www.openbiomed.info

Short Story- eLife, PLOS ONE, mBio

I received the email invitation to the eLife Open House, as many of you did.

I sent off the invitation with a brief commentary for my colleagues, then thought that my message could also make is as a blog post.  Here it is:

 I will be away at this time.

 The open access war between PLoSOne, MBio, and eLife is about to erupt, and eLife’s first volley (besides the virtual press conference)  is no author fee for at least three years.

 PLoS is countering with community service by giving away its article-level metric package http://article-level-metrics.plos.org/

 MBio already boasts an impact factor of 5.311 and ranks 16th among all microbiology-centered journals in less than two years of publishing. (http://mbio.asm.org/site/misc/announcements.xhtml)

 CG

Tags: article metrics, eLife, mbio, PLoS ONE

AAAS missed a public service opportunity with Sci TM

I became aware of a dramatic health story published recently in Science Translational Medicine though a write-up in the New York Times.  The Times tries to balance their subscription access with a reputation of public service, granting articles with public interest a permanent archival URL.

New York Times Permalink Generator

Of course, I was reading in my institutional office and could go right to the article.  But I spent a couple of minutes looking at the article page, still committed to the optimistic idea that the editors of Science Translational Medicine still knew when to choose the open access high road of giving a research article public access status, in particular because a proportion of the authorship, including the lead author Evan S. Snitkin, work in divisions of the National Institutes for Health(NIH).  Instead, on settling into my blogging chair at home and lacking my institutional IP access, I hit what many members of the public,  unaffiliated physicians, and independent researchers, are used to hitting:

The pay wall.

Science Translational Medicine is published by the American Association for the Advancement of Science or AAAS.  I must admit I had a wonderful time at the AAAS reception for librarians at the Medical Library Association 2012 Annual Meeting in Seattle last May, which featured four of my colleagues providing insight into how they are making a difference for scientific researchers in their institutions with an ability to discover, organize, and apply genomic information. These are the presentations that AAAS has made available:

Personalized Genomics, Personalized Medicine, and You
Carrie Iwema, Ph.D., MLS, Molecular Biology Health Sciences Library System,
University of Pittsburgh

Genomic Literacy: How Much is Enough? (And How Can the Library Help?)
Pamela Shaw, MSLIS, M.S., Galter Health Sciences Library, Northwestern University

Personalized Medicine is Not Just for People: Genomics in Companion and Food Animals
Kristine Alpi, MLS, MPH, AHIP, William Rand Kenan, Jr. Library of Veterinary Medicine,
North Carolina State University

A Role for Every Library in Support of Genomic Medicine
Kristi Holmes, Ph.D., Bernard Becker Medical Library, Washington University at St. Louis

I am so happy that AAAS decided that these presentations were worth giving away, but there was also an expectation from both my colleagues and the AAAS sales and marketing staff that work most closely with them that scientific information wants to be free, particularly genomic research that is heavily supported by NIH extramural funds and the NIH research lab expertise, to the tune of billions of dollars derived from tax revenue.  The wealth of science published under commercial contract has to be balanced with opportunities for the tax-paying public to get access to quality research sooner.

Source: http://officeofbudget.od.nih.gov/pdfs/FY12/Tab%201%20Executive%20Summary.pdf

I think there is precedent for some editorial intervention by Science Translational Medicine editorial staff to make certain significant articles immediately open access because of their clinical or public health importance. After all, the New England Journal of Medicine, in some ways comparable to Science and its sister journals for their commitment to publish knowledge before their competitors and maintain a profitable business model, has a recent tradition of releasing some articles immediately (Online First) and openly as a public health service. Online First is also a free taste that might lead to subscriptions.

Science Translational Medicine authors have a couple of post-publication avenues for releasing a version of their article for unimpeded access, and Science Translational Medicine allows posting of the accepted version of the paper to a funding body’s repository (such as PubMed Central) six months after publication, provided that a link to the final version  is included. 

None of these author options really makes up for the public deficit of a pay wall for salient and attention-grabbing public health translational research funded by taxpayers and conducted at federal facilities.

Tags: AAAS, librarians, NEJM, new york times, science translational medicine

Predatory open access hashtag survey results

After a week of voting, we have a winner!

