instrument-data-to-allotrope
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 standardsThis pattern can be adapted for any data transformation workflow where you need to convert between formats or validate against organizational standards.
Workflow Overview
- Detect instrument type from file contents (auto-detect or user-specified)
- Parse file using allotropy library (native) or flexible fallback parser
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