381,784 Collected SKILL.md files

Explore AI Agent Skills & Claude Prompts

Discover open-source agent skills for Claude Code, Codex, ChatGPT, and any tool that uses SKILL.md.

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monarch-initiative
Showing 12 of 26 skills
monarch-initiative

odk

by monarch-initiative
star 307

Use when running any ODK-backed command in this repo — owltools, robot, make NORM, robot verify, or any other tool that lives inside the ODK docker image

navigation main article SKILL.md
schedule Updated 1 month ago
monarch-initiative

analyse-issue

by monarch-initiative
star 305

Analyze MONDO GitHub issues for validity, suggest improvements, and generate structured reports with duplication checks and identifier validation

navigation main article SKILL.md
schedule Updated 7 months ago
monarch-initiative

merge-terms

by monarch-initiative
star 305

Use when asked to merge two MONDO terms — obsoleting one and transferring its metadata to the surviving term

navigation main article SKILL.md
schedule Updated 28 days ago
monarch-initiative

release-announcement

by monarch-initiative
star 305

Generate a formatted Mondo release announcement with statistics table from release diff reports

navigation main article SKILL.md
schedule Updated 2 months ago
monarch-initiative

update-publications

by monarch-initiative
star 35

Updates the Monarch Initiative publications page with latest data from Google Scholar. Use this when the user asks to update publications, refresh citation metrics, or add new papers to the publications page.

navigation main article SKILL.md
schedule Updated 7 months ago
monarch-initiative

cancer-curator

by monarch-initiative
star 28

Skill for curating cancer and neoplastic disease entries in the dismech knowledge base. Use this skill when creating or enhancing cancer entries, adding oncogene/tumor suppressor pathophysiology, curating histopathology findings, adding targeted therapy information, and linking genetic drivers to treatment responses. Covers fusion genes, two-hit hypothesis, oncogene addiction, and precision oncology concepts.

navigation main article SKILL.md
schedule Updated 21 days ago
monarch-initiative

disease-classification

by monarch-initiative
star 28

Skill for populating the `classifications` top-level block of a dismech Disease entry. Covers Harrison's Part assignment, mechanistic nosology, lysosomal storage, IUIS immunodeficiency, channelopathy, and ICD-O morphology fields, with a lookup table from common clinical phrasing to controlled-vocabulary keys.

navigation main article SKILL.md
schedule Updated 1 month ago
monarch-initiative

disease-trajectories

by monarch-initiative
star 26

Mine Disease Trajectories (DT/DisTraj) outputs for comorbidity/trajectory candidates, including parsing DT JSON/TSV, extracting directed pairs, filtering by sex or significance, and mapping signals into dismech comorbidity YAML.

navigation main article SKILL.md
schedule Updated 4 months ago
monarch-initiative

dismech-compliance

by monarch-initiative
star 26

Skill for analyzing and improving compliance in the dismech knowledge base. Use this skill when checking disorder file completeness, identifying missing fields (ontology terms, evidence, descriptions), understanding weighted priority scoring, and systematically improving knowledge base coverage.

navigation main article SKILL.md
schedule Updated 6 months ago
monarch-initiative

dismech-references

by monarch-initiative
star 26

Skill for validating and repairing evidence references in the dismech knowledge base. Use this skill when working with evidence items in disorder YAML files, validating that snippet text matches PubMed abstracts, and repairing misquoted or fabricated evidence. Critical for ensuring scientific accuracy and preventing AI hallucinations.

navigation main article SKILL.md
schedule Updated 5 months ago
monarch-initiative

dismech-terms

by monarch-initiative
star 26

Skill for adding and validating ontology term references in the dismech knowledge base. This skill should be used when working with disorder YAML files that need ontology term annotations (HPO for phenotypes, CL for cell types, GO for biological processes, MONDO for diseases, UBERON for anatomical entities). Use this skill when adding phenotype_term, cell_types term, biological_processes term, or other ontology-bound fields to disorder files.

navigation main article SKILL.md
schedule Updated 2 months ago
monarch-initiative

microbiome-curation

by monarch-initiative
star 26

Skill for curating microbiome-related pathophysiology in the dismech knowledge base. Use this skill when adding dysbiosis mechanisms, ecological concepts (Anna Karenina, keystone taxa, colonization resistance), SCFA/metabolite pathways, and linking microbial ecology to disease pathophysiology. Covers IBD, C. diff, obesity, and other microbiome-associated conditions.

navigation main article SKILL.md
schedule Updated 4 months ago
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Browse Agent Skills by Occupation

23 major groups · 867 SOC occupations

Browse by Category

Explore agent skills organized by their primary use case

SKILLMD / CREATORS AND OCCUPATION CATEGORIES

Explore the agent skills ecosystem by occupation and creator

SkillMD is not just a keyword search box. It is an open map that organizes public skills by occupation, creator, and repository, helping you see which workflows, judgment criteria, and domain habits people are writing for AI agents.

