%0 Journal Article %1 RoldanGarcia:2009:BMC-Bioinformatics:19796402 %A d e l M Roldán-García, M %A Navas-Delgado, I %A Kerzazi, A %A Chniber, O %A Molina-Castro, J %A Aldana-Montes, J F %D 2009 %J BMC Bioinformatics %K biopax dataintegration ontology %R 10.1186/1471-2105-10-S10-S5 %T KA-SB: from data integration to large scale reasoning %U http://www.ncbi.nlm.nih.gov/pubmed/19796402 %V 10 Suppl 10 %X 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.

@article{RoldanGarcia:2009:BMC-Bioinformatics:19796402, 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.}, added-at = {2010-03-25T09:34:57.000+0100}, author = {d e l M Rold{\'a}n-Garc{\'i}a, M and Navas-Delgado, I and Kerzazi, A and Chniber, O and Molina-Castro, J and Aldana-Montes, J F}, biburl = {https://www.bibsonomy.org/bibtex/2eba0067bf91e7b1b3d409837085efee0/wnpxrz}, description = {KA-SB: from data integration to large scale reason... [BMC Bioinformatics. 2009] - PubMed result}, doi = {10.1186/1471-2105-10-S10-S5}, interhash = {81f4337a5221aaa6db16f128a80967cf}, intrahash = {eba0067bf91e7b1b3d409837085efee0}, journal = {BMC Bioinformatics}, keywords = {biopax dataintegration ontology}, pmid = {19796402}, timestamp = {2010-03-25T09:34:57.000+0100}, title = {KA-SB: from data integration to large scale reasoning}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19796402}, volume = {10 Suppl 10}, year = 2009 }