obsidian

obsidian-second-brain-research-skills

Agent skills for managing a second-brain research vault in Obsidian.

These skills follow the Agent Skills specification so they can be used by any skills-compatible agent, including Claude Code and Codex CLI.

Installation

npx skills

npx skills add [email protected]:D0miH/obsidian-second-brain-research-skills.git

Manually

Claude Code

Add the contents of this repo to a /.claude folder in the root of your Obsidian vault (or whichever folder you're using with Claude Code). See more in the official Claude Skills documentation.

Codex CLI

Copy the skills/ directory into your Codex skills path (typically ~/.codex/skills). See the Agent Skills specification for the standard skill format.

OpenCode

Clone the entire repo into the OpenCode skills directory (~/.opencode/skills/):

git clone https://github.com/D0miH/obsidian-second-brain-research-skills.git ~/.opencode/skills/obsidian-second-brain-research-skills

Do not copy only the inner skills/ folder — clone the full repo so the directory structure is ~/.opencode/skills/obsidian-second-brain-research-skills/skills/<skill-name>/SKILL.md.

OpenCode auto-discovers all SKILL.md files under ~/.opencode/skills/. No changes to opencode.json or any config file are needed. Skills become available after restarting OpenCode.

Skills

Skill	Description
ask_paper	Answer questions about a paper in the vault, using note first and arXiv HTML as fallback
read_paper	Convert a research paper into structured Obsidian notes and link research projects
create_project	Create atomic research project notes with minimal overhead
create_proposal	Create research proposal notes with proper linking and structure
merge_projects	Identify overlapping projects and merge them into consolidated notes
update_moc	Manage research area hubs (MOCs) with lean, project-focused organization
update_vault_index	Keep vault_index.md synchronized with current vault structure
audit_links	Validate vault graph consistency and structural integrity
validate_paper_links	Validate paper note links against actual paper references and influence
vault_maintenance	Run all vault maintenance skills in sequence — audit_links, update_vault_index, validate_paper_links