instrument-data-to-allotrope

SKILL.md

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

Convert laboratory instrument output files (PDF, CSV, Excel, TXT) to Allotrope Simple Model (ASM) JSON format or flattened 2D CSV. Use this skill when scientists need to standardize instrument data for LIMS systems, data lakes, or downstream analysis. Supports auto-detection of instrument types. Outputs include full ASM JSON, flattened CSV for easy import, and exportable Python code for data engineers. Common triggers include converting instrument files, standardizing lab data, preparing data for upload to LIMS/ELN systems, or generating parser code for production pipelines. Source: anthropics/life-sciences.

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