biodb

biodb provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...) as well as in-house local database files (CSV, SQLite), enabling retrieval of entries, web service access, compound search by mass and/or name, and mass spectra matching for LCMS and MSMS.

Key Features:

• Remote database access: Connects to standard remote chemical and biological databases including ChEBI, KEGG, and HMDB.
• Local database support: Reads in-house local database files in CSV and SQLite formats.
• Entry retrieval: Retrieves entries from connected databases.
• Web services access: Provides access to database web services.
• Compound search: Searches compounds by mass and/or name.
• Mass spectra matching: Performs mass spectra matching for LCMS and MSMS.
• Development framework: Facilitates development of new database connectors for local projects or separate published packages.

Scientific Applications:

• Metabolomics and mass spectrometry: Supports mass spectra matching for LCMS and MSMS data analysis.
• Chemical compound identification: Enables search and retrieval of chemical compounds from major biochemical databases.
• Database integration: Integrates remote and local chemical and biological data sources for research workflows.

Methodology:

The package implements an architecture as a development framework for creating database connectors.