npm - @cyanheads/pubmed-mcp-server - Versions diffs - 1.4.3 → 1.4.5 - Mend

@cyanheads/pubmed-mcp-server 1.4.3 → 1.4.5

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package/README.md CHANGED Viewed

@@ -1,98 +1,162 @@
 <div align="center">
+  <h1>pubmed-mcp-server</h1>
+  <p><b>A production-grade Model Context Protocol (MCP) server that empowers AI agents and research tools with comprehensive access to PubMed's vast repository of biomedical and scientific literature.</b></p>
+</div>
-# pubmed-mcp-server
-**Empower your AI agents and research tools with seamless PubMed integration!**
+<div align="center">
-[![TypeScript](https://img.shields.io/badge/TypeScript-^5.8.3-blue.svg?style=flat-square)](https://www.typescriptlang.org/)
-[![Model Context Protocol](https://img.shields.io/badge/MCP%20SDK-^1.17.2-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
-[![Version](https://img.shields.io/badge/Version-1.4.2-blue.svg?style=flat-square)](./CHANGELOG.md)
-[![License](https://img.shields.io/badge/License-Apache%202.0-blue.svg?style=flat-square)](https://opensource.org/licenses/Apache-2.0)
-[![Status](https://img.shields.io/badge/Status-Stable-green.svg?style=flat-square)](https://github.com/cyanheads/pubmed-mcp-server/issues)
-[![GitHub](https://img.shields.io/github/stars/cyanheads/pubmed-mcp-server?style=social)](https://github.com/cyanheads/pubmed-mcp-server)
+[![Version](https://img.shields.io/badge/Version-1.4.5-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.19.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Status](https://img.shields.io/badge/Status-Stable-brightgreen.svg?style=flat-square)](https://github.com/cyanheads/pubmed-mcp-server/issues) [![TypeScript](https://img.shields.io/badge/TypeScript-^5.9.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/)
 </div>
-A production-grade Model Context Protocol (MCP) server that empowers AI agents and research tools with comprehensive access to PubMed. Enables advanced, automated workflows for searching, retrieving, analyzing, and visualizing biomedical and scientific literature via NCBI E-utilities.
+---
+## 🛠️ Tools Overview
+This server provides five powerful tools for accessing and analyzing biomedical literature from PubMed:
+| Tool Name | Description |
+| :--- | :--- |
+| `pubmed_search_articles` | Searches PubMed for articles based on your query. |
+| `pubmed_fetch_contents` | Retrieves detailed information for specific PubMed articles by PMID. |
+| `pubmed_article_connections` | Finds related articles (cited by, similar, references) or formats citations. |
+| `pubmed_research_agent` | Generates a standardized JSON research plan from component details. |
+| `pubmed_generate_chart` | Generates a chart image (PNG) from structured publication data. |
-Built on the [`cyanheads/mcp-ts-template`](https://github.com/cyanheads/mcp-ts-template), this server follows a modular architecture with robust error handling, logging, and security features.
+### `pubmed_search_articles`
-## 🚀 Core Capabilities: PubMed Tools 🛠️
+**Search and discover millions of biomedical articles** using free-text queries and advanced filters.
-This server equips your AI with specialized tools to interact with PubMed:
+**Key Features:**
-| Tool Name                                                                        | Description                                                                             | Example                                                                                                  |
-| :------------------------------------------------------------------------------- | :-------------------------------------------------------------------------------------- | :------------------------------------------------------------------------------------------------------- |
-| [`pubmed_search_articles`](./src/mcp-server/tools/pubmedSearchArticles/)         | Searches PubMed for articles based on your query.                                       | [View Example](./examples/pubmed_search_articles_example.md)                                             |
-| [`pubmed_fetch_contents`](./src/mcp-server/tools/pubmedFetchContents/)           | Retrieves detailed information for PubMed articles.                                     | [View Example](./examples/pubmed_fetch_contents_example.md)                                              |
-| [`pubmed_article_connections`](./src/mcp-server/tools/pubmedArticleConnections/) | Finds related articles (cited by, similar, references) or formats citations for a PMID. | [Ex. 1](./examples/pubmed_article_connections_1.md), [Ex. 2](./examples/pubmed_article_connections_2.md) |
-| [`pubmed_research_agent`](./src/mcp-server/tools/pubmedResearchAgent/)           | Generates a standardized JSON research plan outline from component details.             | [View Example](./examples/pubmed_research_agent_example.md)                                              |
-| [`pubmed_generate_chart`](./src/mcp-server/tools/pubmedGenerateChart/)           | Generates a chart image (PNG) from given input data.                                    | [View Examples](./examples/generate_pubmed_chart/)                                                       |
+- Free-text search across all article fields (title, abstract, author, journal).
+- Filter by publication date range and specific publication types (e.g., "Review", "Clinical Trial").
+- Sort results by relevance, publication date, author, or journal name.
+- Optionally fetch brief summaries for top results in the same call.
+**Example Use Cases:**
+- "Find recent review articles on CRISPR gene editing."
+- "Show me all publications by Dr. Anthony Fauci in 2023."
+- "List the latest articles on neuroinflammation in the journal 'Nature'."
+📖 **[View detailed examples →](./examples/pubmed_search_articles_example.md)**
 ---
-## Table of Contents
+### `pubmed_fetch_contents`
-| [Overview](#overview)           | [Features](#features)                          | [Installation](#installation) |
-| :------------------------------ | :--------------------------------------------- | :---------------------------- |
-| [Configuration](#configuration) | [Project Structure](#project-structure)        |
-| [Tools](#tools)                 | [Development & Testing](#development--testing) | [License](#license)           |
+**Retrieve detailed, structured metadata** for specific articles using their PubMed IDs (PMIDs).
-## Overview
+**Key Features:**
+- Fetch single or multiple articles (up to 200 at once).
+- Use ESearch history (`queryKey`, `WebEnv`) for batch retrieval of large sets.
+- Choose from multiple detail levels:
+  - `abstract_plus`: Rich, parsed data including abstract, authors, journal, DOI, and keywords.
+  - `full_xml`: The complete, raw PubMedArticle XML structure in JSON format.
+  - `medline_text`: The classic MEDLINE plain-text format.
+  - `citation_data`: Minimal data required for generating citations.
+- Include optional data like MeSH terms and grant information.
