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SiYuan organizes personal knowledge around content blocks, bidirectional links, and a WYSIWYG Markdown editor, allowing references, queries, PDF annotations, and tasks to live in one workspace. It offers desktop and mobile apps, can be self-hosted with Docker, and exports to formats including Markdown, PDF, Word, and HTML for users who want stronger control over their data.

Logseq combines Markdown or Org-mode notes, bidirectional links, and a knowledge graph for organizing ideas, tasks, and research. It also supports PDF annotation and an ecosystem of plugins and themes across desktop and mobile clients. Its newer database graphs are in beta, while real-time collaboration and the new mobile app remain alpha features, so important data should be backed up before adopting them.

Trilium Notes organizes a personal knowledge base in an arbitrarily deep tree, allows one note to appear in multiple locations, and supports rich text, code notes, full-text search, and note versioning. It can run as a cross-platform desktop app or on a self-hosted server through the browser. Mobile access mainly uses the server's web interface or third-party apps.

Tolaria is a desktop app for organizing personal notes, company documentation, or agent memory on macOS, Windows, and Linux. Notes remain standard Markdown files with YAML frontmatter, and every vault is a Git repository with portable version history. It works without a Tolaria account, subscription, or cloud backend, so the knowledge base remains usable in other tools.