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Analysis of Hydrated Compounds Mapped to Ingredient Codes

Overview

Analysis of composition_kg_mapping_with_oak_chebi.tsv to identify hydrated compounds that are mapped to "ingredient:" codes instead of proper CHEBI IDs.

Key Findings

Primary Pattern: MnCl2 x 4 H2O → ingredient:2003

The main hydrated compound consistently mapped to an ingredient code is:

MnCl2 x 4 H2O → ingredient:2003

Occurrences Found

From the sections analyzed (approximately 4,200 lines out of ~40,000+ total lines), the following instances were identified:

  1. Line 521: Medium 1590 - MnCl2 x 4 H2O → ingredient:2003 (0.00181 g/L)
  2. Line 573: Medium 846 - MnCl2 x 4 H2O → ingredient:2003 (9.97009e-05 g/L)
  3. Line 1064: Medium 486 - MnCl2 x 4 H2O → ingredient:2003 (0.00248509 g/L)
  4. Line 1091: Medium 663 - MnCl2 x 4 H2O → ingredient:2003 (0.000496524 g/L)
  5. Line 1124: Medium 265 - MnCl2 x 4 H2O → ingredient:2003 (0.0018 g/L)
  6. Line 1148: Medium 40 - MnCl2 x 4 H2O → ingredient:2003 (0.000104 g/L)
  7. Line 1167: Medium 559 - MnCl2 x 4 H2O → ingredient:2003 (9.96016e-05 g/L)
  8. Line 2005: Medium 873 - MnCl2 x 4 H2O → ingredient:2003 (9.98004e-05 g/L)
  9. Line 2085: Medium 1299 - MnCl2 x 4 H2O → ingredient:2003 (9.98004e-05 g/L)
  10. Line 2120: Medium 992 - MnCl2 x 4 H2O → ingredient:2003 (0.00036 g/L)
  11. Line 2134: Medium 144b - MnCl2 x 4 H2O → ingredient:2003 (0.001 g/L)
  12. Line 2169: Medium 1647 - MnCl2 x 4 H2O → ingredient:2003 (0.0001 g/L)
  13. Line 3060: Medium 1101 - MnCl2 x 4 H2O → ingredient:2003 (2.99103e-05 g/L)
  14. Line 3149: Medium 1539 - MnCl2 x 4 H2O → ingredient:2003 (0.00098912 g/L)
  15. Line 3191: Medium 457d - MnCl2 x 4 H2O → ingredient:2003 (3e-05 g/L)
  16. Line 4013: Medium 1639 - MnCl2 x 4 H2O → ingredient:2003 (0.0001 g/L)
  17. Line 4055: Medium 1002 - MnCl2 x 4 H2O → ingredient:2003 (3e-05 g/L)
  18. Line 4080: Medium 778a - MnCl2 x 4 H2O → ingredient:2003 (9.97009e-05 g/L)
  19. Line 4105: Medium 1160 - MnCl2 x 4 H2O → ingredient:2003 (0.00036 g/L)
  20. Line 4113: Medium 856 - MnCl2 x 4 H2O → ingredient:2003 (0.001 g/L)
  21. Line 4196: Medium 1487 - MnCl2 x 4 H2O → ingredient:2003 (0.00098912 g/L)

Related Observation

  • Line 4164: Medium 1282 contains MnCl2 x 2 H2O → CAS-RN:20603-88-7 (different hydrate form mapped to a CAS registry number rather than an ingredient code)

Comparison with Proper CHEBI Mappings

The file contains many examples of hydrated compounds that ARE properly mapped to CHEBI IDs, including:

  • MgCl2 x 6 H2O → CHEBI:6636
  • CaCl2 x 2 H2O → CHEBI:91243
  • FeSO4 x 7 H2O → CHEBI:75836
  • ZnSO4 x 7 H2O → CHEBI:35176
  • Na2S x 9 H2O → CHEBI:76209
  • L-Cysteine HCl x H2O → CHEBI:17561
  • MgSO4 x 7 H2O → CHEBI:32599
  • CoCl2 x 6 H2O → CHEBI:35696
  • NiCl2 x 6 H2O → CHEBI:34887
  • Na2MoO4 x 2 H2O → CHEBI:86473

Summary Statistics

  • From analyzed sections (~10% of file): 21 instances of MnCl2 x 4 H2O mapped to ingredient:2003
  • Affected media: 21 different growth media
  • Single ingredient code: All instances map to the same ingredient:2003
  • Concentration range: From 2.99103e-05 g/L to 0.00248509 g/L

Recommendations

  1. Create CHEBI mapping: MnCl2 x 4 H2O (Manganese(II) chloride tetrahydrate) should be mapped to a proper CHEBI ID instead of ingredient:2003

  2. Verify completeness: Based on this sample, there are likely more instances throughout the full file (estimated 100+ total occurrences)

  3. Check related compounds: Review other manganese compounds and hydrated metal chlorides for similar mapping issues

  4. Quality control: Implement validation to ensure hydrated compounds get proper chemical ontology mappings rather than generic ingredient codes

Impact

This mapping issue affects the semantic consistency of the knowledge graph, as MnCl2 x 4 H2O should be linked to chemical ontology terms rather than generic ingredient identifiers for proper chemical reasoning and integration with other chemical databases.