-The PubMed MCP Server acts as a bridge, allowing applications (MCP Clients) that understand the Model Context Protocol (MCP) – like advanced AI assistants (LLMs), IDE extensions, or custom research tools – to interact directly and efficiently with PubMed's vast biomedical literature database.
+**Example Use Cases:**
-Instead of complex API integration or manual searches, your tools can leverage this server to:
+- "Get the full abstract and author list for PMID 31772153."
+- "Fetch citation data for these three PMIDs: 31535994, 29749963, 33836086."
+- "Retrieve the MEDLINE record for PMID 12345678."
-- **Automate research workflows**: Search literature, fetch full article metadata, track citations, and generate research plans programmatically.
-- **Gain research insights**: Access detailed publication data, author information, journal details, MeSH terms, and citation networks without leaving the host application.
-- **Integrate PubMed into AI-driven research**: Enable LLMs to conduct literature reviews, analyze research trends, and support evidence-based decision making.
-- **Visualize research data**: Generate charts and visualizations from publication metadata and search results.
+📖 **[View detailed examples →](./examples/pubmed_fetch_contents_example.md)**
-Built on the robust `mcp-ts-template`, this server provides a standardized, secure, and efficient way to expose PubMed functionality via the MCP standard. It achieves this by integrating with NCBI's E-utilities API, ensuring compliance with rate limits and providing comprehensive error handling.
+---
-> **Developer Note**: This repository includes a [.clinerules](.clinerules) file that serves as a developer cheat sheet for your LLM coding agent with quick reference for the codebase patterns, file locations, and code snippets.
+### `pubmed_article_connections`
-## Features
+**Explore the citation network** and generate formatted citations for any article.
-### Core Utilities
+**Key Features:**
+- Discover related literature by finding:
+  - **`pubmed_similar_articles`**: Articles with similar content.
+  - **`pubmed_citedin`**: Articles that have cited the source article.
+  - **`pubmed_references`**: Articles that the source article references.
+- Generate citations in multiple standard formats in a single call:
+  - `ris`: Research Information Systems format for reference managers.
+  - `bibtex`: For use with LaTeX and BibTeX.
+  - `apa_string` and `mla_string`: Plain-text citations in APA and MLA style.
-Leverages the robust utilities provided by the `mcp-ts-template`:
+**Example Use Cases:**
-- **Logging**: Structured, configurable logging (file rotation, stdout JSON, MCP notifications) with sensitive data redaction.
-- **Error Handling**: Centralized error processing, standardized error types (`McpError`), and automatic logging.
-- **Configuration**: Environment variable loading (`dotenv`) with comprehensive validation using Zod.
-- **Input Validation/Sanitization**: Uses `zod` for schema validation and custom sanitization logic.
-- **Request Context**: Tracking and correlation of operations via unique request IDs using `AsyncLocalStorage`.
-- **Type Safety**: Strong typing enforced by TypeScript and Zod schemas.
-- **HTTP Transport**: High-performance HTTP server using **Hono**, featuring session management and authentication support.
-- **Authentication**: Robust authentication layer supporting JWT and OAuth 2.1, with fine-grained scope enforcement.
-- **Deployment**: Multi-stage `Dockerfile` for creating small, secure production images with native dependency support.
+- "Find 5 articles that are similar to PMID 30310041."
+- "Who has cited the paper with PMID 29089531?"
+- "Get the BibTeX and RIS citation for PMID 33577065."
-### PubMed Integration
+📖 **[View detailed examples →](./examples/pubmed_article_connections_1.md)**
-- **NCBI E-utilities Integration**: Comprehensive access to ESearch, EFetch, ELink, and ESummary APIs with automatic XML parsing.
-- **Advanced Search Capabilities**: Complex query construction with date ranges, publication types, author filters, and MeSH term support.
-- **Full Article Metadata**: Retrieve complete publication data including abstracts, authors, affiliations, journal information, DOIs, and citation data.
-- **Citation Network Analysis**: Find related articles, citing articles, and reference lists through ELink integration.
-- **Research Planning**: Generate structured research plans with automated literature search strategies.
-- **Data Visualization**: Create PNG charts from publication metadata (bar, line, scatter, pie, bubble, radar, polarArea).
-- **Multiple Output Formats**: Support for JSON, MEDLINE text, full XML, and formatted citations (RIS, BibTeX, APA, MLA).
-- **Batch Processing**: Efficient handling of multiple PMIDs with pagination support.
+📖 **[View a second example →](./examples/pubmed_article_connections_2.md)**
-## Installation
+---
-### Prerequisites
+### `pubmed_research_agent`
-- [Node.js (>=20.0.0)](https://nodejs.org/)
-- [npm](https://www.npmjs.com/) (comes with Node.js)
-- **NCBI API Key** (recommended for higher rate limits) - [Get one here](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/)
+**Bootstrap a new research project** by generating a formal, structured research plan.
+**Key Features:**
+- Assembles a comprehensive JSON-based research plan from high-level inputs.
+- Outlines every phase of research: conception, data collection, analysis, and dissemination.
+- Includes sections for hypotheses, literature search strategies, experimental design, and data analysis pipelines.
+- Can optionally embed detailed prompts to guide a research agent in executing the plan.
+**Example Use Cases:**
+- "Draft a research plan to investigate the role of TREM2 in Alzheimer's disease."
+- "Outline a project on the effects of intermittent fasting on metabolic health, including a PubMed search strategy."
+- "Create a formal plan for a comparative multi-omics analysis of gut microbiome data."
+📖 **[View detailed examples →](./examples/pubmed_research_agent_example.md)**
+---
+### `pubmed_generate_chart`
+**Visualize publication trends** and data with server-side chart generation.
+**Key Features:**
+- Create PNG charts from structured data arrays.
+- Supports a wide range of chart types: `bar`, `line`, `scatter`, `pie`, `doughnut`, `bubble`, `radar`, and `polarArea`.
+- Customize chart title, dimensions, axes, and data series.
+- Ideal for quickly visualizing search results or publication metadata.
+**Example Use Cases:**
+- "Plot the number of articles published on 'immunotherapy' per year since 2015."
+- "Create a bar chart showing the top 10 journals by publication count for 'nanotechnology'."
+- "Make a scatter plot of articles by citation count vs. publication year."
+📖 **[View detailed examples →](./examples/generate_pubmed_chart/)**
+---
+## ✨ Features
+This server is built on the [`mcp-ts-template`](https://github.com/cyanheads/mcp-ts-template) and inherits its rich feature set:
+- **Robust Error Handling**: A unified `McpError` system ensures consistent, structured error responses.
