Here are the top 10 clinical genetics journals for 2011,  according to SCImago Journal Rank for today, limited to journals with at least 100 articles over the last three years:

1. Nature Genetics is the highest ranked journal by a wide margin.  In a reputation strong position, Nature Publishing Group (NPG) does not offer optional gold open access to authors of articles in Nature Genetics, as is done for some other NPG journals. NPG does offer publisher processing for NIH-funded articles bound for PubMed Central.  Authors do not assign copyright for NPG articles, though they also grant NPG an exclusive license to publish. NPG also offers guidance and support for author self-archiving after a 6-month embargo.  Stevan Harnad took them to task for their resistance to immediate self-archiving and self-labeling their efforts as “liberal.”  I would give them an Openbiomed open access grade of  C.
2. PLoS Genetics, published by the Public Library of Science (PLoS), offers the a gold open access business model which funds the enterprise with an author fee.  For PLoS Genetics, the current publication fee is US$2250. Authors who are affiliated with one of our Institutional Members are eligible for a discount on this fee. PLoS applies the Creative Commons Attribution License (CCAL) to articles, and authors retain ownership of the copyright.  Articles are automatically eligible for immediate self-archiving. An Openbiomed open access grade of  A is well-deserved.
3. Nature Reviews Neuroscience also comes from the NPG, part of the Nature Reviews family.  According to this page, In 2009 NPG rebranded the Nature Clinical Practice journals into Nature Reviews, for eight clinical specialties. For authors, no particular open access enhancement in comparison to Nature Genetics. The Openbiomed open access grade of  C also applies.
4. Circulation: Cardiovascular Genetics is published by the American Heart Association and is representative of journal literature publishing the results of translational science that seeks to move laboratory discoveries aggressively into clinical practice. All AHA journals use the same author copyright transfer agreement, which causes the author to give away control and publication rights,with the one exception that  the author may post an accepted version of an article in a non-profit funders web archive and/or an author’s institutional repository, no earlier than 6 months after publication.  Nothing said about a personal web site. The Openbiomed open access grade is  C- .
5. Molecular Biology and Evolution (MBE) is published by Oxford University Press under the umbrella of Oxford Journals.MBE is one of the more than 100 journals that offer the Oxford Open option for a publication charge of £1700/$3000/€2550.  Authors from developing countries receive a significant publication charge discount. Post-Print version of articles can be placed on personal websites, your institution’s website and in institutional or subject-based repositories such as PubMed Central, as long as a 12 month embargo is respected. Authors do not assign copyright, though they also grant OUP an exclusive license to publish. The Openbiomed open access grade is  B .
6. DNA Repair is a subscription journal from Elsevier. Optional sponsored open access is available for this  journal. Only 2 articles in 2010 from this journal were sponsored open access. The charge for the sponsored option is us$3,000 plus tax where applicable.  Elsevier is fully green, which may be a reason why the number of sponsored articles is so low. Elsevier is also a full partner in Research4life, (as is OUP) and most of their article  reach developing nations that way.  The Openbiomed open access grade is  B+.
7. The Orphanet Journal of Rare Diseases(OJRD) is an open access journal on the Biomed Central(BMC) open access platform. An article processing charge of £950/US$1500/€1145 is required, though an institutional membership in BMC can provide a discount. Authors retain the copyright to their work, licensing it under the Creative Commons Attribution License which allows articles to be re-used and re-distributed without restriction,provided the original work is correctly cited. BioMed Central is owned by Springer Science+ Business Media. With a APC fee substantially below PL0S, this journal rates an Openbiomed open access grade of  A+.
8. BMC Medical Genomics is another open access, peer-reviewed journal on the Biomed Central platform. Blessed with all the open access attributes of BMC, with an APC of £1230/$1945/€1485.  Being a little more than OJRD without a clear compelling reason, his journal rates an Openbiomed open access grade of  A.
9. The American Journal of Medical Genetics Part C: Seminars in Medical Genetics is a subscription journal from Wiley-Liss, a imprint of Wiley-Blackwell.  Wiley-Blackwell offers a hybrid OnlineOpen access option for over 500 journals, including this one. The OnlineOpen APC fee is fixed at US$3000 for most journals.  Wiley-Blackwell expects to receive either a signed Copyright Transfer Agreement  or an Exclusive License Form before publication; in most cases this is the copyright transfer. Only OnlineOpen submission get explicit permission to post the  final PDF of the contribution on a personal website or in a personal repository. For non-open articles, only a pre-print copy is allowed in a personal website or repository. The Openbiomed open access grade is  B.
10. Evolution, the International Journal of Organic Evolution, is a subscription journal from Blackwell, acquired by Wiley.  The open access opportunities and constraints are similar to  The American Journal of Medical Genetics Part C: Seminars in Medical Genetics  , including the OnlineOpen option. Same open access grade: B .

