ai-gene-review: Instructions file for Claude Code

CLAUDE.md

ai-gene-review CLAUDE.md is an instructions file for Claude Code from ai4curation/ai-gene-review. It costs 13,716 tokens per session, scanned A, original, BSD-3-Clause.

Repository instructions for reviewing gene annotations, which describe how to assess links between genes and biological functions. They cover the project layout, review criteria, source files, and where to keep notes and results.

In plain words
What is it for?
Use them when reviewing a human gene, consulting UniProt and QuickGO records, recording notes, running bioinformatics analyses, or preparing an AI review.
Why use it?
They help reviewers use the project’s required evidence and file conventions consistently without editing downloaded source data.

Instructions file for Claude Code

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

This is ai4curation/ai-gene-review's own configuration. It tells Claude Code how to work on ai-gene-review 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 ai-gene-review configures →

Reuse

Borrowing it

Nothing to install: this file belongs to ai4curation/ai-gene-review. 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/ai4curation/ai-gene-review/main/CLAUDE.md
Clone the repo
git clone --depth 1 https://github.com/ai4curation/ai-gene-review

Made for: Claude Code.

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Per session 13,716 This file is loaded in full into every session.
When invoked 13,716 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 $0.13716 $0.13716
Opus 5.5 $0.05486 $0.05486
Sonnet 5.5 $0.02743 $0.02743
Haiku 4.5 $0.01372 $0.01372

Measured today against content hash 4cc645ad5ad8, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

ai-gene-review 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 today.

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 · 938 lines

How it starts

The opening of the file, as written. The whole thing — 938 lines — stays where its author put it; the contents beside it link to each section on GitHub.

AI instructions for ai-gene-review

Project Overview

This project is for managing AI reviews of gene annotations. The overall goal is to both review existing GO annotations using strict defined criteria, and to summarize the resulting high quality annotations.

Repository layout

src/ ai_gene_review/ schema/ gene_review.yaml <-- linkml schema for review docs genes/ human/ CFAP300/ CFAP300-notes.md <-- keep your notes here CFAP300-ai-review.yaml <-- the output of your AI review CFAP300-notes.md <-- your own notes, edit this, use it like a journal and keep appending. CFAP300-uniprot.txt <-- the uniprot record downloaded from the UniProt website (do not edit this file) CFAP300-goa.tsv <-- the GO annotation downloaded from the QuickGO API (do not edit this file, no need to view it) CFAP300-deep-research.md <-- the deep research for the gene review (do not edit this file, it is automatically generated for you) CFAP300-citations.md <-- the citations for the gene review (do not edit this file) CFAP300-bioinformatics/ <-- the folder for any bioinformatics analyses (create this if necessary) CFAP300-predictions-review.yaml <-- review of computational predictions NOT in GOA (optional) / ... worm/ lrx-1/ SCHPO/ <-- other orgs use uniprot species codes ... publications/ PMID_123456.md <-- cached publication text (this should be available for you, DO NOT EDIT) reactome/ R-HSA-NNNNNN.md <- cached reactome entry gocams/ MODEL/ <-- one folder per production GO-CAM model (bare local id) MODEL-src.yaml <- cached gocam-py model (activities/annotons; DO NOT EDIT) MODEL-review.yaml <- optional reviewer assessment index.tsv <- gene_product -> GO-CAM activity (annoton) index; join key to reviews/modules history/ genes/// <- append-only curation session records (see docs/history.md) modules//, gocams//, projects//, schema/, other/

Read the full file on GitHub · 938 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. today Changed · +36 lines · +650 tokens per session 4cc645ad5ad8
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  10. 21d ago First seen · 763 lines · 10,522 tokens per session scan A 9fd5884451de

Subscribe to this mod's changes

ai-gene-review CLAUDE.md is an instructions file published in the GitHub repository ai4curation/ai-gene-review (24 stars, last pushed today), licensed BSD-3-Clause. It adds 13,716 tokens to every session, about $0.0549 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 2026-08-30.

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