Posts Tagged PMC

Questions about uptake of Springer’s hybrid OA option

A news release, Springer Open Choice uptake affects 2011 journal pricing (EurekAlert, June 18, 2010), raised questions about uptake of the Springer Open Choice option, a hybrid OA option.  Searches of PMC (PubMed Central) can provide some relevant information. Examples:

Q#1: Was uptake of Springer Open Choice greater in 2009 than in 2008?

A: Yes. When “Limit by Journal” was used to restrict the search of PMC to “Springer Open Choice” (“Journal Name”), then the number of articles published in the date range “2009/01/01” to “2009/12/31” was found to be (Search #1): 2186. For the date range “2008/01/01” to “2008/12/31”, the result was (Search #2): 1079. So, these results indicate that the uptake of the Springer Open Choice option did increase substantially between 2008 and 2009.

Q#2: Does the Springer Open Choice option account for a substantial proportion of the OA publications available via PMC?

A: No. The proportion of the PMC Open Access Subset identified as being associated with the Springer Open Choice option was found (on June 21, 2010) to be 2186/40196=5.4% in 2009. This is an increase in this proportion in comparison with the previous year. The results for 2008 were:  1079/31006=3.5%.

Q#3: How does uptake of the Springer Open Choice option compare with that of other hybrid OA options?

A: Quite well. Data were obtained, using searches analogous to those considered above, for the percentages of “Elsevier Sponsored Documents” (PMC’s nomenclature) in the PMC Open Access Subset (1.1% in both 2009 and 2008) and for the percentages of “Wiley-Blackwell Online Open” (PMC’s nomenclature) publications in the PMC Open Access Subset (1.0% in 2009 and 1.6% in 2008).

Of course, many other publishers provide hybrid OA options. For a list, see: Publishers with Paid Options for Open Access (via SHERPA/RoMEO, University of Nottingham).  The hybrid OA options of only a few of the major publishers on this list could be identified among PMC’s “Journal Names”. These included (in order of decreasing uptake into PMC): “BMJ Unlocked“, “ACS AuthorChoice“, “Taylor & Francis iOpenAccess” and “SAGE Open“. The uptake into PMC of the latter four hybrid OA options was less than that found for the Springer, Elsevier and Wiley-Blackwell hybrid OA options.

Data for the Oxford Open hybrid OA option could not be obtained via searches of PMC. However, a recent press release, Open Access Uptake for OUP Journals: Five years on (Oxford Journals News, June 10, 2010) , included the information that: “On a like-for-like basis, the average uptake in 2009 for journals which entered the scheme prior to 2008 was stable (6.7%, compared with 6.8% in 2008).” (These percentages represent the average uptake of the Oxford Open option for papers in participating OUP journals, taking into account a lower uptake amongst 11 new titles joining Oxford Open in 2009. They should not be compared with the percentages of hybrid OA publications in the PMC Open Access Subset).

Q #4: How does uptake of the Springer Open Choice option compare with data for PLoS ONE?

A: Better than anticipated. Data were obtained, using searches analogous to those considered above, for the percentages of publications in the PMC Open Access Subset that were published in PLoS ONE. The results, 11.0% in 2009 and 8.7% in 2008, are only approximately twice as large as the results for the Springer Open Choice option (5.4% in 2009 and 3.5% in 2008, see Q#2 above).  PLoS ONE was selected for this comparison because it’s a broad based (and very high volume) fully OA journal that seems likely to grow even larger in the future (see Comments, below).


Data have been obtained, via PMC, about the uptake of the hybrid OA options of several major publishers. The Springer Open Choice option appears to have had the greatest uptake in 2008 and 2009. Perhaps this is because Springer was one of the earliest adopters of a hybrid OA option, which it launched in 2004 (see: Springer’s Open Choice program, Peter Suber, Open Access News, July 3, 2004). Springer has also actively marketed this option, via deals such these, also reported in Open Access News: Max Planck and Springer strike a deal (February 4, 2008) and Springer’s first US deal in which subscriptions cover publication fees for affiliated authors (January 21, 2009).

Of course, like it or not, one of the major marketing tools for journals is their Journal Impact Factor (JIF). Fully OA journals can have an JIF, but the hybrid OA components of otherwise toll-access journals currently do not.

Thomson Reuters recently released its 2009 Journal Citation Report. An excerpt from: New impact factors yield surprises (The Scientist, June 21, 2010):

PLoS ONE debuted in the Journal Citation Report for the first time with a respectable impact factor of 4.351. This score puts the open access journal in the top 25th percentile for biology publications. But might this sudden success be more of a bane than a boon to PLoS ONE, blogger Philip Davis asks. It may turn out that accepting 70 percent of the manuscripts submitted to your journal gets a bit trickier when you’re flooded with papers.

Thus, a surprisingly large initial JIF for PLoS ONE provides support for the prediction that this OA journal will grow even larger in the future. Will such growth pose problems of scalability for PLoS ONE? Perhaps – but these will be problems arising from success. Nice problems to have. Much better than the most unattractive alternative, which is failure.

Can the hybrid OA options offered by toll-access journals also increase their uptake? Perhaps, if these options are actively marketed, and can compete successfully in prestige and price with fully OA journals. Springer also has a nice problem. It now owns BioMed Central (BMC) a pioneering OA publisher. See: Springer acquisition FAQ. An excerpt from the FAQ:

7. Will BioMed Central’s article processing charges be raised to match those of the Springer Open Choice option?

No, BioMed Central will continue to set its own article processing charges, and no increases are planned as a results of the acquisition. As ever, BioMed Central reserves the right to adjust article processing charges from time to time in the light of economic factors.

So, Springer’s Open Choice option is competing with Springer’s own fully OA publisher. Might both of Springer’s approaches to Gold OA fail to compete successfully with those of other publishers? Seems unlikely.


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Ten Years of PubMed Central

The blog post PubMed Central Turns Ten – Dr. David Lipman, by Dean Giustini (Open Medicine Blog, April 21, 2010), includes a link to
a video (51 min), entitled “Ten Years of PubMed Central “.

It’s a video of a talk given by David Lipman, Director of the National Center for Biotechnology Information at the National Library of Medicine, on March 23, 2010. He provides an overview of the past, present, and future of the National Institutes of Health’s archive of biomedical research articles, PubMed Central (PMC). Some noteworthy sections of the video are:

0 – 3:30 min: Introduction by Ian Lapp, Mailman School of Public Health (which cosponsored the event).

3:30 – 22:40 min: David Lipman describes the past of PMC.

22:40 – 31:30 min: He discusses the “Discovery Initiative”, an effort to “improve the quantity, quality and relevance of information obtained/viewed by users“. The value of weblog analyses is emphasized.

31:30 – 32:25 min: PMC statistics (as  of January 2010) are discussed.

32:25 – 38:50 min: Changes in written communication are considered.  Some very interesting comments are made about use of the Google knol authoring system to produce a new kind of journal, PLoS Currents: Influenza. Plans to produce other journals using this same authoring system are mentioned. These plans include additional PLoS Currents journals, but also journals initiated by other groups.

39:20 – 51 min: Discussion. The initial question is about the process for starting a Google knol journal.

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More about PMC Canada

The webpage entitled: Update on PubMed Central Canada (PMC Canada), at the Canadian Institutes of Health Research (CIHR) website, was modified on November 30, 2009. Excerpt:

The first element of the PMC Canada system-the search interface-was launched in October 2009. It allows users to browse, search and download articles.
A manuscript submission system is being developed for PMC Canada.

Also, there’s a section on “PMC Canada: Now Open for Business” by Andrea Szwajcer in the November 2009 issue [5-page PDF] of a newsletter from the St. Boniface Hospital Library (one of the University of Manitoba Libraries). An excerpt (from page 3 of the newsletter):

The digital platform to locate and access publications includes a basic and advanced search function for PMC Canada as well as alphabetical index list to search the PMC Journals by title. The manuscript submission system is not yet available but is promised “later this year”.
This webpage is a little deceiving as you may assume that if you do a search in the search box, you are limited to strictly Canadian publications or have that ability somehow. The reality is a little more disappointing. ….

Comment: Relevant information is available via the webpage for PMC International (PMCI). Excerpts:

To date, NLM has authorized two PMCI centers: UKPMC and PMC Canada.


Like the UKPMC, PMC Canada receives all of its content through the US PubMed Central.


With the introduction of PMC Canada, all current PMC participants have been asked for permission to make their PMC content available to the Canadian site. NLM will not redistribute a journal’s PMC content to PMC Canada without the explicit permission of the publisher. These permissions are included automatically in PMC agreements signed in June 2009 forwards.

So, all articles in PMC Canada that are marked “In PMC Canada” will also be available in US PMC. Those marked “Only in US PMC” aren’t currently available in PMC Canada because the publisher has not yet provided explicit permission for them also to be archived there.

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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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Finding articles on CSC via OAIster or PMC

A mentioned in a previous post, in addition to this OA-oriented blog, I’m currently also editing another blog, Cancer Stem Cell News. I recently, using OAIster, searched the “entire record” field for the phrase “cancer stem cell*”. The search for articles about CSC was limited to resource type “text”, and the results were sorted in “date descending” order. This search yielded 167 records. Of these 167, 136 (81%) were obtained from 5/29 (17%) of the contributors. These 5 were: PubMed Central (PMC) [41 records]; CiteBase [39]; HighWire Press, Stanford University [20]; BioMed Central (BMC) [19] and Defense Technical Information Center (DTIC) Repository [17]. The remaining 24/29 contributors (83%) provided 31/167 (19%) of the records. Perhaps, another example of the Pareto principle (for many events, 80% of the effects come from 20% of the causes)?

The most recent article, dated 2008-06-09, was Mammosphere culture of metastatic breast cancer cells enriches for tumorigenic breast cancer cells by Matthew J Grimshaw, Lucienne Cooper, Konstantinos Papazisis, Julia A Coleman, Hermann R Bohnenkamp, Laura Chiapero-Stanke, Joyce Taylor-Papadimitriou and Joy M Burchell.  Publisher: BMC. PubMed Citation: Breast Cancer Res 2008; 10(3): R52. Epub 2008 Jun 9. (The full citation for this article isn’t included in the OAIster record).

This same article can also be accessed via PMC. The Conclusion section of the PMC Abstract:

This paper shows, for the first time, that mammosphere culture of pleural effusions enriches for cells capable of inducing tumours in SCID mice. The data suggest that mammosphere culture of these metastatic cells could provide a highly appropriate model for studying the sensitivity of the tumorigenic ‘stem’ cells to therapeutic agents and for further characterisation of the tumour-inducing subpopulation of breast cancer cells.

Comment: A search of PMC for the phrase “cancer stem cells” yielded access to articles published more recently than the one cited above. For example, a search limited to articles added to PMC in the last 30 days (done on November 9) yielded 3 citations, all published in November 2008.

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