Only 3 journals rated a C or less, and there were a few A‘s and several B‘s.   A guess I am an easy grader.

I was looking at the web site for one of the newer biomedical open access publishers, e-Century Publishing Corporation, and I noticed this statement:

By submitting a manuscript to AJCR, all authors agree that all copyrights of all materials included in the submitted
manuscript will be exclusively transferred to the publisher – e-Century Publishing Corporation once the manuscript is
accepted.

Also,

All PDF, XML and html files for all articles published in this journal are the property of the publisher, e-Century Publishing
Corporation (www.e-Century.org). Authors and readers are granted the right to freely use these files for all academic
purposes. By publishing paper in this journal, the authors grant the permanent right to the publisher to use any articles
published in this journal without any restriction including, but not limited to academic and/or commercial purposes.

So no real news here, but I began to wonder if this is as universal an open access publisher process as presumed. So I decided to do a quick survey. Here’s the result:

**Libertas Academica-  “Unless your work appears in a Clinical Medicine Reviews journal (i.e. a journal with a title that begins “Clinical Medicine Reviews in…”) then copyright in your Work rests with the author(s).  If your Work appears in a Clinical Medicine Reviews journal (i.e. a journal with a title that begins “Clinical Medicine Reviews in…”) then copyright in your Work rests with Libertas Academica Ltd.”

In most cases of required copyright transfer, publishers cite the need to create revenue with adaptations or assignments of submitted research. Co-Action Publishing stated:

Revenues from commercial reprints and sales allow us to keep our publishing fees down. Moreover, a major portion of the profits generated from commercial reprints are placed in a fund to cover publication fees for researchers from developing nations and in some cases for young researchers.

Once again, I used the SCImago Journal Rank for the medicine category Nephrology in 2011 (also requiring that each journal had to exist for three years and have at least 100 articles over the three years) to see how many of the top-10 journals had an open access option, typically an extra author article processing charge for immediate free non-subscription access from the journal’s home page or immediate, non-embargoed access in PubMed Central. Here are the results of my quest:

Seven of these 10 journals had an open access option for a fee, while three did not. Two of those three less-open titles, the American Journal of Kidney Diseases (AJKD) and Advances in Chronic Kidney Disease (AJKD) come from the National Kidney Foundation (NKF). Why is this organization sponsoring journals that have not woken up to the advantage of an open access option? No clear reason.   They do have a public advocacy effort underway, the NKF People Like Us campaign:

Here is their pitch to be someone like them:

BE A “PEOPLE LIKE US” ADVOCATE

The NKF’s “People Like Us” is the fastest-growing and most influential advocacy movement for people affected by CKD, transplant candidates and recipients, living and potential donors, donor families and caregivers. “People Like Us” empowers, educates and encourages you to get involved on issues relating to CKD, donation and transplantation (of all organs)

So while it is technically true that all of their target PEOPLE do not have to be taxpayers, I would think there is a high probability that most are.  With a well-organized marketing effort underway to constituencies that care about organ donation and other medical issues, it must have occurred to someone that science in the open helps cures to be discovered earlier.  This is a very successful and well supported organization of $51,774,362 public support and revenue in 2011.  Salaries in 2o11 totaled $20,163,279, including very healthy salaries for Directors:

NKF FY IRS Form 990 Schedule J

Of course, this is not a public or government entity, and they get considerable financial support from the pharmaceutical industry.  Still, perhaps there should be some discussion about open access publishing options for the American Journal of Kidney Diseases (AJKD) and Advances in Chronic Kidney Disease (AJKD), providing more rapid access to the research results. That kind of advocacy is also likely to find a response from readers.

There are actually observers and players in scholarly communication  that think the 100 or so open access blogs out there are merely a bunch of shrill malcontents bent on breaking up the marriage of convenience between overburdened faculty and experienced publishers that have historical precedent to prosper and profit from selling it right back to the institutional libraries of those that created it, or merely vending  individual articles, easily discovered through PubMed or Google Scholar.

Clicking on this image will download a 20MB PPT Morality Tale of innocence, vanity, greed, betrayal and hope as a series of photo-slides with toy animals.

