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hvantk:resource-uniprot-ptm

Builds locus-keyed Hail Tables from UniProt PTM data for variant annotation.

Updated Feb 2, 2024
Search Tags:#data pipeline#bioinformatics#proteomics#uniprot#variant annotation#hail
One-click install
npx skills add https://github.com/bigbio/hvantk --skill hvantk-resource-uniprot-ptm
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: hvantk:resource-uniprot-ptm
Source: https://github.com/bigbio/hvantk/tree/main/hvantk/skills/uniprot_ptm
Command: npx skills add https://github.com/bigbio/hvantk --skill hvantk-resource-uniprot-ptm

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires hail, requests, click, pytest, requests-mock, and includes scripts (resource) components.

What problem does it solve?

This skill automates the complex pipeline of acquiring, mapping, and building high-quality UniProt post-translational modification (PTM) datasets into Hail Tables, ensuring researchers have consistent, versioned, and analysis-ready proteomics data.

Core Features & Use Cases

  • Automated Data Lifecycle: Handles the entire flow from UniProt REST API download to genomic coordinate mapping and final Hail Table materialization.
  • Drift Detection: Includes a drift probe to monitor upstream UniProt schema changes, ensuring data integrity across updates.
  • Use Case: A researcher needs to annotate gnomAD-scale variant tables with PTM sites; this skill provides the optimized, locus-keyed Hail Table required for high-performance proximity joins.

Quick Start

Use the hvantk reprocess uniprot-ptm:sites command to build the latest PTM dataset into a Hail Table at the specified output path.

Frequently Asked Questions about hvantk:resource-uniprot-ptm

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

FAQPage Schema
How do I map UniProt post-translational modification sites to genomic coordinates for variant annotation?▼

You can build UniProt post-translational modification datasets into locus-keyed Hail Tables by automating REST API downloads and performing coordinate mapping against reference genomes, yielding analysis-ready proteomics data for variant annotation.

Can I annotate large-scale genetic datasets with UniProt PTM data using Hail?▼

Yes, you can materialize UniProt PTM data into optimized, locus-keyed Hail Tables, which facilitate high-performance proximity joins for annotating gnomAD-scale variant tables with experimental PTM sites.

Does this pipeline detect upstream UniProt schema changes during data updates?▼

The pipeline includes a drift probe to monitor upstream UniProt schema changes, ensuring data integrity and enabling reproducible data builds across dataset version updates.

How do I build and update a UniProt PTM Hail Table for multiomics analysis?▼

You can use the hvantk reprocess command to acquire, map, and materialize the latest UniProt PTM dataset into a Hail Table at a specified output path, automating the entire data lifecycle.

Do I need to handle contig remapping manually when integrating proteomics data with genomic loci?▼

No, the pipeline automatically performs contig remapping and coordinate mapping against reference genomes, integrating experimental PTM sites with genomic data without manual intervention.

What is the best way to ensure reproducible data builds for UniProt PTM datasets?▼

Automating the data lifecycle from UniProt REST API download to Hail Table materialization with schema validation and drift monitoring ensures reproducible, versioned, and high-quality proteomics data builds.

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