Funder Dispatch – First 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, look for more increased participation in the sciences of the CC0 tool (read “CC Zero”), and advances on scientific norms and best practices to accompany the waiver. Also look for progress in our Materials Transfer work, as we continue our work towards implementing the system with a set of biobanks and foundations. In terms of our technical work, look for more advances in our standards work as we continue to push for adoption of various recommendations for ontologies in larger standards bodies.

What has been achieved this quarter?

This quarter, we have announced the launches of a number of very important tools:  the CC0 waiver, which builds upon our Protocol for Open Access Data; the integration of NeuroCommons into Microsoft Word; and the launch of GreenXchange, a collaboration of Creative Commons, Nike and Best Buy. We have also been furthering our work to expand and strengthen our ties in the philanthropic community and continuing discussions regarding a pilot for our Materials Transfer work.

We continue to work with the data and database sharing community on a number of fronts. Recently, we provided policy guidance to the Open Data Commons on their new Open Database License (OdBL). (See our statement at

We have also begun work with a project of the National Cancer Institute, called caBIG – the cancer bioinformatics grid, to study data sharing agreements, with the goal of ultimately developing an ontology of data sharing contracts that can be used in tagging.

Project Updates

Personal Genome Project and Tranche release their data to the Public Domain with CC0

Following the public launch of CC0, two early adopters in the sciences released significant amounts of data to the public domain. The two early adopters of CC0 related to scientific databases – Tranche and the Personal Genome Project (“PGP”) – both publicly announced their commitment to open data and use of CC0 in mid-March at the time of the launch. Tranche is a free and open source data sharing tool for sharing large sets of scientific data. PGP is an effort to sequence and interpret genes at an individual level (“personal genomics”) to help individuals better understand their personal disease risk profiles, biological characteristics, and ancestry. Tranche will offer CC0 as a default option for sharing scientific data sets. PGP, in addition to releasing a significant data set at the launch of CC0, is planning to release all future genomic data under CC0, showing their ongoing commitment to the public domain and belief in the benefits of open data.

NeuroCommons add-in for Microsoft Word

Science Commons and Microsoft announced this March the integration of the Neurocommons knowledgebase with the Microsoft Word package. Microsoft Research staff have built a “plugin” to Word that allows authors to quickly and easily add hyperlinks to their life sciences articles using a system very similar to the familiar Word “spell check” functionality – but instead of checking for spelling errors, the plugin looks up the words in the Neurocommons, and then tags the word with the stable, semantic web-enabled hyperlinks Science Commons has carefully developed through our technical work. Microsoft is releasing both this plugin and the plugin that allows Creative Commons licenses for Office documents into the commons via an OSI-approved open source software license, a major step towards the creation of more open platforms for scholarly authorship that integrate the literature directly into the emerging web of data.

Announcing the launch of GreenXchange

This past February, Creative Commons, in collaboration with Nike and Best Buy, announced the launch of a new project – GreenXchange – which will explore how the digital commons can help holders of patents collaborate for sustainability. GreenXchange will be hosted inside the Science Commons wing of CC.

GreenXchange draws on the experience of Creative Commons in creating “some rights reserved” regimes for artists, musicians, scientists, and educators, but also on the hard-won successes of patent “commons” projects like the Linux Patent Commons, the BIOS project, FreePatentsOnline and the Eco-Patent Commons. We will examine how best to reconstruct the academic research exemption eliminated in the United States in the Madey v. Duke case, how to extend that exemption to corporate research, how private contract systems can be used to construct a commons for use in sustainability. There is also a technical component – we are very interested in how tools like ccMixter and the semantic web will allow for new methods of tracking use and re-use of patents and integration of shared patents into climate and sustainability model.

GreenXchange is very much an exploratory project. Our goal is to stimulate innovation in the operational space by increasing research use and rights through the some rights reserved model, and to extend the model itself all the way into standard commercial patent licensing for sustainability purposes. Our model is open innovation, our methods are those of the digital commons, and we are very excited to be working with our new partners to help them overcome “failed sharing” to help us all work towards a sustainable world.

