Biological web data sources have now become essential information sources for researchers. However, their use is tedious, labor-intensive, repetitive, and possibly involve the integration of data from multiple web data sources. In this paper, as a first step towards the full integration of web data sources, we propose a framework that allows an integrated use of biological sources in a task-oriented manner. We define and experimentally evaluate a toolkit-based framework for semi-automatically constructing an integrated (software) system that automates and optimizes the execution of a biology-related computational task at hand. To test and refine the principles of the framework, we build and evaluate "Pathway-Infer" as a benchmark integrated system.