+- **Full-Stack Observability**: Deep insights with structured logging (Winston) and optional, auto-instrumented OpenTelemetry for traces and metrics.
+- **HTTP/STDIO Transports**: Flexible deployment with support for both standard I/O and a high-performance Hono-based HTTP server.
+- **Pluggable Authentication**: Secure your HTTP transport with out-of-the-box support for `none`, `jwt`, or `oauth` modes.
+- **Input Validation**: All tool inputs are rigorously validated against Zod schemas.
+- **Request Context**: `AsyncLocalStorage` provides end-to-end tracing of operations via unique request IDs.
+- **Edge-Ready**: Write code once and run it on your local machine or at the edge.
+Plus, specialized features for **PubMed**:
+- **Official API Integration**: Type-safe, comprehensive access to the NCBI E-utilities API (ESearch, EFetch, ELink).
+- **Compliant & Resilient**: Built-in rate limiting and retry logic to ensure compliance with NCBI policies.
+- **Optimized Data Handling**: Automatic parsing and normalization of complex XML responses into clean, agent-consumable JSON.
+## 🚀 Getting Started
 ### MCP Client Settings
-Add the following to your MCP client's configuration file (e.g., `cline_mcp_settings.json`).
-This configuration uses `npx` to run the server, which will automatically install the package if not already present.
-All environment variables are optional, but recommended for production use. NCBI API key is recommended to avoid rate limiting issues.
+Add the following to your MCP Client configuration file (e.g., `cline_mcp_settings.json`). This ensures the server is automatically installed and run when needed.
 ```json
 {
@@ -101,7 +165,7 @@ All environment variables are optional, but recommended for production use. NCBI
       "command": "npx",
       "args": ["@cyanheads/pubmed-mcp-server"],
       "env": {
-        "MCP_LOG_LEVEL": "debug",
+        "MCP_LOG_LEVEL": "info",
         "MCP_TRANSPORT_TYPE": "http",
         "MCP_HTTP_PORT": "3017",
         "NCBI_API_KEY": "YOUR_NCBI_API_KEY_HERE"
@@ -111,142 +175,71 @@ All environment variables are optional, but recommended for production use. NCBI
 }
 ```
-### If running manually (not via MCP client for development or testing)
-#### Install via npm
-```bash
-npm install @cyanheads/pubmed-mcp-server
-```
-#### Alternatively Install from Source
-1.  Clone the repository:
-    ```bash
-    git clone https://github.com/cyanheads/pubmed-mcp-server.git
-    cd pubmed-mcp-server
-    ```
-2.  Install dependencies:
-    ```bash
-    npm install
-    ```
-3.  Build the project:
-    ```bash
-    npm run build
-    ```
-## Configuration
-### Environment Variables
-Configure the server using environment variables. For local development, these can be set in a `.env` file at the project root or directly in your environment. Otherwise, you can set them in your MCP client configuration as shown above.
-| Variable              | Description                                                                              | Default       |
-| :-------------------- | :--------------------------------------------------------------------------------------- | :------------ |
-| `MCP_TRANSPORT_TYPE`  | Transport mechanism: `stdio` or `http`.                                                  | `stdio`       |
-| `MCP_HTTP_PORT`       | Port for the HTTP server (if `MCP_TRANSPORT_TYPE=http`).                                 | `3017`        |
-| `MCP_HTTP_HOST`       | Host address for the HTTP server (if `MCP_TRANSPORT_TYPE=http`).                         | `127.0.0.1`   |
-| `MCP_ALLOWED_ORIGINS` | Comma-separated list of allowed origins for CORS (if `MCP_TRANSPORT_TYPE=http`).         | (none)        |
-| `MCP_LOG_LEVEL`       | Logging level (`debug`, `info`, `notice`, `warning`, `error`, `crit`, `alert`, `emerg`). | `debug`       |
-| `MCP_AUTH_MODE`       | Authentication mode for HTTP: `jwt` or `oauth`.                                          | `jwt`         |
-| `MCP_AUTH_SECRET_KEY` | **Required for `jwt` auth.** Minimum 32-character secret key for JWT authentication.     | (none)        |
-| `NCBI_API_KEY`        | **Recommended.** Your NCBI API Key for higher rate limits and reliable access.           | (none)        |
-| `LOGS_DIR`            | Directory for log file storage.                                                          | `logs/`       |
-| `NODE_ENV`            | Runtime environment (`development`, `production`).                                       | `development` |
-## Project Structure
-The codebase follows a modular structure within the `src/` directory:
-```
-src/
-├── index.ts              # Entry point: Initializes and starts the server
-├── config/               # Configuration loading (env vars, package info)
-│   └── index.ts
-├── mcp-server/           # Core MCP server logic and capability registration
-│   ├── server.ts         # Server setup, capability registration
-│   ├── transports/       # Transport handling (stdio, http)
-│   └── tools/            # MCP Tool implementations (subdirs per tool)
-├── services/             # External service integrations
-│   └── NCBI/             # NCBI E-utilities API client and parsing
-├── types-global/         # Shared TypeScript type definitions
-└── utils/                # Common utility functions (logger, error handler, etc.)
-```
-For a detailed file tree, run `npm run tree` or see [docs/tree.md](docs/tree.md).
-## Tools
-The PubMed MCP Server provides a comprehensive suite of tools for biomedical literature research, callable via the Model Context Protocol.
-| Tool Name                    | Description                                                            | Key Arguments                                                                                             |
-| :--------------------------- | :--------------------------------------------------------------------- | :-------------------------------------------------------------------------------------------------------- |
-| `pubmed_search_articles`     | Searches PubMed for articles using queries, filters, and date ranges.  | `queryTerm`, `maxResults?`, `sortBy?`, `dateRange?`, `filterByPublicationTypes?`, `fetchBriefSummaries?`  |
-| `pubmed_fetch_contents`      | Fetches detailed article information using PMIDs or search history.    | `pmids?`, `queryKey?`, `webEnv?`, `detailLevel?`, `includeMeshTerms?`, `includeGrantInfo?`                |
-| `pubmed_article_connections` | Finds related articles, citations, and references for a given PMID.    | `sourcePmid`, `relationshipType?`, `maxRelatedResults?`, `citationStyles?`                                |
-| `pubmed_research_agent`      | Generates structured research plans with literature search strategies. | `project_title_suggestion`, `primary_research_goal`, `research_keywords`, `organism_focus?`, `p1_*`, etc. |
-| `pubmed_generate_chart`      | Creates customizable PNG charts from structured publication data.      | `chartType`, `dataValues`, `xField`, `yField`, `title?`, `seriesField?`, `sizeField?`                     |
-_Note: All tools support comprehensive error handling and return structured JSON responses._
+### Prerequisites
-## Examples
+- [Node.js (>=20.0.0)](https://nodejs.org/)
+- [npm](https://www.npmjs.com/) (comes with Node.js)
+- **NCBI API Key** (Recommended for higher rate limits) - [Get one here](https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/)
-Comprehensive usage examples for each tool are available in the [`examples/`](examples/) directory.
