O'Really?

February 15, 2012

The Open Access Irony Awards: Naming and shaming them

Ask me about open access by mollyaliOpen Access (OA) publishing aims to make the results of scientific research available to the widest possible audience. Scientific papers that are published in Open Access journals are freely available for crucial data mining and for anyone or anything to read, wherever they may be.

In the last ten years, the Open Access movement has made huge progress in allowing:

“any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers.”

But there is still a long way to go yet, as much of the world’s scientific knowledge remains locked up behind publisher’s paywalls, unavailable for re-use by text-mining software and inaccessible to the public, who often funded the research through taxation.

Openly ironic?

ironicIronically, some of the papers that are inaccessible discuss or even champion the very Open Access movement itself. Sometimes the lack of access is deliberate, other times accidental – but the consequences are serious. Whether deliberate or accidental, restricted access to public scientific knowledge is slowing scientific progress [1]. Sometimes the best way to make a serious point is to have a laugh and joke about it. This is what the Open Access Irony Awards do, by gathering all the offenders in one place, we can laugh and make a serious point at the same time by naming and shaming the papers in question.

To get the ball rolling, here is are some examples:

  • The Lancet owned by Evilseviersorry I mean Elsevier, recently  published a paper on “the case for open data” [2] (please login to access article). Login?! Not very open…
  • Serial offender and über-journal Science has an article by Elias Zerhouni on the NIH public access policy [3] (Subscribe/Join AAAS to View Full Text), another on “making data maximally available” [4] (Subscribe/Join AAAS to View Full Text) and another on a high profile advocate of open science [5] (Buy Access to This Article to View Full Text) Irony of ironies.
  • From Nature Publishing Group comes a fascinating paper about harnessing the wisdom of the crowds to predict protein structures [6]. Not only have members of the tax-paying public funded this work, they actually did some of the work too! But unfortunately they have to pay to see the paper describing their results. Ironic? Also, another published in Nature Medicine proclaims the “delay in sharing research data is costing lives” [1] (instant access only $32!)
  • From the British Medical Journal (BMJ) comes the worrying news of dodgy American laws that will lock up valuable scientific data behind paywalls [7] (please subscribe or pay below). Ironic? *
  • The “green” road to Open Access publishing involves authors uploading their manuscript to self-archive the data in some kind of  public repository. But there are many social, political and technical barriers to this, and they have been well documented [8]. You could find out about them in this paper [8], but it appears that the author hasn’t self-archived the paper or taken the “gold” road and pulished in an Open Access journal. Ironic?
  • Last, but not least, it would be interesting to know what commercial publishers make of all this text-mining magic in Science [9], but we would have to pay $24 to find out. Ironic?

These are just a small selection from amongst many. If you would like to nominate a paper for an Open Access Irony Award, simply post it to the group on Citeulike or group on Mendeley. Please feel free to start your own group elsewhere if you’re not on Citeulike or Mendeley. The name of this award probably originated from an idea Jonathan Eisen, picked up by Joe Dunckley and Matthew Cockerill at BioMed Central (see tweet below). So thanks to them for the inspiration.

For added ironic amusement, take a screenshot of the offending article and post it to the Flickr group. Sometimes the shame is too much, and articles are retrospectively made open access so a screenshot will preserve the irony.

Join us in poking fun at the crazy business of academic publishing, while making a serious point about the lack of Open Access to scientific data.

References

  1. Sommer, Josh (2010). The delay in sharing research data is costing lives Nature Medicine, 16 (7), 744-744 DOI: 10.1038/nm0710-744
  2. Boulton, G., Rawlins, M., Vallance, P., & Walport, M. (2011). Science as a public enterprise: the case for open data The Lancet, 377 (9778), 1633-1635 DOI: 10.1016/S0140-6736(11)60647-8
  3. Zerhouni, Elias (2004). Information Access: NIH Public Access Policy Science, 306 (5703), 1895-1895 DOI: 10.1126/science.1106929
  4. Hanson, B., Sugden, A., & Alberts, B. (2011). Making Data Maximally Available Science, 331 (6018), 649-649 DOI: 10.1126/science.1203354
  5. Kaiser, Jocelyn (2012). Profile of Stephen Friend at Sage Bionetworks: The Visionary Science, 335 (6069), 651-653 DOI: 10.1126/science.335.6069.651
  6. Cooper, S., Khatib, F., Treuille, A., Barbero, J., Lee, J., Beenen, M., Leaver-Fay, A., Baker, D., Popović, Z., & players, F. (2010). Predicting protein structures with a multiplayer online game Nature, 466 (7307), 756-760 DOI: 10.1038/nature09304
  7. Epstein, Keith (2012). Scientists are urged to oppose new US legislation that will put studies behind a pay wall BMJ, 344 (jan17 3) DOI: 10.1136/bmj.e452
  8. Kim, Jihyun (2010). Faculty self-archiving: Motivations and barriers Journal of the American Society for Information Science and Technology DOI: 10.1002/asi.21336
  9. Smit, Eefke, & Van Der Graaf, M. (2012). Journal article mining: the scholarly publishers’ perspective Learned Publishing, 25 (1), 35-46 DOI: 10.1087/20120106

[CC licensed picture "ask me about open access" by mollyali.]

