Structural Genomics, open data and drug development

February 23, 2008

At the scienceblogging conference, someone raised the point that the structural biology community has been depositing raw data into the public domain for a long time and pretty much all protein structures (other than the co-crystal structures generated by pharma companies) are pretty much open access.

So it shouldn’t come as a surprise when the head of the structural genomics effort comes out in support of open data (free registration reqd). Amongst other things Al Edwards equated finding new drugs to the “lottery” and argues that open data is essential to improve our chances of developing better drugs. While the biopharma industry is using more and more sophisticated techniques, both to fail early (rather than expensively in the clinical trial phase) and to find better drugs. Given the fact that there are so many techniques and people addressing different problems, you will find that the industry is increasingly relying on publicly available data, in line with my theory that owning the data is not critical, but what one does with the data.

We are still in early days. If one agrees that virtual collaborations are going to form a big chunk of drug research and development, then data sharing, collaboration and public/private partnerships built on an open data foundation might just be in our future. Perhaps the biggest challenge to this process getting accelerated lies in the quality of our data sources, both in terms of data quality and in the design of those sources. Both are a problem at this time. There are too many data formats, poorly designed data infrastructures and data quality, while much better than it used to me suffers greatly, making it difficult to develop streamlined processes. From a personal bias, I hope that people designing databases for life science data start start thinking about linked data from the start. Just imagine if all of the data in Genbank, or for that matter, the PDB were available in RDF (then you wouldn’t have to do this).

Further reading
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