+### Manual Installation
-- **`pubmed_search_articles`**: [View Example](./examples/pubmed_search_articles_example.md)
-- **`pubmed_fetch_contents`**: [View Example](./examples/pubmed_fetch_contents_example.md)
-- **`pubmed_article_connections`**: [Ex. 1](./examples/pubmed_article_connections_1.md), [Ex. 2](./examples/pubmed_article_connections_2.md)
-- **`pubmed_research_agent`**: [View Example](./examples/pubmed_research_agent_example.md)
-- **`pubmed_generate_chart`**: [View Examples](./examples/generate_pubmed_chart/)
+1.  **Clone the repository:**
+    `git clone https://github.com/cyanheads/pubmed-mcp-server.git`
+2.  **Navigate into the directory:**
+    `cd pubmed-mcp-server`
+3.  **Install dependencies:**
+    `npm install`
+4.  **Build the project:**
+    `npm run build`
-## Development & Testing
+## ⚙️ Configuration
-### Development Scripts
+Configure the server via environment variables. For local development, create a `.env` file in the project root.
-```bash
-# Build the project (compile TS to JS in dist/ and make executable)
-npm run build
+| Variable | Description | Default |
+| :--- | :--- | :--- |
+| `MCP_TRANSPORT_TYPE` | Transport mechanism: `stdio` or `http`. | `stdio` |
+| `MCP_HTTP_PORT` | Port for the HTTP server. | `3017` |
+| `MCP_AUTH_MODE` | Auth mode for HTTP transport: `none`, `jwt`, or `oauth`. | `jwt` |
+| `MCP_AUTH_SECRET_KEY`| **Required for `jwt` auth.** 32+ character secret key. | (none) |
+| `MCP_LOG_LEVEL` | Logging level (`debug`, `info`, `warning`, `error`). | `debug` |
+| `NCBI_API_KEY` | **Recommended.** Your NCBI API Key for higher rate limits. | (none) |
+| `LOGS_DIR` | Directory for log file storage. | `logs/` |
-# Clean build artifacts
-npm run clean
+## ▶️ Running the Server
-# Clean build artifacts and then rebuild the project
-npm run rebuild
+- **Start in STDIO mode (default):** `npm start`
+- **Start in HTTP mode:** `npm run start:http`
+- **Run local checks and tests:** `npm run devcheck` (lint, format, type-check) and `npm test`
-# Lint the codebase
-npm run lint
+## 📂 Project Structure
-# Format code with Prettier
-npm run format
+| Directory | Purpose & Contents |
+| :--- | :--- |
+| `src/mcp-server/tools` | Tool definitions (`logic.ts` & `registration.ts` per tool). This is where you add new capabilities. |
+| `src/mcp-server/transports` | Implementations for HTTP and STDIO transports, including authentication middleware. |
+| `src/services/ncbi` | The core NCBI service client, parsers, and request queue manager. |
+| `src/utils` | Core utilities for logging, error handling, performance, and security. |
+| `src/config` | Environment variable parsing and validation with Zod. |
+| `tests/` | Unit and integration tests, mirroring the `src/` directory structure. |
-# Generate a file tree representation for documentation
-npm run tree
-```
+## 🧑‍💻 Agent Development Guide
-### Running the Server
+For strict rules when using this server with an AI agent, refer to the **[`.clinerules/clinerules.md`](./.clinerules/clinerules.md)** file in this repository. Key principles include:
-```bash
-# Start the server using stdio (default)
-npm start
-# Or explicitly:
-npm run start:stdio
+- **Logic Throws, Handlers Catch**: Never use `try/catch` in your tool's core logic. Always `throw` a structured `McpError` on failure. Handlers are responsible for catching and formatting the final response.
+- **Pass the Context**: Always pass the `RequestContext` object through your call stack for logging and tracing.
+- **Singleton Services**: Access external services (like the `NcbiService`) via their singleton getter (`getNcbiService()`) within the logic file.
-# Start the server using HTTP transport
-npm run start:http
+## 🤝 Contributing
-# Test the server locally using the MCP inspector tool (stdio transport)
-npm run inspector
+Issues and pull requests are welcome! If you plan to contribute, please run the local checks and tests before submitting your PR.
-# Test the server locally using the MCP inspector tool (http transport)
-npm run inspector:http
+```sh
+npm run devcheck
+npm test
 ```
-## License
+## 📜 License
-This project is licensed under the Apache License 2.0 - see the [LICENSE](LICENSE) file for details.
----
-<div align="center">
-Built with the <a href="https://modelcontextprotocol.io/">Model Context Protocol</a>
-</div>
+This project is licensed under the Apache 2.0 License. See the [LICENSE](./LICENSE) file for details.

