Citizendium calls for contributions to Biology week

Biology Week, an online “open house” for biologists, biology students and other interested people, begins today (22 September) on Citizendium, a ‘next-generation’ wiki encyclopedia started by Wikipedia co-founder Larry Sanger. (See this Peer to Peer post for a brief comparison of online encyclopaedias.)

From the Citizendium announcement: "during this week, biologists and anyone interested in the topic are invited to test the Citizendium system. Editors and authors from the project’s Biology Workgroup will be on hand to meet and greet new people on the wiki. “I strongly believe that the Citizendium system will be appealing to many scientists and scholars,” said Sanger. “Many of them just need to give it a try. Biology Week is an excuse for biologists to try out the system together.” Gareth Leng, a professor of Experimental Physiology at the University of Edinburgh, and Citizendium author and editor, described the project: ‘Our role will not be to tell readers what opinions they should hold, but to give them the means to decide, rationally, for themselves. The role of experts is critical—not to impose opinions, but to support accuracy in reporting and citing information’. "

The Citizendium, or “citizens’ compendium”, uses the same software as Wikipedia and is a public-expert hybrid project to produce a general reference resource. The community encourages general public participation, but makes a low-key, guiding role for experts. It also requires real names and asks contributors to sign a “social contract.” As a result, the project is said to be vandalism-free and, despite its youth (its public launch was just 18 months ago), has steadily added more than 8,000 articles.

Further information:

Citizendium website and press release about this project.

Biology Week homepage.

Sample article: Life, said to demonstrate the success of the collaborative-editing system.

(Thank you to Shirley Wu for alerting me to this project.)

Nature’s special issue on ‘big data’

The Big Data special package of articles in this week’s issue of Nature (4 September 2008) looks at how massive influxes of data are changing the way science is done in many fields, and includes a feature story on ‘Wikiomics’ that might be of particular interest to the scientists who work with “web 2.0” tools. Coping with floods of data is now one of science’s biggest challenges, so the Nature special issue assess the need to complement smart science with smart searching; looks at what the next Google will be; interviews the pioneering biologists who are trying to use wiki-type web pages to manage and interpret data; and recalls that the first mass data crunchers were not computers, but the remarkable women of Harvard’s Observatory. All the articles, as well as downloadable PDFs of the print versions, are free online for two weeks from the publication date. We encourage you to download everything you are interested in—and then to spread the word to friends and colleagues about what you like (and don’t like!) via email, blog, by commenting online at the Nature website, or other means. And of course, Nature always welcomes Correspondence submissions.

The contents of the Big Data ‘special’ in full:

Editorial: Community cleverness required

Researchers need to adapt their institutions and practices in response to torrents of new data — and need to complement smart science with smart searching.

Special Report: The next Google

Ten years ago this month, Google’s first employee turned up at the garage where the search engine was originally housed. What technology at a similar early stage today will have changed our world as much by 2018? Nature asked some researchers and business people to speculate — or lay out their wares. Their responses are wide ranging, but one common theme emerges: the integration of the worlds of matter and information, whether it be by the blurring of boundaries between online and real environments, touchy-feely feedback from a phone or chromosomes tucked away on databases.

Party of One column: Data wrangling

Collecting and releasing environmental data have stirred up controversy in Washington, says David Goldston, and will continue to do so.

Features: Welcome to the petacentre

What does it take to store bytes by the tens of thousands of trillions? Cory Doctorow meets the people and machines for which it’s all in a day’s work.

Features: Wikiomics

Pioneering biologists are trying to use wiki-type web pages to manage and interpret data, reports Mitch Waldrop. But will the wider research community go along with the experiment?

Commentary: How do your data grow?

Scientists need to ensure that their results will be managed for the long haul. Maintaining data takes big organization, says Clifford Lynch.

Books & Arts: Distilling meaning from data

Buried in vast streams of data are clues to new science. But we may need to craft new lenses to see them, explain Felice Frankel and Rosalind Reid.

