Funder Dispatch – Third Quarter, 2009

A View of Life in the Commons

To help you stay updated on our projects and relevant developments in the world of open science, Science Commons periodically sends out brief email dispatches to its funders and other stakeholders. We hope these dispatches, which will contain news summaries and links, give you more context for the work we’re doing and help foster a deeper understanding of the issues we address.

As always, we invite your feedback and comments. If you’d like to share your thoughts or get more information about anything you read, please feel free to contact us at

What to keep an eye out for in the coming quarter ….

This coming quarter will see significant development for the GreenXchange project, as we work to prepare for its presentation at Davos 2010 hosted by the World Economic Forum this January. We will also be co-hosting a series of meetings for Sage Bionetworks, a non-profit launched out of Merck & Co., Inc., to solicit input and feedback as Sage moves forward in pursuing a commons approach to data sharing. Stay tuned also for future developments on the Materials Transfer front, as we continue discussions with various stakeholders and implementation.

What has been achieved this quarter?

There have been a number of advances to note from this past quarter, the most prominent being the Personal Genome Project’s implementation of the Science Commons Materials Transfer System. Alongside this development, key members of the materials community, specifically working with mouse models and stem cells, have endorsed the use of Creative Commons tools to make content and materials widely available and accessible with the least restrictions imposed on reuse. Beyond that, our advocacy efforts continue within various communities such as in the publishing world, ontologies and Semantic Web, as well as within various projects we are working in such as Sage and the GreenXchange, a project of Creative Commons, Best Buy and Nike.

Project Updates

Personal Genome Project employs Science Commons Materials Transfer system

For the first time, the Science Commons Materials Transfer Agreements (MTAs), created to facilitate the sharing of biological specimens, have played a vital role in advancing the promise of personalized medicine. This month, the Personal Genome Project (PGP) announced that it is making the Science Commons MTAs a core component of its informed consent process, the first group to employ our MTA work.

PGP has been a leader in genomic sequencing and also data sharing, currently making all of their data available in the public domain using CC0 – Creative Commons’ public domain waiver released last March. Their use of standardized MTAs takes their dedication to openness one step further, in making available another important component of the research cycle – the physical materials.

An important benefit of our MTA system is that it enables the use of Web-enabled software tools, similar to the Creative Commons license formats. Science Commons continues its work with Coriell and PGP to enrich the Coriell online catalog with MTA-related metadata, icons, and deeds for PGP’s cell collection, which will ultimately make it easier to find and order these materials online. For more information about PGP’s use of Science Commons MTAs, visit their Web site at . Also, stay tuned for a press release and more news this fall.

CC0 formally endorsed in Nature opinion piece

A new opinion piece in Nature on post-publication sharing of tools explicitly recommends open sharing and the use of CC0 to put data in the public domain. The special issue of Nature focuses on data sharing and is now online and accessible free of charge.

The piece “Post-publication sharing of data and tools” comes out of this year’s CASIMIR conference in Rome, and discusses the sharing of biological materials, specifically but not limited to mice and embryonic stem cells.

The piece is chock-full of stellar recommendations that Science Commons supports, from better and more explicit resource sharing policies at journals and funding bodies, to the use of standard MTAs, to making data open and putting it in the public domain using CC0, our public domain waiver. To read the article in its entirety, visit .

Global Biodiversity Information Facility works on web-based interoperability standards

This summer, Science Commons’ Jonathan Rees had a seat on a task force of the Global Biodiversity Information Facility (GBIF) concerned with persistent identifier lookup for entities such as taxon data and species occurrence records. The task force has advised GBIF to take a leadership role in establishing standard, sustainable practices for the provision of biodiversity information on the Web. The particular approaches advocated by the task force will help to harmonize knowledge interchange practices between the biodiversity and biomedical informatics communities. Keep an eye out for a finalized report from this meeting in the next quarter on

News & Developments In the Community

Sage formally launches, begins series of planning meetings

Sage, the non-profit entity formed out of Merck & Co, Inc, has formally launched. Sage will be the home of an open access disease biology platform based on the work previously done at Rosetta Inpharmatics and will be led by Stephen Friend and Eric Schadt, two leading thinkers in biotechnology. Over the next few weeks, Sage and Science Commons will convene a series of regional forums with experts and stakeholders from the funding community, Open Access, and research world to help shape their work as we move forward. The first of these meetings will be on October 6 in Birmingham, UK, with another that week at the Massachusetts Institute of Technology (MIT) on October 9. Following those meetings, there will be another forum in San Francisco on October 12, and one in Beijing, China on November 17. This is all leading up to a larger Congress tentatively scheduled for April 2010. Stay tuned for more news.

