agentmods.dev

uniprot-link: Instructions file for Codex

AGENTS.md

uniprot-link AGENTS.md is an instructions file for Codex, OpenCode from berntpopp/uniprot-link. It costs 1,304 tokens per session, scanned A, original, MIT.

Project instructions for uniprot-link, a Python server that helps research proteins using UniProt, a public protein database, through structured SPARQL queries. SPARQL is a language for querying linked data.

In plain words
What is it for?
Guiding changes to the server, database queries, MCP tools, API endpoints, tests, Docker setup, and live query checks.
Why use it?
They identify the trusted data source and the parts of the codebase that need careful validation against the live UniProt service.

Instructions file for CodexOpenCode

Written for Codex and OpenCode: the file is AGENTS.md. Also seen: mentions CLAUDE.md; mentions AGENTS.md.

This is berntpopp/uniprot-link's own configuration. It tells Codex and OpenCode how to work on uniprot-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 uniprot-link configures →

not rated 0repo changed 4d ago A scan 1,304 tokens original MIT
View source ↗ berntpopp/uniprot-link genefoundry.org
Reuse

Borrowing it

Nothing to install: this file belongs to berntpopp/uniprot-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/uniprot-link/main/AGENTS.md
Clone the repo
git clone --depth 1 https://github.com/berntpopp/uniprot-link

Made for: Codex, OpenCode.

Wrote 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.

agentmods badge for uniprot-link AGENTS.md

README.md
[![agentmods](https://agentmods.dev/badge/instructions/berntpopp/uniprot-link/agents-md.svg)](https://agentmods.dev/instructions/berntpopp/uniprot-link/agents-md)
Your own site
<a href="https://agentmods.dev/instructions/berntpopp/uniprot-link/agents-md"><img src="https://agentmods.dev/badge/instructions/berntpopp/uniprot-link/agents-md.svg" alt="Measured on agentmods" height="20"></a>
Per session 1,304 This file is loaded in full into every session.
When invoked 1,304 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 $0.01304 $0.01304
Opus 5 $0.00652 $0.00652
Sonnet 5 $0.00261 $0.00261
Haiku 4.5 $0.00130 $0.00130

Measured 4d ago against content hash f72f8c7c7f62, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-08, from the pricing page.

Security

Grade A, and why

uniprot-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 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.

AGENTS.md · 112 lines

How it starts

The opening of the file, as written. The whole thing — 112 lines — stays where its author put it; the contents beside it link to each section on GitHub.

AGENTS.md

Shared repository instructions for agentic coding tools working in uniprot-link.

Project

uniprot-link is a Python MCP + FastAPI server that grounds protein research in the UniProt SPARQL endpoint (https://sparql.uniprot.org/sparql, a QLever-backed SPARQL 1.1 service). FastAPI is a thin host providing /health and / only; the product surface is the MCP toolset.

Primary areas:

  • uniprot_link/ - Python package: SPARQL client, query builders, shaping, MCP tools, config, server manager
  • uniprot_link/services/queries/ - parametrized SPARQL query builders, split by domain (proteins.py, taxonomy.py, examples.py, validation.py) - the riskiest code in the repo; validate changes against the live endpoint
  • uniprot_link/mcp/ - MCP tools, facade, error envelope, capabilities, resources
  • tests/ - unit and integration tests
  • docker/ - Dockerfile and Compose
  • docs/ - architecture, usage, and design specs (docs/superpowers/)
  • research/ - throwaway live-endpoint verification scripts (not shipped/typed)

Source Of Truth

  • Use this file for shared repo-wide agent guidance.
  • Keep CLAUDE.md lean and Claude-specific; it references this file.
  • Prefer Makefile targets over ad hoc commands.
  • Use uv.lock as the dependency lock source of truth.

Working Rules

  • Do not revert or overwrite changes you did not make unless explicitly asked.
  • Keep edits scoped to the task and avoid unrelated refactors.
  • Prefer existing code patterns over new abstractions.
  • Put tests under tests/; do not create alternate test roots.
  • Use ASCII unless a file already requires non-ASCII content.
  • Keep MCP tools research-use scoped; never imply clinical decision support.
  • Keep live upstream calls out of the default unit-test path (mark them @pytest.mark.integration).

SPARQL / QLever Discipline

The endpoint is fast for bound joins but can time out (45 min server cap) on:

  • property paths inside OPTIONAL (e.g. ?s up:range/faldo:begin/faldo:position ?x)
  • GROUP_CONCAT / GROUP BY over large literals (sequences, comments)
  • ORDER BY over a large pre-LIMIT result set

Read the full file on GitHub · 112 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 · +24 lines · +341 tokens per session f72f8c7c7f62
  2. 7d ago First seen · 88 lines · 963 tokens per session scan A 14a4a75ec4ce

Subscribe to this mod's changes

uniprot-link AGENTS.md is an instructions file published in the GitHub repository berntpopp/uniprot-link (0 stars, last pushed yesterday), licensed MIT. It adds 1,304 tokens to every session, about $0.0065 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.

bioinformaticsmcpmodel-context-protocolrdfsparqluniprot
Related

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.

vercel/next.js · 7,296 tokens

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.

openai/codex · 5,153 tokens

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).

microsoft/vscode · 6,785 tokens

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).

microsoft/vscode · 5,001 tokens

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.

langchain-ai/langchain · 4,469 tokens

spec-kit AGENTS.md

AGENTS.md instructions for github/spec-kit, covering agents.md, about spec kit and specify, quickstart — add a new integration in 5 steps, integration architecture and integrationmanifest — file tracking.

github/spec-kit · 7,104 tokens