Generate SDRF files for proteomics datasets from PXD accessions.
npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-annotate
Please help me install this Agent Skill. Skill: sdrf:annotate Source: https://github.com/bigbio/sdrf-skills/tree/main/skills/sdrf-annotate Command: npx skills add https://github.com/bigbio/sdrf-skills --skill sdrf-annotate
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.
parse_sdrf validation against selected templates, fixing errors before delivery.Ask the assistant to create an SDRF for a ProteomeXchange dataset by providing its PXD identifier, e.g., “Create an SDRF for PXD012345”.
High-intent search queries and answers about installing and using this skill.
To create an SDRF file for a ProteomeXchange dataset, provide the PXD accession identifier to the assistant. The workflow then coordinates template selection, ontology lookup, and technical metadata extraction from PRIDE to generate the file.
SDRF annotation is the process of generating structured metadata files for proteomics datasets. It involves selecting templates, looking up ontology terms via OLS, and extracting technical metadata to ensure compliance with community standards.
You validate an SDRF file by generating a temporary file and running the parse_sdrf validation tool against selected templates. This process identifies and fixes formatting or ontology errors before final delivery.
Yes, you can use literature descriptions and raw file metadata instead of PXD accessions. The workflow accepts experiment descriptions to guide template selection and sample metadata collection for the SDRF file.
Yes, SDRF annotation requires ontology term lookups for cell type, disease, organism, and modifications. The workflow searches the OLS ontology lookup service to ensure precise terminology and SDRF standard compliance.
Creating SDRF files is limited by the need for accessible PRIDE APIs for project metadata and OLS for ontology terms. Without access to these external services, the automated template selection and validation workflow cannot function correctly.
bigbioSubmit validated SDRF annotations as pull requests to the bigbio/proteomics-sample-metadata GitHub repository.
bigbioExplain SDRF column definitions, format rules, and validation errors for proteomics metadata.
bigbioFix formatting errors in SDRF files and validate with parse_sdrf.
bigbioLoad SDRF content, detect templates, and validate against PRIDE data.