KA-SB: from data integration to large scale reasoning

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.

Figure 1

KOMF architecture. This mediator is based on the use of ontologies to integrate heterogeneous data through data services.

Figure 2

DBOWL Storage System. DBOWL Storage System.

Figure 3

KA-SB, tool information flow. KA-SB, tool information flow.

Figure 4

KA-SB structure. The methodology is based on the use of KOMF to retrieve information as ontology instances. When a user retrieves information that needs further analysis, the tool allows him/her to create a persistent knowledgebase. This knowledgebase could be used to perform more detailed and complex analysis over a specific set of information.

Figure 5

KA-SB implementation details. The internal elements of KOMF allow users to perform online queries, while DBOWL provides a persistent reasoner to perform more complex analysis over specific sets of information.

Figure 6

Part of the ontology BioPax Level 3. This ontology has been registered for integrated access to biological data in this use case.

Figure 7

Query Interface. This part of the tool enables building user queries easily.

Figure 8

Step by step query building. The user selects the name and organism of the target protein, and then introduces the predicates to search for interacting proteins.

Figure 9

Instance visualization. Results obtained from the mediator can be visualized as RDF instances, flat files and a graphical representation.