Open Data Category


eLife Editor Wins Nobel Prize for Cellular Research



The 2013 Nobel Prize for Physiology or Medicine was awarded to James E. Rothman, Thomas C. Sudhof and Randy W. Schekman for their research on cell transport systems. This work has strengthened the medical community’s understanding of neurological diseases, diabetes, and immunological disorders. Schekman, a Cell Biologist at the University of California at Berkeley, is a prominent support of Open Access publishing and is the Editor-in-Chief at eLife, an innovative Open Access journal in the biomedical sciences. eLife joins The Public Library of Science and PeerJ in offering a cutting-edge Open Access publishing platform for prestigious scientists to share their work, data, and rich media. eLife is currently free to publish (no author-side fees). For more information, please visit the journal’s website or watch the video.


MSNBC’s Morning Joe Discusses Big Data, Open Access, and Cancer Research

Kathy Giusti, co-founder of the Multiple Myeloma Research Foundation (MMRF), was featured on MSNBC’s Morning Joe this week to talk about how the open sharing of data can improve cancer research. The MMRF recently launched the MMRF Research Gateway to serve as an open access portal for data on Multiple Myeloma, a common form of blood cancer. The goal is to make the data openly available so that progress in cancer treatment can be accelerated. The MMRF Research Gateway requires registration, however non-profit academic, private, and governmental users can access the data free of charge. Watch the clip.


This week in Open Access: SHARE

Yesterday, the Scholarly Publishing & Academic Resources Coalition (SPARC) released a letter sent to John Holdren, the Director of the White House Office of Science and Technology Policy (OSTP), requesting copies of U.S. government agency plans to make the results of federally funded research freely available to the public. This follows up on a February 22nd, 2013, White House OSTP memorandum directing federal agencies that annually provide $100 million in funding for research and development to “develop a plan to support increased public access to the results of research funded by the Federal Government. This includes any results publishing in peer-reviewed scholarly publications.” The deadline for these proposals was August 22nd, 2013, and there has been no official word on the specifics of these plans yet.

To comply with these policy changes (once they take effect), the SHared Access Research Ecosystem (SHARE) has been proposed by the Association of American Universities (AAU), the Association of Public and Land-grat Universities (APLU), and the Association of Research Libraries (ARL). This system will leverage current digital repository infrastructure already in place and in use at large state and publically funded Universities to create a network of publically funded, open access research through a common metadata schema. Here at the University of Iowa, our digital repository system is called Iowa Research Online.

Toward the making SHARE a reality, the AAU, APLU, and the ARL announced yesterday the formations a Joint Steering Group comprised of University Administrators, Librarians, and Technologists was formed to see this project through completion. You can read more about SHARE here.


Elsevier allows experimental text mining of its journals at UBC

In an agreement with the University of British Columbia (UBC) Elsevier recently agreed to allow researchers there to text-mine Elsevier content for a number of purposes. The agreement came about through the efforts of Heather A. Pinowar, a post-doc at UBC whose “work depends on text mining, using computers to automatically pull certain kinds of information from large amounts of text, including databases of journal articles.”  See details in Jennifer Howard’s article in the Chronicle of Higher Education.


Berlin 9 Open Access Conference held in Bethesda.

The ninth Berlin Open Access Conference, and the first to be held in the US, concluded last week in Bethesda, Md. See for details on the program. The Conference follows on the Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities, “issued in 2003 by international research, scientific, and cultural institutions, to promote the Internet as a medium for disseminating global knowledge.”

Some interesting quotes from the meeting from Jen Howard’s coverage in the Chronicle of Higher Education:

“One or two people in this room will die in the next five years because of research that didn’t make its way to clinics fast enough,” one presenter, Cameron Neylon, told the crowd. Mr. Neylon, a biophysicist, is a senior scientist at Britain’s Science and Technology Facilities Council. He spoke at a session on how open access can create new opportunities for business as well as for scholarship. “This is not about ideology anymore,” it’s about creating the best, most efficient mechanisms for getting research to those who need it, he said.

“To me this is a design challenge,” said Michael Crow, president of Arizona State University. In an ideal world, knowledge would be as evenly distributed as sunlight, he said, recommending that universities need to be redesigned so they don’t work on exclusivity.


Open access might not be the real issue issue for the future of research communication

Dr. David Rosenthal, engineer and co-creater of LOCKSS (Lots of Copies Keep Stuff Safe) recently spoke on the topic of Open Access at the University of British Columbia.

He choseto look at five audiences where OA may have an effect: general public, researchers, libraries, publishers, and software developers.  He discusses his thoughts on peer-review or in his opinion bad peer-reviewing and whether or not open access increases or decreases bad research publishing; the creation of the big deal journal bundling by publishers to fight off the cost decrease due to the transition to Web publishing and lack of library initiative to fight off the big deals; and how the increase of OA data versus OA articles might be more beneficial for researchers.  Essentially, he believes a combination of reducing publication costs, finding new technology driven publishing models, less restrictions on intellectual property and publishing of better quality articles may be the issues that face the future of research and that OA may just be a way to work on those real issues.

