Welcome to the SPARC Open Access Newsletter, issue #88
August 2, 2005

Read this issue online

First fruits of the NIH public-access policy

Since the NIH policy took effect on May 2, grantees have submitted 340 papers to PubMed Central (PMC) for public access.  Of those, 11 are now processed, online, and ready to read.

Each is available in HTML and PDF editions.  Here are the links to HTML editions:


What follows is a little tour of these articles, highlighting what PMC has added in its processing.

* The first thing to notice is that PMC has added many useful links to the HTML editions, but not to the PDF editions, which are intended for printing.  For navigation, reference linking, and other purposes, researchers should use the HTML editions.  You can reach the PDFs either from the PMC search box or from the sidebar of the HTML editions.

* Each article displays a full, standard citation to the published edition at the top of the front page.  In the HTML edition, the citation includes the publisher's DOI and a link to the publisher's edition.  Both editions clearly label the files as author manuscripts.

* Each article has a PMC identifier or PMCID, though these are only visible from the PMC search page, not the article pages.

* The HTML edition links to the email address of the corresponding author.

* The HTML edition links from note calls in the text to endnotes, and from endnotes to PubMed entries and full-text.  If there is a free online edition of the cited article, then the reference link says "Free Full Text".  Otherwise it just says "Full Text".  If there is a free edition at both the publisher's web site and PMC, then the "Free Full Text" link points to the PMC copy. 

* The HTML edition has a TOC with links to every section of the paper.  The TOC is repeated in the left sidebar at every section break.  This not only aids navigation for readers, but gives each section a unique URL for external links.

* Both editions put the figures and tables at the bottom of the file.  The HTML edition links to that section from the TOC.  It also links from individual figure calls in the text to the individual figures themselves.

* In each HTML edition, there is a drop-down box of links near the top of the sidebar.  It contains article-specific links to related material in NIH databases, such as similar articles in PubMed, PubMed Central, or PubMed LinkOut. 

According to the PMC page on Author Manuscripts, "If the journal participates in NCBI's LinkOut service (as is frequently the case) the reference to the published article also provides a direct link to the full text of the article at the journal site."

In the drop-down box in the third article above, by Norio Takamoto et al., there are links to related material in GenSat, Gene, HomoloGene, Nucleotide, Protein, Taxonomy, and Taxonomy Tree.  In the fifth, by Mirko Schmidt et al., there are links to all of these as well as to PubChem Compound and PubChem Substance.  In the ninth, by Kerry Grens et al., there are links to GenBank Accession numbers --not from the pull-down box but directly from references in the text.  These forms of integration with other public-access material available at or through NIH are a major benefit of the program.

* The HTML edition links to other articles in PubMed by the same authors.  It also links to the NIH public-access policy, a page on the submission process, a page explaining the difference between author manuscripts and published articles, the list of all PMC journals, the list of all author manuscripts in PMC, and the PMC search box.  A footer  links to the PMC email address, and the home pages of the PMC, PubMed, NCBI, NLM, NIH, Department of Health and Human Services.  It also links to the NIH Privacy Policy and to the Freedom of Information Act.

* Finally, the HTML edition links to the PMC copyright page and PMC disclaimer.  On the whole, these pages are both generic (not journal- or article-specific).  But the bottom of the PMC copyright page lists links to publisher-specific copyright policies added at the request of publishers.  The PMC disclaimer page will soon offer publishers the same option.
* Both the HTML and PDF editions show the date of deposit in PMC.

* The first of the 11 articles above was written by intramural NIH scientists, the rest by extramural scientists with NIH funding.  This is important merely as proof that the NIH policy applies to and accommodates researchers of both kinds.

* The 11 articles were published in a mix of profit and non-profit journals:  Epilepsia (Blackwell), Journal of Applied Physiology (American Physiological Society), Development (Company of Biologists) (two articles), Chemistry & Biology (Elsevier), Journal of Biological Chemistry (American Society for Biochemistry and Molecular Biology) (two articles), Trends in Immunology (Elsevier), Journal of Bone and Joint Surgery (The Journal of Bone and Joint Surgery, Inc.), Brain, Behavior and Evolution (Karger), and Hormones and Behavior (Elsevier). 

