Under the Hood of PLoS ONE: The Open Source TOPAZ E-Publishing System

PLoS is building its innovative PLoS ONE e-journal, which will incorporate both traditional and open peer review, using the open source TOPAZ software. (For a detailed description of the PLoS ONE peer review process, check out "ONE for All: The Next Step for PLoS.")

What is TOPAZ? It’s Web site doesn’t provide specifics, but "PLoS ONE—Technical Background" by Richard Cave does:

The core of TOPAZ is a digital information repository called Fedora (Flexible Extensible Digital Object Repository Architecture). Fedora is an Open Source content management application that supports the creation and management of digital objects. The digital objects contain metadata to express internal and external relationships in the repository, like articles in a journal or the text, images and video of an article. This relationship metadata can also be search using a semantic web query languages. Fedora is jointly developed by Cornell University’s computer science department and the University of Virginia Libraries.

The metastore Kowari will be used with Fedora to support Resource Description Framework (RDF) http://en.wikipedia.org/wiki/Resource_Description_Framework metadata within the repository.

The PLoS ONE web interface will be built with AJAX. Client-side APIs will create the community features (e.g. annotations, discussion threads, ratings, etc.) for the website. As more new features are available on the TOPAZ architecture, we will launch them on PLoS ONE.

There was a TOPAZ Wiki at PLoS. It’s gone, but it’s pages are still cached by Google. The Wiki suggests that TOPAZ is likely to support Atom/RSS feeds, full-text search, and OAI-PMH among other possible features.

For information about other open source e-journal publishing systems, see "Open Source Software for Publishing E-Journals."

Overcoming Obstacles to Launching and Sustaining Non-Traditional-Publisher Open Access Journals

As I noted in "What Is Open Access?," there is a fairly long history of non-traditional publishers producing free electronic journals:

During the late 1980s and early 1990s, the Internet had developed to the point that scholars began to publish free digital journals utilizing existing institutional infrastructure and volunteer labor (e.g., EJournal, PostModern Culture, and The Public-Access Computer Systems Review. These journals were not intended to generate income; they were "no-profit" journals. Although many of these journals allowed authors to retain their copyrights and they had liberal copyright statements regarding noncommercial use, they preceded by a decade or more the Creative Commons, and, consequently, did not embody that kind of copyright stance. While some of these journals ceased publication and others were transformed into non-profit ventures, they provided a model that others followed, especially after the popularization of the Internet began in the mid-1990s, which followed the earlier introduction of Web browsers. In recent years, the availability of free open source journal management and publishing systems, such as the Open Journal Systems, further simplified and streamlined digital journal publishing, fueling additional growth in this area. Now, a wide variety of academic departments or schools, institutes and research centers, libraries, professional associations, scholars, and others publish digital journals, a subset of which comply with the strictest definition of an open access journal and a larger subset which comply with the looser definition of an open access journal as a free journal. Since these diverse "publishers" would have been unlikely to be engaged in this activity without facilitating digital technologies and tools, I refer to them as "non-traditional publishers." Many of them are also "no-profit" publishers as well.

Given open source digital journal publishing systems, the idea of starting an OA journal has become more attractive than it was in the days when digital journals required a fair amount of specialized, labor-intensive technical support. However, the obstacles that non-traditional-publisher OA journals (hereafter called NTP OA journals) face are not primarily technical.

Here are some issues that NTP OA journals can face:

