb/pubcrawl/actions/workflows/build.yml)
+[![npm](https://img.shields.io/npm/v/@pharmatools/pubcrawl?color=cb3837&logo=npm)](https://www.npmjs.com/package/@pharmatools/pubcrawl)
+[![downloads](https://img.shields.io/npm/dm/@pharmatools/pubcrawl?color=cb3837)](https://www.npmjs.com/package/@pharmatools/pubcrawl)
+[![node](https://img.shields.io/node/v/@pharmatools/pubcrawl?color=339933&logo=node.js&logoColor=white)](https://nodejs.org)
+[![MCP Registry](https://img.shields.io/badge/MCP_Registry-listed-6E56CF)](https://registry.modelcontextprotocol.io/?q=pubcrawl)
+[![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE)
+[![PRs welcome](https://img.shields.io/badge/PRs-welcome-brightgreen.svg)](CONTRIBUTING.md)
+
+[Quick start](#-quick-start-60-seconds) · [Tools](#-tools) · [Examples](#-examples) · [Architecture](#-architecture) · [Roadmap](ROADMAP.md) · [Contributing](CONTRIBUTING.md)
+
+</div>
+
+---
+
+## ✨ What is PubCrawl?
+
+PubCrawl connects your AI assistant (Claude Desktop, Cursor, or any MCP-compatible client) directly to the primary sources clinicians and researchers actually use — so you can ask a question in plain English and get an answer grounded in **PubMed**, **Europe PMC**, **FDA/UK drug labelling**, and **ClinicalTrials.gov**, with real PMIDs, NCT IDs, and DOIs you can verify.
+
+Every tool is a thin, deterministic wrapper over an official API. Nothing is invented; every result cites its source.
+
+- 🔬 **14 tools** across literature, drug labelling, and clinical trials
+- 🧾 **Verifiable by design** — results link back to DailyMed, the eMC, PubMed, and ClinicalTrials.gov
+- 🌍 **US *and* UK labelling** — a side-by-side `compare_labels` no other MCP server offers
+- 📰 **Preprints** via Europe PMC — surface work ahead of formal publication
+- 🆓 **No API keys required** (an optional free NCBI key raises PubMed rate limits)
+- 🧪 Fully **typed, tested, and CI-checked**
 
 Built by [PharmaTools.AI](https://pharmatools.ai).
 
-## Tools
+---
+
+## 🚀 Quick start (60 seconds)
+
+**1. Add PubCrawl to your client config** — no install step needed, `npx` fetches it on first run.
+
+For **Claude Desktop**, edit `claude_desktop_config.json`:
 
-### Literature
+- **macOS:** `~/Library/Application Support/Claude/claude_desktop_config.json`
+- **Windows:** `%APPDATA%\Claude\claude_desktop_config.json`
+
+```json
+{
+  "mcpServers": {
+    "pubcrawl": {
+      "command": "npx",
+      "args": ["-y", "@pharmatools/pubcrawl"]
+    }
+  }
+}
+```
+
+**2. Restart your client.** PubCrawl appears under **+ → Connectors**.
+
+**3. Ask away:**
+
+> _"Compare the US and UK labelling for atorvastatin, and find recent Phase 3 trials for it."_
+
+That's it. → [More examples](#-examples) · [API key & other options](#-configuration)
+
+---
+
+## 🧰 Tools
+
+### 📚 Literature
 
 | Tool | What it does |
 |------|-------------|
 | `search_pubmed` | Search PubMed with filters for date range, article type, and sort order. Returns PMIDs, titles, authors, journals, and DOIs. |
+| `search_europepmc` | Search Europe PMC — a broader corpus than PubMed that also indexes preprints (bioRxiv, medRxiv) and patents. Each result includes an abstract snippet, citation count, open-access status, and a preprint flag. Filter to preprints or open-access only. |
 | `get_abstract` | Get the full structured abstract for an article — broken into labeled sections (background, methods, results, conclusions) with keywords and MeSH terms. |
 | `get_full_text` | Retrieve the full text of open-access articles from PubMed Central, with parsed sections, figure/table captions, and reference counts. |
 | `find_related` | Find similar articles using PubMed's neighbor algorithm, ranked by relevance score. |
 | `format_citation` | Generate a formatted citation in APA, Vancouver, Harvard, or BibTeX style. |
 | `trending_papers` | Find recent papers on a topic, with optional filtering to high-impact journals (Nature, Science, Cell, NEJM, Lancet, JAMA, etc.). |
 
-### Drug Labelling
+### 💊 Drug labelling
 
 | Tool | What it does |
 |------|-------------|
-| `get_uspi` | Pull US Prescribing Information sections from DailyMed — indications, dosing, warnings, contraindications, and more. Parsed from FDA structured product labels. |
+| `resolve_drug_name` | Convert a brand drug name to its generic (or a generic to its US brand names), with drug class and common indications. Deterministic, via RxNorm/openFDA — no AI. |
+| `get_uspi` | Pull US Prescribing Information sections via openFDA (cited to DailyMed) — indications, dosing, warnings, contraindications, and more. |
 | `get_smpc` | Retrieve UK Summary of Product Characteristics from the eMC — the UK equivalent of US prescribing information, with numbered SmPC sections. |
 | `compare_labels` | Side-by-side comparison of US (USPI) and UK (SmPC) labelling for the same drug. Spot regulatory differences in indications, warnings, and dosing. |
-| `search_by_indication` | Find drugs approved for a medical condition. Searches FDA labelling via OpenFDA, then cross-references UK availability on the eMC. |
+| `search_by_indication` | Find drugs approved for a medical condition. Searches FDA labelling via openFDA, then cross-references UK availability on the eMC. |
 
-### Clinical Trials
+### 🧫 Clinical trials
 
 | Tool | What it does |
 |------|-------------|
 | `search_trials` | Search ClinicalTrials.gov for clinical trials. Filter by condition, intervention, recruitment status, and phase. Returns NCT IDs, sponsors, enrollment, and links. |
 | `get_trial` | Get full details for a clinical trial by NCT ID — eligibility criteria, study design, arms, primary/secondary outcomes, locations, and associated PubMed IDs. |
 
-## Setup
+---
+
+## 💬 Examples
+
+Once connected, just ask naturally:
+
+**Literature**
+- "Search PubMed for recent clinical trials on semaglutide."
+- "Search Europe PMC for preprints on GLP-1 receptor agonists, most cited first."
+- "Get the abstract for PMID 38127654, then find related papers and cite them all in Vancouver style."
+- "What are the trending papers on CRISPR gene therapy this month, high-impact journals only?"
+- "Pull the full text of that PMC article and summarise the methods section."
+
+**Drug labelling**
+- "Get the FDA prescribing information for metformin — just the indications and warnings."
+- "Pull the UK SmPC for atorvastatin."
+- "Compare US and UK labelling for lisinopril and highlight the differences."
+- "What's the generic name and drug class for Ozempic?"
+- "What drugs are approved for type 2 diabetes in both the US and UK?"
+
+**Clinical trials**
+- "Find recruiting Phase 3 trials for pembrolizumab in breast cancer."
+- "Get the eligibility criteria and primary outcomes for NCT03086486."
+
+**Cross-source (where PubCrawl shines)**
+- "For semaglutide: summarise the US label's cardiovascular indication, then find the pivotal trial and its NEJM publication."
+
+---
+
+## 🏗 Architecture
+
+Three layers — **tools** register the MCP interface, **lib clients** talk to each external API, and shared **cache** + **parsers** keep it fast and consistent.
+
+```mermaid
+flowchart LR
+    Client["🖥  MCP client<br/>Claude Desktop · Cursor · …"]
+
+    subgraph Server["PubCrawl MCP server"]
+        direction TB
+        Transport["stdio · Streamable HTTP"]
+        Tools["14 tools — src/tools/*"]
+        Shared["LRU cache · XML/JATS/SPL parser"]
+        Transport --> Tools --> Shared
+    end
+
+    Client -->|MCP| Transport
+
+    Tools --> NCBI["NCBI E-utilities"]
+    Tools --> EPMC["Europe PMC REST"]
+    Tools --> FDA["openFDA + DailyMed"]
+    Tools --> EMC["UK eMC"]
+    Tools --> CT["ClinicalTrials.gov v2"]
+
+    NCBI --> S1[("PubMed / PMC")]
+    EPMC --> S2[("Preprints · patents")]
+    FDA --> S3[("US labels")]
+    EMC --> S4[("UK labels")]
+    CT --> S5[("Trials")]
+```
+
+Each tool file exports a `register*Tool(server)` function with a zod schema and an async handler. All network calls are rate-limited, cached, and time-bounded. See [`CLAUDE.md`](CLAUDE.md) for a full architecture walkthrough and [`CONTRIBUTING.md`](CONTRIBUTING.md) to add a tool.
 