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package/dist/mcp-server/tools/pubmedArticleConnections/logic/citationFormatter.js CHANGED Viewed

@@ -4,10 +4,10 @@
  * @module src/mcp-server/tools/pubmedArticleConnections/logic/citationFormatter
  */
 import Cite from "citation-js";
-import { getNcbiService } from "../../../../services/NCBI/core/ncbiService.js";
+import { getNcbiService } from "../../../../services/ncbi/core/ncbiService.js";
 import { logger, requestContextService, } from "../../../../utils/index.js";
-import { extractAuthors, extractDoi, extractJournalInfo, extractPmid, getText, } from "../../../../services/NCBI/parsing/index.js";
-import { ensureArray } from "../../../../services/NCBI/parsing/index.js";
+import { extractAuthors, extractDoi, extractJournalInfo, extractPmid, getText, } from "../../../../services/ncbi/parsing/index.js";
+import { ensureArray } from "../../../../services/ncbi/parsing/index.js";
 // Main handler for citation formats
 export async function handleCitationFormats(input, outputData, context) {
     const eFetchParams = {

package/dist/mcp-server/tools/pubmedArticleConnections/logic/elinkHandler.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"elinkHandler.d.ts","sourceRoot":"","sources":["../../../../../src/mcp-server/tools/pubmedArticleConnections/logic/elinkHandler.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AASH,OAAO,EAAU,cAAc,EAAE,MAAM,4BAA4B,CAAC;AACpE,OAAO,KAAK,EAAE,6BAA6B,EAAE,MAAM,YAAY,CAAC;AAChE,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC;AAwBjD,wBAAsB,wBAAwB,CAC5C,KAAK,EAAE,6BAA6B,EACpC,UAAU,EAAE,cAAc,EAC1B,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,IAAI,CAAC,CAiQf"}

package/dist/mcp-server/tools/pubmedArticleConnections/logic/elinkHandler.js CHANGED Viewed

@@ -3,10 +3,10 @@
  * for the pubmedArticleConnections tool.
  * @module src/mcp-server/tools/pubmedArticleConnections/logic/elinkHandler
  */
-import { getNcbiService } from "../../../../services/NCBI/core/ncbiService.js";
+import { getNcbiService } from "../../../../services/ncbi/core/ncbiService.js";
+import { extractBriefSummaries } from "../../../../services/ncbi/parsing/index.js";
+import { ensureArray } from "../../../../services/ncbi/parsing/xmlGenericHelpers.js"; // Added import
 import { logger } from "../../../../utils/index.js";
-import { extractBriefSummaries } from "../../../../services/NCBI/parsing/index.js";
-import { ensureArray } from "../../../../services/NCBI/parsing/xmlGenericHelpers.js"; // Added import
 export async function handleELinkRelationships(input, outputData, context) {
     const eLinkParams = {
         dbfrom: "pubmed",

package/dist/mcp-server/tools/pubmedArticleConnections/logic/elinkHandler.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ {"version":3,"file":"elinkHandler.js","sourceRoot":"","sources":["../../../../../src/mcp-server/tools/pubmedArticleConnections/logic/elinkHandler.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,cAAc,EAAE,MAAM,+CAA+C,CAAC;AAC/E,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AACnF,OAAO,EAAE,WAAW,EAAE,MAAM,wDAAwD,CAAC,CAAC,eAAe;AAKrG,OAAO,EAAE,MAAM,EAAkB,MAAM,4BAA4B,CAAC;AA0BpE,MAAM,CAAC,KAAK,UAAU,wBAAwB,CAC5C,KAAoC,EACpC,UAA0B,EAC1B,OAAuB;IAEvB,MAAM,WAAW,GAA2B;QAC1C,MAAM,EAAE,QAAQ;QAChB,EAAE,EAAE,QAAQ;QACZ,EAAE,EAAE,KAAK,CAAC,UAAU;QACpB,OAAO,EAAE,KAAK;QACd,+DAA+D;KAChE,CAAC;IAEF,QAAQ,KAAK,CAAC,gBAAgB,EAAE,CAAC;QAC/B,KAAK,gBAAgB;YACnB,WAAW,CAAC,GAAG,GAAG,kBAAkB,CAAC;YACrC,WAAW,CAAC,QAAQ,GAAG,uBAAuB,CAAC;YAC/C,MAAM;QACR,KAAK,mBAAmB;YACtB,WAAW,CAAC,GAAG,GAAG,kBAAkB,CAAC;YACrC,WAAW,CAAC,QAAQ,GAAG,oBAAoB,CAAC;YAC5C,MAAM;QACR,KAAK,yBAAyB,CAAC;QAC/B,SAAS,8BAA8B;YACrC,WAAW,CAAC,GAAG,GAAG,gBAAgB,CAAC;YACnC,oFAAoF;YACpF,MAAM;IACV,CAAC;IAED,MAAM,OAAO,GAAG,IAAI,GAAG,CACrB,yDAAyD,CAC1D,CAAC;IACF,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,OAAO,CAAC,CAAC,GAAG,EAAE,EAAE,CACvC,OAAO,CAAC,YAAY,CAAC,MAAM,CAAC,GAAG,EAAE,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,CAC3D,CAAC;IACF,UAAU,CAAC,WAAW,GAAG,4DAA4D,OAAO,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC;IAEnH,MAAM,WAAW,GAAG,cAAc,EAAE,CAAC;IACrC,MAAM,WAAW,GAAgB,CAAC,MAAM,WAAW,CAAC,KAAK,CACvD,WAAW,EACX,OAAO,CACR,CAAgB,CAAC;IAElB,yCAAyC;IACzC,MAAM,CAAC,KAAK,CAAC,mCAAmC,EAAE;QAChD,GAAG,OAAO;QACV,iBAAiB,EAAE,IAAI,CAAC,SAAS,CAAC,WAAW,EAAE,IAAI,EAAE,CAAC,CAAC;KACxD,CAAC,CAAC;IAEH,iFAAiF;IACjF,MAAM,iBAAiB,GAAG,WAAW,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;IAChE,MAAM,gBAAgB,GAAG,iBAAiB,CAAC,CAAC,CAAC,CAAC;IAE9C,sCAAsC;IACtC,MAAM,aAAa,GAAG,WAAW,CAAC,gBAAgB,EAAE,OAAO,CAAC,CAAC;IAC7D,MAAM,OAAO,GAAG,aAAa,CAAC,CAAC,CAAC,CAAC;IAEjC,IAAI,UAAU,GAAuC,EAAE,CAAC;IAExD,IAAI,gBAAgB,EAAE,KAAK,EAAE,CAAC;QAC5B,MAAM,QAAQ,GACZ,OAAO,gBAAgB,CAAC,KAAK,KAAK,QAAQ;YACxC,CAAC,CAAC,gBAAgB,CAAC,KAAK;YACxB,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,gBAAgB,CAAC,KAAK,CAAC,CAAC;QAC7C,MAAM,CAAC,OAAO,CAAC,4BAA4B,QAAQ,EAAE,EAAE,OAAO,CAAC,CAAC;QAChE,UAAU,CAAC,OAAO,GAAG,gBAAgB,QAAQ,EAAE,CAAC;QAChD,UAAU,CAAC,cAAc,GAAG,CAAC,CAAC;QAC9B,OAAO;IACT,CAAC;IAED,IAAI,OAAO,EAAE,gBAAgB,EAAE,CAAC;QAC9B,6DAA6D;QAC7D,MAAM,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,gBAAgB,CAAC;YACrD,CAAC,CAAC,OAAO,CAAC,gBAAgB,CAAC,CAAC,CAAC;YAC7B,CAAC,CAAC,OAAO,CAAC,gBAAgB,CAAC;QAE7B,IAAI,OAAO,EAAE,QAAQ,IAAI,gBAAgB,