Because the NIH request applies to past NIH grants as well as future ones, we cannot assume that these 11 articles were all published recently.  In fact, 9 of the 11 were published in 2005 (from January to June) and two were published in 2004 (one in March, one in November).  Moreover, these dates only refer to the labels on the journal issues in which they appeared, not the true dates of publication.  Without knowing the true dates of publication, we can't measure the delays between publication and public access.  But even if we knew the true delays, we couldn't assume anything about the embargoes, if any, requested or demanded by these journals.

* Some PMC articles that are *not* author manuscripts under the public-access policy contain links to (1) commentaries and (2) lists of other PMC articles that cite them.  Here's an example with both kinds of link,

Author manuscripts under the public-access policy will eventually get both kinds of links.

* For a list of all the author manuscripts currently in PMC, either click the "Author Manuscripts" link near the top of any HTML edition or run the "author manuscript" filter in the PMC search box.  Or just bookmark this URL:

The results page gives you a tally.  If you run the search periodically, you can watch the tally climb over time.  This will not give you the "denominator" --or the number of articles eligible for deposit that are either not yet deposited or not yet processed.  But it will show you the growing volume of this body of publicly-funded, free online literature.

* For some background on the compliance rate of NIH grantees, here are some highlights of the data distributed by the NIH at the July 11 meeting of the NIH Public Access Working Group of the NLM Board of Regents.

(1) How long were the requested embargoes?  Of the articles in the pipeline as of July 11, most (68.3%) authors requested immediate public access.  7.9% requested six month embargoes, and 14.3% requested 12 month embargoes.

(2) How long did it take for grantees to complete the submission process?  The largest plurality (48%) completed it in just three minutes.  The second largest plurality (19%) completed it in 10 minutes.  A total of 84% completed it in 10 minutes or less.  Only 8% took longer than 20 minutes.

(3) How long are grantees waiting after publication before submitting their work to PMC?  28% submit to PMC in less than six months, 11% wait from 7 to 12 months, and 21% wait more than a year.  (40% of NIH grants have not yet resulted in publication.)

(4) How many submissions should PMC expect if there were 100% compliance?  On average over the past two years (May 2003 - March 2005) NIH grants have resulted in 5,500 publications per month or 250 per workday.  The current compliance rate (340 submissions in two months) is just 3% of that. 


Congress wants to see results from the NIH policy

Last month I described the House of Representatives appropriations report for 2006 and its language supporting the NIH policy and PubChem.  Since then the Senate has adopted its own appropriations report.

House Report 109-143, June 21, 2005 (House appropriations bill for 2006)

Senate Report 109-103, July 14, 2005 (Senate appropriations bill for 2006)

July SOAN story on the House language

Here's what the Senate said about the NIH public-access policy on July 14:

Public Access- The Committee has noted that the National Institutes of Health has begun to implement its public access policy which is geared to ensuring that NIH-funded research results are made available as soon as possible to the public, health care providers, educators, and scientists through the National Library of Medicine's PubMed Central database. The Committee agrees with the need for, and a goal of, issuing a balanced policy to help promote increased public access to NIH-funded research while maintaining the integrity of the peer review system which is essential to ensure the quality and accuracy of medical research in the United States. The Committee urges NIH to work with all stakeholders as it moves forward in implementing this policy. To assist the Congress in assessing the degree of success of this new policy, the Committee requests a progress report by no later than February 1, 2006. Specifically, the Committee requests that the report contain the following information: (1) the total number of peer-reviewed articles deposited in PubMed Central since the May 2, 2005 implementation date and the distribution of chosen delay periods; (2) an assessment of the extent to which the implemented policy has led to improved public access; (3) an assessment of the impact of the policy on the peer review system; and (4) the cost of operating the database.

Here's what it said about PubChem:

PubChem- The Committee is aware of the development of PubChem, the informatics component of the Molecular Libraries project of the NIH Roadmap for Medical Research. The Committee understands that the purpose of PubChem is to create a database of chemical structures and their biological activities. PubChem will house both data from the new NIH molecular libraries screening center network and compound information from the scientific literature. The Committee expects the NIH to work with private sector chemical information providers, with a primary goal of maximizing progress in science while avoiding unnecessary duplication and competition with private sector databases.

Both paragraphs differ from their House counterparts.  The differences will have to be worked out in a conference committee after the summer recess. 

