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The cell biology literature contains manipulated data that distort findings, usually in an attempt to 'beautify' and, rarely, to commit fraud, states the September Editorial in Nature Cell Biology (11, 1045; 2009, free to read online) According to the Editorial, a National Academy of Sciences (NAS) report, 'Ensuring the Integrity, Accessibility, and Stewardship of Research Data in the Digital Age', "arrives at no hard and fast rules; the panel found that different fields have quite different requirements. In the words of panel chairs Phillip Sharp and Daniel Kleppner, "the report provides a framework for dealing with the challenges to the community generated by the onrush of digital technology." Nevertheless, the key tenets that researchers are responsible for ensuring the integrity and accuracy of their data and appropriate training in the management of research data, that all data and experimental details from papers be publicly accessible and carefully archived to allow verification and to facilitate future discoveries, and that field-specific standards have to be developed by researchers, funders, societies and journals, benefit from being spelled out in one document."
Many of the recommendations in the report already are the policy of Nature Cell Biology and the other Nature journals: the Editorial provides further information about these, including references to past Editorials, with particular emphasis on various aspects of data manipulation and plagiarism -- which, although widely unrealised, extends to concepts as well as to copying text and illustrations.

Posted by Maxine Clarke on September 07, 2009
Categories: Access, Data availability, Ethics | Permalink | Comments (0)

Joerg Heber, a senior editor at Nature Materials, announces that access to all Editorials in the journal is now free to registered users of nature.com. This follows a similar decision taken at Nature some years ago, and more recently, by Nature Cell Biology. The August Editorial of Nature Materials (8, 611; 2009) discusses publishing models more broadly: "As moves towards open-access schemes gain momentum, the choice between 'author pays' and subscription-based models may come down to fundamental business considerations rather than limits in access to original research." In 'open access' publishing, authors pay for publication costs, and online access and dissemination of those papers is free for readers. The Editorial goes on to describe the publication model of the Nature journals, which is (in the main) subscription-based (in which the reader or institution pays for access), and which also offer various open-access services to authors, who retain copyright of their articles...."at every stage of manuscript handling we provide an expensive, high-quality service. This not only involves the professional subediting and production of accepted papers, but also an exhaustive prescreening of submitted manuscripts. At Nature Materials, we prescreen well above 80% of submitted manuscripts without peer review. This means that, at a cost, we rely much less on the 'free' peer-reviewing services of scientists than journals with lower screening rates. As open access certainly should not be considered as a way to lower publication standards, the overall expenses related to the dissemination of scientific results should be considered so that the costs remain the same. This means that research-intensive institutions in particular (or those paying for their research grants) may well end up paying proportionally more under author-pays models than they would under subscription-based models. Researchers from less research-intensive institutions on the other hand would benefit."
Read the full version of the Nature Materials editorial here.
Comments on the Editorial are welcome at the Nature Publishing Group news forum at Nature Network.

Posted by Maxine Clarke on July 29, 2009
Categories: Access | Permalink | Comments (0)

This month's (July) Nature Chemical Biology includes two articles describing how access to the highest quality chemical probes will ensure their prominent position in the biological and drug discovery toolboxes.
Aled M Edwards, Chas Bountra, David J Kerr and Timothy M Willson, in their Commentary (Nature Chemical Biology 5, 436 - 440; 2009) Open access chemical and clinical probes to support drug discovery, say that drug discovery resources in academia and industry are not used efficiently, to the detriment of industry and society. Duplication could be reduced and productivity increased, they write, by performing basic biology and clinical proofs of concept within open access industry-academia partnerships. Chemical biologists could play a central role in this effort.
The authors' main argument is that the development of new medicines is being hindered by the way in which academia and industry advance innovative targets. By generating freely available chemical and clinical probes and performing open-access science, the overall system will produce a wider range of clinically validated targets for the same total resource, arguably the most effective way to spur the development of treatments for unmet needs.
In a related article in the same issue of the journal, 'A crowdsourcing evaluation of the NIH chemical probes', Tudor I. Opera et al. (Nature Chemical Biology 5, 441-447; 2009) write that between 2004 and 2008, the US National Institutes of Health Molecular Libraries and Imaging initiative pilot phase funded 10 high-throughput screening centres, resulting in the deposition of 691 assays into PubChem and the nomination of 64 chemical probes. The authors 'crowdsourced' the Molecular Libraries and Imaging initiative output to 11 experts, who expressed medium or high levels of confidence in 48 of these 64 probes. Crowdsourcing is a cross-disciplinary alternative way to assess confidence for both chemical probes and drug leads: it pools multiple levels of expertise from translational disciplines, providing a rigorous chemical-probe evaluation process.

