Archive for August, 2009

Updates sent to Twitter, August 2009

Updates related to OA, sent to Twitter during August 2009:

RT @petersuber: For news about open access, follow @oatp (OA Tracking Project) [August 28].

RT @petersuber: The Twitter version of the OATP feed is now available at the OATP Twitter account [August 27]:

RT @petersuber: For a short time, the OATP feed was available here. No more.  [August 27] Details:

OA tracking project (OATP) via Twitter [August 27]:

Peter Suber is sending updates about #openaccess to Twitter [August 26]:

Business Week Runs Sloppy Science Policy Analysis (critique re errors and omissions about OA) [August 25]:

Peter Scott’s Library Blog: Scholas – social file-sharing for academics [August 24]:

Michael Smith Foundation for Health Research adopts an OA mandate [August 21]:

What You Might Not Know About (Biomedical) Journals [August 18]:

“The Strength of Weak Ties: Why Twitter Matters in Scholarly Communication” [August 17]:

Elsevier is going the wrong way [August 16]:

A taxonomy of articles in PubMed Central [August 12]:

Protocol for implementing #openaccess #data for #research #databases [August 2]

Journal publishers that have formally indicated cooperation with Harvard’s open access policies [August 1]:


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Michael Smith Foundation for Health Research adopts an OA mandate

On July 6, 2009, the Board of Directors of the Michael Smith Foundation for Health Research (MSFHR),  adopted an Open Access to Research Outputs Policy [see 2-page PDF]. The MSFHR is the provincial support agency for health research in British Columbia (BC, Canada) and is funded by the Government of BC. A pivotal paragraph of the policy statement is also available at Managing Your Award [from the MSFHR]:

All MSFHR Award Recipients who receive an award or an award renewal after July 7, 2009 must ensure that all final peer-reviewed journal manuscripts that arise from research supported by that award (in whole or in part) are made freely accessible through either the Publisher’s website or an online repository within six months of publication.

Other excerpts from the policy statement:

Additionally, Award Recipients are now required to deposit bioinformatics, atomic, and molecular coordinate data, as already required by most journals, into the appropriate public database immediately upon publication of research results.

Authors are encouraged, but are not required, to submit final peer-reviewed manuscripts accepted before July 7, 2009, if they have appropriate copyright permission. MSFHR Award Recipients are responsible for ensuring that any publishing agreements concerning submitted manuscripts fully comply with this Policy.


Compliance with this Policy is a requirement and a term of the Condition of Awards that the Award Recipient agrees to upon acceptance of MSFHR funds. This policy applies to MSFHR Award Recipients who have received award notification or renewal letters after July 7, 2009. Compliance will be monitored through annual reporting requirements. Non-compliance to this policy may result in the termination of the award.


Costs related to the publication of research outputs are considered eligible expenses as defined in the Eligible Expenses section under each Program area on the MSFHR website. ….. In the event that Award Recipients encounter additional publications costs than the amount budgeted in the original application, they may approach MSFHR for supplemental funding to cover publication costs. …..

Comment: This policy is a strong OA mandate.

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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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Whither blogging?

Two OA-related blogs that I’ve been following for quite a long time have recently undergone major changes. One is Caveat Lector, by Dorothea Salo, who has provided many credible (and readable) commentaries about repositories.This blog is no longer actively maintained. The reason? “It’s just too big” (excerpt from “Hanging up the keyboard“, June 23, 2009). She does continue to contribute to The Book of Trogool, where “an academic librarian confronts the way computers are changing academic research“.

Another major change is that Peter Suber, as of July 1, 2009, has curtailed his blogging on the Open Access News blog. Instead (among other activities) he’s tagging news items for the OA tracking project (OATP), via Connotea.

In addition to following the items tagged for the OATP, I’ve been paying attention to OA-related news items that are mentioned on Twitter and FriendFeed. See, for example, a search on Twitter for the hashtag #openaccess and a similar search on FriendFeed for #openaccess. These  searches can yield overlapping results, because posts from members of Twitter who are also members of FriendFeed will appear at both sites.

Because of Twitter and FriendFeed, the role of blogs may be evolving. For a relevant blog post, see: W(h)ither blogging and the library blogosphere?, by Meredith Farkas (July 22, 2009).  Excerpt:

With Twitter (and even more easily in FriendFeed) you can have the sort of discussion one might have in the comments of a blog post, nearly in real time. And it’s really cool, because you can feel much closer to the people you’re conversing with since the conversation is happening so quickly and in a single space that everyone is on equal footing in.

The comments about this blog post are also interesting. An example is Comment #17, posted by Walt Crawford. Excerpt:

Twitter et al (I really dislike the term “microblogging,” but can’t win that one) have, in a way, strengthened essay-length blogging while weakening short-form blogging (maybe)–and essays have always been harder to do than quick notes.

Meanwhile, a new OA journal has been announced: Journal of Scholarly and Research Communication. The International Editorial Board includes several people who have made pioneering contributions to the OA movement. An anecdote: I learned about the existence of this new journal via a FriendFeed entry from Bill Hooker (August 2, 2009). I then found that the same news was also available via a tweet from Shana Kimball (July 10, 2009) and a FriendFeed entry from Marin Dacos (July 20, 2009). Then, I noted that the new journal is mentioned by Peter Suber in the SPARC Open Access Newsletter of August 2, 2009. It’s also been bookmarked by Heather Morrison for the OATP (July 17, 2009). Unfortunately, at present, links to individual bookmarks in Connotea aren’t functioning properly. See: Update on recent and ongoing service problems for Connotea by Ian Mulvany (Nature Network, July 29, 2009).

Why the anecdote? I first became aware of the new journal via FriendFeed. This illustrates the advantage of short-form blogging as a means to disseminate news items.

Bora Zivkovic has compared Twitter and FriendFeed in PLoS ONE on Twitter and FriendFeed (March 30, 2009). Excerpt:

Despite online debates – which one is better: Twitter or FriendFeed, sometimes serious, sometimes tongue-in-cheek – the fact is that these are two different ‘animals’ altogether. Asking one to make a choice between the two is like asking one to make a choice between e-mail and YouTube – those are two different services that do different things. Thus, they are to be used differently. …

Comment: From the perspective of the OA movement, these microblogging services provide novel opportunities for wider dissemination of  information about OA. I regard these services as useful supplements to journal articles, blogs and mailing lists.

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