Posts Tagged repositories

About the first phase of PMC Canada

As noted in a previous post, 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.The next element, a manuscript submission system, has been launched. Excerpts from a press release (dated April 28, 2010) that’s available via the website of National Research Council Canada:

PMC Canada supports CIHR’s Policy on Access to Research Outputs, which requires CIHR grant recipients to make their peer-reviewed publications freely accessible online within six months of publication. PMC Canada’s manuscript submission system will enable CIHR-funded researchers to deposit their peer-reviewed articles, exposing their research to a global audience and facilitating collaboration to advance scientific progress.


This first phase of PMC Canada includes a basic bilingual interface, a manuscript submission system for CIHR researchers and a bilingual help desk. Plans for the second phase of the repository will incorporate a customized web front-end along with enhanced reporting and alerting features for system funders and users. An advisory committee of Canadian health researchers and other stakeholders will guide PMC Canada’s future development.


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AgEcon Search: A case study of a subject repository

AgEcon Search: A case study on the differences between operating a subject repository and an institutional repository by Julie Kelly and Louise Letnes, Journal of Digital Information, 2010(Mar); 11(10) [Full text PDF][FriendFeed entry][In an issue on: Open Repositories 2009]. Abstract:

AgEcon Search is a subject repository containing the full text of working papers, conference papers and small press journals in agricultural and other areas of applied economics. In existence since 1995, it contains material from 170 organizations. Comparisons are made between the operations of a subject repository and those of an institutional repository, with each having easier and more challenging aspects. The field of economics has characteristics that contribute to the success of a subject repository, such as a pre-print culture and an interest in intellectual property and the economics of publishing.

Examples of excerpts from the full text:

[From page 3/9]: A number of factors have made creating and sustaining a subject repository an easier undertaking than doing the same for an institutional repository. An obvious one is the fact that AgEcon Search covers just one subdiscipline, although a variety of work is done under the umbrella of agricultural and applied economics.

[From page 4/9]: Much to the consternation of some college and university administrators, researchers often have more loyalty to their discipline than to their institution. In the repository world, this may translate into more interest in subject repositories than institutional ones.

[From page 8/9]: Including data sets in AgEcon Search is a topic that continues to come up, and possibilities in that area are being monitored. The current software platform, DSpace, was not designed with data as its main file type, so data-related issues will be carefully investigated before the migration to a new platform.

Comment: The full text is recommended. Some of the areas that may be more challenging for a subject repository than for an institutional one are discussed.

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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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Can the costs of quality-filtration be reduced?

The costs of the conventional ‘hierarchy of journals’ approach to the quality-filtration of the research and scholarly literature can be very high.

For example, Mike Rossner, Executive Director of the Rockefeller University Press, has quoted a figure of US$10,000 as the average cost per article for the online versions of the three journals that this press publishes. These journals (and their 2008 Journal Impact Factors) are: J Cell Biol (9.1), J Exp Med (15.5) and J Gen Physiol (4.7). He provided this cost figure at the 07:50 min. point during his presentation at an event held on March 9, 2010 by the Scholarly Communication Program at Columbia University.

The full 97 min. video of the presentations is available at: Who Pays for Open Access?. Mike Rossner is the first of three speakers. He called these Rockefeller University Press journals ‘selective journals’, and described their business model, which provides free public access to articles after a 6-month embargo period. He suggested (at the 18:25 min. point in the video) that, for biomedical research journals, “charging for information in only the first 6 months after publication is a clear-cut way to know how valuable it is“.

The costs per article for these ‘selective journals’ are high mainly because of staffing costs of the ‘publication platform’. Tasks such as the management of the peer review system and the performance of copy-editing are done by paid staff. These people must deal with all of the manuscripts that are received, even though only about 10% of them are published.

Mike Rossner also suggested (at the 14:00 min. point in the video) that PLoS ONE provides an example of his definition of an ‘archival journal’ – one where: “Reviewers ask if data support conclusions, not whether the research represents an advance in the field “. An ‘archival journal’ publishes a higher proportion of submitted articles than does a ‘selective journal’. This higher volume reduces costs.

The current publication fee for PLoS ONE is US$1,350. This figure probably overstates the actual cost per article, if PLoS is indeed using PLoS ONE to subsidize its more selective journals (see the 14 min. point in the video, and, for example, Bulk Publishing Keeps PLoS Afloat, Philip Davis, The Scholarly Kitchen, July 7, 2008).

In contrast, Green OA costs much less. To date, an exemplar for Green OA is the arXiv repository, which provides OA to e-prints in Physics, Mathematics, Computer Science, Quantitative Biology, Quantitative Finance and Statistics. The cost of per submission for an article in the arXiv repository is much, much lower than the publication fee for PLos ONE. It’s less than US$7 per article (see the section on “How much does arXiv cost to operate? ” in the arXiv Support FAQ).

This much lower cost was mentioned (at the 48:35 min. point in the video) by Ivy Anderson, Director of Collection Development and Management at the California Digital Library, the second speaker in the event at Columbia University (whose presentation begins at the 18:50 min. point in the video). However, she also pointed out that arXiv is primarily a repository. It’s not a publishing platform.