  • NTP OA journals are new journals. New journals have much more difficulty attracting authors, especially high-visibility authors, than established journals. Therefore, they also have more difficulty attracting readers, especially scholars who will cite their articles. This is a vicious circle. There are three key strategies for overcoming this problem: (1) focus your journal on a specialized, emerging topic of great interest that is not covered or not well covered by existing journals; (2) establish a high visibility editorial team and editorial board; and (3) actively recruit articles from authors.
  • NTP OA journals are digital-only journals. Certainly there is less prejudice against digital-only journals today than in the late 1980s; however, there may still be residual feelings by some scholars that digital journals are not "real" journals, and many scholars may have legitimate concerns about whether these journals will be available 10, 20, 30 or more years into the future. Regarding the latter point, it is highly desirable to have a convincing digital preservation strategy in mind, such as LOCKSS (a growing number of academic libraries are using this system to preserve digital journals). Authors who must face the prejudices of tenure committees against digital journals may be reluctant to publish in them or wish that they hadn’t when facing a promotion review. Provosts, department chairs, and others need to tackle the difficult issue of separating the digital wheat from the chaff so that junior faculty can be comfortable publishing in sanctioned NTP OA journals in their disciplines.
  • NTP OA journals often lack strong "branding." Conventional journal publishers typically have well-established reputations and they invest significant resources in promoting their journals, especially new journals.
  • NTP OA journals typically publish fewer articles than their conventional counterparts. In my view, this is not an intrinsic problem, but it can lead to negative perceptions of these journals.
  • NTP OA journals may not be indexed in traditional disciplinary indexing and abstracting services, they may lack standard identifiers (ISSN numbers), and they may not be cataloged by libraries in systems such as the OCLC Online Union Catalog (now publicly available as WorldCat). Fortunately, the latter two issues can be fairly easily addressed by NTP OA journal editors working with the National Serials Data Program at the Library of Congress and their local libraries; getting in I&A systems may require both time (to demonstrate that the journal warrants indexing) and persistent effort. The existence of directories of freely available digital journals, such the Directory of Open Access Journals, ameliorates the I&A problem somewhat, and NTP OA journal editors should make every effort to get their journals in such directories.
  • For the reasons noted above, NTP OA journals may lack citation impact; however, if they do have impact this may not be known because they are not included in prominent ISI publications that are widely used to measure such impact. However, with the advent of Google Scholar and similar systems that provide alternative ways of measuring citation impact, there is a glimmer of hope on the horizon, but these new methods of determining impact need to be widely recognized as being legitimate for them to be effective. One favorable impact factor is that, since NTP OA journals’ contents can be freely indexed by commonly used search engines (e.g., MSN Search), scholars are more likely to find their articles and cite them.
  • NTP OA journals require copy editing. This seems like an obvious point; however, novice editors can easily underestimate how much copy editing is required to produce a high-quality journal and how demanding this can be.
  • NTP OA journals survival may depend on the continued interest of their founders. Founders can lose interest in their journals, they can move to new jobs (leading to issues of their continued affiliation with the journal or the transfer of the journal to a new organization), they can retire, and they can die (see Walt Crawford’s "Free Electronic Refereed Journals: Getting Past the Arc of Enthusiasm").

For the reasons outlined above, NTP OA journals have a higher probability of success and survival if they are produced by a formal digital publishing program that has the firm backing of a nonprofit organization (or a unit of such an organization) than they do if they are published by a loose confederation of individuals. This digital publishing program does not need to invest anywhere near the level of resources that conventional publishers do, but it needs to have a parent organization that is committed to the continued operation and preservation of its journals, a distinct brand identity, a small core of subsidized part- or full-time editorial staff supported by a much larger number of editorial volunteers, a minimal level of supported technical infrastructure that relies on open source software, an active vs. passive content recruitment orientation, and a vigorous targeted promotion effort that integrates its journals into conventional finding tools and uses disciplinary and dedicated mailing lists, RSS feeds, Weblogs, and other free or low-cost communication tools to publicize them.

Open Source Software for Publishing E-Journals

Want to publish an open access journal, but you don’t want to license a commercial journal management system, develop your own system, or to do it all by tedious HTML hand-coding? Here’s summary information about two existing open source e-journal management systems (and one emerging system) that may do the trick.

HyperJournal

  • "HyperJournal is a software application that facilitates the administration of academic journals on the Web. Conceived for researchers in the Humanities and designed according to an intuitive and elegant layout, it permits the installation, personalization, and administration of a dedicated Web site at extremely low cost and without the need for special IT-competence. HyperJournal can be used not only to establish an online version of an existing paper periodical, but also to create an entirely new, solely electronic journal."
  • Overview
  • Documentation
  • Download

Open Journal Systems, Public Knowledge Project

  • "Open Journal Systems (OJS) is a journal management and publishing system that has been developed by the Public Knowledge Project through its federally funded efforts to expand and improve access to research. OJS assists with every stage of the refereed publishing process, from submissions through to online publication and indexing. Through its management systems, its finely grained indexing of research, and the context it provides for research, OJS seeks to improve both the scholarly and public quality of referred research."
  • Open Journal Systems (Overview)
  • FAQ
  • OJS Technical Reference
  • Download

DPubS (Digital Publishing System), Cornell University Library (In development)

  • "DPubS’ ground-breaking software system will enable publishers to cost-effectively organize, deliver, present and publish scholarly journals, monographs, conference proceedings, and other common and evolving means of academic discourse."
  • About DPubS
  • FAQ

Postscript: Peter Suber suggests adding several other software packages, including:

  1. ePublishing Toolkit
  2. SciX Open Publishing Services (SOPS)

The Economics of Free, Scholar-Produced E-Journals

While highly visible, large-scale STM open access publishing ventures such as BioMed Central loom large in the free e-journal scene, small-scale scholar-produced e-journals continue to quietly publish new scholarly articles as they have done for at least 18 years now.