I think many librarians blog about open knowledge and open access, not as uninformed agitators, but rather as concerned  survivors of  the extraordinary last decade of the old millenium and first decade of the new millenium that saw the exponential growth of the digital library and the exponential demand by institutional clients for electronic journals and their cost.  When the cost of electronic journals began a rapid escalation at a much greater rate than inflation, coupled by the initial need to subscribe to both print and electronic,  the so-called serials crisis in library expenditures became a budgetary crisis as well.

Source: ARL Statistics 2003-04, Association of Research Libraries, Washington, D.C. *Includes electronic resources from 1999-2000 onward. http://www.arl.org/bm~doc/monser04.pdf

Inevitably, there are limits to what any library can afford. Biomedical libraries are also charged with maintaining subscriptions to an increasing variety of research databases and electronic clinical bedside tools at a time when budgets are finite or shrinking.  The ability to maintain popular subscriptions and tactfully drop subscriptions to under-utilized resources (complemented by funding inter-library loan for articles from dropped titles) continues in most academic medical libraries.

The reaction in 2004 by the Dartmouth Biomedical Libraries was typical.  There was awareness of open access alternatives and great trepidation from faculty used to a longstanding publishing-editorial partnership that created predictable and useful knowledge distribution on a need-to-know basis among peers, with libraries buying back from publishers the content and editorial expertise “donated”  by faculty.  The taxpayer access advocacy movement had not gained the traction and attraction it has now. There was still uncertainty voiced about whether the author-pays open access business model of PLoS or BioMed Central could survive.  Still, at that moment at Dartmouth in 2004, four years before the dawn of the economic crisis, there was still concern:” …there is one matter on which research librarians, academicians, government officials, openaccess proponents, and journal editors are in agreement: the current cost of biomedical journals is too high and not in the best interests of medicine, science, or the public.” (source)

In 2012, there is still a serials crisis, because there are even greater demands on  medical libraries to afford new products and face the unpleasant reality of reducing journal subscriptions as an offset for trying new things:

• The Columbia University Health Sciences Library in 2012 can only afford new titles by cutting underutilized titles
• The City of Hope Hospital Graff Library is also cutting journal titles and packages in FY2012.
• the University of Texas Health Sciences Center in San Antonio is initiating cuts in FY2012
• The UCSF Library proposed 2012 cancellations that essentially eliminated print where electronic existed and was waiting for faculty response.

However, in 2012, there are successful open access publishers, and since 2009 some very important universities have been nurturing the Compact for Open Access Publishing Equity. The number of academic medical center and university institutional repositories and their use has steadily increased, providing a place for faculty to deposit open access copies of articles from an Elsevier published journal since 2004, even from Elsevier journals that the university had to cut.

Given all this trending toward multiple versions of open access and the ongoing existing problems with library resource budgets, there is a lot of education that has to take place. So think of occasional shrill and fanatical behavior as PTSCB… Post Traumatic Serials Crisis Behavior and generally well-intentioned attempts to educate scholars and librarians to open access alternatives.  I mentioned Green open access publisher behavior to some colleagues, and one person thought no publisher was trying to cut down less trees.  I did reorient this sincere person.

One of my most popular posts, the one on Amy Bishop’s open access publishing, made use of the google cache to cite evidence that the publisher had removed from their web site.  Similarly, the Internet Archive, AKA the wayback machine,by maintaining a history of periodically sampling websites, allows librarians to do things such as….find out what a publisher charged for an e-journal title or package some time in the past.

The case in point I want to focus on in this post is the announcement by the Royal Society of Chemistry (RSC) of their expected 2012 subscription costs.  This was done very forthrightly in a very public forum, the MEDLIB-L electronic discussion list I was reading in my openbiomed email inbox. As the message I was reading  is found in a publicly-accessible archive, and this is in fact a marketing attempt and not a contractual negotiation or any kind of privileged information (email going to thousands of  librarians will hardly remain privileged or private), I wanted to share the good news that was being spread:

RSC Publishing would like to announce pricing for 2012. We’ve achieved over 150% growth in international quality content in last three years with 70+ countries contributing published articles. This growth has been supported by well thought out price increases reflective of customer feedback, increases in costs related to the growth in quality content, and changes in the global economy.

If you followed the URLs provided by this publisher’s Library Marketing Specialist, you could eventually find the price list for 2012.   I decided to check the the wayback machine to see if we could find the pricing from previous years.  In fact,  the archive.org page for RSC tells us that

“http://www.rsc.org has been crawled 417 times going all the way back to January 27, 1998.”

