An ontological-based knowledge organization for bioinformatics workflow management system

Abstract

Motivation and Objectives In the field of Computer Science, ontologies represent formal structures to define and organize knowledge of a specific application domain (Chandrasekaran et al., 1999). An ontology is composed of entities, called classes, and relationships among them. Classes are characterized by features, called attributes, and they can be arranged into a hierarchical organization. Ontologies are a fundamental instrument in Artificial Intelligence for the development of Knowledge-Based Systems (KBS). With its formal and well defined structure, in fact, an ontology provides a machine-understandable language that allows automatic reasoning for problems resolution. Typical KBS are Expert Systems (ES) and Decision Support Systems (DSS). ESs gather and formalize the knowledge of a human expert of a domain in order to produce inferences and recommendations given an initial query. DSSs are more interactive KBS, in the sense they offer support, rather than replacement, for the decision making process during the execution of a task, suggesting one possible strategy or tool given a set of initial conditions. DSSs are mainly adopted in the clinical field, where they are called Clinical DSS (CDSS). Ontology specification, structure and organization are then of fundamental importance for the development of a KBS. In this paper we present an improvement of our ontological approach for knowledge organization in DSS design. In our previous publication (Fiannaca et al., 2012) we defined a paradigm for ontology specification named Data Problem Solver (DPS) and we showed how our approach can be applied to bioinformatics domain, modeling the Protein-Protein Interaction Network extraction scenario. In the proposed approach, we aim at integrating into our ontology the concept of Workflow as a set of processes. Our main objective is to provide a general schema in order to add the functionalities and capability of a DSS to the more recent Workflow Management Systems, that especially in bioinformatics, with the Taverna workbench (Hull et al., 2006), represent a powerful instrument for researchers. We called our extended ontological approach Data Problem Solver Workflow (DPSW).