The Encyclopedia
of Composable Characteristics

🖥️ Development

To bootstrap a development environment, please use the following commands.

# Clone the repository
git clone git@github.com:stjudecloud/ecc.git
cd ecc

# Build the crate in release mode
cargo build --release

# List out the examples
cargo run --release --example

🤖 Authoring characteristics with Claude

This repository ships a Claude Code skill, create-ecc, that guides an agent through researching and authoring a new composable characteristic — not just writing YAML, but producing an evidence-backed entry a domain expert would sign off on. It lives at .claude/skills/create-ecc/SKILL.md and is discovered automatically by any agent started in this repository.

What it does

1. Research first. Before writing anything, the agent builds an evidence brief: a precise definition and scope, the correct category (morph vs molec), primary-literature citations with resolvable URLs, how the property is measured/reported (which decides binary vs. enumerated values and any thresholds), and alignment with existing ontologies (NCIt/MONDO). A quality bar rejects thin or unsourced entries.
2. Scaffold correctly. It allocates the next identifier (ECC-{MORPH|MOLEC}-NNNNNN, six zero-padded digits) and a matching NNNNNN-slug.yml filename in the right folder, and writes a schema-valid entry honoring the state lifecycle (draft → proposed → provisional → adopted) and deny_unknown_fields.
3. Validate. It runs cargo run -p ecc-cli -- check ecc and fixes any failures before finishing.

Usage

Start an agent in the repository root and describe the characteristic, e.g.:

Use the create-ecc skill to add a molecular characteristic for MYCN amplification.

See .claude/skills/create-ecc/SKILL.md for the full workflow and schema reference.

## 🚧️ Tests

Before submitting any pull requests, please make sure the code passes the
following checks (from the root directory).

```bash
# Run the project's tests.
cargo test --all-features

# Run the tests for the examples.
cargo test --examples --all-features

# Ensure the project doesn't have any linting warnings.
cargo clippy --all-features

# Ensure the project passes `cargo fmt`.
# Currently this requires nightly Rust
cargo +nightly fmt --check

# Ensure the docs build.
cargo doc

🤝 Contributing

Contributions, issues and feature requests are welcome! Feel free to check issues page.

📝 License

This project is licensed as either Apache 2.0 or MIT at your discretion.

Copyright © 2024-Present St. Jude Children's Research Hospital.