Nature Chemical Biology website.
Nature Chemical Biology guide to authors.
Nature Chemical Biology focuses and supplements.
Nature Chemical Biology symposium 2009: Chemical biology in drug discovery.

Posted by Maxine Clarke on July 02, 2009
Categories: Access, Data availability, Disciplines | Permalink | Comments (0)

In a Correspondence in the current issue of Nature (458; 967, 2009), Raf Aerts of the Katholieke Universiteit Leuven writes:

Your Commentaries on 'How to survive the recession' devote much discussion to the effects of the global recession on science (Nature 457, 957–963; 2009). However, the financial squeeze may also be affecting the publication output of research institutions in a more subtle way. It could be boosting the traditional reader-pays publication model for scientific journals at the expense of the author-pays, or open-access, model.
Open-access journals ask authors to pay for processing their manuscripts (which involves organizing a form of quality control, formatting and distribution) so that the final product becomes freely available, and free to use if properly attributed. This model is widely believed to increase the visibility, dissemination and, eventually, the citation and impact of research findings.
However, few peer-reviewed open-access journals have so far had a high impact factor in their field, except for a small number such as those published by the Public Library of Science and BioMed Central. They are therefore struggling to emerge and to attract the most prestigious research findings.
This situation could deteriorate further if open-access journals are forced to move to (partial) site licensing in order to cover their production costs — a shift recently undertaken by the Journal of Visualized Experiments, for example as authors become increasingly reluctant or unable to pay in the current financial climate.

(This is an slightly shortened version of the Correspondence. The full version is available online at Nature's website.)

Posted by Maxine Clarke on April 28, 2009
Categories: Access, Publishing | Permalink | Comments (2)

Roy Welch and Laura Welch of Syracuse University, New York, examine why researchers seem reluctant to be more directly involved in the annotation of microbial genomes in the February issue of Nature Reviews Microbiology (7, 90; 2009). They write:

"To annotate an organism's genome, biological information about the organism must be matched to the genes and genetic elements in the sequenced genome. The process is iterative and open-ended: new information is constantly incorporated into the annotation. It can also be recursive: analysis of the annotation may provide insight about the organism that in turn leads to changes to the annotation. Unfortunately, the generation of new information and annotation of the genome are at present completely separate processes. Often new information does not become incorporated into the annotation in a timely manner, a costly loss for those who rely on it to advance their research.
The community of expert researchers who study an organism produce most of the information that becomes part of the annotation and are also the primary group of end-users. It is therefore curious that the annotation process is circuitous and inefficient: researchers communicate new information not as direct updates to the annotation, but as research papers that must later be interpreted and incorporated into the annotation separately — most often by a third party! Indeed, some information never finds its way into the annotation. It would be far more efficient for the research community to contribute directly to genome annotation. Yet the life science community as a whole remains stuck in the old, inefficient paradigm."

The authors go on to argue that technology is not the impediment, given the wide availability of wikis (collaborative editing websites) and the databases that have been created using these technologies, including EcoliWiki, GONUTS, Myxopedia and Wikipathways. Rather, state the authors, the impediment seems to be sociological: until contributions to a genome-annotation collaborative information repository can be credited by inclusion in a PhD thesis, curriculum vitae, tenure application or grant proposal, direct collaborative annotations are unlikely to fulfil their promise and potential to accelerate scientific achievement.

Posted by Maxine Clarke on January 26, 2009
Categories: Access, Data availability | Permalink | Comments (0)

