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.

Kurt Elling playing “Steppin’ Out” (Joe Jackson) at the New Morning in Paris on May 26, 2011.

“We so tired of all the darkness in our lives

With no more angry words to say can come alive

Get into a car and drive to the other side”

You may not learn anything new in this post if you are already following this issue, but I imagine some readers are not and need some pointers.

NATURE PUBLISHING GROUP AND DIGITAL SCIENCE

“Nature Publishing Group (NPG) and Digital Science note the concern amongst the scientific and library communities about the Research Works Act (H.R. 3699), currently under consideration by the U.S. federal government, and wish to clarify our position.

NPG and Digital Science do not support the Research Works Act. ”   READ THE ENTIRE STATEMENT

AMERICAN ASSOCIATION FOR THE ADVANCEMENT OF SCIENCE (AAAS)

“The nonprofit American Association for the Advancement of Science (AAAS), the world’s largest general scientific society and publisher of the journal Science, today reaffirmed its support for the current public access policy of the U.S. National Institutes of Health (NIH).

Contrary to recent news reports, AAAS does not endorse the Research Works Act, which would prevent the NIH from requiring its grantees to make biomedical research findings freely available via the National Library of Medicine’s Web site.”   READ THE ENTIRE STATEMENT

ROCKEFELLER UNIVERSITY PRESS

“Dear Representative Maloney,  I am the Executive Director of The Rockefeller University Press, a nonprofit organization that publishes three biomedical research journals. I am contacting you as a publisher and as your constituent in the 14th Congressional District of New York to express my strong opposition to the Research Works Act (H.R. 3699), which you and Representative Issa introduced into the House on December 16, 2011.  I want to state emphatically that I support the NIH Public Access Policy and think it should be expanded to other federal funding agencies.”   READ THE ENTIRE LETTER

The Harvard Open Access Project (HOAP) at the Berkmann Center for Internet & Society is tracking other publishers that  step into the light  at their Notes on the Research Works Act page, including:

• AAP members who reject the RWA and publicly disavow the AAP position on RWA
• AAP members who apparently reject the RWA, but whose positions require confirmation.
• Publishers who reject the RWA but are not members of AAP

No, this is not  a new word game.  There is a flow of ideas, starting with a publisher’s genuine attempt to connect scientists to science educators.

I saw the tweeting about Scientific American and the Nature Publishing Group starting an initiative called “1,000 Scientists in 1,000 Days” to try to introduce scientists to science teachers in American schools, so that career scientists can volunteer to advise on curricula, answer a classroom’s questions, or visit a school. File this under the category “Doing something is better than doing nothing,” also known as a high profile drop in the bucket.

I then thought about what the educational philosopher Nell Noddings called “continuity and caring.”   This is the best personal example I am proud to have encountered of continuity and caring in science: a physician scientist retires and decides to teach full-time in  a New Haven school…teach science.  I am talking about Robert Gifford M.D.

source: Medicine@Yale

Here is how he did science:

On a Wednesday morning in early January, Robert H. Gifford, M.D., HS ’67, took nine of his eighth-grade students out onto New Haven’s Columbus Avenue for an experiment. Braving a wind chill of 4 degrees, they measured the length of the block in front of Sacred Heart/St. Peter School and prepared to calculate the speed of passing cars. The parochial school is the last of several serving the Hill neighborhood, which borders the medical school campus to the south and west, and Gifford, the former deputy dean of education at Yale, is the school’s new science teacher. In fact, he is its only full-time science teacher.

The hours are long, the work is challenging and the pay is modest. (Gifford, who volunteered his services during his first semester at the school, now receives a small salary.) But it fulfills the goal he set several years before his retirement in 1999 [“Goodbye, Dr. Gifford,” Fall 1999|Winter 2000] of teaching science to children in New Haven’s inner city. The lack of a required state teaching certificate thwarted Gifford’s original plan to teach in city public schools. But his name came to the attention of Geraldine Giaimo, M.S., the principal of Sacred Heart/St. Peter, who was looking for a way to offer students more science than the classroom teachers could incorporate into their lessons.

