PML:PAGE-OM Markup Language

The study of correlations between genome variation and phenotype diversity is a key theme in the current biosciencefield. This has lead to a large number of different studies generating huge amounts of data, which typically must be shared amongst many collaborators and researchers. To store and use such data efficiently, it is paramount that biomedical researchers describe the data in a compatible and similar way. To this end, the Japan Biological Informatics Consortium has developed a data model termed DVAR (DNA Variation and Phenotype Data Model) under the auspices of an international collaboration since 2005. An initial submission of DVAR was made to the Object Management Group (OMG) standardization organization, and this was approved in 2006. The latest meeting to continue this model development was held in Tokyo in September 2007. The meeting discussed extensions and changes needed for DVAR to appropriately model biomedical phenotypic information as well as modeling experimental results for associations between genotype and phenotype. The outcome of that meeting was a significantly improved model, which was submitted to the OMG under a revised name of PaGE-OM(Phenotype and Genotype-Object Model). PaGE-OM was approved at the OMG Technical Meeting in March 2008 and should be finalized by the end of fiscal year 2008. We have validated PaGE-OM by applying it to various existing phenotype and genotype databases, and will demonstrating how further databases can be expressed in the PaGE-OM. In ongoing and collaborative work, PaGE-OM will be improved with a view to expand its application in healthcare and pharmaceutical industry.

About IBIC

6th IBIC PhotoIn November 2003, we organized the 1st International Bio-data Interoperability Conference (IBIC) to have international discussions on the standardization of genomic variation data description form. It was an outcome of the conference that we proposed the initial submission of PML to Life Science Research (LSR) of Object Management Group (OMG) in response to the request for proposal
for the standardization of genomic variation data description form in January 2004. Because the 1st international conference was fruitful, we decided such international conference to be executed continuously.
In June 2004, we held the 2nd IBIC to improve PML. Subsequently, we proposed the final submission in October 2004. In June 2005, our proposal for the standardization of genome sequence variation data description form became readily available as an official standard specification.
In September 2005, the 3rd IBIC was held to discuss the expansion PML to phenotype/genotype data description format and we made the RFP of data description standard form of phenotype/genotype data named DVAR(DNAVariation and Phenotype Data Model). It was approved by OMG in December 2005.In October 2006, the 4th IBIC was held to discuss the DVAR. We made the OMG initial submission of DVAR and this initial submission was approved in December 2006. In September 2007, the 5th IBIC wasn held to improve the model development . New data model was submitted to OMG under a revised name of PAGE-OM(Phenotype And Genotype Experiment-Object Model). PAGE-OM was approved in March 2008. In October 2008, we held the 6th IBIC to discuss the Finalization Task Force of OMG process.

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