-### Prerequisites
+---
 
-- Node.js 20+
-- An MCP-compatible client (Claude Desktop, Cursor, etc.)
+## 🔧 Configuration
 
-### Install via npm
+### Install options
 
 ```bash
+# Zero-install (recommended): npx fetches it on demand — see Quick start above.
+
+# Or install globally:
 npm install -g @pharmatools/pubcrawl
+
+# Config for a global install:
+#   { "mcpServers": { "pubcrawl": { "command": "pubcrawl" } } }
 ```
 
-### Configure Claude Desktop
+### NCBI API key (optional)
 
-Add to your `claude_desktop_config.json`:
+Without a key, PubMed requests are limited to 3/second. A free key raises this to 10/second.
 
-**macOS:** `~/Library/Application Support/Claude/claude_desktop_config.json`
-**Windows:** `%APPDATA%\Claude\claude_desktop_config.json`
+1. Create a free NCBI account at <https://www.ncbi.nlm.nih.gov/account/>
+2. Account Settings → API Key Management → create a key
+3. Add it to your config:
 
 ```json
 {
   "mcpServers": {
     "pubcrawl": {
-      "command": "pubcrawl"
+      "command": "npx",
+      "args": ["-y", "@pharmatools/pubcrawl"],
+      "env": { "NCBI_API_KEY": "your_key_here" }
     }
   }
 }
 ```
 
-Restart Claude Desktop. PubCrawl will appear under **+ → Connectors**.
+### HTTP transport
 
-### Install from source
+PubCrawl also ships a stateless Streamable HTTP transport for browser-based and hosted clients:
 
 ```bash
-git clone https://github.com/nickjlamb/pubcrawl.git
-cd pubcrawl
-npm install
-npm run build
+npm run start:http   # serves POST /mcp and GET /health on PORT (default 3000)
 ```
 
-Then point the config at the built file:
+---
 
-```json
-{
-  "mcpServers": {
-    "pubcrawl": {
-      "command": "node",
-      "args": ["/path/to/pubcrawl/dist/index.js"]
-    }
-  }
-}
-```
+## 🗺 Roadmap
 
-### NCBI API key (optional)
+Highlights of what's planned — see [`ROADMAP.md`](ROADMAP.md) for the full list.
 
-Without an API key, requests are rate-limited to 3/second. With one, you get 10/second.
+- `get_europepmc_fulltext` — read preprints & OA articles surfaced by `search_europepmc`
+- `get_adverse_events` — openFDA FAERS adverse-event lookups
+- EMA / EPAR labelling to complement the US + UK `compare_labels`
+- MeSH query helper for sharper PubMed searches
+- MCP **resources** & **prompts** for common review workflows
 
-1. Create a free NCBI account at https://www.ncbi.nlm.nih.gov/account/
-2. Go to Account Settings → API Key Management
-3. Add the key to your config:
+Ideas welcome — [open an issue](https://github.com/nickjlamb/pubcrawl/issues/new/choose).
 
