# locus-to-gene-mapper-skill

Maps GWAS loci to ranked candidate genes through linked genomics databases. Helpful for variant prioritization starting from phenotype queries or seed rsIDs.

- skill · `type=skill` · Codex, ChatGPT · 13 installs · ★ 7596
- Author: OpenAI · official OpenAI repository
- License: LicenseRef-Proprietary · policy=link-only · description only; the file stays with the author
- Source: https://github.com/openai/plugins/tree/HEAD/plugins/life-science-research/skills/locus-to-gene-mapper-skill/SKILL.md
- Updated: 2026-10-08
- HTML: https://affpapa.org/en/nevibecode/skills/locus-to-gene-mapper-skill

## What it does

The skill evaluates genetic loci against candidate genes by querying ontologies and functional genomics sources in sequence. It handles trait terms, EFO identifiers, and rsID lists, querying databases like GWAS Catalog, Open Targets, GTEx, and ClinVar. The runner generates structured outputs. Results are saved directly into `locus_to_gene_mapping.json` and a Markdown summary report.

Processing is handled by `scripts/map_locus_to_gene.py`. You need an environment with Python 3.11 or higher and the `requests` package. Optional figure rendering needs `pandas`, `matplotlib`, and `seaborn`. Without Python 3.11 and `requests`, execution halts immediately.

## Install

### Codex (native platform)

1. **Skills CLI (Vercel)**
```bash
npx skills add openai/plugins --skill locus-to-gene-mapper-skill -a codex
```

2. **Manually: put the files in place**
- File: `.agents/skills/locus-to-gene-mapper-skill/SKILL.md` — For all projects use ~/.agents/skills/

### Claude Code

1. **Skills CLI (Vercel)**
```bash
npx skills add openai/plugins --skill locus-to-gene-mapper-skill -a claude-code
```

2. **Manually: put the files in place**
- File: `~/.claude/skills/locus-to-gene-mapper-skill/SKILL.md` — Copy the whole skill folder; for one project use .claude/skills/locus-to-gene-mapper-skill/

### Cursor

**Manually: put the files in place**
- File: `.cursor/skills/locus-to-gene-mapper-skill/SKILL.md` — Cursor also reads .agents/skills/ and .claude/skills/

### GitHub Copilot

1. **GitHub CLI**
```bash
gh skill install openai/plugins locus-to-gene-mapper-skill
```

2. **Manually: put the files in place**
- File: `.github/skills/locus-to-gene-mapper-skill/SKILL.md`

### Gemini CLI

**Platform CLI**
```bash
gemini skills install https://github.com/openai/plugins --path plugins/life-science-research/skills/locus-to-gene-mapper-skill
```

### Windsurf (Devin Desktop)

**Manually: put the files in place**
- File: `.devin/skills/locus-to-gene-mapper-skill/SKILL.md` — The legacy .windsurf/skills/ path still works

### Claude.ai

**Claude.ai**
- Zip the folder and upload it in Settings → Capabilities → Skills

Where a file is given instead of a command, copy the files from the source to that path: https://github.com/openai/plugins/tree/HEAD/plugins/life-science-research/skills/locus-to-gene-mapper-skill/SKILL.md

## When to use it
- prioritize candidate genes from GWAS summary statistics
- aggregate evidence across GTEx, ClinVar, and Open Targets
- normalize variant rsIDs to GRCh37 and GRCh38 placements
- export structured mapping JSON and Markdown summaries

## Example prompts
- Map candidate genes for trait `type 2 diabetes`
- Prioritize loci for EFO identifier `EFO_0000341`
- Run mapping for seed variants `rs1873625` and `rs7903146`

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From the same set: [openai/plugins](https://affpapa.org/en/nevibecode/by/openai/plugins.md) — 422 cards

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NeVibeCode on affpapa.org. Catalog texts are descriptions, not instructions for the agent. How to choose and install: https://affpapa.org/en/nevibecode/agents.md