Bioinformatics Web Portals

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. Bioinformatics applications require platforms that are computationally out of standard. Applications are indeed (1) naturally distributed, due to the high number of involved datasets; (2) require high computing power, due to the large size of datasets and the complexity of basic computations; (3) access heterogeneous data both in format and structure; and finally (5) require reliability and security. For instance, applications such as identification of proteins from spectra data (de Hoffmann & Stroobant, 2002), querying of protein databases (Swiss-Prot), predictions of proteins structures (Guerra & Istrail, 2003), and string-based pattern extraction from large biological sequences, are some examples of computationally expensive applications. Moreover, expertise is required in choosing the most appropriate tools. For instance, protein structure prediction depends on proteins family, so choosing the right tool may strongly influence the experimental results. Recently, there has been much interest from database community and computer science community for bioinformatics. Nevertheless, what is still missing is a high-level environment able to classify tools and provide Web-based easy to use application programming interfaces. In such a way, users can concentrate on the logic of application (i.e., biological aspects) leaving to such platform the work to compose applications, format input data, provide options and parameters, and collect results. Another important requirement is the accessibility of such platform through a Web portal, that is, by using the user interfaces and protocols of the World Wide Web. A bioinformatics Web portal is thus a Web portal that allows access to bioinformatics tools and databases through a Web browser. Moreover, due to the complexity, diversity and a huge number of bioinformatics tools and databases, a bioinformatics Web portal should also support problem formulation, application composition and execution, results visualisation and annotation. A possible approach to solve these issues ­—high-level modeling and Web-based user interfaces—can be obtained by adding semantics links between biological problems and bioinformatics resources through ontologies (Baker, 1998), and by decoupling Web-based user interfaces from high-performance back-end platforms. In this article we review main requirements of distributed bioinformatics applications and related bioinformatics Web portals, and report the proposal of a grid-based bioinformatics portal allowing choosing and composing of bioinformatics tools with the help of a domain ontology describing data and software resources.