Posts Tagged NIH

Political theater about public access to federally funded research

On July 29, 2010, the Information Policy, Census, and National Archives Subcommittee of the US House Committee on Oversight and Government Reform held a hearing entitled: “Public Access to Federally-Funded Research”. The hearing was chaired by Subcommittee Chairman Representative William Lacy Clay (D-MO).

The Alliance for Taxpayer Access has posted a news item about the hearings, entitled: Summary: Hearing on Public Access to Federally Funded Research, dated August 12, 2010.  Excerpt from the last paragraph of this summary: “Next steps: Congress will be in recess until September 9, so any further action on this issue or related legislation will happen after that point.”

There was a webcast of the hearings (2 hr 14 min) and a video is available. Copies of the Opening Statement of Chairman Clay and of the Prepared Testimony of the ten panel members are available here.

Some information about the video (the total duration of the hearing was 2:14:00):

  • 3:10 End of Chairman’s Opening Statement.
  • 7:30 End of statement from Representative Jason Chaffetz (R-UT).
  • 7:35 Introduction of Panel I.
  • 9:40 Beginning of reading of Prepared Testimony by each of three members of the first panel. Each member was given 5 minutes to present their testimony. (All had concerns about government-mandated public access to the outputs of federally funded research).
  • 26:10 End of Panel I presentations and beginning of first question period. Representatives Jason Chaffetz (R-UT), Judy Chu (D-CA), Carolyn Maloney (D-NY) and Chairman Clay asked questions.
  • 1:07:25 End of first panel.
  • 1:09:00 Introduction of Panel II.
  • 1:13:35 Beginning of reading of Prepared Testimony by each of six members of the second panel. (All were supporters of public access to the outputs of federally funded research).
  • 1:43:15 End of Panel II presentations and beginning of second question period. Chairman Clay was the only Representative still present, and he asked several questions.
  • 1:59:10 End of second panel.
  • 2:00:15 Introduction of Panel III.
  • 2:01:30 Beginning of reading of Prepared Testimony by the single member of the third panel, Dr. David Lipman (Director, NCBI, NLM, National Institutes of Health).
  • 2:05:50 End of Panel III presentation and beginning of third question period. Again, Chairman Clay was the only Representative still present, and he asked several questions.
  • 2:14:00 End of hearing.

Summaries of Twitter messages (tweets) about the webcast have been posted here and here. The emphasis is on the Panel II session.

Another commentary about the hearings is: House Holds Hearing on Status of Open Access, FASEB Washington Update, August 6, 2010. The emphasis is on the Panel I session.

Comments: How to review this video, as an example of political theater? First impression: it was based on three one-act plays. Each one was nicely staged. Second impression: the model for these plays was one of the “Judge So-and-So” programs that can be seen on television. In such programs, the judge listens while various people present their different versions of a dispute, and tries to decide who is being deceitful and who isn’t. Representative Clay played the role of “Judge Clay” very well. Most of the supporting cast were also excellent (although perhaps Representative Maloney spent more time in the spotlight than was really necessary). There were even some humorous moments.

What was the purpose of this particular example of political theater? It served well as a tutorial about the OA movement. However, Representative Clay was the only member of the House to benefit from the full tutorial. The other three Representatives were present and asked questions only during the first act. Then, they left.

Were these hearings simply a prelude to further legislative action or an executive pronouncement? Stay tuned for the next exciting episode.

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UCLA survey of knowledge about the NIH Public Access Policy

Measuring Capacity and Effectiveness of NIH Public Access Policy Programming as a Model for Open Access by Tania Bardyn and 4 co-authors, UCLA Louis M Darling Biomedical Library. Dated July 24, 2010 in the University of New Mexico DSpace repository.

Abstract: This file contains the presentation slides from Ms. Bardyn’s presentation at the Evidence Based Scholarly Communication Conference, March 11-12, 2010, in Albuquerque, NM. [PDF of 44 presentation slides].

This was a “Survey of Translational and Other Researchers’ Knowledge of the NIH Public Access Policy at UCLA“.