-```json
-{
-  "mcpServers": {
-    "pubcrawl": {
-      "command": "pubcrawl",
-      "env": {
-        "NCBI_API_KEY": "your_key_here"
-      }
-    }
-  }
-}
+---
+
+## 🛠 Development
+
+```bash
+git clone https://github.com/nickjlamb/pubcrawl.git
+cd pubcrawl
+npm install
+
+npm run dev      # TypeScript watch mode
+npm run build    # compile to dist/
+npm start        # run the stdio server
+npm test         # Vitest unit suite
+npm run lint     # ESLint
 ```
 
-## Example prompts
+Unit tests live in `tests/` and cover the parsing, caching, citation, and formatting logic with fixture payloads (no network calls). CI runs lint → test → build on every push and pull request. New to the codebase? Start with [`CONTRIBUTING.md`](CONTRIBUTING.md).
 
-Once connected, just ask naturally:
+---
 
-- "Search PubMed for recent clinical trials on semaglutide"
-- "Get the abstract for PMID 38127654"
-- "Find papers related to this one and format citations in APA"
-- "What are the trending papers on CRISPR gene therapy this month?"
-- "Get the full text of that paper from PMC"
-- "Get the FDA prescribing information for metformin — just the indications and warnings"
-- "Pull the UK SmPC for atorvastatin"
-- "Compare US and UK labelling for lisinopril"
-- "What drugs are approved for type 2 diabetes?"
-- "Find recruiting Phase 3 trials for pembrolizumab in breast cancer"
-- "Get details on clinical trial NCT03086486"
+## 📦 Releases & changelog
 
-## Development
+Versions follow [Semantic Versioning](https://semver.org). See the [**CHANGELOG**](CHANGELOG.md) for a full history and [Releases](https://github.com/nickjlamb/pubcrawl/releases) for notes and assets.
 
-```bash
-npm run dev    # TypeScript watch mode
-npm run build  # Compile to dist/
-npm start      # Run the server
-```
+## 🤝 Contributing
+
+Contributions are welcome and appreciated — bug reports, new data sources, new tools. Read the [contributing guide](CONTRIBUTING.md) to get started, then [open an issue](https://github.com/nickjlamb/pubcrawl/issues/new/choose) or a pull request.
+
+## 📄 License
 
-## License
+[MIT](LICENSE) © [PharmaTools.AI](https://pharmatools.ai)
 
-MIT
+<div align="center">
+<sub>Data from NCBI E-utilities, Europe PMC, openFDA, DailyMed, the UK eMC, and ClinicalTrials.gov. PubCrawl is not affiliated with these providers.</sub>
+</div>

package/dist/http.js

@@ -5,6 +5,7 @@ import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { StreamableHTTPServerTransport } from "@modelcontextprotocol/sdk/server/streamableHttp.js";
 import { setApiKey } from "./lib/ncbi.js";
 import { registerSearchTool } from "./tools/search.js";
+import { registerSearchEuropePmcTool } from "./tools/search-europepmc.js";
 import { registerAbstractTool } from "./tools/abstract.js";
 import { registerFullTextTool } from "./tools/fulltext.js";
 import { registerRelatedTool } from "./tools/related.js";
@@ -14,6 +15,7 @@ import { registerUspiTool } from "./tools/uspi.js";
 import { registerSmpcTool } from "./tools/smpc.js";
 import { registerCompareLabelsTool } from "./tools/compare-labels.js";
 import { registerSearchIndicationTool } from "./tools/search-indication.js";
+import { registerResolveNameTool } from "./tools/resolve-name.js";
 import { registerTrialsSearchTool } from "./tools/trials-search.js";
 import { registerTrialDetailTool } from "./tools/trials-detail.js";
 // Configure NCBI API key if available (10 req/s vs 3 req/s)
@@ -23,9 +25,10 @@ if (process.env.NCBI_API_KEY) {
 function createMcpServer() {
     const server = new McpServer({
         name: "pubcrawl",
-        version: "2.0.0",
+        version: "2.4.0",
     });
     registerSearchTool(server);
+    registerSearchEuropePmcTool(server);
     registerAbstractTool(server);
     registerFullTextTool(server);
     registerRelatedTool(server);
@@ -35,6 +38,7 @@ function createMcpServer() {
     registerSmpcTool(server);
     registerCompareLabelsTool(server);
     registerSearchIndicationTool(server);
+    registerResolveNameTool(server);
     registerTrialsSearchTool(server);
     registerTrialDetailTool(server);
     return server;

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+{"version":3,"file":"http.js","sourceRoot":"","sources":["../src/http.ts"],"names":[],"mappings":";AACA,OAAO,eAAe,CAAC;AACvB,OAAO,EAAE,YAAY,EAAE,MAAM,WAAW,CAAC;AACzC,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACpE,OAAO,EAAE,6BAA6B,EAAE,MAAM,oDAAoD,CAAC;AACnG,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAC;AAC1C,OAAO,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AACvD,OAAO,EAAE,2BAA2B,EAAE,MAAM,6BAA6B,CAAC;AAC1E,OAAO,EAAE,oBAAoB,EAAE,MAAM,qBAAqB,CAAC;AAC3D,OAAO,EAAE,oBAAoB,EAAE,MAAM,qBAAqB,CAAC;AAC3D,OAAO,EAAE,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AACzD,OAAO,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AACnD,OAAO,EAAE,oBAAoB,EAAE,MAAM,qBAAqB,CAAC;AAC3D,OAAO,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AACnD,OAAO,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AACnD,OAAO,EAAE,yBAAyB,EAAE,MAAM,2BAA2B,CAAC;AACtE,OAAO,EAAE,4BAA4B,EAAE,MAAM,8BAA8B,CAAC;AAC5E,OAAO,EAAE,uBAAuB,EAAE,MAAM,yBAAyB,CAAC;AAClE,OAAO,EAAE,wBAAwB,EAAE,MAAM,0BAA0B,CAAC;AACpE,OAAO,EAAE,uBAAuB,EAAE,MAAM,0BAA0B,CAAC;AAEnE,4DAA4D;AAC5D,IAAI,OAAO,CAAC,GAAG,CAAC,YAAY,EAAE,CAAC;IAC7B,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC;AACtC,CAAC;AAED,SAAS,eAAe;IACtB,MAAM,MAAM,GAAG,IAAI,SAAS,CAAC;QAC3B,IAAI,EAAE,UAAU;QAChB,OAAO,EAAE,OAAO;KACjB,CAAC,CAAC;IAEH,kBAAkB,CAAC,MAAM,CAAC,CAAC;IAC3B,2BAA2B,CAAC,MAAM,CAAC,CAAC;IACpC,oBAAoB,CAAC,MAAM,CAAC,CAAC;IAC7B,oBAAoB,CAAC,MAAM,CAAC,CAAC;IAC7B,mBAAmB,CAAC,MAAM,CAAC,CAAC;IAC5B,gBAAgB,CAAC,MAAM,CAAC,CAAC;IACzB,oBAAoB,CAAC,MAAM,CAAC,CAAC;IAC7B,gBAAgB,CAAC,MAAM,CAAC,CAAC;IACzB,gBAAgB,CAAC,MAAM,CAAC,CAAC;IACzB,yBAAyB,CAAC,MAAM,CAAC,CAAC;IAClC,4BAA4B,CAAC,MAAM,CAAC,CAAC;IACrC,uBAAuB,CAAC,MAAM,CAAC,CAAC;IAChC,wBAAwB,CAAC,MAAM,CAAC,CAAC;IACjC,uBAAuB,CAAC,MAAM,CAAC,CAAC;IAEhC,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,MAAM,IAAI,GAAG,QAAQ,CAAC,OAAO,CAAC,GAAG,CAAC,IAAI,IAAI,MAAM,EAAE,EAAE,CAAC,CAAC;AAEtD,MAAM,YAAY,GAA2B;IAC3C,6BAA6B,EAAE,GAAG;IAClC,8BAA8B,EAAE,oBAAoB;IACpD,8BAA8B,EAAE,qDAAqD;IACrF,+BAA+B,EAAE,gBAAgB;CAClD,CAAC;AAEF,MAAM,UAAU,GAAG,YAAY,CAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE;IACjD,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,GAAG,CAAC,GAAG,IAAI,GAAG,EAAE,UAAU,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,CAAC,CAAC;IAElE,wBAAwB;IACxB,IAAI,GAAG,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC;QAC7B,GAAG,CAAC,SAAS,CAAC,GAAG,EAAE,YAAY,CAAC,CAAC;QACjC,GAAG,CAAC,GAAG,EAAE,CAAC;QACV,OAAO;IACT,CAAC;IAED,oCAAoC;IACpC,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE,CAAC;QACxD,GAAG,CAAC,SAAS,CAAC,GAAG,EAAE,KAAK,CAAC,CAAC;IAC5B,CAAC;IAED,wBAAwB;IACxB,IAAI,GAAG,CAAC,QAAQ,KAAK,SAAS,IAAI,GAAG,CAAC,MAAM,KAAK,KAAK,EAAE,CAAC;QACvD,GAAG,CAAC,SAAS,CAAC,GAAG,EAAE,EAAE,cAAc,EAAE,kBAAkB,EAAE,CAAC,CAAC;QAC3D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC,CAAC,CAAC;QAC9D,OAAO;IACT,CAAC;IAED,qEAAqE;IACrE,IAAI,GAAG,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;QAC5B,MAAM,MAAM,GAAG,eAAe,EAAE,CAAC;QACjC,MAAM,SAAS,GAAG,IAAI,6BAA6B,CAAC;YAClD,kBAAkB,EAAE,SAAS;SAC9B,CAAC,CAAC;QACH,MAAM,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;QAChC,MAAM,SAAS,CAAC,aAAa,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC;QACxC,OAAO;IACT,CAAC;IAED,0BAA0B;IAC1B,GAAG,CAAC,SAAS,CAAC,GAAG,EAAE,EAAE,cAAc,EAAE,kBAAkB,EAAE,CAAC,CAAC;IAC3D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,KAAK,EAAE,WAAW,EAAE,CAAC,CAAC,CAAC;AAClD,CAAC,CAAC,CAAC;AAEH,UAAU,CAAC,MAAM,CAAC,IAAI,EAAE,SAAS,EAAE,GAAG,EAAE;IACtC,OAAO,CAAC,KAAK,CAAC,iDAAiD,IAAI,MAAM,CAAC,CAAC;AAC7E,CAAC,CAAC,CAAC"}

package/dist/index.js

@@ -4,6 +4,7 @@ import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import { setApiKey } from "./lib/ncbi.js";