Essay: The Harvard computers

The first mass data crunchers were people, not machines. Sue Nelson looks at the discoveries and legacy of the remarkable women of Harvard’s Observatory.

Review: The future of biocuration

To thrive, the field that links biologists and their data urgently needs structure, recognition and support. Doug Howe, Maria Costanzo, Petra Fey, Takashi Gojobori, Linda Hannick, Winston Hide, David P. Hill, Renate Kania, Mary Schaeffer, Susan St Pierre, Simon Twigger, Owen White & Seung Yon Rhee

Podcast Extra: Big Data

As Google celebrates its 10th anniversary, we find out how science is coping with massive datasets generated by unprecedented computing power. BoingBoing blogger Cory Doctorow tells us about his visits to the LHC data storage facility and the genome sequencing Sanger Centre.

Creating a digital library of mathematics

A recent Nature News story highlights efforts to create a free digital library of mathematics (Nature 454, 263; 2008). From the Nature report:

All the mathematical literature ever published runs to more han 50 million pages, with around 75,000 articles added each year. Over the past decade there have been several attempts to make this prodigious body of work accessible in a single digital archive, but so far none has succeeded.

A group of mathematicians intends to change this. They have started small, with a handful of digitization projects in Poland, Russia, Serbia and the Czech Republic. In a few years they hope to unite these repositories with their western European counterparts in an archive to be hosted by the European Union, according to the organizer, Petr Sojka, an informatics scientist at Masaryk University in Brno in the Czech Republic. Eventually this pan-European archive could be expanded globally, he says.

To make such an archive easier to search, researchers have found ways to guess the subject of a paper on the basis of the frequency of symbols in it. But there will be many more-practical challenges, such as finding the funds to scan millions of old papers and striking deals with publishers who hold rights to them.

It may already be too late to build a single free mathematical archive, according to John Ewing, head of the American Mathematical Society, which maintains a list of more than 1,500 journals whose archives have already been digitized. “A few years ago, this model had the potential to change the mathematics journal literature in profound ways,” he says. But most publishers have rushed to scan their own archives in order to lock them up and sell them to libraries.

“While the effort to digitize the smaller collections is admirable, and it’s certainly worthwhile, it’s unlikely to effect a larger change,” says Ewing.

Importance of archiving for authors in developing countries

Massimo Sandal of the University of Bologna writes in Nature Correspondence (454, 158; 2008):

Raghavendra Gadagkar (Nature 453, 450; 2008) argues that the open-access ‘pay to publish and read for free’ model leads to a disadvantage for scientists in developing countries. I disagree. Gadagkar correctly states: “page charges may be waived for authors who cannot afford to pay.” He then adds: “a model that depends on payment by authors can afford only a few such waivers.” This is not necessarily true: for example, some open-access journals provide discounts to particular institutions.

I would prefer to see what little money is available to a developing country spent on helping to publish their scientists’ papers rather than financing publishing houses based in First World countries. At present, open-access publication may be hard for those in the developing world to afford, but in the long run it will be advantageous, offering them free access to educational and academic resources.

Most important, the future of open access probably does not lie in journal publishing models. The huge success of online literature databases such as arXiv, free to publish and access, is significant. Such databases currently host mostly non-peer-reviewed preprints, and so are of little value for career building. But academic organizations throughout the world could, if they wished, build an equivalent archive of peer-reviewed papers.

I also disagree with Gadagkar’s view: “If I must choose between publishing or reading, I would choose to publish”. No one can expect to do serious science without access to the current academic literature.

Although many subscription journals are free to access online in developing countries through the HINARI, AGORA and OARE initiatives of the United Nations, the principle remains that if you cannot afford to read, you automatically cannot afford to publish. Perhaps Gadagkar will agree next time he is denied access to a fundamental paper for his research because his institution does not subscribe to it.

NPG will archive for authors

Nature Publishing Group announced this week that it will provide a free service to help authors fulfil funder and institutional mandates for the archiving of primary research papers. NPG has encouraged self-archiving since 2005. The new arrangements will provide uploading for NPG authors, starting later this year. See here for NPG’s press release announcing the service.

