Explain SDRF column definitions, format rules, and validation errors for proteomics metadata.
npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-explain
Please help me install this Agent Skill. Skill: sdrf:explain Source: https://github.com/bigbio/sdrf-skills/tree/main/skills/sdrf-explain Command: npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-explain
Helps researchers and annotators understand SDRF columns, error messages, and format rules so they can produce valid, analysis-ready proteomics metadata and avoid common annotation mistakes.
Ask the skill to explain the purpose, format rules, and example values for the column characteristics[biological replicate].
High-intent search queries and answers about installing and using this skill.
An SDRF file structures proteomics metadata for reproducible annotation and PRIDE submissions. It defines experimental variables, characteristics, and factor values so downstream tools can correctly interpret sample attributes and experimental design.
To fix SDRF validation errors, identify the violated rule, correct the specific column value, and check ontology terms against the specification. Common fixes involve correcting reserved words, updating characteristics columns, and ensuring proper factor value formatting.
Characteristics describe inherent sample properties, comments add free-text metadata, and factor values represent experimental variables. SDRF annotation distinguishes these to ensure downstream analysis correctly separates biological attributes from experimental design factors.
Select an SDRF template by matching your experimental design to the specification's defined templates. The right template provides required columns, expected ontology terms, and format rules, ensuring valid PRIDE submissions and reproducible dataset curation.
SDRF column annotation requires controlled vocabulary and ontology terms recognized by the specification. Using custom terms triggers validation errors; you must select valid ontology terms from approved sources to ensure successful PRIDE submissions and reproducible annotation.
SDRF validation fails on biological replicate columns when values violate formatting rules, use reserved words incorrectly, or lack required ontology terms. Correct the column by applying exact expected value types and plain-language definitions from the SDRF specification.
bigbioGenerate SDRF files for proteomics datasets from PXD accessions.
bigbioSubmit validated SDRF annotations as pull requests to the bigbio/proteomics-sample-metadata GitHub repository.
bigbioValidate SDRF files for structural, template, and ontology issues.
dailycafiSearch MetaboLights studies and retrieve ISA-Tab metadata via the EMBL-EBI REST API.