Although Sacred Heart/St. Peter is a parochial school, only about 30 percent of its students are Roman Catholic. Of the 224 students enrolled, 96 percent are African-American or Latino and 62 percent meet federal guidelines for free or reduced-rate breakfasts and lunches at the school. “We were actually in tears when [Gifford] said he would come here,” said Giaimo, herself an alumna of Sacred Heart, which merged with St. Peter School in 1994. “He’s not just the science teacher. He’s the science department.”

You can read the rest of this piece here.   Getting back to the 1000 scientists. In 2008-09, in the United States, there were about 13,800 public school districts containing about 99,000 public schools, including about 4,700 charter schools.

Can the initiative 1,000 Scientists in 1,000 Days make a dent in the need?  Sure.  But what could make a bigger dent? Awareness by every science teacher and school librarian of where to find high quality science research without choosing between online subscriptions and school supplies.

Today, we have an incredibly rich portfolio of  science that is instantly available to every science teacher in every one of these 99,000 schools, exciting stories of discovery, previously unknown animal models for human illness, and the burgeoning field of the genetic basis of life. I think quite sincerely that these 1000 scientists could create much value by endorsing barrier-free access to inspiring research knowledge, starting with PubMed Central and institutional repositories. There are 1182 scientist author-deposited Nature articles in PubMed Central.

Perhaps a few of the 1000 can see this as a natural extension to advice on curricula, answering classroom questions, or visiting a school.

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.

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.

On June 4th the University of California Library System issued a very public complaint about Nature Publishing Group‘s proposed triple-digit increase in institutional subscription costs, coupled with a threat of author and editorial boycott by faculty.

On June 24th, David Carlson, the Dean of Library Affairs at Southern Illinois University(SIU), Carbondale, and Associate Dean Connie Poole at the SIU School of Medicine, Springfield, issued a memo to their own faculty regarding the recent NPG controversy with California State University Libraries.

Here are the major recommendations to SIU faculty on the Carbondale and Springfield campuses, if you don’t have time to read the entire memo:

• Be aware of the financial value of the work you contribute when you write, review, and edit articles.
• Whenever possible, choose to publish in journals with equitable business models – open-access journals, or those with reasonably priced subscriptions.
• Assert your rights as an author. Negotiate with publishers for better control of and broader access to your published work through an author addendum such as the Scholar’s Copyright Addendum (http://scholars.sciencecommons.org/).
• Place a copy of your work in SIU’s digital repository, OpenSIUC, and encourage your colleagues to do the same. This will not only be a positive contribution, but will advance the visibility, impact, and reach of your research.
• This past year, the SIU Faculty Senate and Graduate Council endorsed a resolution for faculty to support Open Access. A second resolution called for faculty to “grant SIUC permission to make his or her scholarly journal articles… openly accessible in OpenSIUC.” Support this effort and provide your permission when you are surveyed in the Fall.

Pianist George Cables wrote and played Dark Side, Light Side.  It came to mind in thinking about Nature Publishing Group (NPG) and the recent dust-up with the University of California Libraries.  Yes, that million dollar misunderstanding.

Last week a letter to University of California (UC) faculty by librarians from the 10 UC campuses was sent  to NPG and posted publicly.  The letter describes a 400% increase in the cost of access to the 67 NPG journals published by Nature Publishing Group, as well as mentioning that this would come on the heals of NPG subscription agreements that increased 137% in the past five years.  The letter also suggests a tool to get attention and redress:  a article submission boycott, or perhaps resigning from NPG peer review assignments.

So Nature posts the typical knee jerk response on their site, admonishing the University of California Libraries to be satisfied with the substantial discount off of list price they are receiving, something like 50%.   Perhaps the author has not recently gone into Stop and Shop for a “buy one, get one free”  package of hot dogs, only to find that the list price for the hot dogs has mysteriously risen to $4.⁹⁹ ( or, these days, $4.⁴⁹ for 14 oz.).  Not quite the bargain you are seeking….

But enough on the dark side of NPG.  There are genuine interesting and useful things Nature is doing:

• Scitable by Nature Education, a free science library and personal learning tool.

• Nature.com Blogs, Nature Publishing Group’s community-run blog tracking and indexing service.

• Twenty-five journals published by NPG now offer authors an open access option.

There are two sides to every coin, and certainly NPG is giving us an eye-opening and temporarily maddening view of both the lighter and darker tendencies in commercial publishing today.