I was checking out The Digital Access to Scholarship at Harvard (DASH) repository and saw the announcement that Open Access Fellows are Harvard students (both undergraduate and graduate) who help faculty to make deposits into DASH, answer questions about the Open Access Policies, and help depositors complete metadata descriptions of items being placed in the repository.   Great idea!

As student jobs in academic libraries have been relegated to staffing evening service points or shelving a declining number of circulated books,  providing a student job for direct open access repository assistance and indirect advocacy among student peers  and classroom instructors satisfies many constituencies on  campus.

In terms of biomedical open access, DASH currently holds 1185 articles from the Harvard Medical School and 564 articles from the Harvard School of  Public Health. 457 of the articles from the Medical School are in PLoS publications, and there are direct links to the publisher’s open access copy. There is also a deposit waiver option, which I think the Open Access Fellows must become intimately acquainted.

So far, my advanced searching of Google for “open access fellows” has not turned up any other university explicitly copying this model.  But if it is anything like the “personal librarian program” that was started at my library more than 10 years ago, there certainly will be followers.  Particularly as more academic libraries establish an “Office of Scholarly Communication” and decide student jobs are a priority.

In the top 30 2009  Evolutionary Biology Journal Citation Reports(JCR) impact factor journals, we find only two titles from open access publishers:

• BMC Evolutionary Biology
• Evolutionary Bioinformatics

Another open access evolutionary biology title has not been around long enough to start being tracked in JCR. Genome Biology and Evolution (GBE) comes from Oxford University Press and has been published since May 2009.  You can find 164 open access articles from GBE available in  PubMed and PubMed Central.

Nearly two years old, the output of GBE does not compare quantitatively with the PLoS One publishing model. It is hard for any journal to catch up quantitatively to PLoS ONE.   GBE is one of six fully open scientific journals in the Oxford Open initiative.

Article-level Metrics from PLoS on Vimeo.

I am a firm believer in quality peer review for open access biomedical journals.  After all, these journals affect the health of individuals and communities all over the globe.  But we are beyond the monopoly on quality health information, according to Harnad and others,  that was characteristic of the pre-digital era when journals prided themselves on claiming to support the public interest by limiting access  to paying subscribers, including libraries.

Still, there is interest in establishing qualitative criteria for open access publishing, as there is a hill to climb for established biomedical researchers with well-conceived and executed research to buck tradition and select an immediate open access alternative to a long-standing, highly-impact-factor-ranked  peer reviewed journal. [For example, the researchers in my institution with big news that they think will be more respected in Science (Hey, you taxpayers, you get your uninhibited view in 12 months, so pipe down) than more widely read by the global and NIH taxpayer audience  in PLoS Genetics.  Still, there are scientists, even at my instition, that use the NIH’s encouragement (use of NIH grant proceeds for open access author processing fees is welcome)  to cast their traditional behavior to the wind and let everyone know what genetic research avenues hold progress.

So what kind of peer review takes place in Science?  From their Manuscript selection web page:

“Papers are assigned to a staff editor who has knowledge of the field discussed in the manuscript. Most submitted papers are rated for suitability by members of Science‘s Board of Reviewing Editors. The editors atScience consider this advice in selecting papers for in-depth review. Authors of papers that are not highly rated are notified promptly, within about 1 to 2 weeks.

Research papers that are selected for in-depth review are evaluated by at least two outside referees. Reviewers are contacted before being sent a paper and asked to return comments within 1 to 2 weeks for most papers. We are able to expedite the review process significantly for papers that require rapid assessment. Selected papers are edited to improve accuracy and clarity and for length. Papers cannot be resubmitted over a disagreement on interest or relative merit. If a paper was rejected on the basis of serious reviewer error, resubmission may be considered.”

What about that upstart PLoS Genetics? What is their version of peer review?

“Once a new manuscript has passed technical quality control, it is assigned to one of our senior editors—comprising the Editor-in-Chief, Deputy Editor, and Section Editors—depending on the subject matter, workload, and any potential competing interests. This first step usually occurs within a few working days of submission and is followed by an initial evaluation, sometimes in consultation with one or more members of the editorial board. For manuscripts that are considered further, an Associate Editor is assigned who then decides whether to invite external peer reviewers. We aim to have external reviews returned within ten days, although this can take longer depending on personal circumstances. After receipt of the reviewers’ comments, the Associate Editor makes a decision, often after consultation with other editorial board members. For manuscripts that are peer reviewed externally, the average duration between submission and first decision has been just over 30 days.”

Sounds like either publication has a peer review process in place, though such simple directions may obscure the fact of editors dealing with unmanageable quantities of submissions, as was pointed out in TheScientist back in 2006 which questioned the traditional method of peer review in the electronic age.   Although dated, this article also contains a chart comparing the submissions and reviewing patterns of several well-known subscription and open access journals.

So if the editorial board is in the driver’s seat for the standard of peer review, I have been pondering if we could come up with a metric of assessing the quality of the collective editors of a biomedical open access  journal.   I will be away this weekend for relaxation and back Monday night, but I will carry some nerdy index cards at all times, in case the vision of this editorial metric suddenly appears.

