February 18, 2005

NIH Grant Recipients Are 'Asked' to Post Data: New Policy on 'Public Access' Draws Criticism

By Rick Weiss
Washington Post Staff Writer
Friday, February 4, 2005; Page A15

Researchers who receive grant money from the National Institutes of Health will be "asked" to submit their results to a public Web site within a year after they are published in a scientific journal, under a new and controversial NIH policy announced yesterday.

The highly anticipated "public access" policy -- which aims to make it easier for Americans to see the results of research they paid for with their tax dollars -- represents a compromise between competing forces that had lobbied the agency intensely during the past year.

On one side were the publishers of highly profitable scientific journals who feared that free access -- even months after paper publication -- would undermine their subscription base. They were joined by some not-for-profit scientific societies that count on revenue from their print journals to support their research and training programs.

On the other side were patient advocacy groups and others who argued that taxpayers should not have to pay subscription or per-article fees to see the results of federally supported medical research.

They argue that journals would not be significantly harmed because the policy applies to only the 10 percent or so of published biomedical articles that result from NIH-funded research. Individuals and libraries would still subscribe, they say, to read the other 90 percent of the contents.

Both sides expressed irritation with the decision, which NIH Director Elias A. Zerhouni said at a news briefing yesterday would take effect May 2.

Proponents of quick access complained that the policy marks a retreat from an earlier version, floated by NIH in September, which had called for public access within six months. Even the 12-month deadline is voluntary, they noted.

The policy "falls short of the bright light of transparency that Dr. Zerhouni promised," said Rick Johnson, director of the Scholarly Publishing and Academic Resources Coalition and a member of the Alliance for Taxpayer Access, a coalition of groups that support changes in scientific publishing.

Former NIH director Harold Varmus, now president of Memorial Sloan-Kettering Cancer Center in New York and a longtime proponent of public access, called the new policy "a significant move" but echoed others' disappointment that it does not use stronger language. Instead of requesting that scientists submit their results, the policy could have said scientists are "expected" to do so, he said.

But the publishing industry's campaign to oppose NIH's efforts -- spearheaded by former House member Patricia Schroeder (D-Colo.), who is now president of the Association of American Publishers -- also fell short of its goals. The AAP yesterday said it is "concerned" about the outcome. Not-for-profits also complained.

"It's wasteful and duplicative of what we're already doing," said Martin Frank, chairman of the DC Principles Coalition for Free Access to Science and executive director of the American Physiological Society, one of several not-for-profit science organizations that Frank said already make their articles available to the public relatively quickly after publication. "The $2.5 million to $4 million that the NIH is going to spend on this could be better spent on biomedical research," he said.

Zerhouni has said there are advantages to having the articles all in one federally managed database, including easier cross-comparisons of data among different articles.

Both sides had at least one complaint in common: The policy leaves it up to scientists to decide when to make their articles public. That puts scientists in an awkward position of wanting to release them quickly to please the NIH -- their funding source -- and slowly to please their paper publishers -- upon whom they are equally dependent for professional prestige.

"For many authors, the dilemma will be painful and career-jeopardizing," said Johnson, noting that life would have been much easier for scientists had the NIH simply demanded public access as a condition of receiving grant money.

Details of the new policy can be seen at: www.nih.gov/about/publicaccess/publicaccess_imp.pdf

Posted by Kevin Messner at 1:32 AM

February 14, 2005

The Public Library of Science Urges Researchers to Comply With the National Institutes of Health's New Public Access Policy

February 3, 2005: San Francisco, CA - The Public Library of Science [PLoS] applauds the US National Institutes of Health [NIH] for today's announcement that it expects all of its grantees to make articles arising from their NIH-funded research freely available online in the National Library of Medicine's PubMed Central.

While NIH's Public Access Policy could, and PLoS believes should, have been stronger in several respects, it sets an important precedent for all sponsors of scientific research. "The US government has now endorsed the principle that the results of federally funded research should be freely available to the public," said Michael B. Eisen, Ph.D., co-founder of PLoS. "Scientists and the scientific community now have an historic opportunity to make this principle a reality."

Read the full statement at http://www.plos.org/news/announce_nihpapolicy.html

Posted by Kevin Messner at 1:52 AM

Open Mass Spectrometry Search Algorithm (OMSSA)

The Open Mass Spectrometry Search Algorithm [OMSSA] is an efficient search engine for identifying MS/MS peptide spectra by searching libraries of known protein sequences. OMSSA scores significant hits with a probability score developed using classical hypothesis testing, the same statistical method used in BLAST. OMSSA is free and in the public domain.

OMSSA is available at http://pubchem.ncbi.nlm.nih.gov/omssa/ A research article on OMSSA is available to U Minn TC affiliates at J Proteome Res. 2004 Sep-Oct;3(5):958-64.

