Members of the RIKEN, MGI, EuroPhenome, TPC and CASIMIR groups met at Lake Biwa near Kyoto on July 13th 2009 to discuss developing a basic standard for transferring "shallow" phenotype data between databases. A summary of this meeting can be found on the Meetings page.
We will be following up this meeting with a discussion at the forthcoming meeting in La Jolla , which will deal with issues including what conditions, if any, should be imposed on individuals accessing phenotype data through shared portals and how whether mechanisms such as microattribution could be used to track the origins of pieces of data.
To understand relationships between genotype and phenotype we need to be able to relate genomics and phenomics data. There are well-established databases for genomics information, but phenomics data are fragmented, and much is not publicly available. For mouse data, this is partly because various types of phenomics information have been gathered (e.g. baseline data on inbred strains in the Mouse Phenome Project and EUMORPHIA; recombinant inbred strain data in GeneNetwork.org; phenotype characterization of mutant genotypes by Mouse Genome Informatics; high throughput data from various mutagenesis and knockout projects, notably in Europhenome ) and partly because different groups have different conceptions of how to represent data of this type. Unlike sequence data, there has been no international effort to collect mouse phenotype data in one place.
Since February 2006 a group representing many of the centres holding these disparate types of mouse phenotype data have met to discuss how to make their resources accessible to the mouse community as seamlessly as possible. Our aim is that it should be possible to establish portals that allow phenome data to be collectively searched for phenotypes and associated information. This will involve us in implementing some unifying technology and raises important issues, such as what should be the common ontological representation of phenotype information, and whether it is necessary to define minimum information for the description of phenotyping experiments.
The Mouse Phenotype Database Integration Consortium (2007) Integration of mouse phenome data resources. Mamm Genome. 2007 Apr 10; 18(3), 157-163. PUBMED