Archive for May, 2009

Updates sent to Twitter, May 2009

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

Which web 2.0 services do scientists use? Euan Adie, Nascent, May 29, 2009 [May 29]:

Article-Level Metrics at PLoS, Peter Binfield (May 27, 2009) [May 28]:

Discussion on FriendFeed about the Liebert Open Option (for paid OA) [May 28]:

Article-level citation count reports available from UKPMC [May 24]:

Open Access mandates: Judging success [May 23]:

Mendeley Bookmarklet added to PLoS articles [May 13]:

A question about Advanced Research Journals [May 10]:

What it means to be Bold in Science Publishing, Barak Shahen, May 3, 2009 [May 10]:

Searched Twitter for #openaccess [May 6]:

Bookmarks on Connotea matching the tag oa.twitter (one as of May 3, posted by Peter Suber) [May 3]:

CANADA: Open access – promises and challenges, Leslie Chan, May 3, 2009 (reprint of: [May 3]:

Research Councils UK planning to increase support for open access (BioMed Central Blog, 1 May 2009) [May 2]:

Concern about accepted manuscripts & the possibility of open access publishing (Open Research Online) [May 1]:


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Exploring OA-related tags on Twitter and FriendFeed

In a previous post, I commented that I’m experimenting with Twitter as an adjunct to the two blogs that I edit (this one, and Cancer Stem Cell News). I’m also in the early stages of experimenting with FriendFeed. For more information about these two sites, see the Wikipedia entries for Twitter and FriendFeed. Twitter is “a free social networking and micro-blogging service“, while FriendFeed is a “real-time feed aggregator” that uses “your existing social network as a tool for discovering interesting information“.

A hashtag that’s used on both sites is #OpenAccess. Results of a Twitter search for #OpenAccess revealed that a number of Twitterers have added this hashtag to “tweets” that are related to OA. (Tweets are micro-blog posts on Twitter. “Tweeps” are Twitter persons, or followers of Twitterers). See: Twitter Types – what kind of Tweep are you?).

[The next two paragraphs were revised on July 16, 2009, to remove outdated text and links, and to add some new information]:

Results of a FriendFeed search for #OpenAccess also reveals posts that have been hashtagged #OpenAccess (or #openaccess). There’s some overlap between the results of a Twitter search for this hashtag, compared with the results of a FriendFeed search for the same hashtag. Such overlap will occur if the Twitterer is also a member of FriendFeed.

The social bookmarking site Delicious (see Wikipedia entry) can also be searched for the hashtag #OpenAccess. When this search was done (on July 16, 2009), only one recent bookmark tagged #openaccess was found. It was bookmarked by Keita Bando.  Another social bookmarking site is Connotea (see Wikipedia entry) . I’ve found (on July 16, 2009) only one use of a Connotea bookmark by Keita Bando on Delicious. It’s a bookmark of this shortened URL: (which links to: The open access tracking project (OATP), Peter Suber, Open Access News, April 16, 2009). [End of revised section].

More about the OATP is available from a section of the SPARC Open Access Newsletter, issue #133, May 2, 2009. The purpose of the OATP is to use tags on Connotea in a collaborative effort to track new OA developments worldwide. For example, there’s a pipe, based on Yahoo Pipes, which starts with a Connotea feed of the most recent 100 items tagged and then removes any duplicates. An RSS feed is available (OATP 100 items no dups) via (for example) Google Reader.

Comment: Yahoo Pipes is quite a remarkable resource. For example, I’ve built a pipe which combines a Twitter search for #OpenAccess (the most recent 15 items) with the OATP pipe (but with only the most recent 15 items from Connotea, no duplicates) sorted by publication date in descending order. It shouldn’t be difficult to build a pipe that would display a combined total number of items larger than 30.

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A question about Advanced Research Journals

The post: Invitation for research paper (by Rajesh, The Scientist Community, May 5, 2009) provides information about Advanced Research Journals. The first sentence of the post:

Advanced Research Journals is one of the international publishers for Open Access journals devoted to various disciplines in science and technology.

There are links to individual journals on the left frame of the webpage. Of these, only the first three links are active at present, those to: International Journal of Drug Delivery, International Journal of Phytomedicine and International Journal of Cancer Science. To date, there have been no issues of any of these journals.

The home page of the journal provides no information about the publisher of these journals. However, when I clicked today on the logo in the upper left corner of the page, I was taken to Elsevier’s ScienceDirect.