Here I'd like to focus on the NIH policy.  The differences between the two paragraphs are individually small but taken together reveal a larger difference of attitude. 

(1) The House is "pleased" that the NIH is implementing its policy.  The Senate "has noted" that the NIH is implementing its policy.

(2) The House regards the policy as "a first step" toward "free and timely access" to NIH-funded research.  The Senate says nothing of the kind.

(3) The House "endorses NIH's expressed goals for the policy".  The Senate "agrees with the need for" such a policy.

(4) The House supports the goal without qualification.  The Senate supports the goal of "a balanced policy" that promotes increased public access "while maintaining the integrity of the peer review system".

(5) The House "is concerned...that the final policy may not achieve" its good goals.  The Senate expresses no such concern. 

(6) Both houses instruct the NIH to report back to Congress next year on two aspects of the policy:  how many articles grantees deposited in PubMed Central and what embargo periods they requested.  The House but not the Senate asks for the number of articles that could have been deposited.  The Senate but not the House asks for "an assessment of the impact...on the peer review system" and "the cost of operating the database".  The House asks for the report on March 1, 2006, the Senate on February 1.

(7) The House "is concerned that grant recipients may not fully understand the NIH policy" and calls for "an aggressive education and outreach initiative".  The Senate says nothing of the kind.

No doubt, the House is more enthusiastic about public access than the Senate and more troubled by the weakening of the policy before its adoption.  The Senate clearly heard from publisher lobbyists, who not only scaled back the plaudits for the policy's goals and the qualms about its toothless means, but insinuated that the line-up of existing non-OA publishers and journals is "the peer review system". 

We can hope that the conference committee will retain more of the House language than the Senate's, though of course the opposite is also possible. 

However, the common ground between the two bills will certainly survive the conference.  Both bills support the goal of the public-access policy and both ask the NIH to report on the compliance rate.  The NIH will get the message that both houses of Congress are monitoring the rate of progress toward a reaffirmed goal.  Even without a statement of concern, the message is that Congress wants to see results.  If so, then meager compliance will be a reason to strengthen the policy, for example, by requiring compliance rather than merely requesting it.

The early evidence is that compliance is very meager.  See the data at the end of the previous story, above.

The Alliance for Taxpayer Access issued a press release on the Senate report, July 15, 2005.

The publishers behind the DC Principles wrote a letter to Senator Arlen Specter in an attempt to curb the NIH public access policy, July 7, 2005.  Sen. Specter is chairman of the Senate committee that funds the NIH.

Letter from Elias Zerhouni, Director of the NIH, to the Alliance for Taxpayer Access, thanking it for its public call for data on the rate of compliance, June 16, 2005.


Top stories from July 2005

This is a selection of open-access developments since the last issue of the newsletter, taken from the Open Access News blog, which I write with other contributors and update daily.  I give both the item URL and blog posting URL so that you can read the original story as well as what I or another blog contributor had to say about it.  For other developments, the blog archive is browseable and searchable.

Here are the top stories from July:

* Celera released its genome data to the public domain.
* OSI and SPARC released two new publishing guides.
* PLoS launched one new OA journal and previewed another.
* The German Research Foundation studied author attitudes toward OA.
* The RCUK draft OA policy elicited more news and comment.

* Celera released its genome data to the public domain.

On July 1, Celera Genomics released its genome data to GenBank, the OA database maintained by the NIH.  According to Ted Agres, the company made "hundreds of millions of dollars selling access to its proprietary genome sequence information".  But Maureen McDounough reports that the revenue eventually dropped below costs and the decision to make the data OA was strictly business.  "David Speechly, Celera's senior director of investor relations and corporate communications...[said that] the subscription revenue no longer justified the cost of maintaining the online service....'It was pure cost-benefit analysis.'"

Celera Genomics


Lewis Hyde, How to explore the unknown, On the Commons, July 13, 2005.

Ted Agres, Dueling Databases, The Scientist, July 4, 2005

Maureen McDonough, Celera Releases Genome Data at Last, Bio IT World, June 8, 2005.

Jocelyn Kaiser, Celera to End Subscriptions and Give Data to Public GenBank, Science Magazine, May 6, 2005.

* OSI and SPARC released two new publishing guides.

In the OSI guide, Jan Velterop helps society journals convert to OA.  Velterop is the former Publisher of BioMed Central.