This is not a perfect system, as there are billions of possible web pages that can potentially be sampled, and certainly most sites are not sampled every day or even every month. But you can usually find something intriguing from the past, and I found an RSC price list for 2010, giving me and you a two-year range of comparison for price increases.  So here the 2010 and 2012 prices for some packages and journals, as well as the percentage price increase over two years:

So you can see that my sample of 2010 and  2012 list prices for a few packages and individual journals shows 2-year increases ranging from 15% – 34%. The publisher explains that cost increases are necessary: “increases in costs related to the growth in quality content, and changes in the global economy.”

Back in 2007  an RSC publication, Chemistry World, published an article “Chemistry’s open access dilemma” reflecting the ambiguity of their readership.  RSC has also implemented an Open Science initiative which allowed authors to pay a gold open access fee to make their article available.   Of course, this open option still requires authors to assign RSC the exclusive right to do all the official publishing, while granting authors some personal deposit alternatives.

How do librarians feel about the price increases above?  Do you accept the publisher’s rationalization? Please post a blog comment, if you desire…  You can also send me email (charles dot greenberg at openbiomed dot info), and I would be happy to reprint your comments anonymously in my next post.

Open Research Computation is a new open access journal launched on the BioMed Central (BMC) platform. Here’s the description of what to expect:

So who is the competition for this new journal?

• Computer Physics Communications, an Elsevier published journal,  does have an open access option.
• Software Quality Journal, from Springer, will accept articles with their Open Choice option.
• Computational Statistics, also from Springer, also will accept articles with their Open Choice option.
• Software: Practice and Experience, from the Wiley Online Library, does not appear as a Wiley OnlineOpen qualified journal.
• Computational Intelligence and Neuroscience, from Hindawi, is an open access title.

Probably the greatest competition for this new journal, at least from my perspective of biomedicine, will come from BMC itself: BMC Bioinformatics is a well-established open access journal seeking “all aspects of the development, testing and novel application of computational and statistical methods for the modeling and analysis of all kinds of biological data, as well as other areas of computational biology.”  BMC Bioinformatics is also a top-10 impact factor journal in the category of Mathematical and Computational Biology.

So what does Open Research Computation offer as incentive?  Several of the most outspoken supporters of open science on their editorial board, including Editor in Chief Cameron Neylon,  advocate for open science. He explains the founding Open Research Computation (ORC) by emphasizing open source licensed reproducibility:

The primary consideration for publication in ORC is that your code must be capable of being used, re-purposed, understood, and efficiently built on. You work must be reproducible. In short, we expect the computational work published in ORC to deliver at the level that is expected in experimental research.

So now we eagerly await the first articles…this event is a nice complement to the post I did on the fledgling open hardware movement.

I do occasionally look at the Association of Learned and Professional Society Publishers (ALPSP) web site, if only to compare their tag-line  Shaping the Future of Learned and Professional Publishing with their behavior.   For instance, their April 2011 report  Heading for the open road: costs and benefits of transitions in scholarly communications acknowledged my blog theme, the acceleration toward open aspects of publishing and access and compared several assumption I and others make.

I preparation for their upcoming conference, ALPSP highlights the finalists for the Best New Journal and Publishing Innovation Awards. Among the new publication nominees is Bioanalysis, published by FutureScience Ltd.  I decided to look at the instructions for authors that FutureScience provides.  Besides the classic gold open access option, I also noticed that FutureScience also provides Access Tokens for authors.

What is access with tokens? Here is a snapshot from today’s explanation, linked back to the page where the most up-to-date version is found.

My first inclination was to read whatever Peter Suber or whatever trusted source I could find about the SWOT analysis (Strengths, Weaknesses, Opportunities, and Threats) of access tokens offered to authors as an alternative to gold open access.  One article in the Scholarly Kitchen blog talked about access tokens that might give small libraries a cheaper subscription to at least one scientific journal that was going to offer them.  I also found a thesis online, TOKEN-BASED ACCESS TO DIGITAL INFORMATION from 1999 that laid out much technical theory about how a token system could work.  My quick check (please comment if you can add to this discussion) of Peter Suber, Stefan Harnad, google blog search, etc. did not really turn up any opinion considering what tokens could do to open access.

Then I read about the Irish Journal of Medical Sciences providing tokens to  members of the Members/ Fellows of the Royal Academy of Medicine in Ireland  to bypass that little dilemma of their local library lacking funds for  subscriptions by having access token subscriptions as part of their society or association membership.   Since it is a similar author benefit in the case of the FutureScience implementation,  I guess  I can form my own opinion.

