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instrument-data-to-allotrope

Convert laboratory instrument output files to Allotrope ASM JSON and CSV.

23.4k|2.8k|Updated Jan 23, 2026
Search Tags:#data conversion#data standardization#asm#allotrope#instrument data#lab informatics
One-click install
npx skills add https://github.com/anthropics/knowledge-work-plugins --skill instrument-data-to-allotrope-anthropics
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: instrument-data-to-allotrope
Source: https://github.com/anthropics/knowledge-work-plugins/tree/main/bio-research/skills/instrument-data-to-allotrope
Command: npx skills add https://github.com/anthropics/knowledge-work-plugins --skill instrument-data-to-allotrope-anthropics

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires allotropy, pandas, openpyxl, pdfplumber, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill automates the conversion of raw laboratory instrument output files into the standardized Allotrope Simple Model (ASM) JSON format, streamlining data integration with LIMS, data lakes, and downstream analysis pipelines.

Core Features & Use Cases

  • Automated Conversion: Converts instrument output files (PDF, CSV, Excel, TXT) to ASM JSON.
  • Data Standardization: Ensures lab data conforms to the Allotrope standard for interoperability.
  • Multiple Output Formats: Generates full ASM JSON, flattened 2D CSV, and exportable Python parser code.
  • Auto-Detection: Supports auto-detection of instrument types for seamless processing.
  • Use Case: When scientists need to upload instrument data to a LIMS system, this Skill can convert proprietary instrument files into the required ASM JSON format, ensuring data integrity and compatibility.

Quick Start

Use the instrument-data-to-allotrope skill to convert the attached file 'sample_data.csv' into ASM JSON format.

Frequently Asked Questions about instrument-data-to-allotrope

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I convert raw laboratory instrument output files to Allotrope Simple Model JSON?▼

To convert laboratory instrument output files to Allotrope Simple Model (ASM) JSON, you can automate the transformation of raw PDF, CSV, Excel, and TXT files into standardized ASM JSON format. This process auto-detects instrument types to streamline data integration with LIMS and data lakes.

What is the best way to standardize lab instrument data for a LIMS system?▼

The best way to standardize lab instrument data for a LIMS system is converting proprietary instrument files into the Allotrope Simple Model (ASM) JSON format. This ensures data integrity, interoperability, and compatibility for downstream analysis pipelines.

Can I generate a flattened CSV file instead of full ASM JSON?▼

Yes, you can generate a flattened 2D CSV file instead of full ASM JSON. The conversion process supports multiple output formats, allowing data engineers to export either the complete ASM JSON structure or a flattened 2D CSV for simpler downstream analysis.

Does the Allotrope data conversion process support auto-detection of instrument types?▼

Yes, the Allotrope data conversion process supports auto-detection of instrument types. This feature enables seamless processing of various laboratory instrument output files without requiring manual configuration for each specific instrument.

Can I export Python parser code for data engineers to handle instrument data?▼

Yes, you can export Python parser code for data engineers handling instrument data. Along with ASM JSON and flattened 2D CSV outputs, the process generates exportable Python parser code to help standardize data for data lakes and downstream analysis.

What file formats are supported for converting laboratory data to ASM JSON?▼

The supported file formats for converting laboratory data to ASM JSON include PDF, CSV, Excel, and TXT. These raw laboratory instrument output files are processed using libraries like pdfplumber, openpyxl, and pandas to ensure accurate data extraction and standardization.

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