 import { registerSearchTool } from "./tools/search.js";
+import { registerSearchEuropePmcTool } from "./tools/search-europepmc.js";
 import { registerAbstractTool } from "./tools/abstract.js";
 import { registerFullTextTool } from "./tools/fulltext.js";
 import { registerRelatedTool } from "./tools/related.js";
@@ -13,11 +14,12 @@ import { registerUspiTool } from "./tools/uspi.js";
 import { registerSmpcTool } from "./tools/smpc.js";
 import { registerCompareLabelsTool } from "./tools/compare-labels.js";
 import { registerSearchIndicationTool } from "./tools/search-indication.js";
+import { registerResolveNameTool } from "./tools/resolve-name.js";
 import { registerTrialsSearchTool } from "./tools/trials-search.js";
 import { registerTrialDetailTool } from "./tools/trials-detail.js";
 const server = new McpServer({
     name: "pubcrawl",
-    version: "2.0.0",
+    version: "2.4.0",
 });
 // Configure NCBI API key if available (10 req/s vs 3 req/s)
 if (process.env.NCBI_API_KEY) {
@@ -25,6 +27,7 @@ if (process.env.NCBI_API_KEY) {
 }
 // Register all tools
 registerSearchTool(server);
+registerSearchEuropePmcTool(server);
 registerAbstractTool(server);
 registerFullTextTool(server);
 registerRelatedTool(server);
@@ -34,6 +37,7 @@ registerUspiTool(server);
 registerSmpcTool(server);
 registerCompareLabelsTool(server);
 registerSearchIndicationTool(server);
+registerResolveNameTool(server);
 registerTrialsSearchTool(server);
 registerTrialDetailTool(server);
 // Start server

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA,OAAO,eAAe,CAAC;AACvB,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACpE,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AACjF,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAC;AAC1C,OAAO,EAAE,kBAAkB,EAAE,MAAM,mBAAmB,CAAC;AACvD,OAAO,EAAE,2BAA2B,EAAE,MAAM,6BAA6B,CAAC;AAC1E,OAAO,EAAE,oBAAoB,EAAE,MAAM,qBAAqB,CAAC;AAC3D,OAAO,EAAE,oBAAoB,EAAE,MAAM,qBAAqB,CAAC;AAC3D,OAAO,EAAE,mBAAmB,EAAE,MAAM,oBAAoB,CAAC;AACzD,OAAO,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AACnD,OAAO,EAAE,oBAAoB,EAAE,MAAM,qBAAqB,CAAC;AAC3D,OAAO,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AACnD,OAAO,EAAE,gBAAgB,EAAE,MAAM,iBAAiB,CAAC;AACnD,OAAO,EAAE,yBAAyB,EAAE,MAAM,2BAA2B,CAAC;AACtE,OAAO,EAAE,4BAA4B,EAAE,MAAM,8BAA8B,CAAC;AAC5E,OAAO,EAAE,uBAAuB,EAAE,MAAM,yBAAyB,CAAC;AAClE,OAAO,EAAE,wBAAwB,EAAE,MAAM,0BAA0B,CAAC;AACpE,OAAO,EAAE,uBAAuB,EAAE,MAAM,0BAA0B,CAAC;AAEnE,MAAM,MAAM,GAAG,IAAI,SAAS,CAAC;IAC3B,IAAI,EAAE,UAAU;IAChB,OAAO,EAAE,OAAO;CACjB,CAAC,CAAC;AAEH,4DAA4D;AAC5D,IAAI,OAAO,CAAC,GAAG,CAAC,YAAY,EAAE,CAAC;IAC7B,SAAS,CAAC,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAC;AACtC,CAAC;AAED,qBAAqB;AACrB,kBAAkB,CAAC,MAAM,CAAC,CAAC;AAC3B,2BAA2B,CAAC,MAAM,CAAC,CAAC;AACpC,oBAAoB,CAAC,MAAM,CAAC,CAAC;AAC7B,oBAAoB,CAAC,MAAM,CAAC,CAAC;AAC7B,mBAAmB,CAAC,MAAM,CAAC,CAAC;AAC5B,gBAAgB,CAAC,MAAM,CAAC,CAAC;AACzB,oBAAoB,CAAC,MAAM,CAAC,CAAC;AAC7B,gBAAgB,CAAC,MAAM,CAAC,CAAC;AACzB,gBAAgB,CAAC,MAAM,CAAC,CAAC;AACzB,yBAAyB,CAAC,MAAM,CAAC,CAAC;AAClC,4BAA4B,CAAC,MAAM,CAAC,CAAC;AACrC,uBAAuB,CAAC,MAAM,CAAC,CAAC;AAChC,wBAAwB,CAAC,MAAM,CAAC,CAAC;AACjC,uBAAuB,CAAC,MAAM,CAAC,CAAC;AAEhC,eAAe;AACf,KAAK,UAAU,IAAI;IACjB,MAAM,SAAS,GAAG,IAAI,oBAAoB,EAAE,CAAC;IAC7C,MAAM,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;IAChC,OAAO,CAAC,KAAK,CAAC,sCAAsC,CAAC,CAAC;AACxD,CAAC;AAED,IAAI,EAAE,CAAC,KAAK,CAAC,CAAC,KAAK,EAAE,EAAE;IACrB,OAAO,CAAC,KAAK,CAAC,cAAc,EAAE,KAAK,CAAC,CAAC;IACrC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC,CAAC,CAAC"}

package/dist/lib/clinicaltrials.d.ts

@@ -1,4 +1,5 @@
 import { ClinicalTrialSummary, ClinicalTrialDetail } from "../types.js";
+export declare function studyToSummary(study: Record<string, unknown>): ClinicalTrialSummary;
 export declare function searchTrials(params: {
     condition?: string;
     intervention?: string;

package/dist/lib/clinicaltrials.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"clinicaltrials.d.ts","sourceRoot":"","sources":["../../src/lib/clinicaltrials.ts"],"names":[],"mappings":"AACA,OAAO,EACL,oBAAoB,EACpB,mBAAmB,EAKpB,MAAM,aAAa,CAAC;AA6FrB,wBAAsB,YAAY,CAAC,MAAM,EAAE;IACzC,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf,GAAG,OAAO,CAAC;IAAE,OAAO,EAAE,oBAAoB,EAAE,CAAC;IAAC,WAAW,EAAE,MAAM,CAAA;CAAE,CAAC,CA2DpE;AAED,wBAAsB,cAAc,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,mBAAmB,CAAC,CA0FhF"}
+{"version":3,"file":"clinicaltrials.d.ts","sourceRoot":"","sources":["../../src/lib/clinicaltrials.ts"],"names":[],"mappings":"AACA,OAAO,EACL,oBAAoB,EACpB,mBAAmB,EAKpB,MAAM,aAAa,CAAC;AAoCrB,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,oBAAoB,CAuDnF;AAED,wBAAsB,YAAY,CAAC,MAAM,EAAE;IACzC,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,IAAI,CAAC,EAAE,MAAM,CAAC;CACf,GAAG,OAAO,CAAC;IAAE,OAAO,EAAE,oBAAoB,EAAE,CAAC;IAAC,WAAW,EAAE,MAAM,CAAA;CAAE,CAAC,CA2DpE;AAED,wBAAsB,cAAc,CAAC,KAAK,EAAE,MAAM,GAAG,OAAO,CAAC,mBAAmB,CAAC,CA0FhF"}

package/dist/lib/clinicaltrials.js

@@ -26,7 +26,7 @@ async function rateLimitedFetch(url) {
 function str(value) {
     return value != null ? String(value) : "";
 }
-function studyToSummary(study) {
+export function studyToSummary(study) {
     const proto = study.protocolSection;
     if (!proto) {
         return {

package/dist/lib/clinicaltrials.js.map

@@ -1 +1 @@
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+{"version":3,"file":"clinicaltrials.js","sourceRoot":"","sources":["../../src/lib/clinicaltrials.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,YAAY,CAAC;AAUxC,MAAM,QAAQ,GAAG,mCAAmC,CAAC;AACrD,MAAM,gBAAgB,GAAG,IAAI,CAAC,CAAC,cAAc;AAC7C,MAAM,UAAU,GAAG,KAAK,CAAC;AAEzB,IAAI,eAAe,GAAG,CAAC,CAAC;AAExB,KAAK,UAAU,gBAAgB,CAAC,GAAW;IACzC,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;IACvB,MAAM,OAAO,GAAG,GAAG,GAAG,eAAe,CAAC;IAEtC,IAAI,OAAO,GAAG,gBAAgB,EAAE,CAAC;QAC/B,MAAM,IAAI,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE,CAAC,UAAU,CAAC,OAAO,EAAE,gBAAgB,GAAG,OAAO,CAAC,CAAC,CAAC;IAClF,CAAC;IAED,eAAe,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC;IAE7B,MAAM,UAAU,GAAG,IAAI,eAAe,EAAE,CAAC;IACzC,MAAM,OAAO,GAAG,UAAU,CAAC,GAAG,EAAE,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,UAAU,CAAC,CAAC;IAEjE,IAAI,CAAC;QACH,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,GAAG,EAAE,EAAE,MAAM,EAAE,UAAU,CAAC,MAAM,EAAE,CAAC,CAAC;QACjE,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;YACjB,MAAM,IAAI,KAAK,CAAC,iCAAiC,QAAQ,CAAC,MAAM,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAC,CAAC;QAC7F,CAAC;QACD,OAAO,QAAQ,CAAC;IAClB,CAAC;YAAS,CAAC;QACT,YAAY,CAAC,OAAO,CAAC,CAAC;IACxB,CAAC;AACH,CAAC;AAED,SAAS,GAAG,CAAC,KAAc;IACzB,OAAO,KAAK,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;AAC5C,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,KAA8B;IAC3D,MAAM,KAAK,GAAG,KAAK,CAAC,eAAsD,CAAC;IAC3E,IAAI,CAAC,KAAK,EAAE,CAAC;QACX,OAAO;YACL,MAAM,EAAE,EAAE;YACV,KAAK,EAAE,EAAE;YACT,MAAM,EAAE,EAAE;YACV,KAAK,EAAE,EAAE;YACT,UAAU,EAAE,EAAE;YACd,aAAa,EAAE,EAAE;YACjB,UAAU,EAAE,IAAI;YAChB,OAAO,EAAE,EAAE;YACX,UAAU,EAAE,EAAE;YACd,eAAe,EAAE,EAAE;YACnB,UAAU,EAAE,EAAE;YACd,GAAG,EAAE,EAAE;SACR,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,GAAG,KAAK,CAAC,oBAA2D,CAAC;IAC7E,MAAM,MAAM,GAAG,KAAK,CAAC,YAAmD,CAAC;IACzE,MAAM,MAAM,GAAG,KAAK,CAAC,YAAmD,CAAC;IACzE,MAAM,UAAU,GAAG,KAAK,CAAC,gBAAuD,CAAC;IACjF,MAAM,IAAI,GAAG,KAAK,CAAC,uBAA8D,CAAC;IAClF,MAAM,OAAO,GAAG,KAAK,CAAC,0BAAiE,CAAC;IAExF,MAAM,gBAAgB,GAAI,IAAI,EAAE,aAA4D,IAAI,EAAE,CAAC;IACnG,MAAM,aAAa,GAAwB,gBAAgB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;QACtE,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC;QACjB,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC;KAClB,CAAC,CAAC,CAAC;IAEJ,MAAM,eAAe,GAAG,MAAM,EAAE,eAAsD,CAAC;IACvF,MAAM,oBAAoB,GAAG,MAAM,EAAE,oBAA2D,CAAC;IACjG,MAAM,cAAc,GAAG,MAAM,EAAE,cAAqD,CAAC;IACrF,MAAM,WAAW,GAAG,OAAO,EAAE,WAAkD,CAAC;IAEhF,MAAM,MAAM,GAAI,MAAM,EAAE,MAA+B,IAAI,EAAE,CAAC;IAE9D,MAAM,KAAK,GAAG,GAAG,CAAC,EAAE,EAAE,KAAK,CAAC,CAAC;IAE7B,OAAO;QACL,MAAM,EAAE,KAAK;QACb,KAAK,EAAE,GAAG,CAAC,EAAE,EAAE,UAAU,CAAC;QAC1B,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,aAAa,CAAC;QAClC,KAAK,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,IAAI,KAAK;QAChC,UAAU,EAAG,UAAU,EAAE,UAAmC,IAAI,EAAE;QAClE,aAAa;QACb,UAAU,EAAE,cAAc,EAAE,KAAK,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,cAAc,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,IAAI;QAC/E,OAAO,EAAE,GAAG,CAAC,WAAW,EAAE,IAAI,CAAC;QAC/B,UAAU,EAAE,GAAG,CAAC,eAAe,EAAE,IAAI,CAAC;QACtC,eAAe,EAAE,GAAG,CAAC,oBAAoB,EAAE,IAAI,CAAC;QAChD,UAAU,EAAE,GAAG,CAAC,MAAM,EAAE,SAAS,CAAC;QAClC,GAAG,EAAE,KAAK,CAAC,CAAC,CAAC,oCAAoC,KAAK,EAAE,CAAC,CAAC,CAAC,EAAE;KAC9D,CAAC;AACJ,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,YAAY,CAAC,MAQlC;IACC,MAAM,QAAQ,GAAG,aAAa,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,EAAE,CAAC;IACvD,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAA2D,QAAQ,CAAC,CAAC;IAC7F,IAAI,MAAM;QAAE,OAAO,MAAM,CAAC;IAE1B,MAAM,GAAG,GAAG,IAAI,GAAG,CAAC,GAAG,QAAQ,UAAU,CAAC,CAAC;IAE3C,6CAA6C;IAC7C,IAAI,MAAM,CAAC,SAAS;QAAE,GAAG,CAAC,YAAY,CAAC,GAAG,CAAC,YAAY,EAAE,MAAM,CAAC,SAAS,CAAC,CAAC;IAC3E,IAAI,MAAM,CAAC,YAAY;QAAE,GAAG,CAAC,YAAY,CAAC,GAAG,CAAC,YAAY,EAAE,MAAM,CAAC,YAAY,CAAC,CAAC;IACjF,IAAI,MAAM,CAAC,IAAI;QAAE,GAAG,CAAC,YAAY,CAAC,GAAG,CAAC,YAAY,EAAE,MAAM,CAAC,IAAI,CAAC,CAAC;IAEjE,UAAU;IACV,IAAI,MAAM,CAAC,MAAM;QAAE,GAAG,CAAC,YAAY,CAAC,GAAG,CAAC,sBAAsB,EAAE,MAAM,CAAC,MAAM,CAAC,CAAC;IAC/E,IAAI,MAAM,CAAC,KAAK;QAAE,GAAG,CAAC,YAAY,CAAC,GAAG,CAAC,cAAc,EAAE,MAAM,CAAC,KAAK,CAAC,CAAC;IAErE,qCAAqC;IACrC,GAAG,CAAC,YAAY,CAAC,GAAG,CAClB,QAAQ,EACR;QACE,OAAO;QACP,YAAY;QACZ,eAAe;QACf,OAAO;QACP,WAAW;QACX,kBAAkB;QAClB,kBAAkB;QAClB,iBAAiB;QACjB,iBAAiB;QACjB,WAAW;QACX,gBAAgB;QAChB,WAAW;KACZ,CAAC,IAAI,CAAC,GAAG,CAAC,CACZ,CAAC;IAEF,GAAG,CAAC,YAAY,CAAC,GAAG,CAAC,UAAU,EAAE,MAAM,CAAC,MAAM,CAAC,UAAU,IAAI,EAAE,CAAC,CAAC,CAAC;IAElE,OAAO;IACP,MAAM,OAAO,GAA2B;QACtC,SAAS,EAAE,EAAE;QACb,YAAY,EAAE,oBAAoB;QAClC,UAAU,EAAE,oBAAoB;QAChC,UAAU,EAAE,iBAAiB;KAC9B,CAAC;IACF,MAAM,SAAS,GAAG,OAAO,CAAC,MAAM,CAAC,IAAI,IAAI,WAAW,CAAC,CAAC;IACtD,IAAI,SAAS;QAAE,GAAG,CAAC,YAAY,CAAC,GAAG,CAAC,MAAM,EAAE,SAAS,CAAC,CAAC;IAEvD,GAAG,CAAC,YAAY,CAAC,GAAG,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC;IAEvC,MAAM,QAAQ,GAAG,MAAM,gBAAgB,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC;IACxD,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;IAEnC,MAAM,OAAO,GAAI,IAAI,CAAC,OAAsD,IAAI,EAAE,CAAC;IACnF,MAAM,OAAO,GAAG,OAAO,CAAC,GAAG,CAAC,cAAc,CAAC,CAAC;IAC5C,MAAM,UAAU,GAAI,IAAI,CAAC,UAAiC,IAAI,OAAO,CAAC,MAAM,CAAC;IAE7E,MAAM,MAAM,GAAG,EAAE,OAAO,EAAE,WAAW,EAAE,UAAU,EAAE,CAAC;IACpD,KAAK,CAAC,GAAG,CAAC,QAAQ,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;IACxC,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,cAAc,CAAC,KAAa;IAChD,MAAM,QAAQ,GAAG,aAAa,KAAK,EAAE,CAAC;IACtC,MAAM,MAAM,GAAG,KAAK,CAAC,GAAG,CAAsB,QAAQ,CAAC,CAAC;IACxD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package/dist/lib/europepmc.d.ts

@@ -0,0 +1,20 @@
+import { EuropePmcArticle } from "../types.js";
+/**
+ * Build a EuropePmcArticle from a single Europe PMC `core` result object.
+ *
+ * Pure and defensive: every field is optional in the API response, so each is
+ * guarded. Exported so it can be unit-tested against fixture payloads without
+ * a network call.
+ */
+export declare function formatEuropePmcResult(result: Record<string, unknown>): EuropePmcArticle;
+export declare function searchEuropePmc(params: {
+    query: string;
+    maxResults?: number;
+    sort?: "relevance" | "date" | "cited";
+    preprintsOnly?: boolean;
+    openAccessOnly?: boolean;
+}): Promise<{
+    results: EuropePmcArticle[];
+    total_count: number;
+}>;
+//# sourceMappingURL=europepmc.d.ts.map

package/dist/lib/europepmc.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"europepmc.d.ts","sourceRoot":"","sources":["../../src/lib/europepmc.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,gBAAgB,EAAE,MAAM,aAAa,CAAC;AAuC/C;;;;;;GAMG;AACH,wBAAgB,qBAAqB,CACnC,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC9B,gBAAgB,CA4BlB;AAED,wBAAsB,eAAe,CAAC,MAAM,EAAE;IAC5C,KAAK,EAAE,MAAM,CAAC;IACd,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,IAAI,CAAC,EAAE,WAAW,GAAG,MAAM,GAAG,OAAO,CAAC;IACtC,aAAa,CAAC,EAAE,OAAO,CAAC;IACxB,cAAc,CAAC,EAAE,OAAO,CAAC;CAC1B,GAAG,OAAO,CAAC;IAAE,OAAO,EAAE,gBAAgB,EAAE,CAAC;IAAC,WAAW,EAAE,MAAM,CAAA;CAAE,CAAC,CAiChE"}

package/dist/lib/europepmc.js

@@ -0,0 +1,96 @@
+import { cache, TTL } from "./cache.js";
+const BASE_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest";
+const EMAIL = "nick@pharmatools.ai";
+const REQUEST_DELAY_MS = 200;
+const TIMEOUT_MS = 15000;
+let lastRequestTime = 0;
+async function rateLimitedFetch(url) {
+    const now = Date.now();
+    const elapsed = now - lastRequestTime;
+    if (elapsed < REQUEST_DELAY_MS) {
+        await new Promise((resolve) => setTimeout(resolve, REQUEST_DELAY_MS - elapsed));
+    }
+    lastRequestTime = Date.now();
+    const controller = new AbortController();
+    const timeout = setTimeout(() => controller.abort(), TIMEOUT_MS);
+    try {
+        const response = await fetch(url, { signal: controller.signal });
+        if (!response.ok) {
+            throw new Error(`Europe PMC API error: ${response.status} ${response.statusText}`);
+        }
+        return response;
+    }
+    finally {
+        clearTimeout(timeout);
+    }
+}
+const SORT_MAP = {
+    relevance: undefined,
+    date: "P_PDATE_D desc",
+    cited: "CITED desc",
+};
+/**
+ * Build a EuropePmcArticle from a single Europe PMC `core` result object.
+ *
+ * Pure and defensive: every field is optional in the API response, so each is
+ * guarded. Exported so it can be unit-tested against fixture payloads without
+ * a network call.
+ */
+export function formatEuropePmcResult(result) {
+    const source = String(result.source ?? "");
+    const id = String(result.id ?? "");
+    const journalInfo = (result.journalInfo ?? {});
+    const journal = (journalInfo.journal ?? {});
+    const abstractText = String(result.abstractText ?? "");
+    return {
+        id,
+        source,
+        pmid: result.pmid ? String(result.pmid) : "",
+        pmcid: result.pmcid ? String(result.pmcid) : "",
+        doi: result.doi ? String(result.doi) : "",
+        title: String(result.title ?? ""),
+        authors: String(result.authorString ?? ""),
+        journal: String(journal.title ?? "") || String(journal.isoabbreviation ?? ""),
+        year: String(result.pubYear ?? journalInfo.yearOfPublication ?? ""),
+        is_preprint: source === "PPR",
+        is_open_access: result.isOpenAccess === "Y",
+        cited_by_count: result.citedByCount != null ? Number(result.citedByCount) : 0,
+        // inEPMC === "Y" means the full text is readable in Europe PMC; a PMCID is a
+        // reliable fallback signal that an open full text exists.
+        has_full_text: result.inEPMC === "Y" || !!result.pmcid,
+        abstract_snippet: abstractText ? abstractText.slice(0, 300) : "",
+        url: source && id ? `https://europepmc.org/article/${source}/${id}` : "",
+    };
+}
+export async function searchEuropePmc(params) {
+    const cacheKey = `epmc:search:${JSON.stringify(params)}`;
+    const cached = cache.get(cacheKey);
+    if (cached)
+        return cached;
+    // Compose the query with optional filters.
+    let query = params.query;
+    if (params.preprintsOnly)
+        query += " AND (SRC:PPR)";
+    if (params.openAccessOnly)
+        query += " AND (OPEN_ACCESS:Y)";
+    const url = new URL(`${BASE_URL}/search`);
+    url.searchParams.set("query", query);
+    url.searchParams.set("resultType", "core");
+    url.searchParams.set("format", "json");
