/instrument-data-to-allotrope

name: instrument-data-to-allotrope
description: 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.

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/field_classification_guide.md` for guidance, but when ambiguity remains, confirm with the user rather than guessing.

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`:

"calculated-data-aggregate-document": {
  "calculated-data-document": [{
    "calculated-data-identifier": "SAMPLE_B1_DIN_001",
    "calculated-data-name": "DNA integrity number",
    "calculated-result": {"value": 9.5, "unit": "(unitless)"},
    "data-source-aggregate-document": {
      "data-source-document": [{
        "data-source-identifier": "SAMPLE_B1_MEASUREMENT",
        "data-source-feature": "electrophoresis trace"
      }]
    }
  }]
}

**Common calculated fields by instrument type:** | Instrument | Calculated Fields | |------------|-------------------| | Cell counter | Viability %, cell density dilution-adjusted values | | Spectrophotometer | Concentration (from absorbance), 260/280 ratio | | Plate reader | Concentrations from standard curve, %CV | | Electrophoresis | DIN/RIN, region concentrations, average sizes | | qPCR | Relative quantities, fold change |

See `references/field_classification_guide.md` for detailed guidance on raw vs. calculated classification.

Validation

Always validate ASM output before delivering to the user:

python scripts/validate_asm.py output.json
python scripts/validate_asm.py output.json --reference known_good.json  # Compare to reference
python scripts/validate_asm.py output.json --strict  # Treat warnings as errors

**Validation Rules:**

• Based on Allotrope ASM specification (December 2024)
• Last updated: 2026-01-07
• Source: https://gitlab.com/allotrope-public/asm

**Soft Validation Approach:** Unknown techniques, units, or sample roles generate **warnings** (not errors) to allow for forward compatibility. If Allotrope adds new values after December 2024, the validator won't block them—it will flag them for manual verification. Use `--strict` mode to treat warnings as errors if you need stricter validation.

**What it checks:**

• Correct technique selection (e.g., multi-analyte profiling vs plate reader)
• Field naming conventions (space-separated, not hyphenated)
• Calculated data has traceability (`data-source-aggregate-document`)
• Unique identifiers exist for measurements and calculated values
• Required metadata present
• Valid units and sample roles (with soft validation for unknown values)

Supported Instruments

See `references/supported_instruments.md` for complete list. Key instruments:

| Category | Instruments | |----------|-------------| | Cell Counting | Vi-CELL BLU, Vi-CELL XR, NucleoCounter | | Spectrophotometry | NanoDrop One/Eight/8000, Lunatic | | Plate Readers | SoftMax Pro, EnVision, Gen5, CLARIOstar | | ELISA | SoftMax Pro, BMG MARS, MSD Workbench |