Nature Publishing, still smarting from last year’s rejection of  institutional price increases from a couple of academic library systems, has apparently studied the recent success of PLoS ONE ( as an interdisciplinary science journal, PLoSONE instantly ranked in the 2009 top 10 Biology ISI impact factor journals after two previous years of data) and launched a new gold open access journal: Scientific Reports

Some of the interesting goals are presented in the January 6th press release:

• All articles published in Scientific Reports will be open access and subject to an article-processing charge (APC) of US$1350/GB£890/ EURO1046  per accepted manuscript ( an additional 20% discount through the end of 2011)
• Authors will have a choice of two non-commercial Creative Commons (CC) licenses. NPG will make an annual donation to Creative Commons equivalent to $20 per APC paid for publication in Scientific Reports ( a maximum donation of $100,000 per year.
• Authors will be eligible for complimentary membership of the Creative Commons network.
• The focus of Scientific Reports will be natural sciences specialties, and Scientific Reports intends to publish all papers that are judged to be technically valid and original.
• Scientific Reports website will track and publicize most-downloaded, most-emailed, and most-blogged articles.
• All research papers will benefit from rapid peer review and publication, and will be deposited in PubMed Central.
• Scientific Reports will be led by a team of 15 Editorial Advisory Panel members, supported by an editorial board who will make all editorial decisions.  Scientific Reports will not have in-house editors, and will not offer developmental editing.

Now more about the Nature Publishing Group‘s views on and participation in open access, based on a press release issued by David Hoole, Director of their Intellectual Property Policy and Licensing Group.  David’s corporate bio is found with the description of the Executive Committee.   Please read through this press release, as I don’t need to repeat it here.  There is quite a lot of detailed information that only contains one exaggeration, that  one that Stevan Harnad identified a while back:

NPG does not require authors of original (primary) research papers to assign copyright of their published contributions. Authors grant NPG an exclusive licence to publish, in return for which they can reuse their papers in their future printed work without first requiring permission from the publisher of the journal….When a manuscript is accepted for publication in an NPG journal, authors are encouraged to submit the author’s version of the accepted paper (the unedited manuscript) toPubMedCentral or other appropriate funding body’s archive, for public release six months after publication. In addition, authors are encouraged to archive this version of the manuscript in their institution’s repositories and, if they wish, on their personal websites, also six months after the original publication.

Stefan takes issue, as I do, with the dichotomy of intent created by allowing authors to maintain their own copyright yet “encouraging” authors to wait six months to practice green open access.    In his blog entry last June, Stevan addressed Nature’s claims of effective open access practice while regressing on green open access.

This latest statement continues to be perplexing on this point.

Evidence 2010 will bring together international experts from the areas of education, EBM resource development, implementation, health economics and commissioning. Register now at the Early Bird rate and make savings. August 6th is the early-bird deadline.

This 2 day conference will be aimed at:

• Commissioners of evidence-based services
• Those involved in assessing the cost effectiveness of clinical interventions and services
• Developers of evidence-based resources
• Teachers and methodologists
• Those involved in implementation of evidence including front-line healthcare professionals

On the first day of Evidence 2010, there will be a debate of interest to fans of the open future:

Debate: The future of medical publishing in healthcare

Fiona Godlee  Editor in Chief, British Medical Journal

Bill Summerskill  Executive Editor, The Lancet

David Tovey Editor in Chief, The Cochrane Library

Tom Jefferson Scientific Editor PLOs ONE

Register now at the Early Bird rate and make savings.

The Journal of Clinical Oncology (JCO), published by the American Society of Clinical Oncology(ASCO), is considered a top shelf medical journal, ranked 4th for impact in oncology by the current Journal Citation Reports.  JCO follows the historical standard of requiring assignment of author’s copyright to the publisher upon article acceptance.  Authors submit manuscripts with the understanding that, if accepted, the copyright of the article, including the right to reproduce the article in all forms and media, shall be assigned exclusively to ASCO. Posting articles on institutional repositories is prohibited.

The leadership of JCO certainly believe in their mission and want their journal to remain respected and useful to the clinical oncology research community. Here’s how they tell it, in very nice suits.

From the medical library viewpoint, the 2010 cost for a JCO institutional subscription is somewhere in the middle, neither cheap nor expensive, though some hospital libraries would be hard pressed to pay:

What if you are at a hospital that cannot afford a subscription to JCO?  To view a full-text article without a subscription, you can purchase access to the article for 24 hours at a cost of $19.00 per article.

By the way, ASCO had an extremely good year in 2009, ending up with a $7,800,000 surplus and net assets of nearly $50,000,000:

Excerpt from ASCO 2009 Annual Report

Yes, cancer care and research is big business. Now, before you start to think that those ASCO assets are going into ASCO-sponsored scholarships and research funding, you should be reminded that  there is an independently-operated ASCO Cancer Foundation which raises research funds and distributes grants and scholarships.

So what does the ASCO do with a $7,800,000 surplus and net assets of nearly $50,000,000?