In its November Editorial, Nature Reviews Microbiology (6, 794; 2008) reports that the archive of the International Journal of Systematic and Evolutionary Microbiology (IJSEM) has been made available free online: a boon for scientists, historians and the public. The Society for General Microbiology publishes IJSEM on behalf of the International Committee on Systematics of Prokaryotes of the International Union of Microbiological Societies. The society has now provided funding for the entire back archive of the journal to be made freely available worldwide without a journal subscription. (The current content, or past two years, remains subject to access controls.)
From the Nature Reviews Microbiology Editorial: Systematics is the foundation for studies of all types of organisms, because it helps us to understand how one organism relates to another. The value of systematics is often underappreciated, however, for bacteria and viruses. For example, there is a huge imbalance between the 7,000 named bacterial species and the 1,000,000 named insect species. This is particularly important given that it is now well-known that bacteria and viruses are the most populous organisms on Earth, and furthermore, that more than 99% of bacteria have yet to be cultivated. Why should we be interested in naming and characterizing different species of bacteria? The advent of metagenomics has swelled the literature with ever-increasing estimates of numbers and types of bacteria and viruses in the biosphere. An important adjunct to genomics-based approaches is the detailed characterization of these myriad species and investigation of the relationships between them. The availability of the IJSEM archive will hopefully spur renewed interest in this area.
Jean Euzeby, the IJSEM list editor, maintains an incredibly useful web resource that details all those species that have been ratified — the List of Prokaryotic names with Standing in Nomenclature. Another useful site named Bacterial Nomenclature Up-to-Date has an up-to-date list of bacteria and is based on the work of Norbert Weiss, who maintained the database until his retirement in February 2003. The current database is maintained under the supervision of Manfred Kracht. Finally, a comprehensive taxonomy of the Bacteria and Archaea can be found in the Taxonomic Outline of Bacteria and Archaea (TOBA) Release 7.7, which was last updated in 2007.
Other useful resources are described in the Editorial.

Posted by Maxine Clarke on October 30, 2008
Categories: Access, Data availability, Education | Permalink | Comments (0)

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.)

Posted by Maxine Clarke on September 22, 2008
Categories: Access, Communication, Writing | Permalink | Comments (0)

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.

Posted by Maxine Clarke on September 08, 2008
Categories: Access, Author services, Data availability | Permalink | Comments (0)

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.

Posted by Maxine Clarke on August 06, 2008
Categories: Access, Communication, Education | Permalink | Comments (0)

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.

Posted by Maxine Clarke on July 15, 2008
Categories: Access | Permalink | Comments (0)

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.

Posted by Maxine Clarke on July 09, 2008
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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.

Posted by Maxine Clarke on June 16, 2008
Categories: Access, Publishing | Permalink | Comments (5)

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’

Posted by Maxine Clarke on May 07, 2008
Categories: Access, Disciplines, Partners | Permalink | Comments (0)

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."

Posted by Maxine Clarke on April 16, 2008
Categories: Access, Authorship | Permalink | Comments (0)

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.

Posted by Maxine Clarke on April 15, 2008
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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.

Posted by Maxine Clarke on March 26, 2008
Categories: Access, Communication, Data availability, Support | Permalink | Comments (4)

From Nature 451, 879 (2008):
Harvard University has adopted guidelines under which the 'final drafts' of academic papers written by researchers at its Faculty of Arts and Sciences will automatically be published on the university's website, unless the authors request a waiver. Immediate open access to papers could conflict with the copyright policies of many journals including Cell, Nature and Science.
Many institutions keep open-access repositories of papers but the decision makes Harvard the first US university to sign up to default open-access publishing for its research staff. Although the University of California has toyed with the idea for years, it has yet to agree on a policy.
Stuart Shieber, the computer scientist at Harvard who proposed the scheme, says that any request for an exemption will be granted. The university has not yet worked out how to define what constitutes a 'final' draft of a scholarly paper, nor come up with a time limit for submission.
Critics of open-access policies worry that highly selective journals with large readerships will suffer, and that non-peer-reviewed research will become more prominent.
A longer version of this article is available at Nature News.
There is also an online debate on the Harvard announcement in the Publishing in the New Millennium forum at Nature Network, with several updates and links to further information.

Posted by Maxine Clarke on February 27, 2008
Categories: Access | Permalink | Comments (1)

From an Editorial in today's (6 December) issue of Nature (450, 762; 2007):
Although Nature and the Nature journals are built on a business model funded by subscribers and other sources of revenue, various initiatives have been implemented to enhance the accessibility of the research papers published in these journals.
They have long been freely available to researchers in the 100 or so poorest countries through the World Health Organization's Hinari initiative and others like it. Machine access is being enhanced by the open text-mining initiative of the Nature Publishing Group (NPG). Preprints of original versions of papers can be deposited in arXiv and Nature Precedings without compromising their acceptability for publication. And final authors' versions of papers can be deposited in PubMed Central and other public servers from six months after publication. Authors retain copyright of their work, whereas NPG retains the licence to publish it.
For many years, a more generous arrangement has been made for papers reporting full genome sequences. (The paper reporting the sequence and analysis of 12 species of Drosophila is the most recent example, see Nature 450, 203; 2007). These papers are freely accessible on NPG's website from the moment of publication. This recognizes a consistent character of 'genome' papers: they represent the completion of a key and fundamental research resource, describing and reflecting on what has been revealed but not usually providing insights into mechanism. Although some papers in other disciplines might also be characterized in this way, the fundamental character of the genome has led NPG to make a systematic exception.
In the continuing drive to make papers as accessible as possible, NPG is now introducing a 'creative commons' licence for the reuse of such genome papers. The licence allows non-commercial publishers, however they might be defined, to reuse the pdf and html versions of the paper. In particular, users are free to copy, distribute, transmit and adapt the contribution, provided this is for non-commercial purposes, subject to the same or similar licence conditions and due attribution.
In 1996, as human genome sequencing was getting under way, leading players stated: "It was agreed that all human genomic sequence information, generated by centres funded for large-scale human sequencing, should be freely available and in the public domain in order to encourage research and development and to maximise its benefit to society". These principles have continued to guide the field, and NPG has consistently made genome papers freely available in keeping with them. This new licence allows us to formalize the arrangement.