Although submission to the arXiv doesn’t involve peer review, there is an arXiv moderation system. Excerpt:

The arXiv moderators are experts in their fields and in the types of submissions that are appropriate for their subject classifications. They evaluate based on the content of the submission and the policies of arXiv.

In an analogous way, the OA collection PLoS Currents: Influenza also uses a Board of Expert Moderators. In the PLoS Currents FAQs, it’s stated (here) that:

There are currently no publication charges for PLoS Currents. However, it is possible that we will introduce a small publication charge in future to cover the running costs.

It’s also stated, near the bottom of the same FAQs page, that: “We intend PLoS Currents: Influenza to be the prototype for additional PLoS Currents sites“.

Comments: The entire video (Who Pays For Open Access?) is recommended, including the presentation by the third speaker (Bettina Goerner, Manager, Open Access for Springer, beginning at 51:40 min. in the video) and the discussion session (beginning at 72:25 min.).

So, how best to increase the cost-effectiveness of quality-filtration of the research and scholarly literature? One can ask (as does Mike Rossner at the 17:40 min. point in the video): “Has the revolution in searchability negated the utility of selective journals as filters of information?“. He thinks that it hasn’t (and won’t for some time).

Perhaps, if PLoS Currents: Influenza is successful, in that it’s valued by it’s users and it’s running costs are low, then this peer moderation-based approach to quality-filtration of contributions to specified areas of research may flourish, as it has for those specified areas served by the arXiv.

It’s noteworthy that some basic article-level metrics (ALMs) are also provided for each contribution to PLoS Currents: Influenza. These include statistics about “Views” and “Comments“, together with “Ratings“. One need not wait for citation data in order to obtain some guidance about those contributions to this collection that are already attracting attention.

For more about the need for sophisticated ALMs, see: Article-Level Metrics and the Evolution of Scientific Impact by Cameron Neylon and Shirley Wu, PLoS Biol 2009(Nov); 7(11): e1000242. See also the “Metrics” and “Comments” that are attached to this same article.

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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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arXiv repository to be enhanced

Stimulus grant to enhance arXiv e-preprints for scientists by Bill Steele, Chronicle Online, Cornell University, November 17, 2009. Excerpts:

Soon, Cornell’s e-print arXiv of scientific papers will evolve from a simple database to a place where “authors, articles, databases and readers talk to each other” to help users identify a work’s main concepts, see research reports in context and easily find related work.


Other enhancements will provide interoperability with such research sites as PubMedCentral and provisions to allow scientists to contribute in newer, more flexible text formats.

Researchers might be more enthusiastic about participating in open access journals and repositories if they could see that their work was more accessible and usable, [Paul] Ginsparg suggested. “And perhaps the academic community will again play a role at the forefront as the semantic Web 3.0 rolls out,” he said. Academic publishing has lagged behind the commercial Internet in providing interactive enhancements that today’s students take for granted, he explained. “Configuring research communications infrastructure for the next generation of researchers requires getting into the heads of near-term future researchers — undergrads and grad students — coming of age in the Google/Facebook/Twitter era.”

Found via posts in [Digital & Scholarly] and [Open Access News].

Comment: The arXiv repository has been at the forefront of the Green route to OA. The proposed enhancements may once again permit it to play a leadership role. These enhancements are intended to add value of a kind that will enhance the appeal of repositories to a wider range of users.

Green OA mandates implemented by funding agencies and universities can be regarded as “sticks”, designed to push appropriate content into repositories. Enhancements of the kind being proposed for the arXiv can be regarded as “carrots”, designed to pull a variety of users toward repositories. The latter approach has, so far, received less attention from OA advocates than the former.

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OA repository launched by ResearchGATE

News release received via email on September 15, 2009 (Subject: Open Access on ResearchGATE):

ResearchGATE launches Self-Archiving Repository

Scientific Online Network ResearchGATE blazes a new route into the world of Open Access

Boston, September 15th 2009. The last few weeks have been big here at ResearchGATE (, the world’s largest online scientific platform. We have only been online since May last year, but already have 140,000 members. Recently, we introduced our international Job Board for Science and Higher Education. But today is set to be even bigger, as we are launching our Self-Archiving Repository. This will make full-text articles available to the public, for free – the first application of its kind worldwide!

Currently, there is no way for researchers to access millions of publications in their full version online. ResearchGATE is now changing this by enabling users to upload their published research directly to their profile pages (a system called the “green route” to Open Access). Our publication index, containing metadata for 35 million publications, will be automatically matched with the SHERPA RoMEO ( data set of journal and publisher’s self-archiving agreements. As a result, authors will know which versions of their articles they can legally upload. Since nine out of ten journals allow self-archiving, this project could give thousands of researchers immediate access to articles that are not yet freely available.

