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orphanet-link: Instructions file for Claude Code

CLAUDE.md

orphanet-link CLAUDE.md is an instructions file for Claude Code from berntpopp/orphanet-link. It costs 531 tokens per session, scanned A, original, MIT.

A contributor guide for orphanet-link, an MCP and REST server that provides searchable Orphanet rare-disease data from a local SQLite index.

In plain words
What is it for?
Use it when developing, testing, or extending orphanet-link and its data-processing or MCP tool layers.
Why use it?
It explains the project’s architecture, response rules, identifiers, citations, testing, and completion requirements in one place.

Instructions file for Claude Code

Written for Claude Code: the file is CLAUDE.md. Also seen: mentions CLAUDE.md; mentions Claude Code; mentions AGENTS.md.

This is berntpopp/orphanet-link's own configuration. It tells Claude Code how to work on orphanet-link itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything orphanet-link configures →

not rated 0repo changed 4d ago A scan 531 tokens original MIT
View source ↗ berntpopp/orphanet-link genefoundry.org
Reuse

Borrowing it

Nothing to install: this file belongs to berntpopp/orphanet-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.

Copy the file
curl -O https://raw.githubusercontent.com/berntpopp/orphanet-link/main/CLAUDE.md
Clone the repo
git clone --depth 1 https://github.com/berntpopp/orphanet-link

Made for: Claude Code.

Wrote this? Show the measurements

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README.md
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<a href="https://agentmods.dev/instructions/berntpopp/orphanet-link/claude-md"><img src="https://agentmods.dev/badge/instructions/berntpopp/orphanet-link/claude-md.svg" alt="Measured on agentmods" height="20"></a>
Per session 531 This file is loaded in full into every session.
When invoked 531 The same file — it is already loaded in full.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00531 $0.00531
Opus 5 $0.00266 $0.00266
Sonnet 5 $0.00106 $0.00106
Haiku 4.5 $0.00053 $0.00053

Measured 4d ago against content hash 05ddaca63d0d, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-08, from the pricing page.

Security

Grade A, and why

orphanet-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 4d 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.

CLAUDE.md · 43 lines

How it starts

The opening of the file, as written. The whole thing — 43 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.

Essentials

  • orphanet-link is an MCP + REST server over Orphanet's scientific knowledge files (Orphadata), backed by a locally-built SQLite/FTS5 index.
  • Two planes: the data plane (config/constants/identifiers/ingest/ data/services) builds and reads the index and returns plain dicts; the MCP plane (mcp/) is domain-agnostic scaffolding where run_mcp_tool owns success/_meta and returns structured errors (never raised).
  • Invariants: every compact+ (default) response carries _meta.next_commands (minimal opts out of guidance → _meta = {tool, request_id, source, data_version}, keeping the citation anchor); 7-code error taxonomy; each tool has output_schema + READ_ONLY_OPEN_WORLD and a first sentence ending Signature: tool(args...); keep capabilities.TOOLS in sync; normalise ids in identifiers.py; cite the ORPHA code + Orphanet release version.
  • Definition of done: make ci-local green (format-check, lint-ci, lint-loc ≤500 lines/file, mypy strict, tests ≥80% coverage).
  • structlog → stderr only; stdout is reserved for the stdio MCP protocol and for python -m orphanet_link.data_probe, whose single JSON line is the fleet controller's read-only data observation (see AGENTS.md → Fleet Deploy Contract).

Common commands

make install        # uv sync --group dev
make data           # download Orphadata XML and build the local index
make data-status    # print loaded Orphanet release + counts
make dev            # unified REST + MCP server (http://127.0.0.1:8000/mcp)
make mcp-serve      # stdio MCP server
make ci-local       # the full gate

Research use only; not for clinical decision support. Orphadata is CC BY 4.0, © INSERM.

Read the full file on GitHub · 43 lines

Changes

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.

  1. 4d ago Changed · +2 lines · +38 tokens per session 05ddaca63d0d
  2. 7d ago First seen · 41 lines · 493 tokens per session scan A 54bcaba5ec07

Subscribe to this mod's changes

orphanet-link CLAUDE.md is an instructions file published in the GitHub repository berntpopp/orphanet-link (0 stars, last pushed yesterday), licensed MIT. It adds 531 tokens to every session, about $0.0027 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.

bioinformaticsclaudedisease-ontologyepidemiologyfastmcpgenefoundry
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