Posted by Maxine Clarke on December 06, 2007
Categories: Access, Data availability | Permalink | Comments (0)

Via an industry press release, I learn that a new standard for search-engine indexing has just (29 November) been launched, called the Automated Content Access Protocol (ACAP). This standard has been devised by publishers in collaboration with search engines to "revolutionise" (the word used in the press release) the creation, dissemination and use of copyright- and licence-protected content on the internet .
According to the release, ACAP is an open, non-proprietary standard through which publishers, societies, institutions and other content providers can communicate permission for access and use to online intermediaries. ACAP provides a framework that will allow any publisher to express access and use policies in a language that search engines' robot "spiders" can be taught to understand, hence making more content available to users through search engines. Members of ACAP can be seen here.

Posted by Maxine Clarke on December 03, 2007
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Via the SciDev.Net website, I read that a new phase of the international initiative 'Online Access to Research in the Environment' (OARE) was launched on 6 November. In the first phase of the project last year, institutions from 72 countries subscribed. Now, interested institutions from another 36 developing countries will have access to an environmental and related sciences research database.
The United Nations Environment Program (UNEP) and Yale University sponsor the public-private consortium initiative. Around 350 publishing and society partners also support it, including Nature Publishing Group journals.
Primary research papers and other content in our journals are made freely available online to readers in countries that are members of HINARI, AGORA and OARE, greatly extending the reach of the papers as well as providing information in a timely fashion to people who might not otherwise be able to obtain it or obtain it promptly.
SciDev.Net is an independent online science and development network providing news, views and information about science, technology and the developing world. It is a free access website and features several articles a week from Nature, selected by the SciDev.Net editors.

Posted by Maxine Clarke on November 27, 2007
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From the current issue of Nature, News in Brief (Nature 450, 148; 2007).
"US investigators funded by the National Institutes of Health (NIH) may soon be compelled to publish only in journals that make their research papers freely available within one year of publication.
Congress is this week expected to take final votes on a bill incorporating this directive. The measure is contained in a spending bill that boosts the biomedical agency's effective budget by 3.1%, to $29.8 billion in 2008.
President George W. Bush has vowed to veto the bill, which will fund the Department of Health and Human Services and other agencies, because it includes what he calls “irresponsible and excessive” levels of spending.
But congressional Democrats have attached to the measure an unrelated but politically popular bill funding the Department of Veterans Affairs. They hope that this will generate the two-thirds support needed in both houses of Congress to override a presidential veto.
The open-access requirement in the bill would apply only during fiscal year 2008; it would need to be renewed in yearly spending bills in the future."

When a manuscript is accepted for publication in a Nature or other NPG journal, authors are encouraged to submit their version of the accepted paper (the unedited manuscript) to their funding body's archive, for public release six months after publication. Nature journals are hence already more than fulfiling the conditions in the proposed bill. In addition, we encourage authors 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. Authors should cite the publication reference and DOI number on any deposited version, and provide a link from it to the URL of the published article on the journal's website. See here for details of our licence policies.

Posted by Maxine Clarke on November 13, 2007
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Via Seven Stones blog:
Molecular Systems Biology (published by a partnership of the European Molecular Biology Organisation and Nature Publishing Group) has changed its publishing licence for all articles accepted after 1 October 2007 (see updated instruction to authors). The new procedure allows the journal's authors to choose between two Creative Commons licences: one that allows the work to be adapted by users ("attribution-noncommerical-share": by-nc-sa), the other that does not allow the work to be modified ("attribution-noncommercial-no derivative": by-nc-nd). The first articles to be published under the new licence are appearing online at the beginning of this month. The journal's content is therefore not only freely available to all, but also authors can decide to make their research fully open for reuse and adaptation.