Posted by Kevin Messner at 1:47 AM

Entrez Genome Project

A new database, Genome Project, has been added to the Entrez home page
Entrez Genome Project is a companion database to Entrez Genome. The actual data from genome sequencing projects are contained in Entrez Genome (as complete genomes chromosomes) and Entrez Nucleotide (as chromosome or genome fragments such as contigs). The Genome Project database, on the other hand, provides an umbrella view of the status of each genome project, links to project data in the other Entrez databases, and links to a variety of other NCBI and external resources associated with a given genome project. A genome project's status can be complete or in-progress, and the project can include large-scale sequencing, assembly, annotation, and mapping efforts. New genome sequencing projects can be registered through the Genome project submission form. More information about the submission of data from complete genomes is provided in the Resource Guide section on Submission of complete genomes. (Although the Entrez Genome Project database does not include viral genome sequencing projects, data from those projects are submitted to GenBank and are available in the Entrez Nucleotide and Entrez Genome databases. There is also a special set of resources at NCBI dedicated to Viral Genomes.)

Posted by Kevin Messner at 1:40 AM

Public Interest Advocates Question NIH Enhanced Access Policy, Emphasizing NIH Must Be Held Accountable For Bringing Taxpayer-Funded Science to the American Public

Thursday, February 3, 2005 (Washington, DC) ­ Public interest supporters of the NIH Enhanced Public Access Plan today declared the just-announced policy falls short of their expectations and long-standing recommendations. In a letter addressed to Health and Human Services (HHS) Secretary Michael Leavitt, the Alliance for Taxpayer Access outlined its key concerns with the NIH plan:

• The policy is entirely voluntary. Although NIH research in question is funded by taxpayer dollars, the agency is leaving the decision up to each author whether to make their research results available.

• The policy lacks any definitive time frame or deadline by which NIH-funded research must be available for public use.

• The policy puts grant recipients in the untenable position of trying to meet the contradictory expectations of their funding agency and their publisher.

Addressing Leavitt as well as NIH indirectly, members of the Alliance for Taxpayer Access emphasized the need to hold NIH accountable for achieving the stated goals of sharing taxpayer-funded research with the American people and fulfilling the intentions behind the original Congressional mandate. They called on HHS to report to Congress and the public in the near term on progress toward full taxpayer access using two practical metrics:

1. The proportion of eligible research articles that have been deposited in PubMed Central, and

2. The lag time between an article’s publication in a journal and its availability in PubMed Central.

Rick Johnson, Director of the Scholarly Publishing and Academic Resources Coalition (SPARC), said, “Frankly, this just-announced policy is neither what we hoped for nor proposed and it falls far short of the ‘bright light’ of transparency that Dr. Zerhouni promised earlier this week in his ethics reforms.”

Johnson continued, “However, we are eager for it to succeed. The proof is in the pudding. The coming months will tell whether NIH inspires and leads the community of researchers and scholars to accept the public trust invested in them. Today we urge them to do so.”

“What will we consider success?” asked Sharon Terry, president and CEO of the Genetic Alliance. “Plainly put, today a patient with cancer does not have immediate or even timely access to the published results of NIH research. The question we all must ask: A year from now, will the world have changed? Will this same patient have free access to all NIH-funded studies on cancer soon after publication?

“This is a big ‘if’ for all of us,” Terry added. “If six months after enactment, we see a flood of NIH-funded research posted on PubMed Central, then we will be among the first to celebrate. However if the vast majority of taxpayer-funded NIH research produced during this timeframe is not yet available to be used by scientists, patients, physicians and all engaged in promoting public health, then NIH will have failed. It will have failed not only Congress and the President, but more importantly, it will have failed science and the American people. Until the outcome is clear, we can only state emphatically that NIH’s foremost responsibility is to the taxpayer who paid for the research.”

AIDS Vaccine Advocacy Coalition Board Member, Robert Reinhard, expressed concern for the lack of incentive for researchers to provide prompt access: “The potential 12 month delay does not improve much, if any, upon the status quo. NIH guidance also should encourage pursuit of alternative publication venues that commit to free dissemination of knowledge to those who need it.”

“If NIH is going to delegate its responsibility and rely on the good faith of the research community,” Reinhard added, “then NIH should lead by example. What better step could they take than by strongly encouraging NIH intramural researchers to ensure that any paper which bears the name of an NIH employee is posted immediately in PubMed Central.”

Johnson and other members of the Alliance for Taxpayer Access have long argued that there is no legitimate reason for NIH funded research to be withheld from taxpayers for any longer than is absolutely necessary, and that ultimately, it must be available immediately.


