sdrf-skills

sdrf-skills

Turn Claude Code, Cursor, OpenAI Codex, Gemini CLI, or OpenCode into an expert proteomics SDRF annotator.

Pick a dataset → The agent fetches PRIDE + paper → You review a validated SDRF.

Structured skills that give AI assistants expert-level capabilities for annotating, validating, improving, and brainstorming proteomics metadata in the SDRF format.

Workflow

     SETUP             PLAN             ANNOTATE          VALIDATE           REFINE             SHARE
 ┌──────────┐     ┌──────────┐     ┌──────────┐     ┌──────────┐     ┌──────────┐     ┌──────────┐
 │  Conda   │     │ Templates│     │   PXD    │     │ Columns  │     │  Score   │     │ Convert  │
 │   Pip    │────▶│ Strategy │────▶│  PRIDE   │────▶│   OLS    │────▶│  AutoFix │────▶│   PR     │
 │  Tools   │     │  Layers  │     │  Paper   │     │  Rules   │     │ Raw scan │     │ Pipeline │
 └──────────┘     └──────────┘     └──────────┘     └──────────┘     └──────────┘     └──────────┘
  /sdrf:setup   /sdrf:brainstorm   /sdrf:annotate   /sdrf:validate   /sdrf:improve   /sdrf:contribute
                /sdrf:templates                                      /sdrf:fix         /sdrf:convert
                                                                     /sdrf:review
                                                                     /sdrf:techrefine

                  ┌──────────┐     ┌──────────┐     ┌──────────┐     ┌──────────┐
                  │  Format  │     │ Ontology │     │  Plain   │     │  Batch   │
                  │   Spec   │     │  Lookup  │     │   Lang   │     │ Confound │
                  │  Rules   │     │  Verify  │     │ Concepts │     │ Replic.  │
                  └──────────┘     └──────────┘     └──────────┘     └──────────┘
                 /sdrf:knowledge   /sdrf:terms     /sdrf:explain     /sdrf:design

What it does

Instead of an AI guessing at ontology terms or SDRF rules, these skills teach it exactly how to annotate proteomics datasets — using real tools (OLS, PRIDE, PubMed) guided by the methodology of experienced annotators.

The SDRF specification data (column definitions, templates) lives in a git submodule and is read at runtime — so the skills stay current when the spec evolves.

Available skills

All 16 skills are under the sdrf: namespace. In Claude Code, type /sdrf: and autocomplete will show them all.