frumu-ai/tandem/bio-instrument-data

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 skill utilizes the Bio-Informatics Pack.

Scripts and references are located in: src-tauri/resources/packs/bio-informatics-pack/allotrope-conversion/

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)

1. 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?), ask the user for clarification. Refer to the pack's references/field_classification_guide.md for guidance.

Quick Start

# Install requirements first
pip install allotropy pandas openpyxl pdfplumber --break-system-packages
# Core conversion
from allotropy.parser_factory import Vendor
from allotropy.to_allotrope import allotrope_from_file
# Convert with allotropy
asm = allotrope_from_file("instrument_data.csv", Vendor.BECKMAN_VI_CELL_BLU)

Output Format Selection

ASM JSON (default) - Full semantic structure with ontology URIs

• Best for: LIMS systems expecting ASM, data lakes, long-term archival
• Validates against Allotrope schemas

Flattened CSV - 2D tabular representation

• Best for: Quick analysis, Excel users, systems without JSON support
• Each measurement becomes one row with metadata repeated

Both - Generate both formats for maximum flexibility

Calculated Data Handling

IMPORTANT: Separate raw measurements from calculated/derived values.

• Raw data → measurement-document (direct instrument readings)
• Calculated data → calculated-data-aggregate-document (derived values)

Calculated values MUST include traceability via data-source-aggregate-document.

Validation

Always validate ASM output before delivering to the user:

# Run validation script from the pack
python src-tauri/resources/packs/bio-informatics-pack/allotrope-conversion/scripts/validate_asm.py output.json