* Please note, some research articles in BMJ are available by Open Access, but news articles like [7] are not. Thanks to Trish Groves at BMJ for bringing this to my attention after this blog post was published. Also, some “articles” here are in a grey area for open access, particularly “journalistic” stuff like news, editorials and correspondence, as pointed out by Becky Furlong. See tweets below…

July 27, 2010

Twenty million papers in PubMed: a triumph or a tragedy?

pubmed.govA quick search on pubmed.gov today reveals that the freely available American database of biomedical literature has just passed the 20 million citations mark*. Should we celebrate or commiserate passing this landmark figure? Is it a triumph or a tragedy that PubMed® is the size it is? (more…)

August 24, 2009

I bet you think this blog is about you, don’t you?

Science Online London 2009Last Saturday, The Royal Institution of Great Britain (R.I.) hosted a conference called Science Online London (#solo09) co-organised by mendeley.com and network.nature.com. The event centred around the fantastic Faraday Theatre which according to the R.I. is a “beautiful, historic theatre [which] has deeply raked seating that creates an intimate atmosphere, even when full to capacity”. Absolutely. Just like last year, this event attracted delegates and speakers from a wide range of backgrounds in science, publishing and communication from around the world. This post is an approximately alphabetically ordered link-fest of some of the people involved. People are, after all, the most interesting thing about any conference. If you’re not listed here it’s not because I don’t like you (honest!) it’s because we didn’t speak or I didn’t listen or (unlike many people) you’re not vain enough [1] to have a have a blog (yet) :-)

Now I’m told the presentations mentioned above will be on Nature Precedings in due course, which will be good. Thanks to all the organisers, speakers and participants this year that made Science Online London 2009 well worth attending. Hopefully see some more of you again next year!

References

  1. Carly Simon (1972) You’re So Vain
  2. Geoffrey Bilder (2006). In Google We Trust? Journal of Electronic Publishing, 9 (1) DOI: 10.3998/3336451.0009.101
  3. Matt Brown (2008). Venerable institute gets a refit Nature, 453 (7195), 568-569 DOI: 10.1038/453568a
  4. Matt Brown (2008). Reimagining the Royal Institution Nature, 453 (7195), 595-595 DOI: 10.1038/453595a
  5. Duncan Hull (2009). Slides from the author identity session: Authenticating Scientists with OpenID
  6. Jennifer Rohn and Richard P. Grant (2009). Pre-conference video: Live Roof Surfing at Mendeley Fringe Frivolous

April 2, 2009

Upcoming Gig: Science Foo Camp (scifoo) 2009

Google Classic: Please Allow 30 Days for your Search ResultsIn my inbox this morning, an intriguing email from Timo Hannay, Tim O’Reilly and Chris DiBona:

Duncan,

We’d like to invite you to join us for Science Foo Camp (or “Sci Foo”), a unique, invitation-only gathering organized by Nature, O’Reilly Media, and Google, and hosted at the Googleplex in Mountain View, California.

Now in its fourth year, Sci Foo is achieving cult status among those with a passion for science and technology. Nobel laureate Frank Wilczek wrote of last year’s event:

“SciFoo is a conference like no other. It brings together a mad mix from the worlds of science, technology, and other branches of the ineffable Third Culture at the Google campus in Mountain View. Improvised, loose, massively parallel–it’s a happening. If you’re not overwhelmed by the rush of ideas then you’re not paying attention.”

As before, we will be inviting about 200 people from around the world who are doing groundbreaking work in diverse areas of science and technology. Participants will include not only researchers, but also writers, educators, artists, policy makers, investors, and other thought leaders.

The format is highly informal: all delegates are also presenters and demonstrators; the schedule is determined collaboratively on the first evening; and sessions continue to be organized and re-organized throughout the weekend. This creates a unique opportunity to explore topics that transcend traditional boundaries, and discussions are of a kind that happens at the best conferences during breaks and late into the night. Of course, there will also be time to have fun and relax at Google’s legendary campus.

Sci Foo 2009 will run from about 6pm on Friday, July 10 until after lunch on Sunday, July 12. Campers need to make their own way to and from the event, but Google will provide accommodation and meals, and there is no registration fee. For those who don’t have cars, there will also be free shuttle buses between the hotel and the Googleplex.

Please RSVP  etc

We hope to see you at the Googleplex in July!