Of course, this is a non-binding vote. But I will start to use #predOA for future tweets about publishers meeting predator definition.

Tags: Jeffrey Beall, predatory publishing

Time for a predatory open access hash tag- please vote

Now that Jeffrey Beall has published his Criteria for Determining Predatory Open-Access Publishers [PDF], those of us that enjoy hunting predators (with our open commentary) need to be able to track and follow each others efforts in twitter. The lingua franca of following tweets is the hashtag (#).  Sometimes the wisdom of crowds allows logical abbreviations to become the  hash tag, but often one persons logic (e.g. #oa for open access) competes with another group’s logic (#oa for other asians).

Anyway, please share with me your opinion about which of the following hashtag candidates would be the one you would follow to track tweets on predatory open access. I will post the results in a week or so.

Tags: Jeffrey Beall, predatory publishing

Translational science journals: nearly entirely open

Using the SCImago Journal & Country Rank (no subscription required, based on SCOPUS data, for which many libraries pay much), it is relatively simple to put in a word like “translational” and discover how many journals have been launched on that theme (at least those indexed by SCOPUS):

So out of 14 journal titles meeting the “translational” title word criteria, only three have no open access ingest option.  Of course, Elsevier is a green open access publisher (my blog posts on the subject of green OA), and AAAS does have a partial-green policy: “After publication, authors may post the accepted version of the paper on the author’s personal Web site.”  Lots of open access choice with these relatively new journals.

Tags: Gold OA, Green OA, Translational Science

ETD 2012 in Lima: First time in South America, Not the Last

Given the constant news on  open access journal literature, it can be easy to forget that the lifeblood of the institutional repository movement on many campuses is the electronic thesis or dissertation (ETD). The Networked Digital Library of Theses and Dissertations (NDLTD) provides resources, services and meeting opportunities. NDLTD includes members such as universities around the world, profit and non-profit partner organizations, and even individuals, all working toward the goal of delivering open and accessible scholarship. Examples of notable student authors and academic ETD pioneers and are found in ETD Award Winners 2004 – 2010: Case Studies in Success (PDF)

NDLTD is sponsoring the 15th international symposium this year in Lima, Peru.  The early discount registration deadline for the ETD 2012  (September 12-14) has been extended to August 6, 2012. Register today at the NDLTD member rate of only US $225. For complete information about ETD 2012 visit http://www.etd2012.edu.pe/

This is the first time that the international symposium will be in South America, which is quite an honor for Peru. Lots of ETD activity is going on in other South American countries. Biblioteca Digital de Teses e Dissertacoes is a search tool for accessing ETDs produced in Brazilian universities. The Cybertesis program features theses from  the University of Chile and other South American countries.

Tags: dissertations, ETD, NDLTD, theses

A new open access journal for geoscience data can also include health data

I saw the announcement from the SPARC OA Forum news item Open Access Geoscience Data Journal Launched by Wiley posted by Peter Suber about the latest gold OA offering from Wiley Open Access.

 Geoscience Data Journal (GDJ) offers an intriguing opportunity for scientists to distribute all materials related to their  research results in a single place. Author publication charges (APC) are set at $1,500 / €1,200 / £1,000, with a 20% discount offered to members of the Royal Meteorological Society and a fee waiver/discount program offered to researchers in developing nations.

I have blogged earlier about health and geoscience and the lack of an open access journal in this area, based on my friendship with Yale colleague that teaches about medical geology.  While GDJ is not a perfectly scoped match for medical geology, I nevertheless think that GDJ will attract articles with health data sets.  Take, for example, the health effects of fracking.  A Janualry 2012 commentary article in the open access journal Environmental Health Perspectives (Missing from the Table: Role of the Environmental Public Health Community in Governmental Advisory Commissions Related to Marcellus Shale Drilling) was amplified by a JAMA editorial (Rigorous Evidence Slim for Determining Health Risks From Natural Gas Fracking) in May 2012.

There is obvious interest in data-driven research to address the health concerns of this issue and a whole host of other health issues emerging in geologic research, and I hope the editors of GDJ  are tweeting and emailing researchers in a wide variety of fields,  about the opportunities offered in their new open access publication.