+    url.searchParams.set("pageSize", String(params.maxResults ?? 10));
+    url.searchParams.set("email", EMAIL);
+    const sort = SORT_MAP[params.sort ?? "relevance"];
+    if (sort)
+        url.searchParams.set("sort", sort);
+    const response = await rateLimitedFetch(url.toString());
+    const data = (await response.json());
+    const resultList = (data.resultList ?? {});
+    const rawResults = (resultList.result ?? []);
+    const result = {
+        results: rawResults.map(formatEuropePmcResult),
+        total_count: data.hitCount != null ? Number(data.hitCount) : 0,
+    };
+    cache.set(cacheKey, result, TTL.SEARCH);
+    return result;
+}
+//# sourceMappingURL=europepmc.js.map

package/dist/lib/europepmc.js.map

@@ -0,0 +1 @@
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package/dist/lib/pubmed-format.d.ts

@@ -0,0 +1,14 @@
+import { PubMedArticle } from "../types.js";
+/**
+ * Build a PubMedArticle from a single NCBI esummary document.
+ *
+ * Shared by search_pubmed, find_related, and trending_papers so the three
+ * tools return an identical shape from the same code path.
+ *
+ * Note: esummary does NOT return abstract text, so no abstract field is
+ * populated here. (A previous version put `doc.sorttitle` — a normalised copy
+ * of the title — into an `abstract_snippet` field, which duplicated the title
+ * under a misleading key. Use get_abstract to retrieve real abstract text.)
+ */
+export declare function formatSummaryArticle(uid: string, doc: Record<string, unknown>): PubMedArticle;
+//# sourceMappingURL=pubmed-format.d.ts.map

package/dist/lib/pubmed-format.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"pubmed-format.d.ts","sourceRoot":"","sources":["../../src/lib/pubmed-format.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAE,MAAM,aAAa,CAAC;AAE5C;;;;;;;;;;GAUG;AACH,wBAAgB,oBAAoB,CAClC,GAAG,EAAE,MAAM,EACX,GAAG,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC3B,aAAa,CAcf"}

package/dist/lib/pubmed-format.js

@@ -0,0 +1,27 @@
+import { parseSummaryAuthors } from "./xml-parser.js";
+/**
+ * Build a PubMedArticle from a single NCBI esummary document.
+ *
+ * Shared by search_pubmed, find_related, and trending_papers so the three
+ * tools return an identical shape from the same code path.
+ *
+ * Note: esummary does NOT return abstract text, so no abstract field is
+ * populated here. (A previous version put `doc.sorttitle` — a normalised copy
+ * of the title — into an `abstract_snippet` field, which duplicated the title
+ * under a misleading key. Use get_abstract to retrieve real abstract text.)
+ */
+export function formatSummaryArticle(uid, doc) {
+    const authors = parseSummaryAuthors(doc.authors);
+    const pubDate = String(doc.pubdate ?? "");
+    const year = pubDate.match(/\d{4}/)?.[0] ?? "";
+    const doi = String(doc.elocationid ?? "").replace(/^doi:\s*/i, "");
+    return {
+        pmid: uid,
+        title: String(doc.title ?? ""),
+        authors,
+        journal: String(doc.fulljournalname ?? doc.source ?? ""),
+        year,
+        doi,
+    };
+}
+//# sourceMappingURL=pubmed-format.js.map

package/dist/lib/pubmed-format.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"pubmed-format.js","sourceRoot":"","sources":["../../src/lib/pubmed-format.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,mBAAmB,EAAE,MAAM,iBAAiB,CAAC;AAGtD;;;;;;;;;;GAUG;AACH,MAAM,UAAU,oBAAoB,CAClC,GAAW,EACX,GAA4B;IAE5B,MAAM,OAAO,GAAG,mBAAmB,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;IACjD,MAAM,OAAO,GAAG,MAAM,CAAC,GAAG,CAAC,OAAO,IAAI,EAAE,CAAC,CAAC;IAC1C,MAAM,IAAI,GAAG,OAAO,CAAC,KAAK,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;IAC/C,MAAM,GAAG,GAAG,MAAM,CAAC,GAAG,CAAC,WAAW,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;IAEnE,OAAO;QACL,IAAI,EAAE,GAAG;QACT,KAAK,EAAE,MAAM,CAAC,GAAG,CAAC,KAAK,IAAI,EAAE,CAAC;QAC9B,OAAO;QACP,OAAO,EAAE,MAAM,CAAC,GAAG,CAAC,eAAe,IAAI,GAAG,CAAC,MAAM,IAAI,EAAE,CAAC;QACxD,IAAI;QACJ,GAAG;KACJ,CAAC;AACJ,CAAC"}

package/dist/tools/cite.d.ts

@@ -1,3 +1,18 @@
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export interface ArticleInfo {
+    authors: string[];
+    title: string;
+    journal: string;
+    year: string;
+    volume: string;
+    issue: string;
+    pages: string;
+    doi: string;
+    pmid: string;
+}
+export declare function formatApa(info: ArticleInfo): string;
+export declare function formatVancouver(info: ArticleInfo): string;
+export declare function formatHarvard(info: ArticleInfo): string;
+export declare function formatBibtex(info: ArticleInfo): string;
 export declare function registerCiteTool(server: McpServer): void;
 //# sourceMappingURL=cite.d.ts.map

package/dist/tools/cite.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"cite.d.ts","sourceRoot":"","sources":["../../src/tools/cite.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AA4IpE,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAoFxD"}
+{"version":3,"file":"cite.d.ts","sourceRoot":"","sources":["../../src/tools/cite.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AASpE,MAAM,WAAW,WAAW;IAC1B,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,KAAK,EAAE,MAAM,CAAC;IACd,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,EAAE,MAAM,CAAC;IACb,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,MAAM,CAAC;IACd,GAAG,EAAE,MAAM,CAAC;IACZ,IAAI,EAAE,MAAM,CAAC;CACd;AAED,wBAAgB,SAAS,CAAC,IAAI,EAAE,WAAW,GAAG,MAAM,CAgCnD;AAED,wBAAgB,eAAe,CAAC,IAAI,EAAE,WAAW,GAAG,MAAM,CA0BzD;AAED,wBAAgB,aAAa,CAAC,IAAI,EAAE,WAAW,GAAG,MAAM,CA2BvD;AAED,wBAAgB,YAAY,CAAC,IAAI,EAAE,WAAW,GAAG,MAAM,CA0BtD;AAED,wBAAgB,gBAAgB,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAoFxD"}

package/dist/tools/cite.js

@@ -5,7 +5,7 @@ const schema = {
     pmid: z.string().describe("PubMed ID"),
     style: z.enum(["apa", "vancouver", "harvard", "bibtex"]).default("apa").describe("Citation style"),
 };
-function formatApa(info) {
+export function formatApa(info) {
     const authorStr = info.authors.length === 0
         ? ""
         : info.authors.length <= 7
@@ -36,7 +36,7 @@ function formatApa(info) {
     const doiPart = info.doi ? ` https://doi.org/${info.doi}` : "";
     return `${authorStr}${yearPart}${titlePart}${journalPart}${volPart}${issuePart}${pagesPart}.${doiPart}`.trim();
 }
-function formatVancouver(info) {
+export function formatVancouver(info) {
     const authorStr = info.authors.length === 0
         ? ""
         : info.authors.length <= 6
@@ -61,7 +61,7 @@ function formatVancouver(info) {
     const doiPart = info.doi ? ` doi:${info.doi}` : "";
     return `${authorStr}.${titlePart}${journalPart}${yearPart}${volPart}${issuePart}${pagesPart}.${doiPart}`.trim();
 }
-function formatHarvard(info) {
+export function formatHarvard(info) {
     const authorStr = info.authors.length === 0
         ? ""
         : info.authors.length <= 3
@@ -87,7 +87,7 @@ function formatHarvard(info) {
     const doiPart = info.doi ? `. doi:${info.doi}` : "";
     return `${authorStr}${yearPart}${titlePart}${journalPart}${volPart}${issuePart}${pagesPart}${doiPart}`.trim();
 }
-function formatBibtex(info) {
+export function formatBibtex(info) {
     const key = info.authors.length > 0
         ? info.authors[0].split(" ")[0].toLowerCase() + info.year
         : `pmid${info.pmid}`;

package/dist/tools/cite.js.map

@@ -1 +1 @@
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package/dist/tools/related.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"related.d.ts","sourceRoot":"","sources":["../../src/tools/related.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAUpE,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAiE3D"}
+{"version":3,"file":"related.d.ts","sourceRoot":"","sources":["../../src/tools/related.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAUpE,wBAAgB,mBAAmB,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAoD3D"}

