The ontology-based data processing system for international integration , ontology and data mining of mouse phenome information

Mice have been used as a genetically-modifiable model animal of human disease in various biomedical research field. Mouse mutant resources is now on the way of expanding by the collaborative production of knockout mouse for all genes under the umbrella of the International Knockout Mouse Consortium (IKMC) [1]. The next major challenge is, the comprehensive and systematic phenotyping of these resources by the standardized platform such as Japan Mouse Clinic (JMC) and European Mouse Disease Clinic (EUMODIC). To build unified and workable data archive of phenotypic data produced from these multiple platforms, it is required to integrate information about experimental analysis and protocol which are usually not so comparable because of difference of description procedures such as terms and unit among platforms. The “Semantic Web” [3] technology is expected for one of the solutions for such problems as the standard of World Wide Web in next generation. It will transform the Internet into a huge knowledge base retrieved by advanced technologies with data mining and reasoning. In case of an approach in RIKEN, "Life Science Networking System (SciNeS)" [4] has been developed as the common infrastructure in order to implement a large-scale release of data that complies with this standard. In addition, in the mouse phenotyping study, multiple institutes agreed to try the semantic web based technologies to exchange phenotype data in “International Phenome Integration Meeting RIKEN/InterPhenome/CASIMIR” on July 2009 [5]. In this context, we have worked out the development of the system to convert phenotyping and experimental procedure data produced from JMC into the ontology-based “Semantic Web” formats to make use of that for the international integration and data mining.