Tim O’Reilly, O’Reilly Media
Chris DiBona, Google
Timo Hannay, Nature

About Nature Publishing Group

Nature Publishing Group (NPG) is dedicated to serving the information and communication needs of scientists and medics. NPG’s flagship title, Nature, first published in 1869, has now been joined by over 80 other titles, among them the Nature research journals, Nature Reviews, Nature Clinical Practice and a range of prestigious academic journals including society-owned publications. It also operates the leading scientific website, Nature.com, and a range of innovative online services, from databases to collaboration tools and podcasts.

About O’Reilly Media

O’Reilly Media spreads the knowledge of innovators through its books, online services, magazines, and conferences. Since 1978, O’Reilly has been a chronicler and catalyst of leading-edge development, homing in on the technology trends that really matter and spurring their adoption by amplifying “faint signals” from the alpha geeks who are creating the future. Whether it’s delivered in print, online, or in person, everything O’Reilly produces reflects the company’s unshakeable belief in the power of information to spur innovation. An active participant in the technology community, the company has a long history of advocacy, meme-making, and evangelism.

About Google Inc.

Google’s Philosophy – Never settle for the best “The perfect search engine,” says Google co-founder Larry Page, “would understand exactly what you mean and give back exactly what you want.” Given the state of search technology today, that’s a far-reaching vision requiring research, development, and innovation to realize. Google is committed to blazing that trail. Though acknowledged as the world’s leading search technology company, Google’s goal is to provide a much higher level of service to all those who seek information, whether they’re at a desk in Boston, driving through Bonn, or strolling in Bangkok.

About Foo Camps

The “Foo Camp” meeting format has been pioneered by O’Reilly (see when geeks go camping). In this context, “Foo” originally stood for “Friends Of O’Reilly“, but it is also a meaningless ‘placeholder word’ commonly used by computer programmers, rather like the term ‘X’ in algebra. The success of O’Reilly’s original technology Foo Camps has stimulated a wide range of similar events, from Science Foo Camp to Disney’s Pooh Camp.

Obviously I’m thrilled to bits to receive such an email, I’ve been to scifoo once before and it was a fantastic mind-blowing experience. This time, I’m invited as a consolation prize for being a runner-up in the international science blogging challenge 2009 which challenged younger scientists to get a senior scientist to blog. I managed to convince Douglas Kell and David DeRoure to start blogs, so thanks are due to them for entering into the spirit of the competition. This year, the first prize was won by Russ Altman and Shirley Wu at Stanford University, congratulations Shirley and Russ, it will be good to compare scientific blogging notes with you both.

Now, it would have been good to win this prize, but the invite above is probably one of the best runner-up prizes I’ve ever had. Thanks are due to the competition judges Cameron Neylon, Peter Murray-Rust and Richard P. Grant for organising the competition. Thanks also to Tim O’Reilly, Timo Hannay and Chris DiBona, see you in the Googleplex!

[More commentary on this post over at friendfeed]

September 12, 2008

Blogging Professors: Big Boffins with Blogs

Jeffrey Bates by Julian CashI’ve been hunting all over the interweb looking for Professors that have blogs. While it would be a good thing if there were more, (see the science blogging challenge 2008), there are surprising amount of big boffins that already blog. I should say that by big, I mean (full) professor. By boffin I mean a person practicing science including biology, chemistry, physics, mathematics, engineering and hell, even computer “science” and the “dismal science” of economics too. By blog I mean, a web-log or a lab-log which is personal, frequently updated (with web feed) and allows comments. Here is my collection of big boffins with blogs, with a little help from friendfeed.com [1]. It is ordered alphabetically by surname and I hope it gives a flavour of some of the bloggers out there on the Web. If you know any more, please let me know. (more…)

September 4, 2008

Famous for fifteen people

Marilyn Monroe by Andy Warhol (and oddsock)The artist Andy Warhol once said:

“In the future everybody will be world famous for fifteen minutes”.

This well worn saying has been quoted and misquoted in hundreds of different ways in the forty years since Warhol first coined it [1].

Bad Scientist Ben Goldacre, in his keynote speech* at Science Blogging (sciblog) 2008, highlighted one of these deliberate misquotes, which he attributed to NTK.net (Need To Know: Britain’s most sarcastic high-tech weekly newsletter). It goes a little something like this:

“On the internet everybody can be world famous for fifteen people“.

This wonderful expression captures the nature and scale of science blogging on the internet today in a nutshell. Personally, I think it also sums up much of the spirit of the Science Blogging 2008 conference as well. In total, around eight groups of fifteen people, attended the conference. It was physically impossible to talk to all of them in one day, especially since I had to slink off early at 7pm, but I did manage to meet the following people: (more…)

February 29, 2008

Lablogs

Filed under: lablogs — Duncan Hull @ 11:26 am
Tags: , , , , , , , ,

Some notes from a workshop on blog-based laboratory notebooks “LaBlogs” (Laboratory Logs / Weblogs) held at the Cosener’s House in Abingdon, Oxfordshire, hosted by Cameron Neylon, a protein biochemist based at the Rutherford Appleton Laboratory (RAL) and the University of Southampton. (more…)

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