MOTIVATION: Molecular interaction information, such as protein-protein interactions and protein-small molecule interactions, is indispensable for understanding the mechanism of biological processes and discovering treatments for diseases. Many databases have been built by manual annotation of literature to organize such information into structured form. However, most databases focus on only one type of interactions, which are often not well annotated and integrated with related functional information. RESULTS: In this study, we integrate molecular interaction information from literature by automatic information extraction and from manually annotated databases. We further integrate the relationships between protein/gene and other bio-entity terms including gene ontology terms, pathways, species and diseases to build an integrated molecular interaction database (IMID). Interactions can be selected by their associated probabilities. IMID allows complex and versatile queries for context-specific molecular interactions, which are not available currently in other molecular interaction databases. AVAILABILITY: The database is located at www.integrativebiology.org.