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Applying Cheminformatics to Develop a Structure Searchable Database of Analytical Methods
Published on: June 6, 2025
Consistency of systematic chemical identifiers within and between small-molecule databases
Saber A Akhondi1, Jan A Kors, Sorel Muresan
1Department of Medical Informatics, Erasmus University Medical Center, P,O, Box 2040, Rotterdam, CA, 3000, Netherlands. s.ahmadakhondi@erasmusmc.nl.
Journal of Cheminformatics
|December 15, 2012
Summary
Chemical structure identifiers like MOL files and IUPAC names show significant inconsistency across databases, impacting drug discovery. Standardizing chemical structures before data integration is crucial for improving accuracy and reliability in cheminformatics.
Area of Science:
- Cheminformatics
- Computational Chemistry
- Drug Discovery
Background:
- Accurate chemical structures and metadata in databases are vital for drug discovery, influencing quantitative structure-property relationships and novelty checks.
- Ubiquitous chemical identifiers (MOL files, SMILES, IUPAC names, InChI strings) are essential for representing molecular structures.
- Previous research has not addressed the inconsistencies in these identifiers arising from diverse data integration methods and standardization rules.
Purpose of the Study:
- To investigate the consistency of systematic chemical identifiers for small molecules within and between common chemical databases.
- To evaluate the impact of structure standardization on the consistency of chemical identifiers.
Main Methods:
- Examined the consistency between MOL representations and systematic chemical identifiers (IUPAC names, InChI strings) across various chemical resources.
- Assessed consistency with and without structure standardization, including the removal of stereochemistry.
- Analyzed consistency of MOL representations for compounds linked via cross-references.
Main Results:
- Consistency between systematic identifiers and MOL representations varied widely (37.2%-98.5%), with lowest consistency observed for MOL-IUPAC names.
- Excluding stereochemistry significantly improved consistency, raising it from 84.8% to 99.9%.
- Consistency between cross-referenced MOL representations also showed wide variation (25.8%-93.7%), improving to 47.6%-95.6% after removing stereochemistry.
Conclusions:
- Significant inconsistencies exist in structural representations and systematic chemical identifiers within and between databases.
- These inconsistencies can greatly affect data merging and cross-database querying when identifiers are used as keys.
- Standardizing chemical structures using well-defined rules before generating identifiers can dramatically enhance internal consistency.
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