According to the video you might have just watched above, their flagship journal JCO wants to be “the one journal that every hematologist/oncologist has to read.” So what if the cost of that journal’s subscription prevented some hematologist/oncologists in certain hospitals from reading it?  I bet there are plenty of oncologists that understand the critical nature of their research findings and would be willing to use a portion of their grant funding to publish in author-fee based open access journal, the more prestigious and noticed by colleagues, the better. PLoS gold open access has made this point.

My modest proposal is that ASCO use some of its prosperity to fund an experiment in gold open access and test the waters for those that are willing to pay for universal access to their results.  Perhaps even price this gold experiment with the additional waiver of copyright assignment and permission to place the paper on an institutional repository.

There are certainly many major publishers that are trying to maintain revenue while testing the waters of the rising tide of open access with a model such as this.

In a story line out of the post- Reagan excesses of substituting the private sector for governement activity, the Journal of the National Cancer Institute (JNCI), a highly respected research journal for a narrow, exclusive slice of taxpayers, is neither published nor sponsored by the National Cancer Institute(NCI).  It participates in Pubmed Central archiving only at the bare minimum of article availability 12 months after publication.  It earns significant income and profit for Oxford University Press.  It is one of many examples of business as usual where taxpayers subsidize the intellectual content and are told to expect that their investment appears in a clinic or hospital where the promise of cancer research becomes personal.

The history of how JNCI went from public to private property is outlined pretty well on the NCI website with a fact sheet to address the persistent questions that have dogged the privatization since 1996. Under the terms of a 1996 cooperative agreement with NCI, Oxford University Press over a five-year transition gradually took over responsibility for JNCI and became the sole private owner. 

Now here is the game changer, I think, if it happens. On May 17th, President Barack Obama announced his intent to appoint Harold Varmus, M.D., to serve as Director of the National Cancer Institute (NCI).

President Obama said some very gratious things about Dr. Varmus in nominating him: ““…brings unmatched expertise at all levels — not only in cutting edge scientific research, but also as a leader in the development of strategies for improving patient care, in scientific education and training, and in the design of novel public-private partnerships.” 

Another part of Dr. Varmus’ profile is probably creating some sleepless nights for OUP. He is the co-founder and Chairman of the Board of the Public Library of Science, the successful open access publisher; as well as chairs the Global Health Advisory Committee  at the Bill and Melinda Gates Foundation. 

Should not the fruits of cutting edge, federally funded cancer research be immediately and readily available to the public and other researchers? I wait to see if Dr. Varmus is successfully appointed and uses this leadership position to advocate for a more open JNCI.

The American Society for Microbiology(ASM) is one of the most distinguished and successful biomedical science publishers.  ASM is already a full participant in PubMed Central for all of its non-open journals, offering free access at six months after publication, in effect already complying with the six month intent of the FRPAA legislative proposal. Now an open access journal has been added to the ASM journal publication lineup:

As ASM’s first broad-scope, online-only, open access journal, mBio™ will offer rapid review and publication of the best research in microbiology and allied fields. The new journal will continue ASM’s non-profit publishing mission and will be edited by scientists involved in active research. mBio™ will be published in association with the American Academy of Microbiology, from which editors and reviewers will be recruited.  AAM Fellows also will be entitled to submit one paper per calendar year via a special, accelerated submission path. Authors will retain copyright and grant ASM a nonexclusive license to publish their work if it is accepted. Upon publication, the work becomes available to the public to copy, distribute, or display under a  Creative Commons Attribution-Noncommercial-Share Alike 3.0 license. For more details and conditions, see the instructions for authors page for the new journal.

Thomas Shenk, ASM’s Publications Board Chairman and a Princeton Professor, is interviewed about this open access venture in an mBio™ podcast available from their blog.

No doubt the impact factor success of PLoS Pathogens in the Microbiology category of Journal Citation Reports and its similar broad approach to microbiology was useful ammunition in getting ASM and the Academy behind mBio™.

PLoS will be at the 100th meeting of ASM later this month.  Competition is never a bad thing…right?

An article in zeropaid.com amplified the news about BioTorrents, a BitTorrent tracking and repository site created by researchers at the Genome Center of the University of California Davis, announced earlier in April in PLoS One (BioTorrents: A File Sharing Service for Scientific Data).

If you are a denizen of digital bazaar known as BitTorrent, this latest development in scientific data sharing was inevitable, given the expected desire of open science advocates to share large amounts of data faster and more reliably.

If you have heard the term BitTorrent associated with illegally-distributed  music or full-length videos, time to re-orient your thinking to legitimate data transfer needs. The basic function of BitTorrent is to break up a large data set into small pieces, allowing sharing among computers with full copies or partial copies of the dataset. The peer-to-peer network architecture bypasses inaccessible sources and takes advantage of decentralization, and, ultimately, time saving.

BioTorrents automatically tracks popular data sets, as well as features  finding, sharing, and commenting of bioscience torrents, organized by browsing science content categories, sharing license types , and text searching. Google is also fed metadata to allow discovery of shared datasets and find descriptions on the BioTorrents site.  Here is today’s picture of the pioneers for this sharing concept: