Archive for April, 2008

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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More baseline data from PubMed

Heather Morrison has pointed out that one can readily obtain data on the percentages of literature indexed by PubMed for which a link to the free full text is available (see her post: Cancer Literature: 13% Free, March 29, 2008).

The new NIH policy about open access will begin to be implemented on April 7, 2008. So, April 6 is a good time to collect baseline data about the portion of the literature that’s a result of NIH-funded research. An indicator of the amount of such research can be obtained by adding these key words (without the quotation marks) to the PubMed search box: “Research Support, N.I.H., Extramural [pt] OR Research Support, N.I.H., Intramural [pt]”. The key words Research Support, N.I.H., Extramural yield a search for all articles noted in PubMed as resulting from extramural research at any NIH institute. Similarly, the key words Research Support, N.I.H., Intramural yield a search for all articles noted as resulting from intramural research at any NIH institute.

When these key words were used on April 6, with the search limited to articles published within the last 3 years, a total of 215424 articles was identified. When the same search was repeated, but limited to articles published within the last 3 years for which links to the free full text also were available, the result was 73631, or 34% of the total. Over the next couple of years, as the new NIH access mandate continues to be implemented, this percentage can be expected to increase substantially. Indeed, this indicator should provide a simple way of assessing the impact of the new mandate.

Some other data about the percentage of freely-accessible articles, obtained on the same day using the same key words:

Published within the last 2 years: 44366/144166=31%
Published within the last 1 year: 12241/67486=18%
Published within the last 180 days: 3894/30602=13%
Published within the last 90 days: 1012/11947=8%
Published within the last 60 days: 454/6475=7%
Published within the last 30 days: 143/2267=6%

These data suggest that, prior to the implementation of the new NIH policy, less that 10% of NIH-supported articles were freely accessible via PubMed within 90 days after publication. In contrast (after embargo periods of between 6 months and a year have been exceeded) the proportion of NIH-supported articles that were freely accessible via PubMed within 2 years after publication increased to about 30%.

These proportions vary somewhat across topics. When the same search for NIH-supported articles was limited to specified “Topics”, the following results were obtained:

Topic: AIDS
Published within the last 2 years: 2149/6807=32%
Published within the last 90 days: 37/461=8%

Topic: Bioethics
Published within the last 2 years: 167/886=19%
Published within the last 90 days: 2/28=7%

Topic: Cancer
Published within the last 2 years: 16344/48587=34%
Published within the last 90 days: 254/3364=8%

Topic: Complementary Medicine
Published within the last 2 years: 1420/5337=27%
Published within the last 90 days: 36/332=11%

Topic: History of Medicine
Published within the last 2 years: 83/340=24%
Published within the last 90 days: 3/17=about 20%

Topic: Space Life Sciences
Published within the last 2 years: 672/2479=27%
Published within the last 90 days: 10/125=8%

Topic: Systematic Reviews
Published within the last 2 years: 360/1519=24%
Published within the last 90 days: 6/113=5%

Topic: Toxicology
Published within the last 2 years: 6528/21120=31%
Published within the last 90 days: 109/1256=9%

It’ll also be interesting to look for variation in the impact of the implementation of the new NIH policy across topics.

Finally, it should be noted that some bloggers have proposed that the week beginning on April 7, 2008 should be OA week, in recognition of the beginning of implementation of the new NIH policy. Those bloggers who take part are asked to mention at some point during the week that the NIH is, at present, collecting public comments on the policy.

Added April 7, 2008:

A more elaborate search strategy for identification of NIH-supported publications is described at: www.nlm.nih.gov/bsd/funding_support.html

The search strategy involves “all the NIH 2-letter grant codes and institute acronyms as well as the two publication types, Research Support, N.I.H., Extramural and Research Support, N.I.H., Intramural“.

When this strategy was used, the results obtained for the percentages of publications identified in PubMed as freely accessible were:

Published within the last 2 years: 45361/145354=31%
Published within the last 90 days: 1039/11905=9%

These percentages are very similar to those obtained via the search strategy that involves only the two publication types, Research Support, N.I.H., Extramural and Research Support, N.I.H., Intramural.

Results for each of these two publication types were:

Research Support, N.I.H., Extramural:
Published within the last 2 years: 42622/139273=31%
Published within the last 90 days: 981/11425=9%

Research Support, N.I.H., Intramural:
Published within the last 2 years: 2678/7087=38%
Published within the last 90 days: 76/672=11%

The Intramural Support percentages are somewhat larger than the Extramural Support percentages. However, there were substantially fewer Intramural Support publications, so the combined percentages are dominated by the Extramural Support contributions.

Added July 2, 2008: Cite as: Till J. More baseline data from PubMed. Be Openly Accessible or Be Obscure blog. Self-Archived at WebCite® 2008-Jul-2 [http://www.webcitation.org/5Z0oCNM85]

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