Recent advances in the development of new, high throughput screening technologies have resulted in a wealth of life science data. The complexity and volume of these data require technology beyond that of traditional database systems. Open research issues include the seamless, semantic-based integration of geographically distributed, autonomous web databases. Biological And Chemical Integration Information System (BACIIS) addresses these issues. This paper discusses the challenges associated with the integration of life science web databases and the techniques used in BACIIS to address these challenges. Particularly, the execution of life science, multidatabase queries is investigated, and an approach that can overcome the limitations of the query capabilities of each individual life science web database participating in the integration is presented. This approach hides the heterogeneity of the individual databases from the user while providing an efficient execution plan for complex, life science, multidatabase queries.