“”https://www.wikigenes.org/“>WikiGenes is the first wiki system to combine the collaborative and largely altruistic possibilities of wikis with explicit authorship. In view of the extraordinary success of ”https://en.wikipedia.org/wiki/Wikipedia">Wikipedia there remains no doubt about the potential of collaborative publishing, yet its adoption in science has been limited." So writes Robert Hofmann of MIT in a Perspective article in the September edition of Nature Genetics (40, 1047-1051; 2008) about this “dynamic collaborative knowledge base for the life sciences that provides authors with due credit and that can evolve via continual revision and traditional peer review into a rigorous scientific tool.” From the article:

In WikiGenes, authorship tracking technology enables users to directly identify the source of every word. This was not possible in first generation wikis, although authorship is essential to acknowledge contributors and to appraise the reliability of information. On the basis of clear authorship attribution, users can rate each other, and a self-regulating reputation system can be implemented. This is useful to address quality maintenance and the problem of editing conflicts, which used to depend on slow and theoretically refutable top-down decisions. To facilitate contribution and unambiguous use of scientific language, WikiGenes enables editing of articles in their final layout and citation of scientific terminology and references through integrated database and ontology lookups. All contributions to WikiGenes will be open access.

The full article can be read and edited here, at the WikiGenes website.

On the topic of the ‘data deluge’, Sarah Kemmitt notes at Nature Network that the UK Government has opted for an increasingly used technique (see, for example, Elsevier’s Grand Challenge) to scope ideas for a strategy for how to make best use of interrelated information.

Sarah refers to the British Cabinet Office’s Power of Information Taskforce project ‘Show Us a Better Way’, which is asking for suggestions to develop better ways to publish the vast swathes of non-personal information that the government collects and creates, using the incentive of a competition (here is a BBC article about the initiative). From the Show Us a Better Way website:

Ever been frustrated that you can’t find out something that ought to be easy to find? Ever been baffled by league tables or ‘performance indicators’? Do you think that better use of public information could improve health, education, justice or society at large?

The UK Government wants to hear your ideas for new products that could improve the way public information is communicated. The Power of Information Taskforce is running a competition on the Government’s behalf, and we have a £20,000 prize fund to develop the best ideas to the next level. You can see the type of thing we are are looking for here.

To show they are serious, the Government is making available gigabytes of new or previously invisible public information especially for people to use in this competition.

Yesterday (8 July), a week after the competition was announced, 150 ideas had been submitted. Sarah finds it interesting that both business and government are realizing that the ‘power of the crowd’ and offering a prize may be a cost-effective way of harnessing innovative ideas around postmodern challenges. Your views are welcome at her Nature Network post.

Sarah is part of the British Library TalkScience team, and is a co-founder of the Nature Network group Scientific Researchers and Web 2.0: Social Not-working? All are welcome to join the group and contribute to the conversation, in advance of a meeting in September for a focused discussion of the topic.

In its July Editorial Wouldn’t you like to know?, Nature Physics (4, 505; 2008) asks how much of the mass of information available online in encyclopaedic form can be trusted. The Editorial discusses various sources: Wikipedia, of course; Citizendium (with its associated Eduzendium); Scholarpedia ; and a brief mention of Encyclopaedia Britannica, which has just begun experimenting with user-generated input (although not noted in the Editorial).

Scholarpedia is the most recent of these resources, and says of itself that it “feels and looks like Wikipedia – the free encyclopedia that anyone can edit. Indeed, both are powered by the same program – MediaWiki. Both allow visitors to review and modify articles simply by clicking on the edit this article link.” Scholarpedia is said to differ from Wikipedia in that each article is written by an expert (invited or elected by the public); anonymously peer reviewed to ensure accurate and reliable information; and has a curator – typically its author — who is responsible for its content and who has to approve any proposed modifications. The website claims that, by this method, “while the initial authorship and review processes are similar to a print journal so that Scholarpedia articles could be cited, they are not frozen and outdated, but dynamic, subject to an ongoing process of improvement moderated by their curators. This allows Scholarpedia to be up-to-date, yet maintain the highest quality of content.”

The Nature Physics verdict? “Expert authorship and curatorship of free online information are indeed welcome. If scientists embrace Scholarpedia, then perhaps the opportunity to make sure that their own favourite area is well represented in its pages — as well as the possibility of citations — will prove sufficient incentive to the hard-pressed experts. The potential is huge, and so is the challenge.”

Today, 18 June, is the first anniversary of Nature Precedings, where researchers can post their unpublished manuscripts, presentations, posters, white papers, technical papers, supplementary findings and other scientific documents, which can all be “peer-reviewed” online by anyone in the scientific community. (The website was available before June 2007 in ‘beta’ form.) Santosh Patnaik, a user who periodically tracks Nature Precedings at the Nature Network Nature Precedings forum, estimates that the 500th document will be uploaded some time in the next two weeks.