From the "about" page: 'This guide has a limited scope. It is meant to help scholarly societies - and small publishers - assess the options available to them for the future of their journal publishing programmes. Though the option of keeping the status quo of subscription-based journals is discussed, the focus is on conversion of existing journals to open access, either in one go, or via an intermediate managed transition phase.'

From the text: 'Scholarly Societies are 'natural' Open Access publishers....A society serious about furthering the science and practice in its chosen field is bound to consider these benefits [of OA] and to look for ways of using them wherever possible for the attainment of its goals. By switching to open access publishing they will do much to further the widespread dissemination of knowledge in the area of science that they foster and promote....[T]he perception is widespread that the societies benefit more from the traditional publishing model than they are ever likely to do from these new emerging input-paid models, at least if one looks at revenues. As said before, this is a false perception. For societies that make the choice for open access, this guide aims to provide practical help to reduce or even eliminate financial risks and make conversion of an existing journal into an open access one a smooth and professional process.'

Jan Velterop, Guide to Open Access Publishing and Scholarly Societies, Open Society Institute, July 2005.

The SPARC guide helps journals find sponsors.  Excerpt from the announcement:  'This new guide, available free on the web...helps nonprofit publishers evaluate the viability of implementing a corporate sponsorship program and describes ways to develop a sponsorship program as a component of the journal's income stream. The SPARC Guide defines a sponsorship as a relationship between a journal and a provider of funds, resources, or services, in return for which the journal offers rights and associations that may be used for the sponsor's advantage. Under this definition, the notion of sponsorship goes beyond advertising or philanthropy. For a journal, a sponsorship can help advance the journal's mission by enhancing revenue and allowing the publisher a wider range of opportunities to serve readers. In return, as part of a well-conceived marketing strategy, such a sponsorship allows a corporate marketing partner to communicate more effectively with its target market. The SPARC Guide explicitly recognizes that sponsorships will provide a more suitable business model for some journals than for others, and describes how a publisher can determine whether a sponsorship program makes sense for any given journal. Additionally, sponsorships will frequently complement other income-generating models...."SPARC's new guide recognizes the reality that corporate sponsorships of nonprofit journals can be mutually beneficial," said SPARC Director Heather Joseph. "Many publishers are searching for new revenue streams which can in turn allow them to better serve their audience, and sponsorships offer a mechanism to increase their range of options without compromising their editorial mission. A strong match of journal and sponsor can allow sponsors to benefit from association with the journal’s reputation, and from the perception by its readers that the sponsor is providing a societal benefit." '

Sponsorships for Nonprofit Scholarly & Scientific Journals: A Guide to Defining & Negotiating Successful Sponsorships.
NB:  The guide is not yet online, at least at the announced URL. I'd assume the problem is temporary and keep trying. I'll publicize the direct link through the blog as soon as I know it.

SPARC press release announcing the new guide, August 1, 2005.

* PLoS launched one new OA journal and previewed another.

July 25 marked the official launch of PLoS Genetics.

Here's an excerpt from Wayne Frankel's editorial in the inaugural issue:

On behalf of our editorial team, it is my pleasure to welcome you to PLoS Genetics, a new open-access journal from the Public Library of Science (PLoS). Led by an internationally recognized editorial board with broad knowledge and expertise, PLoS Genetics is a journal that celebrates the research of the greater genetics and genomics community. As you see in this first issue, PLoS Genetics is unique --publishing outstanding articles that reflect the full breadth and interdisciplinary nature of this research, all free to read and to use in your own research and teaching....In 2004, when PLoS asked several of us in the genetics community about a need and desire for an open-access genetics/genomics journal, I replied with a resounding "yes!" And I was not alone --others had the same reaction that the time was right for a new genetics journal of high quality. Certainly the open-access element was key --following in the public-domain spirit of genetics and genomics data release, for example, by the Human Genome Project. And creating such a journal --building on the strong experience and reputation of PLoS Biology-- seemed an opportunity not to miss.

PLoS press release on the launch of PLoS Genetics, July 24, 2005.

PLoS also offered a preview of PLoS Pathogens, the OA journal it will formally launch on September 30.

For other PLoS news from July, see the following:

Zara Herskovits, New type of research journal gaining ground, Boston Globe, July 11, 2005.