Then follow creators and GitHub repositories back to the source: compare the skills a team maintains, whether the repo is active, and how the README frames the work before you open, install, or reuse anything.

Use it three ways: learn an unfamiliar field by occupation, study how creators organize skills, then use source context to decide what is worth opening or reusing.

01 Map a field

Browse 23 occupation groups and 867 SOC roles to learn what skills exist in adjacent domains and how they break down real work.

02 Follow creators

Use creator and repository pages to inspect maintained skill collections, recent updates, and source context before trusting a result.

03 Search with sources

Search 1.7M+ collected skills, then use occupation tags, creators, and GitHub source context to decide what is worth opening.

Start with the occupation map, then follow creators and repositories back to real code. SkillMD helps explain why a skill is worth opening, not only what it is named.

SEO KNOWLEDGE HUB & TECHNICAL OVERVIEW

Standardizing Agent Capabilities with SKILL.md and Model Context Protocol (MCP)

In the rapidly evolving landscape of artificial intelligence, LLM agents (Large Language Model agents) have transitioned from simple text predictors to autonomous problem solvers. To orchestrate complex, multi-step agentic workflows, developers require a standardized format to specify agent capabilities, prompt instructions, system rules, and database bindings. This is where SKILL.md and the Model Context Protocol (MCP) have emerged as standard developer paradigms. SkillMD serves as the central directory for indexing, exploring, and sharing these critical agent configurations.

Our open-source registry currently tracks over 1.7 million collected SKILL.md configurations and system prompts. By compiling agent configurations from active developers on GitHub, we bridge the gap between prompt engineering research and production execution. Whether you are building agents with Anthropic's Claude Code, OpenAI's GPT-4, Google's Gemini, or local models using Ollama and LlamaIndex, standardized skill definitions ensure your agents behave predictably across different runtime environments.

What is the Model Context Protocol (MCP)?

The Model Context Protocol (MCP) is an open-source standard designed to connect LLMs to data sources, developer tools, and external environments. MCP establishes a bidirectional communication channel between client applications (like Cursor, Claude Desktop, or custom agent systems) and servers hosting data or capabilities. Standardizing instructions via SKILL.md enables LLMs to query databases, read local files, execute terminal commands, and integrate third-party APIs. SkillMD allows you to find ready-to-run MCP servers and prompt instructions for various occupations and technical tasks.

The Structure of a Professional SKILL.md File

A valid SKILL.md configuration is designed to be easily read by humans and parsed by LLMs. It contains precise system instructions, trigger conditions, required parameters, and execution examples. Below is the typical architectural blueprint of a professional agent skill:

  • Metadata & Core Scope: Declares the name of the skill, author details, target models, and a description of the capability.
  • Triggers & Intent Detection: Details semantic triggers that help the agent decide when to invoke this skill.
  • System Prompts: Explicit system-level instructions that direct the agent's behavior, personality, safety guardrails, and formatting preferences.
  • Capabilities & Tools: Lists the files, databases, or APIs the agent must access to complete the tasks.
  • Few-Shot Examples: Demonstrates real inputs and outputs, helping the model generalize behavior through in-context learning.

Optimizing Agent Workflows for Modern LLMs

Writing effective agent skills requires deep knowledge of prompt engineering. With the release of advanced reasoning models like Claude 3.5 Sonnet, ChatGPT o1, and DeepSeek-V3, prompt templates must focus on structured thinking. Developers are encouraged to use XML tags (e.g., <thought>, <context>, and <rules>) to isolate execution boundaries. Standardized prompts prevent agents from suffering from context drift, ensuring that long-running tasks remain aligned with the initial system parameters.

Exploring by SOC Occupations and Creator Profiles

What makes SkillMD unique is its taxonomy. Instead of simple text search, we parse and organize files according to the Standard Occupational Classification (SOC) system. This means you can discover skills written for Computer and Mathematical roles, Business and Financial operations, Legal, Design, and and Educational Instruction fields. By tracking creator profiles, developers can study how different teams organize their custom instructions, compare version updates, and fork public configs for specialized enterprise use cases.

SkillMD operates as a high-performance index running on a fast Go backend and a highly responsive Astro SSR frontend. All search queries execute in milliseconds, featuring smart debouncing to prevent multiple API requests while keeping user data secure. Join our community of developers to standardize your AI agent instructions and optimize your LLM prompting workflows today.

8 QUESTIONS

Frequently Asked Questions

A practical guide to agent skills: what they are, how to inspect them, and how SkillMD helps you explore the ecosystem.