  • From Slides 3, 9 & 10: Translational researchers at UCLA (N=?) and attendees at 8 NIH Workshops (N=103) were surveyed. The survey took place between Nov. 30, 2009 and Dec. 15, 2009.
  • From Slide 13: 72.5% of responses (50/69) were from the David Geffen School of Medicine.
  • From Slides 15 & 17: Of 69 respondents, 51% did not attend an NIH Workshop at UCLA. And, 51% were Translational Researchers.
  • From Slide 16: 74% (51/69 respondents) answered “Yes” to the question: “Are you currently involved in any NIH funded research?
  • From Slide 26: 50% (32/64 respondents) did not know the stated intention of the NIH Public Access Policy.
  • From Slide 36: Of 65 respondents, 43% had successfully submitted an article to PubMed Central.
  • From Slide 37: Of 65 respondents, 95.4% answered “No” to the question; “Have you made any attempts to retain your copyrights when publishing in an academic journal?“.
  • From Slide 38: Knowledge Sharing: 89% (24 respondents) of NIH Workshop Attendees answered “Yes“; 49% (17 respondents) of Translational Researchers answered “Yes“.
  • From Slide 42: Quote from survey respondent at UCLA, December 2009 (about future training on the NIH Public Access Policy): “I think it is more efficient for the NIH website or other external website to provide such training. The issues are the same at all universities and it is not clear why each institution should provide this information. Since the NIH requires IDs on papers in biosketches and progress reports, that affects investigators competitiveness on grants which is much stronger motivation to comply with the policy than mandated training by UCLA which will force investigators to know the policy, but not necessarily comply with the policy.”
  • From Slide 43: 57% (37/65 respondents) answered “Yes” to the question: “Do you think you need further training on this issue?“.

Comments: The response rate was not high for this survey. Of 103 NIH Workshop Attendees, only 43% of 69 survey respondents were sure that they had attended a Workshop. So, the response rate from NIH Workshop attendees was 0.43×69/103=29%. It’s not stated how many Translational Researchers were surveyed, but it’s unlikely that the response rate for the Translational Researchers was higher than it was for the NIH Workshop Attendees.

Might the survey results be biased in a way that yielded an underestimate of knowledge about the NIH Public Access Policy by translational and other researchers at UCLA? This also seems unlikely.

A question that wasn’t answered in the slide presentation: were the 28 respondents who had successfully submitted an article to PubMed Central (see Slide 36/44) also the most knowledgeable about the NIH Public Access Policy? (If not, does it matter?).

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A taxonomy of articles in PubMed Central

Taxonomy is “the practice and science of classification“. In this post, four subtypes of articles in PubMed Central (PMC) will be identified: 1) Author manuscripts that are publicly accessible; 2) Articles that are embargoed (still under both price and permission barriers); 3) Articles that are Libre OA (all price barriers, and at least some permission barriers, have been removed); 4) Other articles that are publicly accessible, via Gratis OA (price barriers removed, but not permission barriers).

For a definition of “author manuscripts”, see: Author Manuscripts in PMC (webpage last updated: June 30, 2005). An excerpt:

Many of the scientists who receive research funding from NIH publish the results of this research in journals that are not available in PubMed Central (PMC). In order to improve access to these research articles, NIH’s Public Access policy asks these authors to give PMC the final, peer reviewed manuscripts of such articles once they have been accepted for publication.

Get a list of author manuscripts available in PMC.

As of today (August 12, 2009), there was a total of 50704 author manuscripts in PMC. Use of the “Limits” option in a PMC search indicted that none of them were classified as “embargoed”.

The “Limits” option can be used to do a PMC search to find out how many author manuscripts had a publication date within the four months between April 7, 2008 and August 7, 2008. The result of such a PMC search: 7346 (none embargoed).

The initial date for the 4 month interval was chosen because the NIH Public Access Policy is applicable to any NIH-supported manuscript “accepted for publication in a journal on or after April 7, 2008“. The final date for the 4 month interval was chosen because it is more than a year ago. The NIH Policy requires NIH-supported manuscripts to be “accessible to the public on PubMed Central no later than 12 months after publication“. So, after a year, no NIH-supported articles should still be embargoed.