package/dist/tools/related.js

@@ -1,6 +1,6 @@
 import { z } from "zod";
 import { elink, esummary } from "../lib/ncbi.js";
-import { parseSummaryAuthors } from "../lib/xml-parser.js";
+import { formatSummaryArticle } from "../lib/pubmed-format.js";
 const schema = {
     pmid: z.string().describe("PubMed ID to find related articles for"),
     maxResults: z.number().min(1).max(100).default(10).describe("Maximum number of results"),
@@ -27,20 +27,8 @@ export function registerRelatedTool(server) {
                 .filter((uid) => summaryData[uid])
                 .map((uid) => {
                 const doc = summaryData[uid];
-                const authors = parseSummaryAuthors(doc.authors);
-                const pubDate = String(doc.pubdate ?? "");
-                const year = pubDate.match(/\d{4}/)?.[0] ?? "";
-                const doi = (doc.elocationid ?? "")
-                    .toString()
-                    .replace(/^doi:\s*/i, "");
                 return {
-                    pmid: uid,
-                    title: String(doc.title ?? ""),
-                    authors,
-                    journal: String(doc.fulljournalname ?? doc.source ?? ""),
-                    year,
-                    doi,
-                    abstract_snippet: String(doc.sorttitle ?? "").slice(0, 200),
+                    ...formatSummaryArticle(uid, doc),
                     relevance_score: scoreMap.get(uid) ?? 0,
                 };
             });

package/dist/tools/related.js.map

@@ -1 +1 @@
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package/dist/tools/resolve-name.d.ts

@@ -0,0 +1,11 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { type ResolveResult } from "@pharmatools/drug-data";
+/**
+ * Resolve a drug name deterministically via the shared engine (RxNorm, openFDA
+ * fallback). Cached for 1h. Returns { error } when the name isn't recognised.
+ */
+export declare function buildResolveResult(drug: string): Promise<ResolveResult | {
+    error: string;
+}>;
+export declare function registerResolveNameTool(server: McpServer): void;
+//# sourceMappingURL=resolve-name.d.ts.map

package/dist/tools/resolve-name.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"resolve-name.d.ts","sourceRoot":"","sources":["../../src/tools/resolve-name.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AACpE,OAAO,EAAe,KAAK,aAAa,EAAE,MAAM,wBAAwB,CAAC;AASzE;;;GAGG;AACH,wBAAsB,kBAAkB,CACtC,IAAI,EAAE,MAAM,GACX,OAAO,CAAC,aAAa,GAAG;IAAE,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC,CAW5C;AAED,wBAAgB,uBAAuB,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAuB/D"}

package/dist/tools/resolve-name.js

@@ -0,0 +1,44 @@
+import { z } from "zod";
+import { resolveName } from "@pharmatools/drug-data";
+import { cache, TTL } from "../lib/cache.js";
+const schema = {
+    drug: z
+        .string()
+        .describe("Brand or generic drug name to resolve (e.g., 'Lipitor' or 'atorvastatin')"),
+};
+/**
+ * Resolve a drug name deterministically via the shared engine (RxNorm, openFDA
+ * fallback). Cached for 1h. Returns { error } when the name isn't recognised.
+ */
+export async function buildResolveResult(drug) {
+    const cacheKey = `resolve:${drug.toLowerCase().trim()}`;
+    const cached = cache.get(cacheKey);
+    if (cached)
+        return cached;
+    const result = await resolveName(drug);
+    if (!result) {
+        return { error: `Could not resolve "${drug}" in RxNorm or openFDA` };
+    }
+    cache.set(cacheKey, result, TTL.SEARCH);
+    return result;
+}
+export function registerResolveNameTool(server) {
+    server.tool("resolve_drug_name", "Convert a brand drug name to its generic name (or a generic to its US brand names), with drug class and common indications. Deterministic — sourced from RxNorm/openFDA, no AI.", schema, { readOnlyHint: true, destructiveHint: false, openWorldHint: true }, async (params) => {
+        try {
+            const result = await buildResolveResult(params.drug);
+            const isError = "error" in result;
+            return {
+                content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+                ...(isError ? { isError: true } : {}),
+            };
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            return {
+                content: [{ type: "text", text: `Error resolving drug name: ${message}` }],
+                isError: true,
+            };
+        }
+    });
+}
+//# sourceMappingURL=resolve-name.js.map

package/dist/tools/resolve-name.js.map

@@ -0,0 +1 @@
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package/dist/tools/search-europepmc.d.ts

@@ -0,0 +1,3 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+export declare function registerSearchEuropePmcTool(server: McpServer): void;
+//# sourceMappingURL=search-europepmc.d.ts.map

package/dist/tools/search-europepmc.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"search-europepmc.d.ts","sourceRoot":"","sources":["../../src/tools/search-europepmc.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAWpE,wBAAgB,2BAA2B,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAyBnE"}

package/dist/tools/search-europepmc.js

@@ -0,0 +1,30 @@
+import { z } from "zod";
+import { searchEuropePmc } from "../lib/europepmc.js";
+const schema = {
+    query: z.string().describe("Search query (Europe PMC query syntax supported, e.g. field tags like AUTH, TITLE, JOURNAL)"),
+    maxResults: z.number().min(1).max(100).default(10).describe("Maximum number of results"),
+    sort: z.enum(["relevance", "date", "cited"]).default("relevance").describe("Sort order: relevance, date (newest first), or cited (most cited first)"),
+    preprintsOnly: z.boolean().default(false).describe("Restrict to preprints (bioRxiv, medRxiv, etc.)"),
+    openAccessOnly: z.boolean().default(false).describe("Restrict to open-access articles"),
+};
+export function registerSearchEuropePmcTool(server) {
+    server.tool("search_europepmc", "Search Europe PMC — a broader biomedical corpus than PubMed that also indexes preprints (bioRxiv, medRxiv), patents, and agricultural/biomedical databases. Unlike search_pubmed, each result includes an abstract snippet, citation count, open-access status, and whether a preprint. Use preprintsOnly to surface work ahead of formal publication.", schema, { readOnlyHint: true, destructiveHint: false, openWorldHint: true }, async (params) => {
+        try {
+            const { results, total_count } = await searchEuropePmc(params);
+            return {
+                content: [{
+                        type: "text",
+                        text: JSON.stringify({ results, total_count }, null, 2),
+                    }],
+            };
+        }
+        catch (error) {
+            const message = error instanceof Error ? error.message : String(error);
+            return {
+                content: [{ type: "text", text: `Error searching Europe PMC: ${message}` }],
+                isError: true,
+            };
+        }
+    });
+}
+//# sourceMappingURL=search-europepmc.js.map