The Alliance for Taxpayer Access is an informal coalition of stakeholders who support reforms that will make publicly funded biomedical research accessible to the public. The Alliance was formed in 2004 specifically to urge that peer-reviewed articles on taxpayer-funded research at NIH become fully accessible and available online and at no extra cost to the American public. Details and FAQ's on the Alliance may be found at www.taxpayeraccess.org.

Press Contact: Bob Witeck
202-887-0500 ext. 19
202-997-4055 mobile
Witeck-Combs Communications on behalf of the Alliance for Taxpayer Access

* * *


February 3, 2005

The Honorable Michael Leavitt
Secretary of Health and Human Services
Hubert H. Humphrey Building
200 Independence Avenue SW
Room 615F
Washington, DC 20201

Dear Secretary Leavitt:

The Alliance for Taxpayer Access is a coalition of taxpayers, patients, physicians, researchers, and institutions that have played a leading role in the national debate regarding timely and unfettered public access to federally funded biomedical research. We are writing today to share our views on the just-released National Institutes of Health (NIH) Enhanced Public Access Policy.

First, however, we wish to express our appreciation for your responses to questions posed during your recent confirmation hearings in which you stated your support for a public access policy that makes NIH research results available in a timely and accessible manner. These responses exhibited your understanding of the essential issue at stake and the opportunities presented by today's information and communication technologies to accelerate innovation and discovery for the benefit of taxpayers.

Despite our delight with this recognition of the taxpayers’ interests, we are deeply troubled by key aspects of the final policy announced by NIH. We believe an opportunity to demonstrate NIH’s concern with public transparency in its operation has been neglected. Our concerns, which focus on issues that we fear will impair successful achievement of the goals we share with NIH, are these:

• The voluntary nature of the policy. NIH has handed over an essential NIH responsibility and trust ­ to ensure the advancement of scientific knowledge ­ to individual investigators. Before the Internet, there were historical and economic reasons that NIH relied solely on a system that surrenders public research to private interests via the author’s transfer of exclusive ownership of an article to his/her publisher. But today NIH is able to, and should, capture copies of NIH funded research results ­ not just the research that public-spirited authors wish to contribute, but all NIH-funded research. It is able to, and should, track the outputs of its grant portfolio, archive this public treasure, and make it publicly available. The cost is tiny and the benefit great.

• The lack of a definitive time frame for public availability. The NIH policy delegates to investigators the decision on an access embargo period within a 12-month time frame. As a result, there is no assurance that articles reflecting NIH-funded research will be available to the public in PubMed Central on a timely basis. Clearly, 12-months is too lengthy a delay in a field as dynamic as biomedicine. NIH has impaired its effectiveness by yielding its authority to act decisively on behalf of taxpayers.

Because the policy lacks both a deadline and mandatory participation requirements, it risks becoming an unenforceable “paper tiger.” It places ultimate confidence in the willing participation of the research community. Few will be more pleased than the members of ATA if this confidence proves to be well placed. But the reality is that NIH has placed the grant recipient in an untenable position ­ squarely between the contradictory expectations of the funding agency and the publisher. The policy offers no means by which to protect authors from undue pressures from publishing interests to delay making their article readily available on PubMed Central.

Recognizing that the immediate opportunity to re-shape the policy is behind us, we recommend these actions to make the best of the policy:

• Lead by example. Require NIH’s own intramural researchers to deposit all of their final works (which, by law, are in the public domain) into PubMed Central as soon as they are accepted for publication.

• Evaluate the effectiveness of the policy ­ soon and simply. To ensure the policy is achieving its purpose, HHS should adopt the following two evaluation metrics, to be collected on an ongoing basis: 1) the proportion of eligible research articles that have been deposited in PubMed Central; and 2) the average embargo period of deposited material. We urge your department to submit an annual report to the Congress and the public on the policy, focusing especially on these two aspects. We believe it is appropriate that the initial report be submitted by December 1, 2005. If the data do not indicate that the vast majority of NIH research is available in PubMed Central soon after publication, then we believe the policy should be adjusted to better achieve a satisfactory outcome.

In closing, ATA hopes that the NIH Public Access policy will truly provide American taxpayers with greater access to the invaluable biomedical research in which they have invested. We also hope that an effective NIH policy will serve as a role model for other HHS agencies and, eventually, for other departments and agencies throughout the government. We look forward to working closely with you and your staff to ensure achievement of our mutual goal of providing greater public access to taxpayer-funded research.

Richard K. Johnson
Director, SPARC
on behalf of the Alliance for Taxpayer Access

Richard K. Johnson, Director
SPARC (Scholarly Publishing & Academic Resources Coalition)
21 Dupont Circle NW / Washington, DC 20036 USA
Tel +202 296 2296 x157 Fax +202 872 0884
E-mail URL

Posted by Kevin Messner at 1:21 AM

My NCBI Replaces the Cubby: Includes Automatic E-mailing of Search Updates and Filters

he PubMed® Cubby will soon be replaced by My NCBI. My NCBI works similarly to the Cubby in that it retains user information in order to provide additional services. To use My NCBI you must be signed in. You can sign in using an existing Cubby account, or if you do not have an account, you can register for a My NCBI account.