NPG will begin depositing authors’ accepted manuscripts with PubMed Central (PMC) and UK PubMed Central (UKPMC), meeting the requirements for authors funded by the Howard Hughes Medical Institute (HHMI), the US National Institutes of Health (NIH), The Wellcome Trust, the UK Medical Research Council and a number of other major funders in the United States, the United Kingdom and Canada that mandate deposition in either PMC or UKPMC. NPG hopes to extend the service to other archives and repositories in future.

“We are announcing our intention early in the process to solicit feedback from the community and to reassure authors that we will be providing this service,” said Steven Inchcoombe, Managing Director of NPG. “We believe this is a valuable service to authors, reducing their workload and making it simple and free to comply with mandates from their institution or funder.”

Initially, the service will be open to authors publishing original research articles in Nature, the Nature monthly journals that publish original research, and the clinical research section of Nature Clinical Practice Cardiovascular Medicine. NPG will then extend the service to society and academic journals in its portfolio that wish to participate.

For eligible authors who opt-in during the submission process, NPG will deposit the accepted version of the author’s manuscript on acceptance, setting a public release date of 6-months post-publication. There will be no charge to authors or funders for the service.

In 2005, NPG announced a self-archiving policy that encourages authors of research articles to self-archive the accepted version of their manuscript to PubMed Central or other appropriate funding body’s archive, their institution’s repositories and, if they wish, on their personal websites. In all cases, the manuscript can be made publicly accessible six months after publication. NPG’s policies are explained at our author and referees’ website.

Nature’s Managing Director on future trends in publishing

Steven Inchcoombe, who became Managing Director of Nature Publishing Group (NPG) last October, is interviewed in the June/July issue of Research Information. He answers questions about the main information needs of researchers, the role of peer-review, NPG’s position on open access, and provides some predictions for the future.

Open access means that authors or their funders may have to pay to publish papers and I think this will make them demand a higher level of service from publishers. They will want more visibility about what is happening in the publishing process. And once papers are published, authors will want to know who has accessed them as they might want to approach them about possible collaborations.

In addition, self-archiving mandates require authors to do more work. If publishers are clever they will offer authors more help to do this. Also, as more authors are not native English speakers, publishers may have to help them more in how they express themselves in their papers.

There are more and more versions of content available to readers. To justify their versions, publishers must offer serious value such as in forward and backwards citation linking.

Another big challenge will be bringing in rich media such as audio and video.

See the Research Information website for the full article.

UCSD-Nature Signaling Gateway seeks renewed funding

The USCD-Nature Signaling Gateway would like to apply for continued funding from the US National Institutes of Health. If you are a researcher in this field, or if you are interested in this area and have been reading the articles and other content on the Gateway, please show your support by writing a letter to the team via this web form, before 30 May. Your response will help keep the content on the site freely available for all users.

The UCSD-Nature Signaling Gateway is a comprehensive and up-to-the-minute resource for anyone interested in signal transduction. The gateway represents a unique collaboration between the University of California San Diego (UCSD) and Nature Publishing Group, and is designed to facilitate navigation of the complex world of research into cellular signalling. Information and data presented here are freely available to all. It is powered by the San Diego Supercomputer Center (SDSC). It has won the Association of Learned and Professional Society Publishers (ALPSP) Award for Publishing Innovation for ‘a significantly innovative approach to any aspect of publication’.

The Signaling Gateway site has three main components: a data centre (repository and toolkits); Molecule Pages (structured data on key proteins); and Signaling Update (news and comment). The Signaling Gateway is an example of a pioneering business model that allows the scientific community free access to the wealth of cell signaling information through sponsorship, described in an article by Electronic Publishing Services as ‘the door to the future’

Publishing models and publication statistics

Juan-Carlos Lopez discusses the publication process from the authors’ perspective in a couple of posts at Spoonful of Medicine, the blog of Nature Medicine. First, he shares some data to show that the Nature journals are not biased in favour of authors based in the United States. The data shown are the ratio of submitted to published papers as a function of country. Take a look.

