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GTEx Database Integration · mkurman | DecimalAI

scienceby mkurman

GTEx Database Integration

mkurman/gtex-database

Source mkurman/zorai ↗License MIT

Use when you want to retrieve quantitative RNA expression data and variant eQTL information from the GTEx (Genotype-Tissue Expression) Project across 54 non-diseased tissue sites.

SkillScore36Maintained

Automatic

Research pack

Last verified 8/21/2026

What it changes

Passed 4 of 10 test cases with the skill, and 3 of 10 without it.

Without skill27%

With skill36%

Checks it passed that the model alone missed

Executes resolve-gencode-id with GAPDH.
Saves the JSON output into a file under the /tmp/ directory.
Specifies /tmp/gtex_output.json as the default file destination.

and 2 more in the full report

4 fixed4 passed either way12 still failing2 broke

Pass-rate lift: +9 pp
Tokens: +47%
Agent turns: 0%
Response time: -54%

Model gemini-3.6-flashMeasured 8/21/2026v18 of 22 cases passed with skill · 10 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mkurman-gtex-database/SKILL.md https://app.decimal.ai/s/mkurman-gtex-database/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mkurman-gtex-database, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mkurman-gtex-database/ and pins it in .decimal/skills.lock

decimalai skills add mkurman-gtex-database

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mkurman-gtex-database/SKILL.md https://app.decimal.ai/s/mkurman-gtex-database/SKILL.md

Raw file: /s/mkurman-gtex-database/SKILL.md ↗ · machine-readable summary at /s/mkurman-gtex-database.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 4 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 4

Prompt

When making paginated API calls for bulk GTEx records, what is the maximum item limit per page enforced by the skill's guidelines?

What was checked, without and with the skill
Checked	Without skill	With skill
States that page requests are limited to a maximum of 250 items.	Missed	Passed

case-20 · gemini-3.6-flash · 8/21/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md168 lines2 filesincludes scripts

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

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
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

Track record

Benchmark

4 / 10

test cases passed, vs 3 / 10 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mkurman / zorai

skills/scientific-skills-gdm/gtex_database/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1Bundled 1 file · scripts

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

gtex-databaseQuery GTEx (Genotype-Tissue Expression) portal for tissue-specific gene expression, eQTLs (expression quantitative trait loci), and sQTLs. Essential for linking GWAS variants to gene regulation, understanding tissue-specific expression, and interpreting non-coding variant effects.Close match+41 pp pass-rate lift

More skills from the same source and nearby in the registry, with their headline benchmark lift.

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See it in action

What's inside

GTEx Database Integration

Prerequisites

When to Use

Core Rules

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

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