Mereotopological Analysis of Formal Concepts in Security Ontologies

In this paper an analysis of security ontologies, using an mereotopological interpretation of the relationship amongst their classes, based on the entailment in the ontology, is presented. The analysis is carried out by means of a graphical tool (called Paella) that implements such an interpretation and it can suggest the potential debugging of anomalies. The analysis also suggests how to interpret the representational anomalies.Ministerio de Ciencia e Innovación TIN2009-0949

KA-SB: from data integration to large scale reasoning

<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Methods</p> <p>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).</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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 <url>http://khaos.uma.es/KA-SB</url>, which uses the BioPax Level 3 ontology as the integration schema, and integrates UNIPROT, KEGG, CHEBI, BRENDA and SABIORK databases.</p