To make the Connectivity Map "the scientists described the effects of different drugs and diseases using the common language of "genomic signatures" — the full complement of genes that are turned on and off by a particular drug or disease. The scientists compiled the genomic signatures of more than 160 drugs and other biologically active compounds, forming a database of biological "barcodes" that denote cells' responses to the different drugs."
After that, finding the links and connections is just a matter of search strategies. Apparently this has already led to two specific developments, where coincidences between different pieces of research have illuminated each other.
The interesting thing about this development is that it arises from a new way of categorising drugs and diseases - the 'genomic signatures'. Without this, there is no common language to compare the mechanisms involved.
The Broad Institute's press release ends:
"Although the first version of the Connectivity Map is limited mainly to drugs, the same concepts could be applied to almost any aspect of human biology, including diseases, genes and even RNA-based gene inhibitors (RNAi). "Expanding this initial map to encompass all aspects of human biology would provide a valuable public resource for the scientific community," said Eric Lander, an author of the Science paper and the director of the Broad Institute. "Such an effort would parallel the sequencing of the human genome, both in its scope and in its potential to accelerate the pace of biomedical research."