gtex-database

1# GTEx Database Integration
2 
3This skill retrieves transcriptomics data (RNA expression baselines) and
4expression Quantitative Trait Loci (eQTLs) from the GTEx Portal API V2. It
5provides access to median TPM (Transcripts Per Million) values for genes and
6significant eQTLs for variants across 54 human tissue sites.
7 
8## Prerequisites
9 
101.  **`uv`**: Read the `uv` skill and follow its Setup instructions to ensure
11    `uv` is installed and on PATH.
122.  **User Notification**: If .licenses/gtex_database_LICENSE.txt does not
13    already exist in the workspace root directory then (1) prominently notify
14    the user to check the terms at https://gtexportal.org/home/license and
15    https://gtexportal.org/home/documentationPage#gtexApi, then (2) create the
16    file recording the notification text and timestamp.
17 
18## When to Use
19 
20**Use this skill when you need to:**
21 
22-   Map a gene symbol to its Versioned GENCODE ID.
23-   Retrieve the baseline median expression level (in TPM) of a gene across
24    various tissues.
25-   Find the top tissues where a particular gene is most highly expressed.
26-   Fetch significant single-tissue eQTLs for a variant or within a chromosomal
27    window.
28-   Get all significant eQTLs associated with a specific gene.
29-   Contextualise a variant within GWAS loci using eQTL data.
30 
31**Do NOT use when you need to:**
32 
33-   Query for protein-level expression or post-translational modifications
34    (PTMs). GTEx only measures mRNA abundance.
35…