Another PMC search was done to find out how many articles in the PMC Open Access subset were published in the same 4 month interval in 2008. The result of such a PMC search: 3635. This number of (Libre) OA articles (“made available under a Creative Commons or similar license“) is substantially fewer (by about 2-fold) than the 7346 author manuscripts contributed to PMC during the same 4-month interval.

What was the total number of articles publicly (no price barrier) accessible via PMC during this same 4-month interval? The results of such a PMC search: 23582 (plus 378 embargoed). The total (publicly accessible plus embargoed): 23582+378=23960.

The number of articles classified as “not (Libre) OA” and “not author manuscript” can be obtained via another PMC search. The result: 12601 (plus 378 embargoed). The total of “author manuscripts” (7346) plus “Libre OA” (3635) plus “embargoed” (378) plus “not any of these subtypes” (12601) is 23960 (the same as “publicly accessible plus embargoed”, see above).

What was the total number of articles publicly accessible via PubMed during the same 4-month interval? (These include articles that are free at the journal site, in addition to those that are available from PMC). The result of such a PubMed search: 59258. Of these, how many were supported by NIH (either by Extramural or by Intramural research support)? The result of such a PubMed search: 16500 (28% of the  total).

What was the total number of NIH-supported articles identified by PubMed during the same time interval? The result of such a PubMed search: 32504.

So, 16500/32504=51% of the NIH-supported articles contributed during this 4-month interval were publicly accessible via PubMed (either via articles submitted to PMC, or via the journal site, or both).

What percentage of the 16500 NIH-supported, publicly-accessible articles were in PMC (omitting those articles that were accessible only via the journal site)? Inspection of a 6% sample (of 1000 of the 16500 articles) indicated that the proportion is about 17%, at present, for this particular 4-month interval (about 2800 articles). The other 83% (about 13700 NIH-supported articles) were publicly accessible in PMC.

Because the total number of articles publicly accessible in PMC during this same 4-month interval was 23582 (see above), a rough estimate of the proportion of NIH-supported articles published during this 4-month interval, and publicly accessible in PMC, is about 13700/23582=58%. This estimate is somewhat greater than the percentage (51%) of NIH-supported articles, contributed during this 4-month interval, that were publicly accessible via PubMed (either via articles submitted to PMC, or via the journal site, or both). Perhaps the proportion of NIH-supported articles that are publicly accessible in PMC is somewhat greater than the proportion, indexed in PubMed, that only are accessible via the journal site?

Summary: The total number of articles published in the 4-month interval (April 7 to August 7, 2008) and contributed to PMC was 23960. The four subtypes of articles in PMC, and their estimated proportions during this 4-month interval, are: 1) Author manuscripts that are publicly accessible (7346/23960=30.7%); 2) Articles that are embargoed (378/23960=1.6%); 3) Articles that are Libre OA (3635/23960=15.2%); 4) Other articles that are publicly accessible, via Gratis OA (12601/23960=52.5%). These proportions are probably not very different for the subset of NIH-supported articles, if it’s assumed that, during this 4-month interval, about 50-60% of the articles contributed to PMC were NIH-supported.

Comment: It will be of interest to monitor any changes in these proportions, as the time during which the NIH Policy has been in effect increases. The monthly manuscript submission statistics have increased by more than two-fold between April 2008 and April 2009.

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Is academic research a bubble?

An iconoclastic post: The Bubble In Academic Research, The Last Psychiatrist, February 16, 2009. Excerpts:

Open access articles isn’t nearly as big a threat to publishers as simply unbundling the journals from each other, letting universities decide which ones to buy.

So open access doesn’t threaten subscription revenues, it threatens the number of journals they can publish. It’s the multitude of journals, each with its inflated subscription rate, that brings in the real money. Also, each crap journal carries advertisements; even a crap journal with a small niche can have higher ad rates because of the bundling.

…..

Take away the journals and the [academic research] system collapses. Force researchers with NIH grants to publish their findings without the marketing and packaging of a journal, and you’ve effectively halted half of the NIH research, until another generation of researchers with a different research model show up for work. …..

