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.
curl -O https://raw.githubusercontent.com/berntpopp/orphanet-link/main/AGENTS.mdgit clone --depth 1 https://github.com/berntpopp/orphanet-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/orphanet-link/agents-md)<a href="https://agentmods.dev/instructions/berntpopp/orphanet-link/agents-md"><img src="https://agentmods.dev/badge/instructions/berntpopp/orphanet-link/agents-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/orphanet-link/agents-md"><img src="https://agentmods.dev/badge/instructions/berntpopp/orphanet-link/agents-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 | $0.06011 | $0.06011 |
| Opus 5.5 | $0.02404 | $0.02404 |
| Sonnet 5.5 | $0.01202 | $0.01202 |
| Haiku 4.5 | $0.00601 | $0.00601 |
Grade A, and why
orphanet-link AGENTS.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 6d 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 — 443 lines — stays where its author put it; the contents beside it link to each section on GitHub.
AGENTS.md — orphanet-link
Guidance for agents and contributors working in this repository.
What this is
orphanet-link is an MCP + REST server that grounds rare-disease queries in
Orphanet's scientific knowledge files (Orphadata). It builds a local SQLite/FTS5
index from the eight English Orphadata XML products and serves 19 read-only tools
for disease lookup, gene and HPO associations, epidemiology, natural history,
functional consequences, classification hierarchy, and cross-ontology mapping.
It mirrors the sibling mondo-link stack/architecture and slots into
genefoundry-router under the orphanet namespace.
Two planes (non-negotiable boundary)
-
Data plane —
config.py,constants.py,identifiers.py,exceptions.py,logging_config.py,buildinfo.py,ingest/,data/,services/. Downloads the Orphadata XML files (conditional GET with ETag/Last-Modified), atomically builds the SQLite index, and returns plain Python dicts. It raises typed exceptions fromorphanet_link.exceptions; it never builds error envelopes and never imports fromorphanet_link.mcp. -
MCP plane —
mcp/. Domain-agnostic scaffolding copied and adapted frommondo-link.run_mcp_tool(inmcp/envelope.py) ownssuccess/_metaand converts exceptions into returned structured errors (never raised to the client). Tool modules undermcp/tools/call service methods and attach_meta.next_commands; they do not touch SQLite or raise domain exceptions.
The boundary is enforced structurally: the data plane has no knowledge of MCP types; the MCP plane has no knowledge of SQL or XML.
The eight Orphadata products and where each is parsed
| Product | Orphadata file | Parser module | Tables populated |
|---|---|---|---|
| 1 | en_product1.xml |
ingest/parsers/product1.py |
disorder, disorder_synonym, disorder_lookup, disorder_fts, xref |
| 3 | en_product3_<id>.xml (~33) |
ingest/parsers/product3.py |
classification_edge, classification_closure, specialty |
| 4 | en_product4.xml |
ingest/parsers/product4.py |
phenotype |
| 6 | en_product6.xml |
ingest/parsers/product6.py |
gene, disorder_gene |
| 7 | en_product7.xml |
ingest/parsers/product7.py |
linearisation |
| 8 (funct) | en_funct_consequences.xml |
ingest/parsers/funct.py |
disability |
| 9 prev | en_product9_prev.xml |
ingest/parsers/product9_prev.py |
prevalence |
| 9 ages | en_product9_ages.xml |
ingest/parsers/product9_ages.py |
age_of_onset, inheritance |
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.
- 6d ago Changed 80528955f944
- 1mo ago Changed · +103 lines · +1,616 tokens per session 2866acc19f69
- 1mo ago First seen · 340 lines · 4,395 tokens per session scan A 55be9e246544
orphanet-link AGENTS.md is an instructions file published in the GitHub repository berntpopp/orphanet-link (0 stars, last pushed 2d ago), licensed MIT. It adds 6,011 tokens to every session, about $0.0240 per session on Opus 5.5. 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
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).
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.
vscode oss-third-party-notices.instructions.md
Instructions for microsoft/vscode, covering vs code oss third-party-notices pipeline, architecture, pipeline flow in ci, cache eligibility and rollout and applying the notice (cutover).
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.
vscode copilot-instructions.md
Copilot instructions for microsoft/vscode, covering vs code copilot instructions, project overview, root folders, core architecture (src/ folder) and built-in extensions (extensions/ folder).
vscode model-prompts.instructions.md
Model-specific prompt authoring and registry guidelines.