Biotechnology - Genomic and Proteomics/Sage - A Merck Project

Background

There are law review articles about the public domain aspect of life sciences, both as a government policy and as a precompetitive publication / patent defense. There are also articles about the use of collaborative, common platforms as vehicles for innovation.

In the life sciences, we find that the use of the public domain (if conformed to as a standard legal policy) can combine with convergent standardization on data systems and transform the data itself into a platform for innovation and collaboration. Thus, a default legal position by the government, or a defensive legal strategy by a large corporation, can have a "side effect" of enabling new forms of innovative R&D.

Our paper will analyze this effect with a specific focus on genomics.

Skeleton

The paper will cover a set of basic sections.

1. The government created public domain in genomics.
   • Human Genome Project
     • Data access policy
     • Data access reality
     • Bermuda Rules etc.
     • Impact of Celera competition
   • SNPs and HapMap
     • Clickwrap license and intent
     • Corporate participation
     • end of clickwrap
   • ENCODE project
     • data access policy
2. The corporate created public domain in genomics
   • patent defense intent
     • enclosure by patent / startup / university tto
     • Merck Gene Index as "immune" response
   • alliance for cell signaling (AFCS)
     • what else?
3. technical platforms for genomics
   • Government centers
     • NCBI
     • EBI
     • Japan Genome
     • role of PD in global data integration
   • emergence of new PD tools
     • OBO
     • what else?
4. platforms for innovation
   • on ncbi
   • on pubmed
     • pubget
     • hubmed
     • iHOP
     • neurocommons / LOD
     • ingenuity / genstruct etc
   • on the genome
     • DAS
     • companies...
5. Why do some technical platforms make the transition to innovation platforms and not others?
   • information flow analysis
   • "resistance" analysis
   • pubmed and genome v. AFCS and others
6. trying to recapture "lightning in a bottle" - the merck experiment in disease biology (SAGE)
   • analyze decision in merck's history with the gene index
   • analyze contracts
   • analyze technical platform

Other information

MGI > SNP > Sage

HGP > HapMap > Encode

these have been extensively profiled as modes of "property preempting investments" but they also serve as emerging platforms for collaboration. by their very existence - created as anti patent device - they create a pressure to standardize and form networks that did not exist previously. this is because of the now-digital nature of the knowledge, and because of the ability of networks to deliver it. the value now outweighs the value of competitive withholding.

Thus, HGP leads to Distributed Annotation System. Gene ontology. Etc. which in turn create their own commonsense, dependent on the root structure of a public domain of genomes. FLOSS and corporate entities compete as service vendors etc.

Analyze the ecosystem that it takes to convert PPIs into a networked commons platform: the legal tools (PD), the norms (Bermuda Rules), the corporate pressures (journal requirement of GenBank ID), etc. it's not just about dumping into the network.

Find examples of PPIs that did not form a commons.

how the interplay of public and private investments, using the PD for different reasons, has created and sustained a self-perpetuating commons. no one looking at the political economy of collaboration as a result of self-interested investments against patents!

access to what we do actually know - and the right to reformat and integrate it - is the non miraculous way to systematically increase the odds we do something right.