Bioinformatics involves the design and development of advanced algorithms and computational platforms to solve problems in biomedicine (Jones & Pevzner, 2004). It also deals with methods for acquiring, storing, retrieving and analysing biological data obtained by querying biological databases or provided by experiments. Bioinformatics applications involve different datasets as well as different software tools and algorithms. Such applications need semantic models for basic software components and need advanced scientific portal services able to aggregate such different components and to hide their details and complexity from the final user. For instance, proteomics applications involve datasets, either produced by experiments or available as public databases, as well as a huge number of different software tools and algorithms. To use such applications it is required to know both biological issues related to data generation and results interpretation and informatics requirements related to data analysis.