[Editor's Note: This feature was implemented in PubMed on February 1, 2005.]

Read the full NLM Technical Bulletin article at http://www.nlm.nih.gov/pubs/techbull/jf05/jf05_myncbi.html

Posted by Kevin Messner at 1:06 AM

U Libraries purchases subscription to EcoSal

EcoSal is the online successor to the print text, "Escherichia coli and Salmonella: Cellular and Molecular Biology," from American Society for Microbiology Press. It is the premier reference source on the biology of the enteric bacterial cell. The online book encompasses the text of the second print edition, and is now continually expanded, updated, and revised by the editorial board.

The University Libraries now have a license for access to this important bacteriology resource. It is available through the Libraries' catalog, MNCAT, or at http://www.lib.umn.edu/libdata/link.phtml?page_id=1299&element_id=58988

Posted by Kevin Messner at 1:02 AM

February 4, 2005

NIH Calls on Scientists to Speed Public Release of Research Publications: Online Archive Will Make Articles Accessible to the Public

Thursday, February 3, 2005

The National Institutes of Health (NIH) announced today a new policy designed to accelerate the public's access to published articles resulting from NIH-funded research. The policy ? the first of its kind for NIH ? calls on scientists to release to the public manuscripts from research supported by NIH as soon as possible, and within 12 months of final publication.

These peer-reviewed, NIH-funded research publications will be available in a Web-based archive to be managed by the National Library of Medicine (NLM), a component of NIH. The online archive will increase the public's access to health-related publications at a time when demand for such information is on a steady rise.

"With the rapid growth in the public's use of the Internet, NIH must take a leadership role in making available to the public the research that we support," said NIH Director Elias A. Zerhouni, M.D. "While this new policy is voluntary, we are strongly encouraging all NIH-supported researchers to release their published manuscripts as soon as possible for the benefit of the public. Scientists have a right to see the results of their work disseminated as quickly and broadly as possible, and NIH is committed to helping our scientists exercise this right. We urge publishers to work closely with authors in implementing this policy."

"In developing this policy, we made a concerted effort to balance the importance of this archive to NIH's public health mission, with the need to provide flexibility for authors, their institutions, and publishers in those cases where immediate release is not possible," Zerhouni added. "NIH recognizes the importance of preserving quality peer review and the viability of a diversity of publishing models. Nevertheless, we expect that only in limited cases will authors deem it necessary to select the longest delay period."

The NIH policy will achieve several important goals, including:

1. creating a stable archive of peer-reviewed research publications resulting from NIH-funded studies to ensure the permanent preservation of these vital research findings;

2. securing a searchable compendium of these research publications that NIH and its awardees can use to manage more efficiently and to understand better their research portfolios, monitor scientific productivity, and, ultimately, help set research priorities; and

3. making published results of NIH-funded research more readily accessible to the public, health care providers, educators, and scientists.

Beginning May 2, 2005, the policy requests that NIH-funded scientists submit an electronic version of the author's final manuscript, upon acceptance for publication, resulting from research supported in whole or in part by NIH. The author's final manuscript is defined as the final version accepted for journal publication, and includes all modifications from the publishing peer review process.

The policy gives authors the flexibility to designate a specific time frame for public release -- ranging from immediate public access after final publication to a 12 month delay -- when they submit their manuscripts to NIH. Authors are strongly encouraged to exercise their right to specify that their articles will be publicly available through PubMed Central (PMC) as soon as possible.

PMC (http://www.pubmedcentral.nih.gov), a part of the NIH's National Library of Medicine (NLM), is the agency's digital repository of full-text, peer-reviewed biomedical, behavioral, and clinical research journals. It is a publicly-accessible, stable, permanent, and searchable electronic archive.

The release of this policy follows months of intensive deliberations with representatives of patient and scientific organizations, researchers, and publishers. NIH posted the draft policy for public comment in September, and received and reviewed over 6,000 public comments.

As part of on-going efforts to implement this new policy, NIH plans to establish a Public Access Advisory Working Group, as a subgroup of the NLM's Board of Regents. The Working Group will include representatives of the patient advocacy, scientific, library, and publishing communities, and will provide advice on implementation issues and assess progress in meeting the new policy's stated goals.

Additional information on the new policy and related documents, including a "Questions and Answers" fact sheet, can be found at: http://www.nih.gov/about/publicaccess/index.htm.

Don Ralbovsky
OD Office of Communications and Public Liaison

Posted by Kevin Messner at 1:13 AM