The academic research system is flawed because it does not incentivize research, it incentivizes the process of research.

Academic research is a bubble, money keeps flowing into it as long as it produces quality research. Who decides quality? Journals are the rating agencies …..

If someone could look behind the ratings, and take measure of the actual value of the research, the bubble would pop faster than, well, you get the idea. Then there’s the “systemic risk.” Journals collapse, academic centers collapse from lack of funding, Pharma loses the AAA rating on their studies which are done by academics, published in journals, etc.

Research would be forced to change completely– and for the better. But you’ll have a decade or so recession in science and education while the old generation dies out and the new one becomes old enough to start work.

Recommendation: Read the entire post, and the comments about it.

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Demonstrating compliance with the NIH Public Access Policy

A flowchart, How to Demonstrate Compliance with the NIH Public Access Policy [PDF] (last updated December 11, 2008), is available from the Becker Medical Library, Washington University School of Medicine, St Louis.

Found via: Flowchart for Demonstrating Compliance with the NIH Public Access Policy by Cathy Sarli, Bernard Becker Medical Library Scholarly Communications Update, December 31, 2008.

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Assessing medical ethics journals

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Assessing immunology journals

The new NIH policy about open access began to be implemented on April 7, 2008. The new policy can be expected to have impact on the accessibility of NIH-supported publications in all aspects of the biomedical and health sciences. This post has a focus on one of these areas: immunology.

Research in immunology has potential applications to a wide range of areas relevant to human health, including the prevention and treatment of both infectious and chronic diseases. It’s yet another area of research where improved access to research publications can be expected to increase not only the rate of generation of new knowledge, but also the translation of that new knowledge into practical applications.

The Eigenfactor.org site can be used to identify and rank immunology journals. See: Eigenfactor.org: Immunology journals.

This result was obtained via an advanced search (JCR Subject Category: Immunology; Eigenfactor Subject: No Category; Journal name and ISSN number fields left blank). The three highest-ranked journals (omitting those that emphasize reviews):

1. Nature Immunology (Nature Publishing Group).
2. Immunity (Cell Press).
3. Journal of Experimental Medicine (Rockefeller University Press).

Another ranked list of immunology journals can be obtained via the SCImago website. See: SCImago: Immunology journals (obtained via a search of SCImago Journal Indicators, Subject Area: Immunology and Microbiology; Subject Category: Immunology). The rank order of journals is based on the SCImago Journal Rank (SJR) indicator. The same three journals were ranked highest (again, journals that emphasize reviews were omitted).

The Journal-Ranking.com website also identified these same three highly-ranked journals (when a reviews-oriented journal was omitted).

The data shown below include (when available):
a) Journal name and print ISSN;
b) SJR indicator, obtained via a SCImago Journal Search;
c) Subscription prices per citation, obtained via: Journal Cost-Effectiveness 2005-6 BETA;
d) Policies about archiving in repositories (“Green OA“), obtained via the SHERPA/RoMEO database of information about publisher copyright policies & self-archiving, and from Selected Publisher Policies about the NIH Public Access Policy (posted by Charles W. Bailey, Jr., DigitalKoans, April 9th, 2008).
e) Estimates of percentages of NIH-supported publications that are freely accessible, obtained via PubMed. As described in a previous post, NIH-supported publications were identified by searching for these keywords: Research Support, N.I.H., Extramural [pt] OR Research Support, N.I.H., Intramural [pt].

Note that the criteria that can be used to limit PubMed searches include a “Search by Journal” option. This option was used (on April 8th) to search PubMed for articles with NIH support (intramural or extramural), and to estimate the percentage of these identified as freely accessible, for nine Immunology journals. They were:

#1. Nature Immunology: ISSN 1529-2908
SJR(2006)=12.484
Subscription price per citation: 0.48
SHERPA/RoMEO excerpt: Can archive postprint, with 6 month embargo; see also Author licence policy.
Access to the free full text (FFT) of NIH-supported articles:

    published in the last 2 years: 5/162=3% FFT
    published in the last 1 year: 1/80=about 1% FFT
    published in the last 90 days: 0/20=0% FFT

Comment: This very high-profile journal has a satisfactory policy about Green OA. It encourages submission of “the author’s version of the accepted paper (the unedited manuscript) to PubMedCentral or other appropriate funding body’s archive“, and to the repository of the author’s host institution, with a 6-month embargo. Access to the free full text, through PubMed Central, of articles published in this journal is currently low, but can be anticipate to rise dramatically as the new NIH policy is successfully implemented.