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC;YAC3D,MAAM,aAAa,GAAG;gBACpB,EAAE,EAAE,QAAQ;gBACZ,SAAS,EAAE,OAAO,CAAC,QAAQ;gBAC3B,MAAM,EAAE,gBAAgB,CAAC,OAAO,CAAC,MAAM;gBACvC,OAAO,EAAE,KAAK;gBACd,MAAM,EAAE,KAAK,CAAC,iBAAiB,GAAG,CAAC,EAAE,iDAAiD;aACvF,CAAC;YACF,MAAM,aAAa,GACjB,CAAC,MAAM,WAAW,CAAC,OAAO,CAAC,aAAa,EAAE,OAAO,CAAC,CAEjD,CAAC;YACJ,IAAI,aAAa,EAAE,aAAa,EAAE,MAAM,EAAE,EAAE,EAAE,CAAC;gBAC7C,MAAM,GAAG,GAAG,WAAW,CAAC,aAAa,CAAC,aAAa,CAAC,MAAM,CAAC,EAAE,CAAC,CAAC;gBAC/D,UAAU,GAAG,GAAG;qBACb,GAAG,CAAC,CAAC,MAAuD,EAAE,EAAE;oBAC/D,0BAA0B;oBAC1B,IAAI,OAAoC,CAAC;oBACzC,IAAI,OAAO,MAAM,KAAK,QAAQ,IAAI,MAAM,KAAK,IAAI,EAAE,CAAC;wBAClD,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,CAAC;oBAC5B,CAAC;yBAAM,CAAC;wBACN,OAAO,GAAG,MAAM,CAAC;oBACnB,CAAC;oBACD,OAAO;wBACL,IAAI,EAAE,OAAO,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE;wBAClD,mCAAmC;qBACpC,CAAC;gBACJ,CAAC,CAAC;qBACD,MAAM,CACL,CAAC,IAAsB,EAAE,EAAE,CACzB,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,KAAK,KAAK,CAAC,UAAU,IAAI,IAAI,CAAC,IAAI,KAAK,GAAG,CACnE,CAAC;YACN,CAAC;QACH,CAAC;IACH,CAAC;SAAM,IAAI,OAAO,EAAE,SAAS,EAAE,CAAC;QAC9B,wDAAwD;QACxD,MAAM,cAAc,GAAG,KAAK,CAAC,OAAO,CAAC,OAAO,CAAC,SAAS,CAAC;YACrD,CAAC,CAAC,OAAO,CAAC,SAAS;YACnB,CAAC,CAAC,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;QAExB,MAAM,oBAAoB,GAAG,cAAc,CAAC,IAAI,CAC9C,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,QAAQ,KAAK,eAAe,CACxC,CAAC;QAEF,IAAI,oBAAoB,EAAE,IAAI,EAAE,CAAC;YAC/B,MAAM,KAAK,GAAG,WAAW,CAAC,oBAAoB,CAAC,IAAI,CAAC,CAAC,CAAC,2BAA2B;YACjF,UAAU,GAAG,KAAK;iBACf,GAAG,CAAC,CAAC,IAAkB,EAAE,EAAE;gBAC1B,IAAI,SAAsC,CAAC;gBAC3C,IAAI,OAAO,IAAI,CAAC,EAAE,KAAK,QAAQ,IAAI,IAAI,CAAC,EAAE,KAAK,IAAI,EAAE,CAAC;oBACpD,SAAS,GAAG,IAAI,CAAC,EAAE,CAAC,OAAO,CAAC,CAAC;gBAC/B,CAAC;qBAAM,IAAI,IAAI,CAAC,EAAE,KAAK,SAAS,EAAE,CAAC;oBACjC,SAAS,GAAG,IAAI,CAAC,EAAE,CAAC;gBACtB,CAAC;gBAED,IAAI,UAAuC,CAAC;gBAC5C,IAAI,OAAO,IAAI,CAAC,KAAK,KAAK,QAAQ,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE,CAAC;oBAC1D,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC;gBACnC,CAAC;qBAAM,IAAI,IAAI,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;oBACpC,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC;gBAC1B,CAAC;gBAED,MAAM,UAAU,GAAG,SAAS,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;gBAEpE,OAAO;oBACL,IAAI,EAAE,UAAU;oBAChB,KAAK,EAAE,UAAU,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,SAAS;iBACjE,CAAC;YACJ,CAAC,CAAC;iBACD,MAAM,CACL,CAAC,IAAsC,EAAE,EAAE,CACzC,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,KAAK,KAAK,CAAC,UAAU,IAAI,IAAI,CAAC,IAAI,KAAK,GAAG,CACnE,CAAC;QACN,CAAC;IACH,CAAC;IAED,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC5B,MAAM,CAAC,OAAO,CACZ,wDAAwD,EACxD,OAAO,CACR,CAAC;QACF,UAAU,CAAC,OAAO,GAAG,2CAA2C,CAAC,CAAC,8BAA8B;QAChG,UAAU,CAAC,cAAc,GAAG,CAAC,CAAC;QAC9B,OAAO;IACT,CAAC;IAED,MAAM,CAAC,KAAK,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package/dist/mcp-server/tools/pubmedFetchContents/logic.js CHANGED Viewed

@@ -6,10 +6,10 @@
  * @module src/mcp-server/tools/pubmedFetchContents/logic
  */
 import { z } from "zod";
-import { getNcbiService } from "../../../services/NCBI/core/ncbiService.js";
+import { getNcbiService } from "../../../services/ncbi/core/ncbiService.js";
 import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
 import { logger, requestContextService, sanitizeInputForLogging, } from "../../../utils/index.js";
-import { ensureArray, extractAbstractText, extractArticleDates, extractAuthors, extractDoi, extractGrants, extractJournalInfo, extractKeywords, extractMeshTerms, extractPmid, extractPublicationTypes, getText, } from "../../../services/NCBI/parsing/index.js";
+import { ensureArray, extractAbstractText, extractArticleDates, extractAuthors, extractDoi, extractGrants, extractJournalInfo, extractKeywords, extractMeshTerms, extractPmid, extractPublicationTypes, getText, } from "../../../services/ncbi/parsing/index.js";
 export const PubMedFetchContentsInputSchema = z
     .object({
     pmids: z

package/dist/mcp-server/tools/pubmedSearchArticles/logic.js CHANGED Viewed

@@ -5,10 +5,10 @@
  * @module src/mcp-server/tools/pubmedSearchArticles/logic
  */
 import { z } from "zod";
-import { getNcbiService } from "../../../services/NCBI/core/ncbiService.js";
+import { getNcbiService } from "../../../services/ncbi/core/ncbiService.js";
 import { BaseErrorCode, McpError } from "../../../types-global/errors.js";
 import { logger, requestContextService, sanitizeInputForLogging, } from "../../../utils/index.js";
-import { extractBriefSummaries } from "../../../services/NCBI/parsing/index.js";
+import { extractBriefSummaries } from "../../../services/ncbi/parsing/index.js";
 import { sanitization } from "../../../utils/security/sanitization.js";
 export const PubMedSearchArticlesInputSchema = z.object({
     queryTerm: z

package/dist/services/{NCBI → ncbi}/core/ncbiConstants.d.ts.map RENAMED Viewed

	@@ -1 +1 @@
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package/dist/services/{NCBI → ncbi}/core/ncbiConstants.js.map RENAMED Viewed

	@@ -1 +1 @@
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package/dist/services/{NCBI → ncbi}/core/ncbiCoreApiClient.d.ts RENAMED Viewed

@@ -1,7 +1,7 @@
 /**
  * @fileoverview Core client for making HTTP requests to NCBI E-utilities.
