Instrument Data To Allotrope

anthropics/knowledge-work-pluginsOfficial

Converts lab instrument outputs (PDFs, CSVs, Excel files) into Allotrope Simple Model JSON or flattened CSV for LIMS upload and data pipelines. Uses the allotropy library for native parsing when available, falls back to flexible extraction for unsupported formats. Outputs include validated ASM JSON with proper calculated data traceability, 2D CSV for systems that don't handle JSON, and exportable Python code for data engineers. The validation is intentionally soft on unknown units and techniques to stay forward compatible with Allotrope schema updates. Works well as a template you can extend with your own instrument formats or schema mappings through the references directory.

skills.sh installs: 2.4K
GitHub stars: 35.3K
last updated: Aug 21, 2026

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Install

$ npx -y skills add anthropics/knowledge-work-plugins --skill instrument-data-to-allotrope --agent claude-code

Installs into .claude/skills of the current project.

Files

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.