Tags: environmental health, JAMA, Medical Geology, Wiley Interscience

HHMI investigators populate eLife reviewing staff

The forthcoming open access journal eLife recently appointed their Board of Reviewing Editors (BRE), a global team of scientists that will do the challenging work of rapid peer view, under the leadership  the Senior Editors.  Like the Senior Editors, the 175-member BRE represents the wide array of disciplines, covering basic biological research in applied, translational and clinical settings.

As I looked at descriptions of the initial BRE appointments, particularly those in based at U.S. universities and clinical research centers, it is not difficult to find their connection to one of the eLife co-founders, the Howard Hughes Medical Institute (HHMI). HHMI,  one of the nation’s largest philanthropies, plays a powerful role in advancing biomedical research and developing a pipeline of science investigation in the United States. In 2011, HHMI spent $825 million for research and distributed $80 million in grant support. Their annual report proclaims their identity: “Catalysts for Creativity”  and approach basic, clinical, and translational science from a variety of initiatives and directions.  Thousands of scientists are direct or indirect recipients of HHMI funding.

I wrote back in February that Elsevier’s  Cost of Knowledge publicity stumble offered scientists the opportunity to consider alternative scholarly activities, just at the moment that eLife was starting to construct their editorial staff.

HHMI has been unabashedly out front with support for the NIH Open Access Policy and stated their preference  for reviewed research publications and supplemental materials are freely accessible within six months of publication.  Joining forces with the eLife foundation partners provides a way for many previously funded HHMI  investigators to demonstrate tangibly their shared belief in the benefits of open knowledge.  Although  an award committee might decide that a discovery is truly an original, mainstream innovative scientists build their hypotheses on the shoulders of others.  Sharing and openness produce innovation. Here is eLife’s first promotional video by scientists, for scientists.

Tags: eLife, HHMI, Max Planck Society, Wellcome Trust

An explanation for my audience

My blogging has been curtailed to maximize my personal time to prepare for the Medical Library Association annual meeting in May and my visit to the Republican Scientific Medical Library in mid-June to teach my Armenian librarian colleagues about identifying and applying health information research techniques to improve Armenian health care outcomes.  I am preparing a workbook and website which requires much time outside of my MLA and Olympic National Park visit.

Rest assured that I should return to active blogging when all my preparations are ready for a successful training activity.  You can read about my previous expedition to the Republic of Armenia here.

Singing Fountains, Yerevan Armenia, June 2008

Tags: Armenia, RSML, Yerevan, YSMU

Display your own Avian Influenza – Human Virology funded research collection from Pubmed Central…

NIH chief Francis Collins speaks to high school students (SOURCE: USA Today)

On April 20th 2012  NIH Director Francis Collins issued clarification and support for the eventual public release of revised H5N1 journal manuscripts by Dr. Ron Fouchier and Dr. Yoshihiro Kawaoka:

After careful deliberation, the NSABB unanimously recommended the revised manuscript by Dr. Yoshihiro Kawaoka be communicated in full. The NSABB also recommended, in a 12-to-6 decision, that the data, methods, and conclusions presented in the revised manuscript by Dr. Ron Fouchier be communicated fully after a number of further scientific clarifications are made in the manuscript. The recommendation to communicate the research was based on the observation that the information in the revised manuscripts has direct applicability to ongoing and future influenza surveillance efforts and does not appear to enable direct misuse of the research in ways that would endanger public health or national security.

The HHS Secretary and I concur with the NSABB’s recommendation that the information in the two manuscripts should be communicated fully and we have conveyed our concurrence to the journals considering publication of the manuscripts. This information has clear value to national and international public health preparedness efforts and must be shared with those who are poised to realize the benefits of this research.

What Dr. Collins did not share was the reality that there are are already at least 60 articles deposited in PubMed Central that have been funded from US and non-US research grants. Anyone with an email account can establish MyNCBI Collections of research results. I combined a search for Influenza in Birds appearing in the same article with Influenza, Human/virology and limited the result to a variety of publication types for funded research.

View my collection, “Open Access Supported Research on Avian Flu and Human Infection” from NCBI

The precedent has already been well established by NIH that national and international public health preparedness efforts and must be shared with those who are poised to realize the benefits of this research.

Here are video instructions on how to host and build these collections with your MyNCBI account:

Tags: Avian Influenza, MyNCBI, NIH, PubMed Central