- Open Access
Openness as infrastructure
© Wilbanks; licensee Chemistry Central Ltd. 2011
- Received: 24 June 2011
- Accepted: 14 October 2011
- Published: 14 October 2011
The advent of open access to peer reviewed scholarly literature in the biomedical sciences creates the opening to examine scholarship in general, and chemistry in particular, to see where and how novel forms of network technology can accelerate the scientific method. This paper examines broad trends in information access and openness with an eye towards their applications in chemistry.
- Large Hadron Collider
- Open Data
- Data Infrastructure
- Digital Paper
- Radical Incrementalism
Apocryphal, but told to the author by Victoria Stodden.
I owe this phrase to a conversation with Christine Borgman of the University of California of Los Angeles.
See The World Opera project for a fascinating example at http://theworldopera.org/- debates that never occur in a normal opera, such as "should we have a real conductor at one location, an avatar, or just a metronome?" must be resolved before a collaborative performance in real time can be achieved.
Clay Shirky has written a lovely deconstruction of classification called "Ontology is Overrated"-available at http://www.shirky.com/writings/ontology_overrated.html. This paragraph draws on his arguments at multiple points, but I encourage readers to read the whole article, including his high praise of the periodic table of the elements as a high-water mark in classification.
See the Open Knowledge Definition at http://www.opendefinition.org/okd/- although I dispute the idea that data necessarily equals knowledge, I still like the definition's spirit.
See Creative Commons' CC0 legal tool at http://creativecommons.org/publicdomain/zero/1.0/ for an example of an implementation of the OKD for data.
This is a space where the naive "porting" of open infrastructure for software and culture fails. Privacy constraints, especially around human subjects data, are totally orthogonal to the right to make and distribute copies. This is a key area for future work and research.
See the International Virtual Observatory Alliance, at http://www.ivoa.net/, for a remarkable example of international virtual science based on public domain data.
For example, http://www.openphacts.org/, http://semanticweb.com/semantic-chemistry_b10684, http://en.wikipedia.org/wiki/Blue_Obelisk, http://en.wikipedia.org/wiki/Open_Notebook_Science, http://chem2bio2rdf.org
The SNP Consortium (TSC) was established in 1999 as a collaboration of several companies and institutions to produce a public resource of single nucleotide polymorphisms (SNPs) in the human genome. The initial goal was to discover 300 000 SNPs in two years, but the final results exceeded this, as 1.4 million SNPs had been released into the public domain at the end of 2001. In the end, 1.8 million SNPs were released. More than $50,000,000 was contributed to fund this project, the majority by for-profit companies from  and from "The SNP Fact Sheet" at http://www.ornl.gov/sci/techresources/Human_Genome/faq/snps.shtml.
The SGC is a public-private partnership whose mandate is to promote the development of new medicines by carrying out basic science of relevance to drug discovery and placing all information, reagents and know-how into the public domain without restriction. The core mandate of the SGC is to determine 3D structures on a large scale and cost-effectively-targeting human proteins of biomedical importance and proteins from human parasites that represent potential drug targets. In these two areas, the SGC is now responsible for >25% and >50% of all structures deposited into the Protein Data Bank each year. It is funded by public and private institutions, including three of the world's largest pharmaceutical companies. From the SGC FAQ at http://www.thesgc.org/about/faqs.php#faq_3
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