Category Archives: Open Access topics

Models for open access — many flavors

By Karen Grigg, Associate Director of Collection Services at the Duke Medical Center Library:

Open Access comes in a variety of flavors.  The two main types of open access are that of open access journals and self-archiving methods

Open Access journals are those that are freely available to the end-user.  Since the reader does not pay for content, costs must be subsidized by the author or the institution. Along with publication fees, submission fees are sometimes charged.


BioMed Central, an online publisher of free peer-reviewed scientific articles, is sustained by revenue from institutions. However, the new “Shared Support Membership” allows institutions and authors to share article costs.

Public Library of Science, or PloS, charges a publication fee that can be paid by the author or the author’s employer. PLoS also relies on donations from foundations.

Self-archiving allows authors to submit their own material online so that it is accessible to the public.  There are two main varieties of self archiving; institutional repositories (IR), and Subject Based Repositories.  IR are hosted by an institution, such as a university, and bundles all the research output of the institution.  Often, the work is done by librarians or IT staff.  One such IR is eScholarship from the University of California.  A subject-based repository is hosted independently of an individual institution, and bundles the research output of a subject of discipline.  Authors voluntarily self-archive their work on a pre-print server.  An example of a subject repository  is Arxiv, a repository for- physicists and mathematicians.  Finally, authors often post articles on their own web sites, but the ability to do so requires negotiation with the publisher.

There are also some hybrid models of open access. Some publishers allow authors to decide whether or not an article can be openly accessed.  Authors who would like their article to be freely available can opt to pay the publishing fee.  These fees can be several thousand dollars per article.  The Delayed OA model gives public access to journal articles after an embargoed period, often 6 months to 1 year.  With a Partial OA journal, certain parts of the journal; often editorials or abstracts, are freely available, while the bulk of the content is for fee. Finally, Retrospective OA allows access to older journal articles that have been digitized.

For more background on Open Access Models, see:

Zhang, Sha Li. “OCLC Systems & Services | The Flavors of Open Access.” OCLC Systems & Services 23.3 (2007): 229-34. Emerald. Web. 15 Sept. 2010. <>.

“Peter Suber, Open Access Overview (definition, Introduction).” Earlham College — Richmond, Indiana. Web. 15 Sept. 2010. <>.

For more information, see the Open Access at Duke web site.

What is Open Science?

Our next OA Week posting comes from Michael Peper, Librarian for Math and Physics at Duke:

We’ve discussed openness in terms of publications and data, but this same spirit can apply to the research process as well.  Science in some ways is necessarily a shared and collaborative process.  Scientists work together in labs, they share equipment, materials and human resources and share results in publications.  In many cases, however, there was much about the practice of science that has been kept in the dark.  Scientists would not share methods, data, preliminary results, etc. until publication, if ever.  Recently, however, there has been great interest in trying to answer big questions and solve big problems by joining forces to accomplish work that could never be done by one isolated researcher.  Improved cyber infrastructure makes the opportunities for sharing even greater.  Many believe that Open Science should not just be adopted for its admirable ideals, but also because open science also holds promise of being better science.

The title of this post, however, is ‘What is Open Science?’ so perhaps I should actually attempt to answer that question.

The boundaries of Open Science are difficult to define because this idea encompasses other issues related to openness.  Transparency, across the entire practice of science, is what defines Open Science.  Both Science Commons and the Open Science Project lay out their principles of this idea in an attempt to provide it some limits.  The spirit of these principles is that there should be transparency to the methods, observations, data collection, data access, communication, collaboration and research tools.  Instead of limiting the sharing of the practice of science to publication of selected results, the entire scientific process should be exposed to potential users, collaborators and extenders of the work.

There are a growing number of projects that have embraced these ideals and we can point to a few of them here.  Cameron Neylon keeps an open notebook for his work in the biological sciences on producing antibacterial compounds and also writes for the blog Science in the Open.  The Synaptic Leap is another open lab notebook project to create a way for biomedical researchers to collaborate.  The collaborators include Thomas Kepler at the Duke University Medical Center.  A final example is the UsefulChem project which is the brainchild of Jean-Claude Bradley who uses his background as an organic chemist to develop new anti-malarial compounds in an open environment.

For more information, see the Open Access at Duke web site.Open Access logo, designed by PLoS

What is Open data?

From Paolo Mangiafico, Duke’s Director of Digital Information Strategy:

Open Access is about more than just the publications that are the results of research – it’s also about the data generated during the research process.

While publications have always been “public” by definition (even if not universally accessible), data has more frequently been made available only on request, or when there’s some reason to question the published results.

