Borrowing it
Nothing to install: this file belongs to berntpopp/hpo-link. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.
curl -O https://raw.githubusercontent.com/berntpopp/hpo-link/main/CLAUDE.mdgit clone --depth 1 https://github.com/berntpopp/hpo-linkWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/instructions/berntpopp/hpo-link/claude-md)<a href="https://agentmods.dev/instructions/berntpopp/hpo-link/claude-md"><img src="https://agentmods.dev/badge/instructions/berntpopp/hpo-link/claude-md/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/instructions/berntpopp/hpo-link/claude-md"><img src="https://agentmods.dev/badge/instructions/berntpopp/hpo-link/claude-md.svg" alt="Reviewed on agentmods" width="80" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00631 | $0.00631 |
| Opus 5 | $0.00316 | $0.00316 |
| Sonnet 5 | $0.00126 | $0.00126 |
| Haiku 4.5 | $0.00063 | $0.00063 |
Grade A, and why
hpo-link CLAUDE.md scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 9d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 63 lines — stays where its author put it; the contents beside it link to each section on GitHub.
CLAUDE.md
This file orients Claude Code (and other agents) in this repository.
Read AGENTS.md first — it is the authoritative contributor and agent guide (architecture, invariants, conventions, definition of done). This file only highlights the essentials.
Role
hpo-link is an MCP + REST server over the Human Phenotype Ontology (HPO),
backed by a locally-built SQLite database. It serves phenotype term lookup,
is_a hierarchy traversal, cross-ontology mapping, and gene↔phenotype↔disease
association queries (HPOA). It mirrors the sibling mgi-link stack.
Directory layout
hpo_link/ # core package (config, ingest, data, services, mcp)
server.py # unified REST + MCP server entry point
mcp_server.py # stdio MCP entry point (Claude Desktop)
scripts/ # CI helpers (check_file_size.py, check_deployed_freshness.py)
tests/ # unit + integration tests
docker/ # Dockerfile, docker-compose.yml, entrypoint.sh
docs/ # architecture.md, deployment.md, usage.md
See AGENTS.md for the full layout and architecture.
Key make commands
make install # uv sync --group dev
make data # build the local HPO database
make data-status # print loaded HPO release + counts
make dev # unified REST + MCP server on http://127.0.0.1:8000
make mcp-serve # stdio MCP server
make ci-local # the full gate (format-check, lint, lint-loc, mypy, test)
make format # auto-format with ruff
make typecheck # mypy strict
make test # unit tests (not integration)
TL;DR lint / test / build
make ci-local # must be green before any commit
make format # fix formatting issues flagged by ci-local
uv run pytest tests -q -m "not integration" # fast unit tests
Invariants (summary)
- Two planes: data plane returns plain dicts; MCP plane owns
success/_meta. - Every
compact+ response carries_meta.next_commands;minimalopts out. - 7-code error taxonomy; every tool has
output_schema+READ_ONLY_OPEN_WORLD. structlog→ stderr only; stdout is reserved for the stdio MCP protocol.- Files ≤ 500 lines; coverage ≥ 80%;
make ci-localis the definition of done. - Cite HPO id + HPO release version (
hpo_version) in every payload.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 9d ago First seen · 63 lines · 631 tokens per session scan A 91904db36884
hpo-link CLAUDE.md is an instructions file published in the GitHub repository berntpopp/hpo-link (1 stars, last pushed 2d ago), licensed MIT. It adds 631 tokens to every session, about $0.0032 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
Other instructions, from other repositories
next.js AGENTS.md
AGENTS.md instructions for vercel/next.js, covering next.js development guide, codebase structure, monorepo overview, core package: packages/next and other important packages.
codex AGENTS.md
AGENTS.md instructions for openai/codex, covering rust/codex-rs, the codex-core crate, code review rules, crate api surface and model visible context.
vscode buildNext.instructions.md
Working notes and architecture documentation for the new esbuild-based build system in build/next. Use when making changes to the new build pipeline (transpile/bundle commands, NLS plugin, source-map handling, resource copying, or self-hosting watch tasks).
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, applying the notice (cutover) and fallback chain (never fail the build).
langchain AGENTS.md
AGENTS.md instructions for langchain-ai/langchain, covering global development guidelines for the langchain monorepo, corridor security analysis, project architecture and context, monorepo structure and development tools & commands.
deepseek-harness AGENTS.md
AGENTS.md instructions for deepseek-ai/deepseek-harness, covering agents.md, pre-stable apis and released session data, repository layout, commands and host sandbox failures.