note.md

Product Introduction

1. Definition: note.md is a local-first, native Mac application designed as an integrated research IDE and academic writing workspace. It is a specialized productivity tool that combines the core functionalities of a PDF reader, a citation manager (like Zotero), a markdown note-taking app (like Obsidian), and a structured writing editor into a single, unified interface.

2. Core Value Proposition: note.md exists to eliminate workflow fragmentation for researchers, students, and academics. Its core proposition is to provide a private, local-first environment for reading papers, managing sources, taking linked markdown notes, citing evidence, and turning literature into structured writing—all within one application, with no need to sync between multiple tools.

Main Features

1. Reading Studio & Side-by-Side Reading: This feature constitutes a dual-pane PDF reader and markdown editor. It works by allowing users to import and organize PDFs directly within the app's "Knowledge Management" section. The user can then view a PDF in one pane and a markdown article in another, enabling seamless annotation, highlighting, and one-click citation insertion directly from the PDF's metadata into the linked note. It replaces the need for separate apps like Preview or Adobe Acrobat alongside a note-taking application.

2. Smart Citations & Source Management: note.md functions as a powerful citation manager. It automatically extracts metadata (title, authors, journal, etc.) from imported PDFs. Users can then insert BibTeX or APA citations directly into their markdown text with a command. These citations are dynamically linked back to the specific bookmark or highlight in the source PDF. All sources can be structured by topic, tagged, and exported as a standard .bib file, ensuring compatibility with LaTeX workflows and other reference managers.

3. Graph View & Knowledge Management: This feature transforms notes and sources into a visual knowledge graph. How it works: as users create articles, add citations (/cite), and connect notes with bidirectional links ([[link]]), the application automatically maps these relationships. The graph view displays sources and notes together as interconnected nodes, allowing researchers to discover hidden connections and visualize the structure of their research network. This moves beyond simple folder hierarchies to a non-linear, associative knowledge base.

4. Local AI-Powered Semantic Search & Evidence Scan (Premium): This is the core technical innovation. note.md runs local AI models directly on the user's Mac for privacy-preserving intelligence. The Semantic Search uses local embeddings to understand the meaning of a query, finding relevant passages even if the exact wording differs. The Evidence Scan feature can analyze a claim or topic in a draft and automatically retrieve supporting or contradictory passages from the entire local library, citing the source PDF and location. This AI processing happens on-device, with no data sent to the cloud.

Problems Solved

1. Pain Point: The primary problem addressed is research tool fragmentation and context switching. Researchers typically juggle separate applications for managing PDFs (Zotero), reading and annotating them (Preview, PDF Expert), taking notes (Obsidian, Notion, or physical notebooks), and writing (LaTeX, Word, Ulysses). This leads to disjointed workflows, lost connections between notes and sources, and sync issues between libraries.

2. Target Audience: The product is explicitly designed for graduate students, PhD candidates, academic researchers, and professors in fields like STEM, humanities, and social sciences. It targets users who conduct literature reviews, manage extensive paper libraries, write theses, dissertations, or journal articles, and rely on a rigorous, structured, and private research process.

3. Use Cases: Essential scenarios include: conducting a systematic literature review where papers must be sorted, tagged, and synthesized; writing a thesis or research paper where every claim must be traceable to a source; building a long-term personal knowledge base of insights from reading; and performing deep literature analysis where connecting ideas across hundreds of papers is necessary.

Unique Advantages

1. Differentiation: note.md differentiates itself from Zotero + Obsidian + PDF Reader setups by providing a single, cohesive application. Unlike cloud-based tools like Notion or generic markdown editors, it is 100% local-first and offline-capable, ensuring privacy and performance. It surpasses Zotero by integrating the writing environment directly with the citation and PDF management, and surpasses Obsidian by natively understanding and managing the PDF source library with smart citations.

2. Key Innovation: The key innovation is the integration of local AI within a local-first, markdown-based writing environment. The private, on-device AI for semantic search and evidence scanning is a significant advancement over cloud-dependent tools. Furthermore, the philosophy of storing everything in plain-text markdown files ensures data portability, longevity, and user ownership—a direct counter to proprietary formats that lead to vendor lock-in.

Frequently Asked Questions (FAQ)

1. What is the best app for organizing research papers on Mac? For users seeking an all-in-one solution that combines PDF management, note-taking, citation linking, and writing, note.md is a top contender. While Zotero excels at reference management and Obsidian at linked notes, note.md integrates these functions into a single native Mac app, eliminating the need to switch between multiple tools and keeping your workflow, citations, and notes tightly connected.

2. Is there a good Zotero alternative for Mac that includes note-taking and writing? Yes, note.md serves as a comprehensive alternative to using Zotero alongside other apps. It includes a full source and citation manager that can export standard .bib files, but crucially, it places your reference library directly within your markdown writing environment. Every citation in your draft can be traced back with one click to the exact highlight in the source PDF, creating a seamless reading-to-writing pipeline.

3. Can I use note.md without an internet connection for my research? Absolutely. note.md is a local-first application. All your data—PDFs, markdown notes, indexes, and even the local AI features like semantic search—run entirely on your Mac. You do not need an internet connection to read, annotate, write, search your knowledge base, or use AI-powered workflows, ensuring your research remains private and accessible anywhere.

4. Will note.md use my notes and research to train AI models? No. Privacy is a core principle of note.md. Your notes, sources, and all data never leave your machine. All AI processing, including semantic search and evidence scanning, is performed by local AI models on your Mac. There is no cloud server involved, no telemetry uploading your content, and nothing of yours is used for training external models.

5. How does note.md handle different citation formats like BibTeX and APA? note.md automates citation formatting. When you insert a citation using the /cite command, it automatically generates it in either BibTeX or APA format based on the metadata extracted from the PDF. You can switch between these formats. Furthermore, you can export your entire bibliography as a .bib file, making it fully compatible with LaTeX documents and other academic writing tools.