Agent skill · data analytics · anthropics
instrument-data-to-allotrope
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.
Why this skill is useful
Adds executable Python code for converting various instrument output formats to Allotrope ASM JSON and flattened CSV, which the AI wouldn't generate on its own.
What it needs
Requires allotropy, openpyxl, pandas, pdfplumber installed locally. About 6k tokens when loaded. Last updated 2026-08-07. 23,345 stars on the source repository.
What this skill does
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. Refer to references/fieldclassificationguide.md for guidance, but when ambiguity remains, confirm with the user rather than guessing. …
How to use it
Reference it in AdaL, Claude Code, Cursor or any coding agent — nothing to install:
@skills anthropics/instrument-data-to-allotrope