Description
The study of correlations between genome variation and phenotype diversity is a key theme in modern biosciences. Huge amounts of data are routinely generated, 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 logical manner.
To this end, the Phenotype and Genotype Experiment (PaGE-OM) object model has been developed to provide conceptual descriptions for core data elements needed in the handling of genotype, phenotype, and related experiment data. PaGE-OM is under standardization process in the OMG and it is currently available as a beta2-version. The model is platform independent and it can be used as the basis for platform specific implementations such as XML schema and relational databases.
The Polymorphism Markup Language (PML) object model is an earlier version of PaGE-OM, which dealt only with the genotype domain. It was formally approved as an OMG standard in December 2005. Openpml represents an XML exchange format implementation of PML, and this was formally approved by OMG in December 2006.
Background
Modelling work in support of the genotype-phenotype domain has been ongoing since 2003, by an international Consortium that met in a series of annual conferences organised by the Japan Biological Information Consortium (JBIC). Initially, this group devised the main genotype sections of the model, leading to PML. This was then revised and extended to cover phenotype data and genotype-phenotype correlation experiments during 2006 and 2007, and called PaGE-OM. This was submitted to OMG and approved as a standard in March 2008. The project remains ongoing, towards simplified sub-models, use-case schemalets (see here), exchange formats, and harmonisation with other bioscience domain object models, with this work being a partnered effort with the GEN2PHEN project. Additional contributors to this effort are welcome, and interested persons should start by making contact with Juha Muilu.
