A STATUS REPORT ON MAGE

Recently, the Microarray Gene Expression Data Society (MGED, www.mged.org) was awarded funds from NHGRI/NIH to continue development of MAGE, the MGED Ontology (MO) and related technologies for communication and interpretation of microarray data. This award reflects NIH's substantial commitment of resources to microarray experimentation and the recognition that these data should be preserved. In this editorial I discuss MGED's goals, show how MGED's efforts have helped the microarray community and describe MGED's future efforts in the context of the recent award. MGED's efforts are 2-fold. First, it is committed to ensure that microarray experiments are scientifically sound. Second, it is involved in building the infrastructure that will support experimental data, from millions of microarrays. This second goals allows microarray data to be treated similar to DNA sequences which are repeatedly queried, reanalyzed and amalgamated. This is obviously critical because the data are extremely valuable if they are computationally interpretable. MGED's solutions to achieve these two goals are the introduction of scientific guidelines (MIAME), data communications standards (MAGE) and biological annotation systems (MO). Concerning the development of infrastructure for data storage, query and analysis, perhaps it is better to start from what I think MGED is not trying to do. Explicitly MGED's effort is not to build an interoperability and computational infrastructure for a few hundred or a few thousand experiments. This is the current size of the ArrayExpress and GEO data archives, which hold 700 and 2000 experiments, respectively. If a user requires information on the biology of one of these experiments it is simply a matter of reading the paper that describes the experiment. Data standards for interpretation and communication are unnecessary in this case. MGED's efforts are focused squarely on the future; a future where 100 million individual microarrays (or more) are archived and served to the research community. One hundred million publicly available microarrays is an enormous number, but I suspect it will be lower than that exists in 20 years, because as costs go down and experimental systems become more automated, microarrays will be increasingly used in biological research, just as sequencing technologies have. Both ArrayExpress and GEO have doubled in size every six months, which would mean that 100 million microarrays would be available in 2010; assuming a more modest doubling every year, 100 million microarrays will be available by 2015. As a ballpark estimate, 100 million microarrays would account for 2% of public global …