#2. Immunity: ISSN 1074-7613
SJR(2006)=9.337
Subscription price per citation: 0.39
SHERPA/RoMEO excerpt: Can archive postprint on author’s personal or author’s institution’s server.
For NIH-supported authors, the journal will send the postprint to PubMed Central, with a 12-month embargo.
Open Archive: Papers are freely available from the archives of Cell Press journals after 12 months.
Access to the free full text (FFT) of NIH-supported articles:

    published in the last 2 years: = 18/185=10% FFT
    published in the last 1 year: = 6/86=7% FFT
    published in the last 90 days: 0/15=0% FFT

Comment: This high-quality journal has a good policy about the form of Green OA that involves self-archiving in institutional repositories. However, PubMed doesn’t yet provide links to such self-archived articles. Deposition in PubMed Central involves a 12-month embargo. Currently, only 10% of NIH-supported articles are freely accessible via PubMed after 2 years. This percentage should increase as the new NIH policy is successfully implemented.

#3. Journal of Experimental Medicine: ISSN 0022-1007
SJR(2006)=6.785
Subscription price per citation: 0.24
SHERPA/RoMEO excerpt: Can archive postprint (6 month embargo for NIH-supported articles if archived in PubMed Central).
Access to the free full text (FFT) of NIH-supported articles:

    published in the last 2 years: 251/325=77% FFT
    published in the last 1 year: 94/168=59% FFT
    published in the last 180 days: 0/74=0% FFT
    published in the last 90 days: 0/35=0% FFT

Comment: This first-rate journal has an outstanding track record about making articles freely accessible via its own archive and PubMed Central. Already, almost 60% of NIH-supported articles are freely accessible within a year after publication. This percentage should increase further as the new NIH policy is successfully implemented.

Two examples of other journals that publish articles about immunology:

#4. PLoS Pathogens: ISSN 1553-7366
SJR(2006)=2.517
Subscription price per citation: zero (no subscription required).
Publication fee (2008): US$2100 (discount available for authors who are affiliated with an Institutional Member).
Published version deposited by journal in PubMed Central.
Access to the free full text (FFT) of NIH-supported articles:

    published in the last 2 years: 175/175=100% FFT
    published in the last 90 days: 15/15=100% FFT

Comment: A SCImago comparison of this OA journal with the three journals listed above it indicates that the SJR of PLoS Pathogens increased dramatically in 2006.

#5. Journal of Immunology: ISSN 0022-1767
SJR(2006)=2.229
Subscription price per citation: 0.08
SHERPA/RoMEO excerpt: NIH-supported authors can archive postprint in PubMed Central, with a 12 month embargo; see also NIH Public Access Policy: FAQ.
Access to the free full text (FFT) of NIH-supported articles:

    published in the last 2 years: 929/1776=52% FFT
    published in the last 1 year: 13/860=2% FFT
    published in the last 90 days: 1/105=1% FFT

Comment: This popular journal would be more attractive from an OA perspective if its embargo for postprints deposited in PubMed Central could be shortened from 12 months to 6 months.

Four examples of immunology journals that currently have lower SJRs, but satisfactory access policies, are these:

#6. Infection and Immunity: ISSN 0019-9567
SJR(2006)=0.894
Subscription price per citation: 0.26
SHERPA/RoMEO excerpt: Authors can archive postprint.
Journal policy: Published articles freely accessible (and available through PubMed Central) 4 months after publication.
Access to the free full text (FFT) of NIH-supported articles:

    published in the last 2 years: 670/761=88% FFT
    published in the last 1 year: 256/347=74% FFT
    published in the last 180 days: 62/153=41% FFT
    published in the last 90 days: 0/67=0% FFT