Tokens are an extension of a closed system, a tangible benefit extended to authors in exchange for their giving up their copyright and intellectual property.  Once an author has 50 tokens for her/his article and uses them up, the publisher gets a bit more revenue out of their publishing venture when the author wants to re-stock, even as library subscriptions may expire.  It is not open access, and it is not part of the principle of unlimited universal access to electronic publications that is always preferred in academic library.  Perhaps someone from FutureScience will provide some data on their experience with authors and tokens v. author-selected open access.

I forgot to mention in my last post that the Journal Citation Reports (JCR) subscription now provides access to 12 years of data (1999-2010). I really had not noticed this generosity.

Let’s look at another subject discipline to assess whether the top 10  2010 impact factor rankings offer substantial immediate open access options. Integrative & Complementary Medicine cries out for openness, given the public fascination with alternative health.  Unfortunately, some publishers, recognizing the scarcity of evidence-based experimentation, rely on subscription revenue and individual article sales,  fueled by marketing and media curiosity. Here is a summary of those top 10 journals with an open access option:

Interestingly, 50% of the 2010 top-10 impact factor journals in integrative & complementary medicine offer a gold open access option, an identical rate to my last post exploring the top 10 in obstetrics/gynecology.

Now that most academic libraries are announcing the availability of the 2010 edition of Journal Citation Reports(JCR), it is also time to try to find some trends in terms of open access.  I decided to check the new list of top-10 impact factor (IF) journals in a notable subject discipline, Obstetrics and Gynecology (OB/GYN). Did the top-10 IF OB/GYN journals offer an open access option?

Half of the top-10 IF OB/GYN journals provide a gold open access option for immediate public access. This kind of simple analysis could be done at any institution that subscribes to JCR.

I want to compliment the analysis done by Declan Butler in the Nature news blog about the open access shot heard round the world. I’m referring to the announcement that three top-shelf life science foundations– the Howard Hughes Medical Institute (HHMI), the Wellcome Trust (WT), and the Max Planck Society (MPS)– are intending to fund the launch of a premier journal without an author processing fee (at least to start). Declan made many good initial observations and was honest with his reservations.  Probably every open access blogger wants to add to the conversation and not parrot the insights of others.

I immediately thought of the European Research Council commitment to public access that set a guideline for a tolerable non-open embargo by publishers for EU-funded research at six months.  The U.S. National Institute of Health Public Access Policy, well intentioned and certainly precedent setting, is nevertheless fixed for NIH funded research at a political compromise of 12 months.  Two-thirds of this partnership are the leading foundation advocates for the benefits of open research knowledge in Europe.  HHMI has also embraced the philosophy of public accessibility and in its Research Policies of freely available and down-loadable on-line research results within six months of publication.  The assembled partnership for this endeavor seems to be on the same page, comfortable with the idea of using their not-for-profit ethos and funding capability to assert the merits of open knowledge for the needs of the research community and extend the boundaries of scientific knowledge that can be immediately accessible and inspire students and researchers anywhere.  At least that is the goal.

http://www.taxpayeraccess.org/

The Federal Research Public Access Act of 2009 and 2010 was proposed twice in the  U.S. Congress to move toward the a reduced non-open embargo of six months and expand the qualification of any research to all federal agencies that spend more than US$100 million in extramural research, including the National Science Foundation, NASA, and the Department of Energy, to name a handful granting agencies.  The Senate version of the bill was “Read twice and referred to the Committee on Homeland Security and Governmental Affairs.” The House version of the bill was re-introduced in 201o and “Referred to the Subcommittee on Information Policy, Census, and National Archives. “ The general paralysis of our federal legislature has drawn attention away from both the merits of expanding public access in the U.S. and the notion of parity on public access with a European counterpart.  But now three not-for-profit organizations, unencumbered by politics, are making a statement about non-governmental advocacy.

We live within a global scientific community and communication network. As a statement of global open scientific knowledge solidarity, the announcement of this future journal returns attention in the life sciences world to the practical merits of open knowledge.  And a shudder must be felt among publishers, not so much at the most credible open access pioneers with unquestionable commitment to peer review, but among commercial publishers that were relying on their own status or credibility to launch gold open access options while maintaining traditional submissions from scientists that still considered an accepted publication as a golden ticket, regardless of their ability to share it or whether they owned the copyright or how much their library paid for electronic access to that journal.  I foresee  a noticeable uptick in interest to understand open access publishing options in the life sciences and also understanding qualitative factors among a growing variety of open access publishing choices.