  * Handles request construction, API key injection, retries, and basic error handling.
- * @module src/services/NCBI/core/ncbiCoreApiClient
+ * @module src/services/ncbi/core/ncbiCoreApiClient
  */
 import { AxiosResponse } from "axios";
 import { RequestContext } from "../../../utils/index.js";

package/dist/services/{NCBI → ncbi}/core/ncbiCoreApiClient.d.ts.map RENAMED Viewed

	@@ -1 +1 @@
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package/dist/services/{NCBI → ncbi}/core/ncbiCoreApiClient.js RENAMED Viewed

@@ -1,7 +1,7 @@
 /**
  * @fileoverview Core client for making HTTP requests to NCBI E-utilities.
  * Handles request construction, API key injection, retries, and basic error handling.
- * @module src/services/NCBI/core/ncbiCoreApiClient
+ * @module src/services/ncbi/core/ncbiCoreApiClient
  */
 import axios from "axios";
 import { config } from "../../../config/index.js";

package/dist/services/{NCBI → ncbi}/core/ncbiCoreApiClient.js.map RENAMED Viewed

	@@ -1 +1 @@
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package/dist/services/{NCBI → ncbi}/core/ncbiRequestQueueManager.d.ts.map RENAMED Viewed

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package/dist/services/{NCBI → ncbi}/core/ncbiRequestQueueManager.js.map RENAMED Viewed

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package/dist/services/{NCBI → ncbi}/core/ncbiResponseHandler.js.map RENAMED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/services/{NCBI → ncbi}/core/ncbiService.d.ts RENAMED Viewed

@@ -5,7 +5,7 @@
  * retries, and parsing of XML/JSON responses. It aims to provide a robust
  * and compliant interface for other parts of the pubmed-mcp-server to
  * access PubMed data.
- * @module src/services/NCBI/core/ncbiService
+ * @module src/services/ncbi/core/ncbiService
  */
 import { ESearchResult, EFetchArticleSet } from "../../../types-global/pubmedXml.js";
 import { RequestContext } from "../../../utils/index.js";

package/dist/services/{NCBI → ncbi}/core/ncbiService.d.ts.map RENAMED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"ncbiService.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/core/ncbiService.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EACL,aAAa,EACb,gBAAgB,EAEjB,MAAM,oCAAoC,CAAC;AAC5C,OAAO,EAEL,cAAc,EAEf,MAAM,yBAAyB,CAAC;AACjC,OAAO,EAAE,iBAAiB,EAAE,kBAAkB,EAAE,MAAM,oBAAoB,CAAC;AAK3E,qBAAa,WAAW;IACtB,OAAO,CAAC,YAAY,CAA0B;IAC9C,OAAO,CAAC,SAAS,CAAoB;IACrC,OAAO,CAAC,eAAe,CAAsB;;YAQ/B,kBAAkB;IAwBnB,OAAO,CAClB,MAAM,EAAE,iBAAiB,EACzB,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,aAAa,CAAC;IAwBZ,QAAQ,CACnB,MAAM,EAAE,iBAAiB,EACzB,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,OAAO,CAAC;IAON,MAAM,CACjB,MAAM,EAAE,iBAAiB,EACzB,OAAO,EAAE,cAAc,EACvB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,gBAAgB,CAAC;IAcf,KAAK,CAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,OAAO,CAAC;IAMN,KAAK,CAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,EAAE,cAAc,GACtB,OAAO,CAAC,OAAO,CAAC;CAKpB;AAID,wBAAgB,cAAc,IAAI,WAAW,CAY5C"}

package/dist/services/{NCBI → ncbi}/core/ncbiService.js RENAMED Viewed

@@ -5,7 +5,7 @@
  * retries, and parsing of XML/JSON responses. It aims to provide a robust
  * and compliant interface for other parts of the pubmed-mcp-server to
  * access PubMed data.
