Knowledge integration and exchange of data within and among organizations is a universally recognized need in bioinformatics and genomics research through the e-science field. The main problem looming over the lack of integration is the fact that the current Web is an environment primarily developed for human users and micro-array data resources lack widely accepted standards; this leads to a tremendous data heterogeneity. Using semantic technologies as a key technology for interoperation of various datasets enables knowledge integration of the vast amount of biological and biomedical data. In this paper, we aim at providing a semantically-enhanced bioinformatics platform (SEBIO), which handles these issues effectively. We will describe the problems arisen and the solutions applied so far. For that, the SEBIO approach is unfolded and its main components explained, to see in more detail how perfectly it copes with the aforementioned difficulties.