package/dist/tools/search-europepmc.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"search-europepmc.js","sourceRoot":"","sources":["../../src/tools/search-europepmc.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,OAAO,EAAE,eAAe,EAAE,MAAM,qBAAqB,CAAC;AAEtD,MAAM,MAAM,GAAG;IACb,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6FAA6F,CAAC;IACzH,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,2BAA2B,CAAC;IACxF,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,WAAW,EAAE,MAAM,EAAE,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,WAAW,CAAC,CAAC,QAAQ,CAAC,yEAAyE,CAAC;IACrJ,aAAa,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC,gDAAgD,CAAC;IACpG,cAAc,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC,kCAAkC,CAAC;CACxF,CAAC;AAEF,MAAM,UAAU,2BAA2B,CAAC,MAAiB;IAC3D,MAAM,CAAC,IAAI,CACT,kBAAkB,EAClB,wVAAwV,EACxV,MAAM,EACN,EAAE,YAAY,EAAE,IAAI,EAAE,eAAe,EAAE,KAAK,EAAE,aAAa,EAAE,IAAI,EAAE,EACnE,KAAK,EAAE,MAAM,EAAE,EAAE;QACf,IAAI,CAAC;YACH,MAAM,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,MAAM,eAAe,CAAC,MAAM,CAAC,CAAC;YAE/D,OAAO;gBACL,OAAO,EAAE,CAAC;wBACR,IAAI,EAAE,MAAM;wBACZ,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,EAAE,OAAO,EAAE,WAAW,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC;qBACxD,CAAC;aACH,CAAC;QACJ,CAAC;QAAC,OAAO,KAAK,EAAE,CAAC;YACf,MAAM,OAAO,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACvE,OAAO;gBACL,OAAO,EAAE,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,+BAA+B,OAAO,EAAE,EAAE,CAAC;gBAC3E,OAAO,EAAE,IAAI;aACd,CAAC;QACJ,CAAC;IACH,CAAC,CACF,CAAC;AACJ,CAAC"}

package/dist/tools/search.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../src/tools/search.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAiCpE,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAiD1D"}
+{"version":3,"file":"search.d.ts","sourceRoot":"","sources":["../../src/tools/search.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAcpE,wBAAgB,kBAAkB,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAiD1D"}

package/dist/tools/search.js

@@ -1,6 +1,6 @@
 import { z } from "zod";
 import { esearch, esummary } from "../lib/ncbi.js";
-import { parseSummaryAuthors } from "../lib/xml-parser.js";
+import { formatSummaryArticle } from "../lib/pubmed-format.js";
 const schema = {
     query: z.string().describe("PubMed search query"),
     maxResults: z.number().min(1).max(100).default(10).describe("Maximum number of results"),
@@ -9,23 +9,6 @@ const schema = {
     dateTo: z.string().optional().describe("End date (YYYY/MM/DD)"),
     articleType: z.string().optional().describe("Article type filter (e.g., review, clinical trial)"),
 };
-function formatArticle(uid, doc) {
-    const authors = parseSummaryAuthors(doc.authors);
-    const pubDate = String(doc.pubdate ?? "");
-    const year = pubDate.match(/\d{4}/)?.[0] ?? "";
-    const doi = (doc.elocationid ?? "")
-        .toString()
-        .replace(/^doi:\s*/i, "");
-    return {
-        pmid: uid,
-        title: String(doc.title ?? ""),
-        authors,
-        journal: String(doc.fulljournalname ?? doc.source ?? ""),
-        year,
-        doi,
-        abstract_snippet: String(doc.sorttitle ?? "").slice(0, 200),
-    };
-}
 export function registerSearchTool(server) {
     server.tool("search_pubmed", "Search PubMed for biomedical literature. Returns article summaries with PMIDs, titles, authors, journals, and DOIs.", schema, { readOnlyHint: true, destructiveHint: false, openWorldHint: true }, async (params) => {
         try {
@@ -49,7 +32,7 @@ export function registerSearchTool(server) {
             const summaryData = await esummary({ id: searchResult.idlist });
             const articles = searchResult.idlist
                 .filter((uid) => summaryData[uid])
-                .map((uid) => formatArticle(uid, summaryData[uid]));
+                .map((uid) => formatSummaryArticle(uid, summaryData[uid]));
             return {
                 content: [{
                         type: "text",

package/dist/tools/search.js.map

@@ -1 +1 @@
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package/dist/tools/trending.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"trending.d.ts","sourceRoot":"","sources":["../../src/tools/trending.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAqCpE,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAoF5D"}
+{"version":3,"file":"trending.d.ts","sourceRoot":"","sources":["../../src/tools/trending.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAqCpE,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,SAAS,GAAG,IAAI,CAoE5D"}

package/dist/tools/trending.js

@@ -1,6 +1,6 @@
 import { z } from "zod";
 import { esearch, esummary } from "../lib/ncbi.js";
-import { parseSummaryAuthors } from "../lib/xml-parser.js";
+import { formatSummaryArticle } from "../lib/pubmed-format.js";
 const HIGH_IMPACT_JOURNALS = [
     "nature",
     "science",
@@ -66,22 +66,7 @@ export function registerTrendingTool(server) {
             const summaryData = await esummary({ id: searchResult.idlist });
             const articles = searchResult.idlist
                 .filter((uid) => summaryData[uid])
-                .map((uid) => {
-                const doc = summaryData[uid];
-                const authors = parseSummaryAuthors(doc.authors);
-                const pubDate = String(doc.pubdate ?? "");
-                const year = pubDate.match(/\d{4}/)?.[0] ?? "";
-                const doi = (doc.elocationid ?? "").toString().replace(/^doi:\s*/i, "");
-                return {
-                    pmid: uid,
-                    title: String(doc.title ?? ""),
-                    authors,
-                    journal: String(doc.fulljournalname ?? doc.source ?? ""),
-                    year,
-                    doi,
-                    abstract_snippet: String(doc.sorttitle ?? "").slice(0, 200),
-                };
-            });
+                .map((uid) => formatSummaryArticle(uid, summaryData[uid]));
             return {
                 content: [{
                         type: "text",

package/dist/tools/trending.js.map

@@ -1 +1 @@
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package/dist/types.d.ts

@@ -5,7 +5,23 @@ export interface PubMedArticle {
     journal: string;
     year: string;
     doi: string;
+}
+export interface EuropePmcArticle {
+    id: string;
+    source: string;
+    pmid: string;
+    pmcid: string;
+    doi: string;
+    title: string;
+    authors: string;
+    journal: string;
+    year: string;
+    is_preprint: boolean;
+    is_open_access: boolean;
+    cited_by_count: number;
+    has_full_text: boolean;
     abstract_snippet: string;
+    url: string;
 }
 export interface AbstractSection {
     label: string;

package/dist/types.d.ts.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@pharmatools/pubcrawl",
-  "version": "2.2.0",
+  "version": "2.4.0",
   "description": "MCP server for PubMed literature search and US/UK drug labelling — built by PharmaTools.AI",
   "mcpName": "io.github.nickjlamb/pubcrawl",
   "author": "PharmaTools.AI",
@@ -31,6 +31,10 @@
     "start": "node dist/index.js",
     "start:http": "node dist/http.js",
     "dev": "tsc --watch",
+    "test": "vitest run",
+    "test:watch": "vitest",
+    "coverage": "vitest run --coverage",
+    "lint": "eslint .",
     "prepublishOnly": "npm run build"
   },
   "dependencies": {
@@ -42,7 +46,13 @@
   },
   "devDependencies": {
     "@types/node": "^20.0.0",
-    "typescript": "^5.3.0"
+    "@typescript-eslint/eslint-plugin": "^8.0.0",
+    "@typescript-eslint/parser": "^8.0.0",
+    "@vitest/coverage-v8": "^2.1.0",
+    "eslint": "^9.0.0",
+    "typescript": "^5.3.0",
+    "typescript-eslint": "^8.0.0",
+    "vitest": "^2.1.0"
   },
   "engines": {
     "node": ">=20"

package/server.json

@@ -1,17 +1,17 @@
 {
   "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
   "name": "io.github.nickjlamb/pubcrawl",
-  "description": "PubMed literature search and US/UK drug labelling for AI assistants.",
+  "description": "PubMed & Europe PMC literature search, US/UK drug labelling, and clinical trials for AI assistants.",
   "repository": {
     "url": "https://github.com/nickjlamb/pubcrawl",
     "source": "github"
   },
-  "version": "2.0.0",
+  "version": "2.4.0",
   "packages": [
     {
       "registryType": "npm",
       "identifier": "@pharmatools/pubcrawl",
-      "version": "2.0.0",
+      "version": "2.4.0",
       "transport": {
         "type": "stdio"
       },