Funder Dispatch – Second 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 quarter, we will be entering active development on GreenXchange and have big news surrounding our Materials Transfer Project. You can also follow us via our blogs, on twitter, and on our mailing lists – all found on our new “Follow Us” page ( Stay tuned for updates.

What has been achieved this quarter?

Over the past quarter, we have continued to work to promote our data policy, with more and more groups dedicating their data and content to the public domain using the CC0 waiver. The education process continues as the community becomes more interested in open access data, working to include CC0 and the Science Commons Data protocol in their data sharing policies and best practices for their individual disciplines. Our Materials Transfer work continues as we work to finalize implementation technology, as well as continue to cultivate and engage various biobanks, foundations, and institutions critical to discussions on sharing biological materials.

This past quarter also marked the first Shared Names workshop, where our scientist Jonathan Rees discussed the need for common nomenclature and notation in the sciences, and how best to facilitate and create that infrastructure with key members of the community. We also continued to push forth ideas of open innovation and access in disease research, specifically regarding rare and neglected diseases and the pharmaceutical industry.

Project Updates

Experts gather for Shared Names workshop

As the volume of online scientific information increases and as information sources become increasingly cross-linked, inconsistent nomenclature for these links becomes a significant annoyance for computational applications that would recognize and exploit such links. Lack of common notation ultimately means an infrastructure that does not scale and that doesn’t lend itself to experimentation and creativity. Thus nomenclature for cross-references is an area that’s ripe for standardization.

Science Commons has been working since 2006 to understand the social and technical conditions that might bring about such standardization using widely deployed web standards such as URIs, HTTP, and RDF. In fall 2008 we articulated a proposal, strictly limited in scope to references to well known key resources such as PDB, and circulated it to several key bioinformatics projects that would have a significant interest in such a standard were it to be adopted. The proposal was received favorably, and we organized a steering committee to develop and deploy a standard. A workshop was convened on April 29 to educate the larger community about the plan, hear about experience with related systems, and solicit review of requirements. With about 25 attendees and a focused agenda, the workshop was a success.

Although much work remains to be done, we are pleased with the reception that the plan has received in the community, and that the steering committee has chosen to take responsibility for bringing about the technical and organizational infrastructure that will be needed to bring the standard to fruition. For more information on the project, visit <>.

Tropical Disease Initiative and EMBL release data into the public domain

The Tropical Disease Initiative recently released a “kernel” for open source drug discovery, made available in the public domain under the Science Commons Data Protocol.

The kernel ( includes 297 potential drug targets against 10 selected genomes for organisms that cause tropical diseases and is freely and publicly accessible. You can read more about this in Nature Biotechnology (subscription required: or for free in PLoS Neglected Tropical Diseases (

Over at EMBL – the European Molecular Biology Laboratory, they have also made some key data related to drug testing and side effects available ( in the public domain via CC0 – a public domain waiver.

The resource, the SIDER Side Effect Database, contains information on marketed medicines and their recorded adverse side effects and drug reactions. Included in this dataset is information on the frequency of these drug reactions, other drug and side effect classifications, as well as links to other relevant resources. To date, 888 drugs are listed in the database, making it a tremendous resource for research and drug discovery.

The mapping of labels and euphoria-related side effects are now public domain, with some other side effect information available for download under a CC-BY-NC-SA license.

Digg makes a design change, sets CC0 as default

Joining the likes of the Personal Genome Project, Flickr, and a host of others, Digg has now chosen to use the CC0 waiver to put all of their content in the public domain. Digg is a social news web site, where users can share and discover online content by submitting stories and links, which can then be voted on by the community. You can read more about the reasoning behind their switch here: ( Congrats to Digg for taking a step in the right direction and making their content available under CC0.

News & Developments In the Community

PGP goes from 10 to 13,000, with all data public domain

The Personal Genome Project has gone from 10 volunteers to 13,000 since opening itself to the public in late April. All of this genomic data will be put in the public domain, an incredible contribution to the commons, as PGP continues to add to the world’s first publicly accessible genome database. PGP formally announced their decision to use CC0 and make all data available back in March. We applaud the project for showing their ongoing commitment to openness and recognizing its need by using CC0, and look forward to hearing more in the future.