I won’t detour into a lengthy history lesson for those readers who weren’t there. The short version of the story is that New Horizons in Adult Education is typically seen as the first scholarly e-journal published on the Internet (it was established in Fall 1987); however, it’s important to recognize that those were primitive times Internet-wise, when distribution of ASCII article files via list servers and FTP servers were cutting-edge ventures. So, as you would image, finding tools were informal and few and far between. ARL’s publication of the Directory of Electronic Journals, Newsletters, and Academic Discussion Lists in July 1991 was a landmark event that made the invisible visible.

For some reason, there was a mini-surge of activity in the 1989-1991 period, with the emergence of the Bryn Mawr Classical Review, EJournal, Electronic Journal of Communication, Journal of the International Academy of Hospitality Research, Postmodern Culture, Psycoloquy, The Public-Access Computer Systems Review, Surfaces, and other journals. Several editors (myself, Stevan Harnad, and John Unsworth) rocked the house at the Association of Research Libraries’ 1992 Symposium on Scholarly Publishing on the Electronic Networks to the dismay of the assembled conventional publishers, who thought we were mad as hatters because we thought that: (a) e-journals were viable, (b) we could anoint ourselves as publishers, and (c) we were giving it away for free. My recollection is that, after the last speech, there was a stunned silence followed by a spattering of applause and a frenzy of generally hostile, astonished questions.

And, as they say, the rest is history. Peter Suber’s Timeline of the Open Access Movement is a good way to get a handle on subsequent events. Someday, I’ll write more about the early e-volution of e-journals.

So, onto the topic at hand. What are the economics of free, scholar-produced e-journals?

Let’s delimit the field a bit. We are not talking about journals produced by university presses or professional associations. Scholar-produced e-journals are generally labors of love, supported by a small group of scholars who serve without pay as editors, editorial board members, and journal production staff.

They often leverage existing technical infrastructure (e.g., Web servers) at the editors’ institutions. The volume of published papers is typically fairly modest, and the papers themselves are frequently not graphically complex. Editors or other volunteers manage the peer review process (usually via electronic means) as well as copy edit and format articles. HTML and PDF are the usual distribution formats, requiring HTML editors, Word, Acrobat, or similar low-cost or free programs. Increasingly, electronic journal management systems are used to automate editorial functions and simplify journal site creation and maintenance (a prime example is the free Open Journal Systems software). "Marketing" is often done by free electronic means: journal mailing lists, table of contents messages sent to targeted subject-related mailing lists, RSS alerts, etc. Since the content is free and electronic, there is no overhead for subscription/licensing management. Since no one gets paid, human resources functions are not needed. If authors retain copyright or content is under a Creative Commons or similar license, no permissions support is needed. Since existing facilities are used (at work or at home), there is no need to rent or purchase office space. Since no money is changing hands in any form, accounting support is unnecessary.

So, what are the economics of free, scholar produced journals? The glib answer is that there are none. But, the real answer is that the costs are so low and the functions so integral to scholarship that they are easily absorbed into ongoing operational costs of universities. Even if they weren’t and scholars had to do it all on their own, server hosting solutions are so ubiquitous and cheap, free open source software is so functional and pervasive, and commercial PC software is so powerful and cheap (especially at academic discounts) that these minor costs would act as no real barrier to the production of scholar-produced e-journals.

Of course, this is not to say that there are not issues associated with the viability and sustainability of these journals, the perpetual preservation of their contents, and other difficulties, but these are topics for another day.

The Journal of Electronic Publishing Is Reborn

Good news! The Journal of Electronic Publishing is coming back after a long hiatus (the last issue was published in August 2002). New issues will be announced on PACS-P and other lists. See the press release below for details.

Contact: Maria S. Bonn Director, Scholarly Publishing Office, 734-763-3343, mbonn@umich.edu

Journal of Electronic Publishing Re-Launched by Library’s Scholarly Publishing Office

Ann Arbor, May 31, 2005—The Scholarly Publishing Office of the University of Michigan University Library will re-launch The Journal of Electronic Publishing (JEP) in January, 2006.

"JEP is an excellent fit for us in several ways," says Maria Bonn, Director of the Scholarly Publishing Office. "It is another outstanding journal that we can make available free over the Internet, it fits with our commitment to library-based scholarly publishing, and it covers the very area we are involved in, electronic publishing." Michigan’s Scholarly Publishing Office currently publishes 10 journals and four scholarly monograph series online.

JEP was started by the University of Michigan Press in 1995. In 2003 the press agreed to transfer the journal to the Columbia University Press, but the transfer was never completed and the journal—still at http://www.press.umich.edu/jep/—has had no new issues since then.

"Since its first issue, JEP has been a source of innovative ideas, best practices, and leading-edge thinking about all aspects of publishing, authorship, and readership in the electronic environment," says Mark Sandler, Collection Development Officer for the University of Michigan University Library. Returning after a three-year hiatus, JEP will "continue to document the changes in publishing with the growth of the Internet, and to stimulate and shape the direction of those changes."