For more information on the project, we invite you to check out the informational video over at Science Commons <>

News & Developments in the Community

MIT passes university-wide Open Access resolution

On March 18, by unanimous vote, MIT faculty adopted an Open Access resolution that will make scholarly articles available at no charge, freely to the public through DSpace – MIT’s repository service.

The way this policy works is that faculty authors grant the university non-exclusive permission to make their scholarly works available in a repository, with the right for MIT and its faculty to publicly disseminate for all uses except commercial. The resolution is believed to be the first faculty-driven, university-wide policy, and joins other similar initiatives recently adopted at Harvard, Stanford and the National Institutes of Health (NIH).

This follows on our Addendum Generator, created by Science Commons as part of the Scholar’s Copyright project, which hosts the MIT Addendum, among others. The MIT Addendum helps scholars to negotiate with publishers for rights to comply with this new policy, as well as the NIH mandate. Authors can use our Addendum Engine to easily generate a one page document to attach to their submissions to the publishers, stating which rights they’d like to retain. (

We applaud the university for passing this resolution, which is a great step forward for Open Access, and also encourage members of the MIT faculty to consider using one of our addenda to ensure their work can be publicly accessed and shared post-publication.

NIH Open Access mandate made permanent

The NIH Public Access Policy, which was due to expire this year, has now been made permanent by the 2009 Consolidated Appropriations Act, signed into law in early March.

Last year, Science Commons, SPARC, and ARL jointly released a White Paper authored by our board member Mike Carroll called “Complying With the National Institutes of Health Public Access Policy,” explaining the new NIH-mandated PubMed deposit requirement and questions that grant recipients should consider in designing a program to comply with it. At that time, the new mandatory policy had just taken effect, and many recipients were still learning how to comply. Nevertheless, the results were dramatic. Prior to NIH’s mandatory deposit requirement, under a voluntary policy NIH began in 2005, the compliance rate in terms of deposits in PubMed had been very low (4%, as published in an NIH report to Congress in 2006). Shortly after the adoption of the new mandatory policy, submissions spiked to an all time high, prompting an NIH official to project compliance rates of 55-60%. (To read the white paper, visit our Reading Room at

Making the NIH Public Access Policy permanent will provide scholars and institutions with much needed certainty and impetus to focus on implementing these requirements within their institutions. It also creates a opportunity for scholars, universities, and the research community to take a broader look at their institution’s scholarly publishing and open access policies, not only as it applies to deposit in PubMed, but also as it applies to their own institutional repositories and scholarly communities.

Merck donates data to the commons, announces formation of Sage

Merck recently announced the formation of Sage, a new non-profit organization through which it will donate a large amount of data and software to the commons. 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, and John Wilbanks has joined the Sage Board of Directors at the founding of the organization as well.

Science Commons, on the road and on the Web

Common-Use Licensing and Data Sharing in Asia

Open Access content and data accessibility are hot topics in Asia. This past week, Science Commons’ own Kaitlin Thaney participated in a series of roundtables and symposiums on US – China data cooperation and common-use licensing of scientific content, co-sponsored by the National Academies of Science. The first roundtable was held in Qingdao, China – CODATA’s third annual meeting on data cooperation. She also spoke about the benefits of Open Access literature and the issues surrounding data sharing in Beijing, China, as part of a symposium hosted by CC Mainland China and the Chinese Academy of Sciences. A similar event was soon after held in Taipei, Taiwan at Academia Sinica, where she spoke about knowledge sharing in the sciences. The symposium was organized by CC Taiwan, CODATA Taiwan, NARL and the NRC Board on Research Data and Information.

Wilbanks announces Microsoft collaborations, CC0 adopters at ETech

This past March, John Wilbanks  joined technorati and other media and business elite at the Emerging Technologies Conference – “ETech” for short – hosted by O’Reilly Media. Wilbanks, the VP of Science at Creative Commons, gave a keynote in which he announced our latest collaboration with Microsoft, involving the integration of the NeuroCommons into Microsoft Word, as well as announcing the early adopters of CC0 – the Personal Genome Project and Tranche. You can read more about Wilbanks’ talk in this interview before the event and also in this announcement on the day of the presentation.