Our Self-Archiving Repository does not infringe on copyrights because each profile page within ResearchGATE is legally considered the personal website of the user (and the majority of journal publishers allow articles to be openly accessible on personal homepages). Therefore, each user can upload his or her published articles in compliance with self-archiving regulations. Our publication index makes every publication identifiable and is searchable. Since each profile is networked to the larger platform, the uploaded resources will form an enormous pool of research for our members. Of course, it’s free of charge, like the all the other resources at ResearchGATE.

To learn more about ResearchGATE and its many features, visit and sign up for a free profile. Also, feel free to contact me directly or our team at

To learn more about Self-Archiving, visit

Hannah Elmer

Marketing & PR

Excerpt from the Self Archiving webpage:

Self-archive with ResearchGATE

Self-archiving over a ResearchGATE profile page offers many advantages. The ResearchGATE search engines will display your publications among their results and the ResearchGATE semantic matching tool will recommended your articles to other users. These unique resources promote your work to the thousands of researchers who use the site daily. Additionally, publications archived on ResearchGATE are easily found by Google and other external search engines, so they are still retrievable through more traditional means. Since the publications are linked to your personal profile, all traffic they attract will be directed over your site, which further improves the visibility both of you as a researcher and of your other projects.

Comment: No confidentiality statement was attached to the email message, which was sent to members of ResearchGATE. However, so far, this news release doesn’t seem to have been cached by Google. ResearchGATE’s approach to self-archiving differs from that of Scholas. The latter site is intended for “Social File-Sharing for Academics“. For a brief commentary about Scholas, see: SCHOLAS: OnLine Academic Sharing Service, DE Tools of the Trade, August 31st, 2009.

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Medicine needs OA journals?

The blog post: Do We Need Open Access Journals? by Glyn Moody (July 10, 2009) has attracted some attention. [Connotea bookmark][FriendFeed search]. It’s a commentary about: Citing and Reading Behaviours in High-Energy Physics. How a Community Stopped Worrying about Journals and Learned to Love Repositories, by Anne Gentil-Beccot, Salvatore Mele and Travis Brooks (arXiv, June 30, 2009). [Connotea bookmark][Twitter entry].

Examples of Comments about the blog post:

Gunther Eysenbach:

I would argue that there are significant differences depending on the discipline / subject matter involved, and that it is probably not legitimate to extrapolate from high energy physics to the entire [field] of STM publishing. For example, in the field of medicine, where the potential audience is very large and goes well beyond a small group of researchers/experts in a highly specialized field, things like peer-review and sending out press releases – roles fulfilled by open access journals but not repositories – are by no means “ancillary to the main business of getting the information out there”, but rather at the core of knowledge translation from “bench to bedside”, protecting the public from quackery/information tainted by commercial interests (peer-review) and at the same time helping knowledge uptake (press-releases, editorials etc).

Glyn Moody:

Yes, I think that’s a good point. In the HEP community, you’re able to look after yourself (provided you can do the maths), but maybe in the fields of medicine there is a far wider, and less expert audience – GPs, for example. And so the mediating, filtering, authenticating role of open access publishers assumes a greater importance.

Indeed, it’s probably no coincidence that open access began in HEP, with arXiv, and that this result is also in HEP.

Comment: I agree with Gunther Eysenbach that, at present, journals add significant value, including the brand recognition that’s been earned by high-impact journals. However, perhaps the evolving social media may play increasingly important mediating, filtering, authenticating (and even brand recognition) roles?

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Canada joins PMC International

Canada Joins International Effort to Provide Access to Health Research:  “PubMed Central repository will open new pathway to Canadian health research“, News Release, Canadian Institutes of Health Research (CIHR), July 6, 2009. [Connotea bookmark][FriendFeed entry]. Excerpt:

The Canadian Institutes of Health Research (CIHR), the National Research Council’s Canada Institute for Scientific and Technical Information (NRC-CISTI), and the US National Library of Medicine (NLM) have announced a three-way partnership to establish PubMed Central Canada (PMC Canada). PMC Canada will be a national digital repository of peer-reviewed health and life sciences literature, including research resulting from CIHR funding. This searchable Web-based repository will be permanent, stable and freely accessible.

See also: PMC International (PMCI). Excerpt:

To date, NLM [US National Library of Medicine] has authorized two PMCI centers: UKPMC and PMC Canada.

Some background: PubMed Central Canada (PMC Canada) initiative, Kumiko Vezina, OA Librarian, September 17, 2008. Excerpt:

Before this [PMC Canada] can go forward, however, the second and final step of the agreement process must be completed. That would be for CISTI and CIHR to jointly approach the US National Library Medicine to co-sponsor the service, as a mirror site to PubMed Central therefore obtaining a 3-way agreement between CISTI, CIHR and the US National Library of Medicine to ‘officially’ enter into the PubMed Central International (PMCI) network. Once the final agreement is in place, development will begin on the first phase of PMC Canada thus enabling CIHR researchers to deposit their publications into PubMed Central.

More background information is available from the NRC-CISTI Partnership Development Office. (The current version of this webpage was last updated on February 12, 2009).

Comment: It’s good news that the 3-way partnership is now in place. The initial release of PMC Canada is expected to be available in the fall of 2009.

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