gtex-database

Files (2)

• SKILL.md
• gtex_cli.py · scripts/

SKILL.md (first lines)

# GTEx Database Integration

This skill retrieves transcriptomics data (RNA expression baselines) and
expression Quantitative Trait Loci (eQTLs) from the GTEx Portal API V2. It
provides access to median TPM (Transcripts Per Million) values for genes and
significant eQTLs for variants across 54 human tissue sites.

## Prerequisites

1.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
    `uv` is installed and on PATH.
2.  **User Notification**: If LICENSE_NOTIFICATION.txt does not already exist in
    this skill directory then (1) prominently notify the user to check the terms
    at https://gtexportal.org/home/license and
    https://gtexportal.org/home/documentationPage#gtexApi, then (2) create the
    file recording the notification text and timestamp.

## When to Use

**Use this skill when you need to:**

-   Map a gene symbol to its Versioned GENCODE ID.
-   Retrieve the baseline median expression level (in TPM) of a gene across
    various tissues.
-   Find the top tissues where a particular gene is most highly expressed.
-   Fetch significant single-tissue eQTLs for a variant or within a chromosomal
    window.
-   Get all significant eQTLs associated with a specific gene.
-   Contextualise a variant within GWAS loci using eQTL data.

**Do NOT use when you need to:**

-   Query for protein-level expression or post-translational modifications
    (PTMs). GTEx only measures mRNA abundance.
-   Query gene expression in diseased tissues (e.g., tumor samples, cirrhosis).
    GTEx is a baseline atlas of normal, non-diseased tissues.
-   Query embryonic or fetal gene expression. GTEx donors are adults only.

## Core Rules

**CRITICAL**: You MUST respect GTEx Portal API Terms of Use.

-   **Use the Wrapper**: ALWAYS execute the provided helper scripts to query the
    database rather than accessing the database directly. The scripts
    automatically enforce the required rate limit gracefully.
-   Limit requests to maximum 250 items per page where applicable.
-   **Notification**: If this skill is used, ensure this is mentioned in the
    output.

## Command Selection Guide

**Pick the right command on the first try.** Match the user's input to the
correct subcommand below.

-   Map a gene symbol to GENCODE ID: `resolve-gencode-id`
-   Get median expression (TPM) for a gene: `get-median-expression`
-   Find tissues with highest expression for a gene: `get-top-expressed-tissues`
-   Get all eQTLs for a specific gene: `get-gene-eqtls`
-   Find eQTLs within a chromosomal region: `get-eqtls-in-region`

## Quick Start

```bash
# Map the TNF gene symbol to its GENCODE ID
uv run scripts/gtex_cli.py resolve-gencode-id TNF --output /tmp/tnf_id.json

# Get median expression of a gene by GENCODE ID
uv run scripts/gtex_cli.py get-median-expression ENSG00000232810.2 --output /tmp/tnf_expr.json
```

All subcommands write JSON to disk. Always save output in the `/tmp/` directory.
The default output file is `/tmp/gtex_output.json` if `--output` is not
specified.

## Commands

### 1. `resolve-gencode-id` — Gene Symbol → GENCODE ID

Maps a standard gene symbol (e.g., "JUN", "TNF") to its Versioned GENCODE ID.
This ID is required for all other expression and eQTL calls.

```bash
uv run scripts/gtex_cli.py resolve-gencode-id TNF --output /tmp/tnf_id.json
```

*Arguments:*

-   `gene_symbol` (positional): The standard gene symbol (e.g., "TNF").
-   `--output`: Output file path (default: `/tmp/gtex_output.json`).

### 2. `get-median-expression` — Get Median Expression (TPM)

Retrieves the median TPM for a gene across all 54 GTEx tissue sites or specified
tissues.

```bash
uv run scripts/gtex_cli.py get-median-expression ENSG00000232810.2 \
  --tissues "Whole Blood,Spleen" --output /tmp/expr.json
```

*Arguments:*

-   `gencode_id` (positional): The Versioned GENCODE ID.
-   `--tissues`: Comma-separated list of tissue IDs (optional, defaults to all
    54 tissues).
-   `--output`: Output file path (default: `/tmp/gtex_output.json`).

### 3. `get-top-expressed-tissues` — Get Top Expressed Tissues

Returns the `n` tissues with the highest median expression for the target gene.

```bash
uv run scripts/gtex_cli.py get-top-expressed-tissues ENSG00000232810.2 \
  --n 5 --output /tmp/top_tissues.json
```

*Arguments:*

-   `gencode_id` (positional): The Versioned GENCODE ID.

From hanyanphysics/AI-for-Physics, Apache-2.0.

More from hanyanphysics/AI-for-Physics