The full transcript of this talk can be found on his blog:


Open Data for Historical Research: The Trans-Atlantic Slave Trade Database

Culminating several decades of collaboration between researchers and archives spanning four continents, the Trans-Atlantic Slave Trade Database comprises the most comprehensive source of historical data on the slave trade, and is freely available over the Internet. The Voyages Database, its core tool, offers researchers an intuitively friendly interface for searching among nearly 35,000 discrete slave voyages undertaken between 1514 and 1866. Data points for individual voyages include things like: ship name; flag(s); owners; place(s) of slave purchase; place(s) of slave landing; numbers of slaves that died in transit; and much more.

Three ancillary databases provide estimates of the volume of trade for particular periods, regions, and itineraries; images of documents, maps, and illustrations; and the African names of individual slaves that were recorded for particular voyages. Additional resources include a series of interpretive essays by contributing scholars, and a set of lesson plans for the K-12 audience.

Access the Trans-Atlantic Slave Trade Database at


Open Science: some new developments

There have been several interesting articles of late on open science.

Scientists Embrace Openness, by Chelsea Wald, Science, April 9, 2010


History is replete with stories of scientists who hid their ideas from their competition; consider Leonardo da Vinci, whose odd backward writing may have been partly motivated by fear of thieves, or Isaac Newton, who concealed one idea by writing it in the form of an anagram. Science has long been a dog-eat-dog world.

So it may seem odd that a handful of scientists are going to similar lengths to share not just their results but also, sometimes, their raw data — even their lab notebooks — often in real time. They’re part of a movement called Open Science, or, more specifically, Open Notebook Science, whose motto is “no insider information.”

At first glance, going “open” would seem like a serious career risk — years of work could be for nothing if a competitor uses your work to beat you to publication — but many practitioners of openness say the benefits outweigh those risks. The benefits include increased opportunities for collaboration, more feedback from colleagues, and a greater likelihood that the research will get to the people who can use it. Counterintuitively, practitioners say that being open supports their claims of priority and relieves their anxiety about getting ripped off.

Open science: policy implications for the evolving phenomenon of user-led scientific innovation, by Victoria Stodden,  Journal of Science Communication, volume 09, 2010,  Issue 01, March 2010.


From contributions of astronomy data and DNA sequences to disease treatment research, scientific activity by non-scientists is a real and emergent phenomenon, and raising policy questions. This involvement in science can be understood as an issue of access to publications, code, and data that facilitates public engagement in the research process, thus appropriate policy to support the associated welfare enhancing benefits is essential. Current legal barriers to citizen participation can be alleviated by scientists’ use of the “Reproducible Research Standard,” thus making the literature, data, and code associated with scientific results accessible. The enterprise of science is undergoing deep and fundamental changes, particularly in how scientists obtain results and share their work: the promise of open research dissemination held by the Internet is gradually being fulfilled by scientists. Contributions to science from beyond the ivory tower are forcing a rethinking of traditional models of knowledge generation, evaluation, and communication. The notion of a scientific “peer” is blurred with the advent of lay contributions to science raising questions regarding the concepts of peer-review and recognition. New collaborative models are emerging around both open scientific software and the generation of scientific discoveries that bear a similarity to open innovation models in other settings. Public engagement in science can be understood as an issue of access to knowledge for public involvement in the research process, facilitated by appropriate policy to support the welfare enhancing benefits deriving from citizen-science.

My Data, Your Data, Our Data, by Amy Dockser Marcus, Wall Street Journal, April 13, 2010


Researchers Urged to Think Harder About Compiling and Sharing Data

From the Chronicle of Higher Education, June 22, 2009.

By Paul Basken

Data overload is creeping up on everyone, and research scientists are no exception. So it’s time, according to a report out today from the federally chartered National Academies, to think about what to do with all that data.

The report, “Ensuring the Integrity, Accessibility, and Stewardship of Research Data in the Digital Age,” calls on researchers, their universities, and publishers of academic journals to consider new policies for compiling, tracking, storing, and sharing data. Otherwise, the report says, the flood of data coming out of scientific research could be lost, misinterpreted, or misused.

As an example, the report’s authors—more than three dozen experts, mostly at research universities—suggest that scientists try harder to think of what data are relevant to their findings and then include that data in their published work.

Read on…


Publish in Wikipedia or Perish

Declan Butler, Publish in Wikipedia or Perish, Nature News, Dec. 18, 2008

Journal to require authors to post in the free online encyclopaedia.


Wikipedia, meet RNA. Anyone submitting to a section of the journalRNA Biology will, in the future, be required to also submit a Wikipedia page that summarizes the work. The journal will then peer review the page before publishing it in Wikipedia.

The initiative is a collaboration between the journal and the RNA family database (Rfam) consortium led by the UK Wellcome Trust Sanger Institute in Hinxton. “The novelty is that for the first time it creates a link between Wikipedia and traditional journal publishing, with its peer-review element,” says Alex Bateman, who co-heads the Rfam database. The aim, Bateman says, is to boost the quality of the scientific content on Wikipedia while using the entries to update the Sanger database.

…The goal is to encourage more scientists who work on RNA to get involved in creating and updating public data on RNA families, while being rewarded by the traditional method of a citable publication, says Sean Eddy, a computational biologist at the Janelia Farm Research Campus of the Howard Hughes Medical Institute in Ashburn, Virginia, and a co-author of the nematode article.