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Abstract Background The analysis of information in the biological domain is usually focused on the analysis of data from single on-line data sources. Unfortunately, studying a biological process requires having access to disperse, heterogeneous, autonomous data sources. In this context, an analysis of the information is not possible without the integration of such data. Methods KA-SB is a querying and analysis system for final users based on combining a data integration solution with a reasoner. Thus, the tool has been created with a process divided into two steps: 1) KOMF, the Khaos Ontology-based Mediator Framework, is used to retrieve information from heterogeneous and distributed databases; 2) the integrated information is crystallized in a (persistent and high performance) reasoner (DBOWL). This information could be further analyzed later (by means of querying and reasoning). Results In this paper we present a novel system that combines the use of a mediation system with the reasoning capabilities of a large scale reasoner to provide a way of finding new knowledge and of analyzing the integrated information from different databases, which is retrieved as a set of ontology instances. This tool uses a graphical query interface to build user queries easily, which shows a graphical representation of the ontology and allows users o build queries by clicking on the ontology concepts. Conclusion These kinds of systems (based on KOMF) will provide users with very large amounts of information (interpreted as ontology instances once retrieved), which cannot be managed using traditional main memory-based reasoners. We propose a process for creating persistent and scalable knowledgebases from sets of OWL instances obtained by integrating heterogeneous data sources with KOMF. This process has been applied to develop a demo tool http://khaos.uma.es/KA-SB, which uses the BioPax Level 3 ontology as the integration schema, and integrates UNIPROT, KEGG, CHEBI, BRENDA and SABIORK databases.

Summary: Big data technologies enable people to store, analyze, and utilize large amounts of complex data effectively. In this context, NoSQL (Not only Structured Query Language) databases have emerged as the most commonly used infrastructure for handling big Resource Description Framework data. In this paper, we present our proposal to materialize classified OWL (Web Ontology Language) ontologies in a NoSQL database. This materialization process enables the distributed storage of Resource Description Framework data by exploiting the inherent distribution of the NoSQL database nodes. Furthermore, this approach supposes the first step toward a novel approach to scalable OWL reasoning, which enables scalable Linked Data reasoning. To validate our proposal, we developed a prototype for a tool that stores an OWL ontology in a Cassandra database following our approach. Finally, we introduce our reasoning strategy to compute the ontology closure using this Cassandra database. [ABSTRACT FROM AUTHOR]