Hemai Parthasarathy, Measures of Impact, PLoS Biology, August 2005.

* The German Research Foundation studied author attitudes toward OA.

The Deutsche Forschungsgemeinschaft (German Research Foundation) released a major new study of author attitudes toward OA.  It's based on the responses of over 1,000 German scientists to questions about their experiences with OA journals, OA preprint archiving, and OA postprint archiving.

Deutsche Forschungsgemeinschaft, Publikationsstrategien im Wandel? Ergebnisse einer Umfrage zum Publikations- und Rezeptionsverhalten unter besonderer Berücksichtigung von Open Access, 2005.

From Jutta Haider's translation of the executive summary: 'Until now, throughout all disciplines, very few researchers actively publish in Open Access. Of all those questioned only about every tenth had published in an Open Access journal. According to those questioned the distribution of freely accessible preprints on the Internet -­ common practice only in some subjects - is also done infrequently. Somewhat more frequently papers that had already been published elsewhere are secondarily distributed for free online....In contrast to the low Open Access publication activity a majority of those questioned throughout all disciplines approve of an increased advancement of Open Access by the German Research Foundation. Whereas those at earlier stages of their careers in the natural, life, and engineering sciences support the advancement of Open Access somewhat more strongly than their already more established colleagues....The preparedness of scientists to use part of their funding to finance the free availability of their publications is proportionate to the expenditure scientists already have to provide to publish conventionally. Therefore life scientists are most prepared to pay author fees for open access publications, while humanities scholars and social scientists are least prepared....Proposals of the researchers with regards to the question how the German Research Foundation could advance Open Access essentially aim at the following: measures to intensify the debate surrounding freely accessible publications, measures to assure the quality of Open Access journals, and the ­ technical, legal, organizational ­ support of secondary Open Access publication of material that was previously published in a conventional way.'

Also see Richard Sietmann, DFG legt Studie zu Open Access vor, Heise Online, July 23, 2005.

* The RCUK draft OA policy elicited more news and comment.

This is the biggest OA news on the horizon, although July was (and August likely will be) thin in overt developments and public announcements.  There's a lot happening behind the scenes as stakeholders write comments and the Research Councils gear up to finalize the policy.  Don't forget to send your own comments to Dr. Astrid Wissenburg before the August 31 due date.

Michael Seringhaus, Open access revisited, The New Criterion, Summer 2005.

SPARC Europe issued a press release welcoming the RCUK policy, July 14, 2005.

Eliot Marshall, Britain's Research Agencies Endorse Public Access, Science Magazine, July 8, 2005.

BioMed Central issued a press release applauding the RCUK policy, July 5, 2005.

Nick Dempsey, RCUK: Strong Stance But Some Hedging Of The Crucial Repository Issues, EPS Insights, July 4, 2005.

Graham Taylor, Don't tell us where to publish, The Guardian, July 1, 2005.

Also see Stevan Harnad's rebuttal:  Applying Optimality Findings: A Critique of Graham Taylor's Critique of RCUK Policy Proposal, July 9, 2005.


Coming up later this month

Here are some important OA-related events coming up in August.

* August 31, 2005.  The comment period on RCUK draft policy comes to an end.  Send your own comments to Dr. Astrid Wissenburg, astrid.wissenburg@esrc.ac.uk.

* Sometime before the end of August, 2005.  The JISC Common Information Environment (CIE) program should publish its report on using CC licenses for publicly-funded UK research.

* Notable conferences this month

Wikimania - the first international Wikimedia conference (OA and OAI are among the topics.)
Frankfurt, August 5-7, 2005

Establishing a Digital Repository Service (sponsored by the Australian Partnership for Sustainable Repositories)
August 9, 2005, four simultaneous workshops in Canberra, Sydney, Brisbane, and Melbourne.

Workshop for users of publicly-funded research (not the official name)
Edinburgh, August 12, 2005

* Other OA-related conferences



* I've added 18 new conferences to the conference page since the last issue.  In the next few days I'll delete the second asterisk marking them and the new entries will blend into the rest of the collection.


This is the SPARC Open Access Newsletter (ISSN 1546-7821), written by Peter Suber and published by SPARC.  The views I express in this newsletter are my own and do not necessarily reflect those of SPARC.

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