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README.md

Agent Skills for OntoGPT

These directories are Agent Skills: folders with a SKILL.md that an AI coding agent loads when a task matches the skill's description. They teach an agent to operate OntoGPT, whose job is to turn unstructured text into structured, ontology-grounded data.

Skill Use it to
ontogpt-extract run extractions: install, keys, models, inputs, ontogpt extract and friends, reading and converting output
ontogpt-select-template pick the bundled template that fits a text and a goal, or decide none does. Includes a catalog of every template and a script that prints what a template asks for and grounds to
ontogpt-author-template write or change a template: schema reference, a guide to choosing ontologies and OAK annotators, a skeleton, and a validator
ontogpt-troubleshoot diagnose empty outputs, AUTO: values, wrong ids, model and credential errors, cache and download surprises

They are written for the agent, not the end user. Each SKILL.md gives a procedure; references/ holds detail the agent reads on demand; scripts/ holds helpers that run inside the OntoGPT environment (uv run python <script> or an activated venv).

Installing the skills into an agent

The skills are plain directories, so installation is copying or linking.

Claude Code, this repository. Already done: .claude/skills/ holds symlinks to these directories, so a Claude Code session opened in the repo sees them. To use them from other projects, copy or link the directories into ~/.claude/skills/:

for s in skills/ontogpt-*; do ln -s "$(pwd)/$s" ~/.claude/skills/; done

Claude Code, another project that uses OntoGPT. Copy the four directories into that project's .claude/skills/.

Other agents that implement Agent Skills (Codex, Cursor, Gemini CLI, and others). Point the agent's skills directory at these folders, or copy them there. The format is the open specification; nothing here is Claude-specific.

Skills-aware agents without a skills directory. Paste the contents of the relevant SKILL.md into the system prompt and attach the references/ files as documents.

Keeping them current

  • ontogpt-select-template/references/template-catalog.md is generated from src/ontogpt/templates/*.yaml. Regenerate it when templates are added or their descriptions change: the generator is util/gen_skill_template_catalog.py.
  • The helper scripts import ontogpt and linkml_runtime; run them from the repository environment.
  • The CLI tables in ontogpt-extract/references/cli.md mirror ontogpt --help. Update them when options change.

Validating

The reference validator from the Agent Skills project checks frontmatter and naming:

pip install skills-ref
skills-ref validate skills/ontogpt-extract