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COMPOUND_MAPPINGS_COMPARISON_REPORT.md

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Compound Mappings Comparison Report

Files Compared

Baseline (Previous Version)

  • File: pipeline_output/merge_mappings/compound_mappings_strict_final_BASELINE.tsv
  • Size: 3.2 MB
  • Date: Dec 17, 2024 20:54
  • Total Entries: 17,658 (+ 1 header = 17,659 lines)
  • Columns: 36

Current (New Pipeline Output)

  • File: pipeline_output/merge_mappings/compound_mappings_strict_final.tsv
  • Size: 3.2 MB
  • Date: Dec 18, 2024 00:11
  • Total Entries: 17,658 (+ 1 header = 17,659 lines)
  • Columns: 36

Hydrate-Enhanced (New Feature)

  • File: pipeline_output/merge_mappings/compound_mappings_strict_final_hydrate.tsv
  • Size: 3.3 MB
  • Date: Dec 18, 2024 00:16
  • Total Entries: 17,658 (+ 1 header = 17,659 lines)
  • Columns: 39 (3 additional columns)

Baseline vs Current: ID Distribution

ID Type BASELINE CURRENT Change
CHEBI 14,526 14,526 0
PubChem 884 885 +1
CAS-RN 1,176 1,176 0
ingredient 971 970 -1
FOODON 26 26 0
UBERON 28 28 0
KEGG 21 21 0
medium 20 20 0
Unmapped 4 4 0
Other 2 2 0

Semantic ID Coverage

Metric BASELINE CURRENT Change
Total Semantic IDs 15,465 15,465 0
Coverage % 87.6% 87.6% 0

Unique Compounds

Metric BASELINE CURRENT
ChEBI-mapped 686 686
Total unique 1,047 1,047
ChEBI coverage 65.5% 65.5%

Key Difference: BASELINE vs CURRENT

Only 1 entry changed:

Field BASELINE CURRENT
Medium dsmz_973_composition dsmz_973_composition
Compound Na2Se3 x 5 H2O Na2Se3 x 5 H2O
mapped ID ingredient:870 PUBCHEM.COMPOUND:24934.0

Impact:

  • One ingredient code was upgraded to a PubChem ID
  • This represents a semantic mapping improvement (PubChem > generic ingredient code)
  • However, this could also represent a regression if the ingredient code was manually curated

Note: The pipeline appears stable with minimal drift from baseline.

Hydrate-Enhanced Version: New Features

Additional Columns (3 total)

  1. hydrated_chebi_id - ChEBI ID specifically for the hydrated form
  2. hydrated_chebi_label - ChEBI label for the hydrated form
  3. hydrate_mapping_source - Source/method used for hydrate mapping

Hydrate Mapping Statistics

Metric Value
Total entries 17,658
Entries with hydrated ChEBI IDs 1,130
Hydrate coverage 6.4%

What This Means

The hydrate-enhanced file provides:

  1. Dual Mapping: For hydrated compounds, both base and hydrated ChEBI IDs are provided

    • Example: MgCl2 x 6 H2O
      • mapped: Base compound mapping (if available)
      • base_chebi_id: CHEBI ID for MgCl2 (anhydrous)
      • hydrated_chebi_id: CHEBI ID for MgCl2·6H2O (hexahydrate)

  2. Improved Specificity: 1,130 hydrated compounds now have precise ChEBI IDs matching their hydration state

  3. Source Tracking: The mapping source is documented for reproducibility

File Size Comparison

File Size Size Increase
BASELINE 3.2 MB -
CURRENT 3.2 MB 0 KB
HYDRATE 3.3 MB +100 KB

The hydrate file is 3% larger due to the additional columns and hydrate-specific metadata.

Recommendations

1. Verify Na2Se3 Mapping Change

The change from ingredient:870 to PUBCHEM.COMPOUND:24934.0 should be reviewed:

  • Action: Check if PubChem 24934 correctly represents Na2Se3 x 5 H2O
  • Verify: Whether ingredient:870 was a manual curation that should be preserved

2. Use Hydrate File for Downstream Analysis

For media property calculations and semantic analysis:

  • Use: compound_mappings_strict_final_hydrate.tsv
  • Benefit: More accurate molecular weights and ChEBI mappings for 1,130 hydrated compounds
  • Impact: Better pH, salinity, and ionic strength calculations

3. Monitor Pipeline Stability

The current pipeline shows excellent stability:

  • Observation: Only 1 entry changed out of 17,658
  • Confidence: High reproducibility
  • Action: Continue monitoring for unexpected changes

Summary

✅ BASELINE → CURRENT: Highly stable, only 1 mapping changed ✅ CURRENT → HYDRATE: 1,130 compounds enhanced with hydrate-specific ChEBI IDs ✅ Overall Quality: 87.6% semantic coverage maintained ✅ Recommendation: Adopt hydrate-enhanced file for improved chemical accuracy

Generated: 2025-12-18