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sdrf:annotate

Official

Streamline SDRF annotation for proteomics.

Education & Research#ontology#metadata#pipeline#annotation#proteomics#sdrf#pride
Authorbigbio
Version1.0.0
Installs0

System Documentation

What problem does it solve?

Researchers and curators must create highly accurate SDRF files for proteomics datasets, a process that involves complex template selection, ontology term lookup, and detailed technical metadata extraction from PRIDE and raw files.

Core Features & Use Cases

  • End‑to‑end workflow: Guides users from PXD accession or experiment description through template selection, sample and technical metadata collection, file‑sample mapping, and validation.
  • Ontology integration: Searches OLS for precise organism, disease, cell type, and modification terms, ensuring compliance with SDRF standards.
  • Automated validation: Generates a temporary SDRF file and runs parse_sdrf validation against selected templates, fixing errors before delivery.
  • Community contribution: Offers optional steps to submit the final SDRF back to the proteomics‑sample‑metadata repository.

Quick Start

Ask the assistant to create an SDRF for a ProteomeXchange dataset by providing its PXD identifier, e.g., “Create an SDRF for PXD012345”.

Dependency Matrix

Required Modules

None required

Components

Standard package

💻 Claude Code Installation

Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.

Please help me install this Skill:
Name: sdrf:annotate
Download link: https://github.com/bigbio/sdrf-skills/archive/main.zip#sdrf-annotate

Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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