#7. BMC Immunology: ISSN 1471-2172
SJR(2006)=0.701
Subscription price per citation: zero (no subscription required).
Article processing charge (2008): £950 (€1205, US$1890). Discounts offered (e.g. Supporter Member discount).
Published version included in PubMed Central.
Access to the free full text (FFT) of NIH-supported articles:

    published in the last 2 years: 21/21=100% FFT

#8. Microbiology and Immunology: ISSN: 0385-5600
SJR(2006)=0.242
Subscription price per citation: zero (no subscription required).
Access to the free full text (FFT) of NIH-supported articles:

    published in the last 2 years: 4/4=100% FFT

#9. Clinical and Developmental Immunology: ISSN 1740-2522
SJR(2006)=0.219
Subscription price per citation: zero (no subscription required).
Article Processing Charge currently €600.
Access to the free full text (FFT) of NIH-supported articles:

    published in the last 2 years: 3/3=100% FFT

Comment: Of the four journals (#6 to #9), Infection and Immunity appears to be, by a wide margin, the most popular with NIH-supported authors. A SCImago comparison of the same four journals indicates that the SJRs of BMC Immunology have increased steadily since 2001, while those of Infection and Immunity have declined somewhat over the same time interval. The SJRs of Clinical and Developmental Immunology also increased after 2003.

Of course, there are other journals which do not focus on topics related to immunology, but do publish articles about immunology. One example is provided by the Immunology section of the open access journal PLoS ONE.

Comment: A PubMed search indicated that, of a total 1941 articles published in the last 2 years in PLoS ONE (on any subject, not just immunology), only 55 (3%) were by NIH-supported authors. Of 58 publications indexed under the MeSH Heading “Immunity” and published in the last 2 years, only one was NIH-supported. It’ll be of interest to see whether or not these low percentages increase as the new NIH policy is successfully implemented.

The MeSH Heading “Immunity” was also used (on April 15th) to estimate the number of immunity-related and NIH-supported publications in three other journals. The percentages of such articles for which the free full text (FFT) was available via PubMed were:

PNAS: Immunity-related articles, NIH-supported, published in last 2 years: 198/244=81% FFT; published in last 1 year: 66/112=59% FFT;
Science: Immunity-related articles, NIH-supported, published in last 2 years: 38/64=59% FFT; published in last 1 year: 2/26=8% FFT;
Nature: Immunity-related articles, NIH-supported, published in last 2 years: 3/54=6% FFT; published in last 1 year: 2/31=6% FFT.

In conclusion, the results described above should be useful as baseline data for an immunology-oriented case study of the impact of the new NIH policy on access to articles published in the set of journals considered above.

Added May 15, 2008:

The MeSH Heading “Immunity” was used (on May 15th) to estimate the percentages of immunity-related and NIH-supported publications for which the free full text (FFT) was available via PubMed.

Immunity-related articles, NIH-supported:

    published in last 2 years: 3453/8943=39% FFT;
    published in last 1 year: 878/4081=22% FFT.

Total immunity-related articles:

    published in last 2 years: 10101/44181=23% FFT;
    published in last 1 year: 2616/19698=13% FFT.

These immunity-related articles were published in a variety of journals. Overall, however, access to the free full text was available for almost 40% of NIH-supported articles (related to immunity) that were published within the past 2 years.

The number of immunity-related articles for which the free full text (FFT) is available via the PubMed Central (PMC) repository can be estimated by use of the search terms (Immunity AND (free full text[sb])) in the PMC Database. One can also assess the proportion of such articles that are Open Access according to the Bethesda Definition of OA (in which specified permission barriers, as well as price barriers, are absent) by use of the “Limits” option. The results obtained (on May 15) were:

    published in last 2 years: OA/FFT=1952/7283=27%;
    published in last 1 year: OA/FFT=695/2418=29%.

My thanks to Heather Morrison and Peter Suber for their information about how to obtain these OA/FFT estimates.

Added July 2, 2008: Cite as: Till J. Assessing immunology journals. Be Openly Accessible or Be Obscure blog. Self-Archived at WebCite® 2008-Jul-2 [http://www.webcitation.org/5Z0paY8DC]

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