But there are good reasons to make more data more open more often. A 2009 report from the National Academy of Sciences titled “Ensuring the Integrity, Accessibility, and Stewardship of Research Data in the Digital Age” makes the case this way:

The advance of knowledge is based on the open flow of information. Only when a researcher shares data and results with other researchers can the accuracy of the data, analyses, and conclusions be verified. Different researchers apply their own perspectives to the same body of information, which reduces the bias inherent in individual perspectives. Unrestricted access to the data used to derive conclusions also builds public confidence in the processes and outcomes of research. Furthermore, scientific, engineering, and medical research is a cumulative process. New ideas build on earlier knowledge, so that the frontiers of human understanding continually move outward.

Researchers use each other’s data and conclusions to extend their own ideas, making the total effort much greater than the sum of the individual efforts.

Openness speeds and strengthens the advance of human knowledge.” (p. 59)

While not all data should be kept and not all data can be shared, policies, processes, and infrastructure are being developed in many fields and at many institutions to promote openness of research data wherever possible. One example based here at Duke, the Dryad repository, part of the National Evolutionary Synthesis Center, is working with stakeholders from journals and scientific societies to develop data sharing policies, and a place to deposit data underlying scientific publications. Similar policies have been adopted by funding agencies and are becoming an expectation in many fields.

Making your data openly accessible can also bring more attention to your work.

One study that examined the citation history of 85 cancer microarray clinical trial publications found that

48% of trials with publicly available microarray data received 85% of the aggregate citations. Publicly available data was significantly (p = 0.006) associated with a 69% increase in citations, independently of journal impact factor, date of publication, and author country of origin using linear regression.” (Piwowar HA,  Day RS, Fridsma DB, 2007 “Sharing Detailed Research Data Is Associated with Increased Citation Rate.” PLoS ONE 2(3): e308. doi:10.1371/journal.pone.0000308)

Want to learn more about open data and how you can share the results of your work? Here are some starting points:

For more information, see the Open Access at Duke web site.Open Access logo, designed by PLoS

What is Open Access?

Continuing our run-up to Open Access week, another contribution from Pat Thibodeau:

Open access (OA) in its purest sense is making literature free online without any fees or restrictions due to copyright or licenses.

The Budapest Open Access Initiative [ ] was the first to define open access as being publicly free on the Internet, allowing users to read, download, copy, distribute, print, search or link to the full text of articles without legal, financial or technical barriers.  Since their statement, others have followed and Peter Suber, one of the true experts on OA, provides an excellent overview and timeline on his Web site:

Some other important statements are:

Bethesda Statement on Open Access Publishing

Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities

While the OA movement initially focused on journal literature, it is now being applied across the realm of scholarly communication including books, learning objects, repositories of various documents, and data sets.   In all its permutations, its goal is to ensure free access to information to support academic, research and personal pursuits of knowledge and promote innovation and discovery on a global as well as local level.

The OA movement has had an impact on the journal literature.  There are now over 5,300 titles in the Directory of Open Access Journals  [] and a 2009  PL0S One article by Bjork et al. [] reports that now 20% of peer-reviewed articles are freely available across all disciplines.   This is a major shift since the Budapest statement challenged traditional scholarly communications in 2002.

While Peter Suber’s OA chronology []  identifies very early free-access models,  the OA  movement has clearly gained momentum since the Budapest initiative issued its statement in 2002.

For more information, see the Open Access at Duke web site.Open Access logo, designed by PLoS

Collaboration and the open access movement

In anticipation of Open Access Week at Duke, where the theme will be “Collaboration,” we will offer a series of blog posts about basic, and not so basic, issues and opportunities for OA.  This first post if from Pat Thibodeau, Associate Dean for Library Services in the Duke Medical Center.

The simplest definition of collaboration is “to work jointly with others or together especially in an in intellectual endeavor.”   But the open access source Wikipedia []   describes it as a “recursive process” where common goals are achieved “by sharing knowledge, learning and building consensus.”    As multidisciplinary and global projects increase in number that sharing of knowledge or information becomes very critical.  But what happens when one of the collaborators cannot access the information because of a restrictive license, the prohibitive cost of a journal subscription, or the unavailability of publicly funded research data?  Collaboration can be hampered if not halted.

The open access (OA) movement is focused on removing the barriers of price, copyright, and restricted use.  OA promotes the free flow of knowledge and data that makes collaboration possible and ultimately supports the generation of new innovations, creative ideas and scientific discoveries on a global scale.  Collaborators are no longer hampered by institutional or international boundaries.

So has open access actually made a difference?

In fact yes!  A recent NY Times article highlighted a research project where data were openly and publicly shared among commercial industries, universities and nonprofit groups in order to find biological markers of Alzheimer’s disease.  This “collaborative effort” has led to new research on early diagnostic tests as well as treatments.  []

This project is now serving as a model for groups studying other diseases.

In preparation of Open Access Week@Duke (Oct. 18-24), this blog will focus on other topics such as open data, open science, and other elements of the OA movement.  As you follow these blog posts, think about how OA could support collaboration at Duke, within your field, or across the world.

For more information, see the Open Access at Duke web site.Open Access logo, designed by PLoS