instrument-data-to-allotropelisted

# Instrument Data to Allotrope Converter Convert instrument files into standardized Allotrope Simple Model (ASM) format for LIMS upload, data lakes, or handoff to data engineering teams. > **Note: This is an Example Skill** > > This skill demonstrates how skills can support your data engineering tasks—automating schema transformations, parsing instrument outputs, and generating production-ready code. > > **To customize for your organization:** > - Modify the `references/` files to include your company's specific schemas or ontology mappings > - Use an MCP server to connect to systems that define your schemas (e.g., your LIMS, data catalog, or schema registry) > - Extend the `scripts/` to handle proprietary instrument formats or internal data standards > > This pattern can be adapted for any data transformation workflow where you need to convert between formats or validate against organizational standards. ## Workflow Overview 1. **Detect instrument type** from file contents (auto-detect or user-specified) 2. **Parse file** using allotropy library (native) or flexible fallback parser 3. **Generate outputs**: - ASM JSON (full semantic structure) - Flattened CSV (2D tabular format) - Python parser code (for data engineer handoff) 4. **Deliver** files with summary and usage instructions > **When Uncertain:** If you're unsure how to map a field to ASM (e.g., is this raw data or calculated? device setting or environmental condition?), ask the user for clarification. R