The Scholarly Publishing Office (SPO; http://spo.umdl.umich.edu) was founded in 2001 to support academic publishing through a library-based publishing platform. SPO is also teaming with SPARC (the Scholarly Publishing and Academic Resources Coalition; http://www.arl.org/sparc/index.html) on the recently announced Publisher Assistance Program to provide business planning and digital publishing services to facilitate open-access publishing in the social sciences and humanities. Those services will be available to JEP as well, ensuring its future and keeping it at its original University of Michigan home.

SPO’s first issue of JEP will be in January, 2006. "JEP burst on the scene with a focus on experimentation, vision, and prediction," Sandler said. He said that now, ten years later, electronic publishing practices have stabilized for some formats and markets (for instance, scholarly journals have shown significant convergence of distribution and pricing models), but that many unresolved issues remain for newspapers, trade books, magazines, and newer forms of publishing like blogs and wikis. "All aspects of electronic publishing still face considerable change and sometimes upheaval, and a great deal of the creative turmoil that JEP captured in the mid-nineties still challenges publishers, authors, librarians, and readers. We still struggle to understand author and reader preferences, and still search for stable economic models that will allow publishing to flourish in an age of electronic communication," he said. "The new JEP will continue to look back over the past 20 or 30 years to see how we’ve come to this point in the history of publishing, and look forward to where publishing may be heading. It will look inward at key players and practices of publishing, and also look outward at movements on the margins that are challenging traditional publishing interests, and at readers worldwide affected by the interplay of technological and economic forces that have revolutionized social communication."

JEP‘s editor, Judith Axler Turner, will remain at the helm, with editorial input and publishing support from Mark Sandler and Maria Bonn. A new editorial board will be constituted, and JEP will solicit articles that present wide-ranging and diverse viewpoints on contemporary publishing practices, and encourage dialogue and understanding between key decision-makers in publishing and those who are affected by the decisions being made.

The first new issue will focus on the changes in electronic publishing in the past three years, exploring topics such as the rise of open access publishing, the increasingly complicated intellectual property landscape, the rise of new communication technologies, and the new economics of scholarly publishing. JEP is actively seeking feedback on its new direction and is also looking for high-quality submissions on these topics. Authors and others are invited to discuss JEP‘s future or submit articles by contacting the editorial team at JEP-info@umich.edu. Back issues of JEP may currently be found at http://www.press.umich.edu/jep/

The Spectrum of E-Journal Access Policies: Open to Restricted Access

As journal publishing continues to evolve, the access policies of publishers become more differentiated. The open access movement has been an important catalyst for change in this regard, prodding publishers to reexamine their access policies and, in some cases, to move towards new access models.

To fully understand where things stand with journal access policies, we need to clarify and name the policies in use. While the below list may not be comprehensive, it attempts to provide a first-cut model for key journal access policies, adopting the now popular use of colors as a second form of shorthand for identifying the policy types.

  1. Open Access journals (OA journals, color code: green): These journals provide free access to all articles and utilize a form of licensing that puts minimal restrictions on the use of articles, such as the Creative Commons Attribution License. Example: Biomedical Digital Libraries.
  2. Free Access journals (FA journals, color code: cyan): These journals provide free access to all articles and utilize a variety of copyright statements (e.g., the journal copyright statement may grant liberal educational copying provisions), but they do not use a Creative Commons Attribution License or similar license. Example: The Public-Access Computer Systems Review.
  3. Embargoed Access journals (EA journals, color code: yellow): These journals provide free access to all articles after a specified embargo period and typically utilize conventional copyright statements. Example: Learned Publishing.
  4. Partial Access journals (PA journals, color code: orange): These journals provide free access to selected articles and typically utilize conventional copyright statements. Example: College & Research Libraries.
  5. Restricted Access journals (RA journals, color code: red): These journals provide no free access to articles and typically utilize conventional copyright statements. Example: Library Administration and Management. (Available in electronic form from Library Literature & Information Science Full Text and other databases.)

Using this taxonomy, an examination of the contents of the Directory of Open Access Journals quickly reveals that, in reality, it is the Directory of Open and Free Access Journals, because many listed journals do not use a Creative Commons Attribution License or similar license.

Some may argue that the distinction between OA and FA journals is meaningless; however, to do so suggests that the below sections of the "Budapest Open Access Initiative" in italics are meaningless and, consequently, that the Open Access movement is really just the Free Access movement.

By "open access" to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.

Not that there would be anything wrong with the Free Access movement, but some may feel that the broader scope of the Open Access movement is much more desirable.

In any case, the journal universe is not just green or red, and it’s a pity that we don’t know the breakdown of the spectrum (e.g., x number of green journals and y number of cyan journals), for that would give us a better handle on how the world has changed from the days when all journals were red journals.

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