XMetDB: an open access database for xenobiotic metabolism

Area of Science:

• Pharmacology and Toxicology
• Computational Chemistry
• Bioinformatics

Background:

• Xenobiotic metabolism is crucial for drug development and toxicology.
• Existing databases lack detailed biotransformation data, hindering predictive modeling.
• Key information like experimental conditions and specific atoms involved is often missing.

Purpose of the Study:

• To introduce XMetDB, an open-access database for xenobiotic biotransformation data.
• To provide a standardized format for reporting and accessing detailed metabolite information.
• To facilitate the development of improved predictive models for xenobiotic metabolism.

Main Methods:

• Development of XMetDB, an open-access relational database.
• Inclusion of chemical structures, substrate atom annotations, metabolites, enzymes, and experimental details.
• Implementation of a web interface for data submission/retrieval and a web API for programmatic access.
• Establishment of a data curation scheme for quality control.

Main Results:

• XMetDB contains systematically labeled xenobiotic biotransformation data.
• The database includes substrate atoms as reaction centers, products, enzymes, and experimental conditions.
• A web interface and API enable easy data access and submission.
• A comprehensive guide supports data entry.

Conclusions:

• XMetDB formalizes biotransformation data reporting.
• The database provides high-quality, openly available data essential for predictive modeling.
• XMetDB represents a significant advancement for computational metabolism studies.