- * @module src/services/NCBI/core/ncbiService
+ * @module src/services/ncbi/core/ncbiService
  */
 import { logger, requestContextService, } from "../../../utils/index.js";
 import { NcbiCoreApiClient } from "./ncbiCoreApiClient.js";

package/dist/services/{NCBI → ncbi}/core/ncbiService.js.map RENAMED Viewed

	@@ -1 +1 @@
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package/dist/services/{NCBI → ncbi}/parsing/eSummaryResultParser.d.ts.map RENAMED Viewed

	@@ -1 +1 @@
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package/dist/services/{NCBI → ncbi}/parsing/eSummaryResultParser.js.map RENAMED Viewed

	@@ -1 +1 @@
1	- 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package/dist/services/{NCBI → ncbi}/parsing/index.d.ts.map RENAMED Viewed

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package/dist/services/{NCBI → ncbi}/parsing/index.js.map RENAMED Viewed

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package/dist/services/{NCBI → ncbi}/parsing/pubmedArticleStructureParser.d.ts.map RENAMED Viewed

	@@ -1 +1 @@
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package/dist/services/{NCBI → ncbi}/parsing/pubmedArticleStructureParser.js.map RENAMED Viewed

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package/dist/services/{NCBI → ncbi}/parsing/xmlGenericHelpers.d.ts.map RENAMED Viewed

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package/dist/services/{NCBI → ncbi}/parsing/xmlGenericHelpers.js.map RENAMED Viewed

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package/package.json CHANGED Viewed

@@ -1,7 +1,8 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "1.4.3",
+  "version": "1.4.5",
   "description": "Production-ready PubMed Model Context Protocol (MCP) server that empowers AI agents and research tools with comprehensive access to PubMed's article database. Enables advanced, automated LLM workflows for searching, retrieving, analyzing, and visualizing biomedical and scientific literature via NCBI E-utilities.",
+  "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "main": "dist/index.js",
   "files": [
     "dist"
@@ -38,42 +39,41 @@
   },
   "dependencies": {
     "@hono/node-server": "^1.17.1",
-    "@modelcontextprotocol/sdk": "^1.17.2",
+    "@modelcontextprotocol/sdk": "^1.19.1",
     "@opentelemetry/api": "^1.9.0",
-    "@opentelemetry/auto-instrumentations-node": "^0.62.0",
-    "@opentelemetry/exporter-metrics-otlp-http": "^0.203.0",
-    "@opentelemetry/exporter-trace-otlp-http": "^0.203.0",
-    "@opentelemetry/instrumentation-winston": "^0.48.0",
-    "@opentelemetry/resources": "^2.0.1",
-    "@opentelemetry/sdk-metrics": "^2.0.1",
-    "@opentelemetry/sdk-node": "^0.203.0",
-    "@opentelemetry/sdk-trace-node": "^2.0.1",
-    "@opentelemetry/semantic-conventions": "^1.36.0",
-    "@types/node": "^24.2.1",
+    "@opentelemetry/auto-instrumentations-node": "^0.64.6",
+    "@opentelemetry/exporter-metrics-otlp-http": "^0.205.0",
+    "@opentelemetry/exporter-trace-otlp-http": "^0.205.0",
+    "@opentelemetry/instrumentation-winston": "^0.50.2",
+    "@opentelemetry/resources": "^2.1.0",
+    "@opentelemetry/sdk-metrics": "^2.1.0",
+    "@opentelemetry/sdk-node": "^0.205.0",
+    "@opentelemetry/sdk-trace-node": "^2.1.0",
+    "@opentelemetry/semantic-conventions": "^1.37.0",
+    "@types/node": "^24.6.2",
     "@types/sanitize-html": "^2.16.0",
-    "@types/validator": "13.15.2",
-    "axios": "^1.11.0",
+    "@types/validator": "13.15.3",
+    "axios": "^1.12.2",
     "chart.js": "^4.5.0",
     "chartjs-node-canvas": "^5.0.0",
-    "typescript-eslint": "^8.39.0",
     "chrono-node": "^2.8.3",
     "citation-js": "^0.7.20",
     "dotenv": "^16.6.1",
     "fast-xml-parser": "^5.2.5",
     "hono": "^4.8.4",
-    "jose": "^6.0.12",
+    "jose": "^6.1.0",
     "js-yaml": "^4.1.0",
-    "patch-package": "^8.0.0",
-    "tmp": "^0.2.4",
     "node-cron": "^4.2.1",
-    "openai": "^5.12.2",
+    "openai": "^6.1.0",
     "partial-json": "^0.1.7",
+    "patch-package": "^8.0.1",
     "sanitize-html": "^2.17.0",
-    "tiktoken": "^1.0.21",
+    "tiktoken": "^1.0.22",
     "ts-node": "^10.9.2",
-    "typescript": "^5.9.2",
+    "typescript": "^5.9.3",
+    "typescript-eslint": "^8.45.0",
     "validator": "13.15.15",
-    "winston": "^3.17.0",
+    "winston": "^3.18.3",
     "winston-transport": "^4.9.0",
     "zod": "^3.25.74"
   },
@@ -124,12 +124,19 @@
   "devDependencies": {
     "@types/js-yaml": "^4.0.9",
     "@types/node-cron": "^3.0.11",
-    "eslint": "^9.32.0",
+    "ajv": "^8.17.1",
+    "ajv-formats": "^3.0.1",
+    "eslint": "^9.36.0",
     "prettier": "^3.6.2",
-    "typedoc": "^0.28.9",
+    "typedoc": "^0.28.13",
     "vite-tsconfig-paths": "^5.1.4",
     "vitest": "^3.2.4"
   },
+  "overrides": {
+    "patch-package": {
+      "tmp": "0.2.5"
+    }
+  },
   "publishConfig": {
     "access": "public"
   }

/package/dist/services/{NCBI → ncbi}/core/ncbiConstants.d.ts RENAMED Viewed

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/package/dist/services/{NCBI → ncbi}/core/ncbiConstants.js RENAMED Viewed

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/package/dist/services/{NCBI → ncbi}/core/ncbiResponseHandler.d.ts RENAMED Viewed

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/package/dist/services/{NCBI → ncbi}/core/ncbiResponseHandler.js RENAMED Viewed

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/package/dist/services/{NCBI → ncbi}/parsing/eSummaryResultParser.d.ts RENAMED Viewed

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/package/dist/services/{NCBI → ncbi}/parsing/eSummaryResultParser.js RENAMED Viewed

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/package/dist/services/{NCBI → ncbi}/parsing/index.d.ts RENAMED Viewed

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/package/dist/services/{NCBI → ncbi}/parsing/index.js RENAMED Viewed

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/package/dist/services/{NCBI → ncbi}/parsing/pubmedArticleStructureParser.d.ts RENAMED Viewed

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/package/dist/services/{NCBI → ncbi}/parsing/pubmedArticleStructureParser.js RENAMED Viewed

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/package/dist/services/{NCBI → ncbi}/parsing/xmlGenericHelpers.d.ts RENAMED Viewed

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/package/dist/services/{NCBI → ncbi}/parsing/xmlGenericHelpers.js RENAMED Viewed

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