Question: Why this link? I could not find any of the Advanced Research Journals in ScienceDirect. A Google search didn’t provide any further information about these journals.

In view of recent reports, such as this one in The Scientist (May 7, 2009; free registration required) about sponsored journals published by Elsevier, it would be of interest to find out whether or not Advanced Research Journals is sponsored by Elsevier.

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How to create an open scientific culture?

Doing science in the open, Michael Nielsen,, May 1, 2009. Excerpts:

The adoption of the journal system was achieved by subsidizing scientists who published their discoveries in journals. This same subsidy now inhibits the adoption of more effective technologies, because it continues to incentivize scientists to share their work in conventional journals and not in more modern media.


To create an open scientific culture that embraces new online tools, two challenging tasks must be achieved: first, build superb online tools; and second, cause the cultural changes necessary for those tools to be accepted. The necessity of accomplishing both these tasks is obvious, yet projects in online science often focus mostly on building tools, with cultural change an afterthought. This is a mistake, for the tools are only part of the overall picture. It took just a few years for the first scientific journals (a tool) to be developed, but many decades of cultural change before journal publication was accepted as the gold standard for judging scientific contributions.

None of this is to discount the challenge of building superb online tools. To develop such tools requires a rare combination of strong design and technical skills, and a deep understanding of how science works. The difficulty is compounded because the people who best understand how science works are scientists themselves, yet building such tools is not something scientists are typically encouraged or well suited to do. Scientific institutions reward scientists for making discoveries within the existing system of discovery; there is little space for people working to change that system. A technologically challenged head of department is unlikely to look kindly on a scientist who suggests that instead of writing papers they would like to spend their research time developing general-purpose tools to improve how science is done.

What about the second task, achieving cultural change? As any revolutionary can attest, that is a tall order. Let me describe two strategies that have been successful in the past, and that offer a template for future success. The first is a top-down strategy that has been successfully used by the open-access (OA) movement. The goal of the OA movement is to make scientific research freely available online to everyone in the world. It is an inspiring goal, and the OA movement has achieved some amazing successes. Perhaps most notably, in April 2008 the US National Institutes of Health (NIH) mandated that every paper written with the support of their grants must eventually be made open access. The NIH is the world’s largest grant agency; this decision is the scientific equivalent of successfully storming the Bastille.

The second strategy is bottom-up. It is for the people building the new online tools to also develop and boldly evangelize ways of measuring the contributions made with the tools. To understand what this means, imagine you are a scientist sitting on a committee that is deciding whether or not to hire a scientist. Their curriculum vitae reports that they have helped build an open-science wiki, and also that they write a blog. Unfortunately, the committee has no easy way of understanding the significance of these contributions, since as yet there are no broadly accepted metrics for assessing such contributions. The natural consequence is that such contributions are typically undervalued.

To make the challenge concrete, ask yourself what it would take for a description of the contribution made through blogging to be reported by a scientist on their curriculum vitae. How could you measure the different sorts of contributions a scientist can make on a blog — outreach, education and research? These are not easy questions to answer. Yet they must be answered before scientific blogging is accepted as a valuable professional scientific contribution.

Recommendation: Read the entire text of this excellent post. [Found via: The Tree of Life, Jonathan A Eisen, May 9, 2009].

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Updates sent to Twitter, April 2009

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

Association for Computing Machinery (ACM) rejects Harvard’s Copyright Addendum (but does permit Green OA) [April 30]:

The Open-Access Era (about the Personal Genome Project making genotypic and phenotypic information publicly available) [April 29]:

Data sharing in genomics — re-shaping scientific practice [April 26]:

The Semantic Web of Life Science (about the Resource Description Framework, RDF) [April 25]:

Engaging a New Generation of Authors, Reviewers & Readers through Web 2.0 (Michael Habib of Elsevier, on Slideshare) [April 25]:

Libraries around the world support OA to critical research from developing countries (Bioline International News Blog) [April 24]:

Another Canadian Health Research Funder OA Policy: CHSRF [Canadian Health Services Research Foundation][April 23]:

Semantic Enhancements of a Research Article [April 20]:

Towards agreement on best practice for publishing raw clinical trial data [April 9]:

Clickstream Data Yields High-Resolution Maps of Science (PLoS ONE 2009; 4(3): e4803) [April 9]:

From Online Journals, a New Map of Scientific Research [April 9]:

Conference on Open Access Learning, June 11-13, 2009 in Saskatoon SK [April 1]:

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