WisconsinView dedicates 6+ terabytes of data to the public domain

As of July 1, WisconsinView, an effort to make available a variety of types of imagery for the state of Wisconsin, will make their data available in the public domain via CC0. This news was brought to us by Puneet Kishor, a Science Commons fellow.

WiscosinView ( has made aerial photography and satellite imagery of the state of Wisconsin available to the public free over the web since 2004. The effort is a part of the larger AmericaView consortium, and supports access and use of the imagery collections through advocacy and education, as well as continued research on the data.

Science Commons, on the road and on the Web

White House CTO hosts private roundtable on health IT and data sharing

The Chief Technology Officer of the Obama Administration, Aneesh Chopra, called upon our own John Wilbanks this past August for a closed roundtable on healthcare IT. Wilbanks was one of ten at the intimate meeting in Silicon Valley. The event sought to seek input on issues surrounding health technology, data standards and the legal settings needed to optimize data sharing

Wilbanks challenges scholarly publishing societies to think beyond the container

This past September, John Wilbanks stirred the pot a bit at the Society for Scholarly Publishing’s IN meeting in Providence, RI, encouraging publishers to stop thinking about the container, and start thinking about the consumer. The container, in this sense, is the scholarly paper as we know it, a relatively static 2-D document, even in the digital sense. His keynote gave rise to a provocative discussion in the blogosphere about the future of scholarly publishing, and where our focus should lie. For more on his talk, visit Scholarly Kitchen for an overview . You can also find his presentation up online

Knowledge sharing and nanopublication — Why we need Open Access

At the recent Conference on Open Access Scholarly Publishing (COASP), convened this year in Lund, Sweden, there was an increased focus to applications utilizing Open Access and the future of publishing. Science Commons’ Kaitlin Thaney joined the program with other key advocates, publishers and users of Open Access, to emphasize why Open Access to content is needed, even as the technology rapidly advances. She also laid out the issues surrounding making data publicly accessible and interoperable, so that we can begin to stitch together various knowledge sources and build upon existing research. Her talk, Knowledge Sharing and the Commons” can be found online here:

For more information on the event, hosted by the newly formed Open Access Scholarly Publishing Association (OASPA) and the Directory of Open Access Journals based at Lund University, visit their Web site: where you can also find newly updated video of the event, as well as more information on the Association.

Ruttenberg leads international working group aimed at increased sharing of Neuroscience data

Also this September, Principal Scientist Alan Ruttenberg joined esteemed members of the neuroscience community to discuss the Semantic Web and its application to this field of research. The event – the Program on Ontologies of Neural Structures (PONS) meeting was hosted by the International Neuroinformatics Coordinating Facility in Pilzen, Czech Republic. As part of the event, Ruttenberg led an international task force on Representation and Deployment, as well as leading a workshop on the Semantic Web for Neuroscience. In his talk Ruttenberg laid out some of the opportunities available for such a system of sharing knowledge, and also examined a number of key road blocks – scientific, technical, social and legal – in achieving this vision. For more information about the event, visit INCF’s Web site: .

Commoners and digerati come together to discuss how to make the Web work for science

Science Commons organized a landmark event this past July at the Commonwealth Club in San Francisco on the intersection of science adn the Web. The event was hosted by technology visionary Tim O’Reilly, and joined by Wikipedia founder Jimmy Wales, Sage CEO Stephen Friend, and John Wilbanks. The night was dedicated to the idea of bringing Web efficiencies to scientific research – a core theme seen in our work and thinking here at Science Commons. Video of the event is now online at . Stay tuned for upcoming events in the Bay area this fall.