Because the code for Nature Precedings is freely available, Dr Patnaik has mined some data to chart the growth of the website. His results are presented here, in graphical form. The number of posters and presentations, common when the site first launched, is now barely increasing, whereas the number of manuscript uploads has grown at a steady rate over the past year. The most popular discipline, perhaps unsurprisingly, is bioinformatics, although most other disciplines are also becoming more popular, particularly neurosience, ‘evolution and ecology’, and chemistry. (For those interested in statistics, Dr Patnaik has also estimated the productivity of Nature Precedings authors.)

One aspect of this type of open peer-review is that discussion is not limited to the English language, even though the language of uploaded documents is in English. The vast majority of comments are, however, in English: here is an example of constructive review in the neuroscience field, Nature Precedings style. There are many other examples: the most active discussions are here, but one can also filter by subject area.

Update: Hilary Spencer and the Nature Precedings team provide a one-year perspective at Nature Network.

Stephen T Huang, Maged N Kamel Boulos and Robert P Dellavalle write an article in the June issue of EMBO Reports (9, 496-499; 2008) with the title: Scientific discourse 2.0. Will your next poster session be in Second Life?

From the article:

Certainly, peer-reviewed literature and scientific meetings in the physical world will remain the main modes of distributing scientific information and informal communication. Yet, communication through virtual-world technology might become a useful supplement to the traditional discourse. The particular strengths of this technology include: its potential to share, review and comment on information, both with the public and one’s peers; options that allow users to create and develop unique objects, and presentations to educate and inform others and to display data; and, last but not least, the time and cost of bringing people together within and across disciplines can be reduced.

As with any new technology, there are issues that could have an impact on the usefulness of online communication and its acceptance within the scientific community. Scientists who rely on peer-reviewed data for their work might find Web 2.0’s lack of proofreading unacceptable to document research findings. However, we should explore the existing and potential applications of virtual communication for unique ways to discuss ideas, answer questions, educate and debate. Our ability to understand what we can accomplish in online worlds depends on our collective experience with the technology. The more scientists and clinicians who work with and comprehend the applications of virtual worlds for their respective research fields, the sooner we will realize how this technology can be best applied. The next step is to invite ourselves into these online realms, experiment with what they have to offer, and see where our exploration and creativity takes us.

(Stephen T. Huang is at Northwestern University’s Feinberg School of Medicine in Chicago, Illinois, USA; Maged N. Kamel Boulos is at the University of Plymouth, UK; Robert P. Dellavalle is at the Denver Veteran’s Affairs Medical Center and the University of Colorado Denver, Denver, Colorado, USA.)

Noah Gray, an editor at Nature Neuroscience, asks at Action Potential blog why neuroscientists are passing on the seemingly golden opportunity to communicate with one another online, for example on published articles at a journal website, or in an online journal club. Many have expressed opinions about reasons for this reticence: Noah links to some articles in his well-argued post, and you can read other thoughts (and find links to some of the same articles) at Nature Network (for example at Gobbledygook and at Flags and Lollipops).

Here, I’d like to highlight a response by “Michael” in the comment thread to Noah’s Action Potential post, as I believe this summary covers many, if not all, of the reasons why scientists in a discipline tend not to post comments on, and discuss, scientific research papers online. “Michael” writes:

I think there are a number of reasons as to why “Web 2.0” has not played much of a role in discussing neuroscience research. In no particular order:

1) Inefficiency: If I want to know why somebody used buffer x for their biochemistry experiments, or why they didn’t do control experiment xyz I email the authors, or use the phone if I know them. Why post it in the comment section of their paper, and wait for 5 weeks until they bother to check? And why does everybody else need to know about it?

2) Lack of dialogue: Commenting forums are poor venues for true dialogue. If you analyse the comment sections for the more popular entries, either here or elsewhere (for example the New York Times) there rarely is a true back-and-forth of ideas. All too often it’s 50 comments trying to be as witty as possible, with few people attempting to follow and respond to what others have written. There are rare cases where a small number of like-minded people post thoughtful comments at just the right rate to allow for a meaningful discussion. Without some type of moderation, it will remain the exception. The dynamics of a true group discussion, be it at a Journal Club or at your poster, are often taken for granted, but can’t be easily replicated online.

3) Who is commenting: It’s fine to have a democracy of opinions: in science, I don’t care so much about it. The people I want to hear/read often choose not to comment, whereas others who have nothing to say keep posting.

4) The Fear Factor: This one is obvious, and is why scientists have lab meetings or face-to-face Journal Clubs. It’s also why attempts to discuss papers online haven’t quite lived up to expectation. Ideally, we want to be honest in our opinion of a paper, but we are also human and don’t want to suffer the consequences of bruising the ego of a potential reviewer or search committee member. Staying anonymous is not the solution, since that makes it difficult for everybody else to properly evaluate the comment. After all, it does matter who is doing the criticizing.

5) Speed: Even the liveliest online discussion of a paper will drag on over hours or days. If a paper grabs my attention I will discuss at a lab meeting or Journal Club and over the course of one hour we will have thoroughly dissected it. Our attention span only lasts so long. Again, the online dynamics of who logs in at what time don’t allow for a true discourse that leads to some sort of resolution.