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KA-SB: Knowledge-Based Analysis in Systems Biology


The analysis of information in the biological domain is usually focused on the analysis of data from single on-line data sources. Unfortunately, the study of a biological process requires the access to disperse, heterogeneous, autonomous data sources. In this context, an analysis of the information is not possible without the integration of such data. This paper describes how KOMF, the Khaos Ontology-based Mediator Framework, is used to retrieve information and crystallize it in a (persistent) Knowledgebase. This information could be later further analyzed (by means of querying and reasoning).  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 with traditional main memory-based reasoners. We propose a methodology for creating persistent and scalable knowledgebases from sets of OWL instances.


It supports:

  • Ontology Storage in a Relational Database.

  • Tbox reasoning on OWL-DL ontologies.

  • Abox Reasoning on OWL-DL ontologies.

  • Querying OWL-DL ontologies using ECQ (Extended Conjunctive Queries).



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