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Biomedicine relies increasingly on computation. However, despite the evident potential of computational tools to enhance bio-medicine, most experimental biologists – who are often not computer savvy – do not have the time, interest or know-how that could enable them to fully integrate the available tools into their research. More alarmingly, even computational biologists often restrict their usage to a few tools. Among the reasons for this limited utilization of the available knowledge and tools are the genuine difficulty in integrating the output of various tools, each of them usually highly specialized in scope, acceptable input and output format, and applicability. GeneTegrate is a computational platform providing a unifying semantic modeling layer to enrich, simplify and accelerate the analyses of distributed heterogeneous biological data. GeneTegrate encompasses a semantic modeler, providing a repository of enriched object-relationships schemata to represent raw biological data; a schema (model) definition language and a query language, to represent and manipulate the semantic of biological data; adapters to integrate GeneTegrate with multiple biological databases and analysis tools; and caching mechanisms to accelerate analyses of commonly accessed data. Thus, it is possible using GeneTegrate to access numerous services and integrate their output into a comprehensive representation of all available biological knowledge and types of analysis.