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genebass-gene-burden-skill

Fetch Genebass gene burden PheWAS associations for one Ensembl gene ID.

5.3k|765|Updated Mar 4, 2026
Search Tags:#bioinformatics#genomics#Ensembl#PheWAS#genebass#skat-o#gene burden
One-click install
npx skills add https://github.com/openai/plugins --skill genebass-gene-burden-skill
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: genebass-gene-burden-skill
Source: https://github.com/openai/plugins/tree/main/plugins/life-science-research/skills/genebass-gene-burden-skill
Command: npx skills add https://github.com/openai/plugins --skill genebass-gene-burden-skill

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) components.

What problem does it solve?

Querying the Genebass API for gene burden PheWAS results requires constructing correct API URLs, handling burden set naming, and joining phenotype metadata. This Skill wraps that workflow into a single script call that returns compact, readable association summaries for one Ensembl gene ID.

Core Features & Use Cases

  • Gene Burden PheWAS Queries: Submit one Ensembl gene ID with a burden set (pLoF, missense|LC, or synonymous) and receive SKAT-O p-values per phenotype.
  • Phenotype Description Enrichment: Automatically joins results with Genebass phenotype metadata so associations include human-readable descriptions.
  • Controlled Result Size: Limit output with max_results to keep summaries concise, with truncation flags indicating when more associations exist.
  • Use Case: A genetics researcher investigating ENSG00000173531 can request the top 25 pLoF burden associations and immediately see which phenotypes show significant gene burden signals.

Quick Start

Ask the assistant to fetch Genebass pLoF burden associations for Ensembl gene ID ENSG00000173531 with a maximum of 25 results.

Frequently Asked Questions about genebass-gene-burden-skill

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query Genebass gene burden PheWAS data for a gene?▼

Pipe a JSON object with an ensembl_gene_id, burden_set, and optional max_results to the genebass_gene_burden.py script via stdin. The script calls the Genebass API and returns JSON with phenotype associations and SKAT-O p-values.

What burden sets does the Genebass API support?▼

The supported canonical burden sets are pLoF, missense|LC, and synonymous. The script also accepts aliases such as LoF or lof for pLoF and missense for missense|LC, normalizing them before the API call.

Can I use a gene symbol instead of an Ensembl gene ID?▼

No, the script only accepts Ensembl gene IDs matching the ENSG format, with optional version suffixes that are stripped automatically. Gene symbols are not resolved, so convert symbols to Ensembl IDs before querying.

Why does the Genebass query return an HTTP 500 error?▼

Genebass returns HTTP 500 for unknown gene IDs or invalid burden set values. Verify the Ensembl gene ID exists and that the burden set is one of pLoF, missense|LC, or synonymous before retrying.

How do I limit the number of Genebass associations returned?▼

Set the max_results field in the input JSON to a positive integer. The response includes a truncated flag and association_count_total so you know when additional associations were omitted.

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