In a subsequent post, Juan-Carlos describes a talk he gave recently in Madrid, at which he showed these data (and received some puzzling feedback), and also was asked questions about open-access publishing. He writes: “It was fascinating to see how difficult it was for some people to understand that scientific publishing costs money, and that there are different models to recover your costs — the author-pays model, the subscription model, and everything in between …… as there are different models, publishing groups ought to choose the model that works best for each of them. In our case, the subscription-based model is the only one that seems viable for the time being. How difficult is it to get this point?”

There has been some discussion related to this topic over at Nature Network in the past week, summarized here at the blog Gobbledygook. Part of this discussion involves the latest NIH (US National Institutes of Health) policy on self-archiving of research that it has funded, requiring deposition of the author’s version into the PubMedCentral database 12 months after the journal’s publication date. For authors who aren’t sure how this affects them when submitting to Nature journals, the new NIH policy is consistent with Nature Publishing Group’s existing policy, which states: “When a manuscript is accepted for publication in an NPG journal, authors are encouraged to submit the author’s version of the accepted paper (the unedited manuscript) to PubMedCentral or other appropriate funding body’s archive, for public release six months after publication. In addition, authors are encouraged to archive this version of the manuscript in their institution’s repositories and, if they wish, on their personal websites, also six months after the original publication.”

British Library surveys researchers’ attitudes to copyright

In March, the British Library conducted a survey on researchers’ attitudes and needs in the digital age. Of the respondents, 93 per cent stated that access to online research material should be the same as for books. Most of the 320 respondents agreed that, in the age of the Internet, anyone involved in non-commercial research should be allowed, via ‘fair dealing’ or exemptions, to copy parts of electronically published works, including online articles, news broadcasts, film or sound recordings. ‘Fair dealing’ is the ‘right’ to make a copy from an in-copyright work without permission from, or remuneration to, the rights holder for non-commercial research, private study, criticism, review and news reporting. For example, most individual copying by researchers at university for academic purposes is done under the fair-dealing provision in UK law. Two-thirds (68 per cent) of the survey respondents are opposed to having different fair-dealing laws for material in paper or electronic format.

Further details of the survey are available at the British Library website.

Proposal for a centralized grant repository

Noam Y. Harel of Yale University writes in Nature’s Correspondence page (Nature 452, 409; 2008):

Writing grant proposals is difficult enough; keeping track of different deadlines makes for an endless cycle of procrastination and frantic preparation. The added stack of bureaucratic forms, with arcane variations from agency to agency, can tip one over the edge as a deadline nears.

Is it almost too obvious to wish for a centralized proposal repository? Investigators could submit proposals at any time, in a common format that highlights the science rather than obliterates it with red tape. Funding agencies could search the repository for proposals matching their interests. A minimum of bureaucratic information would be required up front. Budget details could be worked out between funding agencies and investigators as necessary.

Ideally, all proposals would be publicly accessible. However, most of the scientific community has not yet accepted the inevitable dawn of truly open science. Submissions to a central repository could therefore be made accessible only to funding agencies that agree to keep proposals private (unless a submitting investigator indicates a willingness to share his or her proposal publicly).

The repository would make life easier for scientists by eliminating the hassle of searching for suitable grant mechanisms and the stress of meeting various deadlines. It would make life easier for funding agencies by expanding the pool of applications from which to choose. Of course, the best proposals could attract offers from multiple agencies. Rather than forcing investigators to choose non-overlapping sources of funding for each project, why not use the repository to mediate shared funding agreements that could benefit everyone involved? In effect, it would serve as the mediator between grant-seekers and grant-providers.

In a world where eBay, Facebook and Google powerfully demonstrate the communal nature of the Web, it is a pity that scientists and funding agencies don’t have a similarly modern forum for matching their interests and offers.