Sage to launch this July

Sage, the non-profit entity formed out of Merck & Co, Inc, will formally launch this July. Through Sage, Merck will donate a large amount of data and software to the commons, the body of work available to the public for free and legal sharing, use, repurposing, and remixing. 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. Sage will be hosted at a set of major US research universities, including UCSF, University of Washington, and Yale University. Science Commons is working with Sage on its sharing strategies and governance plans. Stay tuned for more in the coming weeks.

Science Commons, on the road and on the Web

Wilbanks and Boyle discuss Open Innovation and the Commons

This past May, NESTA, the National Endowment for Science, Technology and the Arts in the UK  hosted a conference on open innovation and intellectual property. The Wellcome Trust and Creative Commons co-sponsored the event, which sought to explore how a Commons approach can unlock innovation. Creative Commons’ own James Boyle (founding member and former chairman of the board) and John Wilbanks (Vice President of Science) both delivered keynotes on Open Innovation and the Commons, detailing the benefits of sharing knowledge through a network and the benefits of such a networked system to stimulate and support innovation. For more information on the event and outcome, visit NESTA’s Web site:; and visit Wilbanks’ blog over at SEED: .

Nguyen discusses the importance of data sharing for biological materials in Cannes, Rome

Representing Science Commons, Thinh Nguyen attended CHDI’s Annual HD Therapeutics Conference, held this year in Cannes. During the four-day conference, Science Commons was invited to present a poster at the conference highlighting our collaboration with Coriell and CHDI regarding transfer of research materials. The audience included leading researchers in Huntington’s Disease (HD) and neurology working on diagnostics, therapeutics, and prevention for HD. The Science Commons presentation supported poster presentations presented by CHDI and Coriell at the conference.

As a result of the presentation, we hope that more researchers will become aware of the MTA system being made available through Coriell, not only as users of the materials but also as potential providers themselves in the future.

Nguyen also joined a recent workshop in Rome hosted by CASIMIR – a EU project working to “coordinate and sustain mouse resources internationally.” The May meeting focused on sharing scientific knowledge – in this case mouse lines and resources, a tacit form of knowledge critical to the scientific research cycle. Nguyen presented our position on data sharing for genetic mouse material and our Materials Transfer work. The event brought together a wide array of participants from various continents and organizations (funding agencies, academics, publishers, mouse repositories, etc.)

Their conclusion – the “sharing problem” needs to be addressed immediately if we are to make use of the genomic output and data – especially as efforts become more coordinated, technology advances, and the process becomes cheaper and more efficient.

For more information on our Materials Transfer work, visit

Health Commons, GreenXchange online has a new piece up on the GreenXchange, a project of Nike and Creative Commons, housed at Science Commons. The article, “Green Xchange: Creating a Meta-Map of Sustainability” details the underlying concepts for the project, the obstacles and includes a look into the future. The project, announced at last January’s World Economic Forum in Davos, pairs together the Creative Commons licensing structure (metadata, human readable aspect, legalese) with the right technology to allow companies to share their patents related to sustainability. The goal – to bring the efficiencies of open collaboration and innovation to the problems of sustainability. You can read the article over at (

In the world of Open Science, the radio program “A World of Possibilities” has a fantastic new piece up on “Open Source science” and Health Commons. The podcast explores the Health Commons approach of creating a more open system for the exchange of medical information that cuts across sectors, medical professionals, cultural boundaries, etc. to leverage the power of the network and accelerate the pace of drug discovery. The segment also takes a look at the personal reasons behind this collaboration and the benefits of an “Open Source” approach to sharing biomedical knowledge. Featured in this segment are representatives from two of Health Commons partners: Marty Tenenbaum, the chairman and chief scientist for CollabRx; and Gavin Yamey and Peter Jerram from the Public Library of Science. To listen to the podcast, visit this Web site (