The recent rapid increase in high-throughput biological data and computational tools has facilitated the establishments of numerous biodatabases as the repositories of biodata and bioinformatics analysis tools. Due to the inefficiency of database categorization, the search of all available information of research interests costs researchers a lot of time and efforts. We have established BioMetaDB for users to systematically identify all the available databases of their interests and to extend databases on relevance biomedical contents. For the purpose of establishing BioMetaDB to provide semantically annotated corpus to markup the instances of biomedical ontology, our BioMetaDB comprises three main tasks: (1) biological information retrieval from public databases; (2) creating an integrated ontology repository for biological and medical studies based on expert-tagged corpus; (3) establish web services to enable users to access all their desired databases by systemically ontology query. Based on biomedical ontologies, we indexed all the databases by their relevant biological features, and further evaluated the relevance among the databases. Our BioMetaDB, a comprehensive compendium of biological databases, is currently integrated from over 1,500 digital sources.