Thomas Lemberger, EMBO editor of Molecular Systems Biology, who runs the Seven Stones blog, notes that he initially wanted to make this announcement only after the first paper published under the new licence (accepted after 1 October) had appeared online, but in light of a recent Editorial in PLoS Biology (“When Is Open Access Not Open Access?”), reviewing in detail the subtleties of publishing licenses and the concept of “open access”, he bought forward the announcement of Molecular Systems Biology's new policy. "Unfortunately, this Editorial, at the time of its publication (16 October), included erroneous information on Molecular Systems Biology, given that we had updated our policy on 1 October.", Thomas writes. "In any case, it is somewhat ironic that MacCallum chose to stigmatize Molecular Systems Biology as an example of a journal that “promulgates” confusion about open access. As it turns out, Molecular Systems Biology is dedicated to the concept of making research freely available and to engage authors themselves in decisions that would achieve this goal with their own research. It is in this spirit of openness and respect for authors that we have recently adapted our license to publish."

Posted by Maxine Clarke on November 02, 2007
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Portico and Nature Publishing Group (NPG) have signed an agreement to preserve Nature and all the other NPG journals and online databases across the life, physical and applied sciences and clinical medicine, to ensure that these publications are preserved and available for future readers.
Portico began as the Electronic-Archiving Initiative launched by JSTOR in 2002 with a grant from the Andrew W. Mellon foundation to extend the foundation's E-journal archiving programme. The goal was to build a sustainable electronic archiving model: for more than two years, project staff developed technology and discussed approaches with publishers and libraries. In 2004, the Electronic-Archiving Initiative became a part of Ithaka Harbors, Inc., a non-profit organization with a mission to accelerate the productive uses of information technologies for the benefit of higher education around the world. The electronic archiving service, known as Portico, was then developed and launched in 2005, with support from JSTOR, Ithaka, the Library of Congress and the Andrew W. Mellon foundation. The service aims to be a permanent electronic archive of scholarly journals. With the addition of the NPG titles, there are more than 6,200 publications in the archive.

Posted by Maxine Clarke on October 02, 2007
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From Nature 449, 13 (2007):
The Association of American Publishers* is taking part in an initiative to protest against what it calls government interference in the scholarly communication process.
Some groups and legislators are pushing for all publicly financed research to be made freely available to the public. Many traditional publishers object, and some have used aggressive tactics to fight the movement (see Nature 445, 347; 2007).
The initiative — called the Partnership for Research Integrity in Science and Medicine — says that it wants to provide the public with more information about scholarly publishing. One of its principles is that "society is best served by sustainable business models and reasonable copyright protections". News of the group's formation did not go down well in the blogosphere, where a number of critics attacked it for implying that open-access publication harms peer review. (*Nature's US division, Nature America, is a member of the Association of American Publishers.)

Timo Hannay, Nature Publishing Group's web publishing director, writes on Nascent blog: "Although Nature America is a member of the AAP, we are not involved in PRISM and we have not been consulted about it. NPG has supported self-archiving in various ways (from submitting manuscripts to PubMed Central on behalf of our authors to establishing Nature Precedings), and our policies are already compliant with the proposed NIH mandate." The Nature journals' policies on archiving and preprint servers can be found at our author and reviewers' website.
Timo's further thoughts and opinions about PRISM, "open-access" publishing and the manners of some individuals involved, are provided in his excellent Nascent post, which I recommend you read if you have any interest in this topic. There is a comment thread at the Nascent posting, to which you are welcome to add, or you may comment here.

Posted by Maxine Clarke on September 11, 2007
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The Nature journals this month (August) feature several editorials on the publishing process. A short round up (with links) follows:

Nature Genetics (39, 931; 2007), in 'Compete, collaborate, compel', calls for procedures for microattribution to be established by journals and databases so that data producers have an overwhelming incentive to deposit their results in public databases and thereby to receive quantitative credit for the use of every published data accession.

In 'Got data?', Nature Neuroscience (10, 931; 2007 ) points out that data sharing is not only good citizenship for researchers, but is also required by funding agencies and many journals. The scientific community needs to develop better incentives to encourage compliance and reward those who share.

And in 'Name that gene!', Nature Structural & Molecular Biology (14, 681; 2007) warns that scientists coin new terms, or neologisms, at a tremendous pace, but name choice can have unforeseen results.

Posted by Maxine Clarke on August 09, 2007
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The July issue of Molecular Systems Biology, NPG's open access journal published in partnership with EMBO (European Molecular Biology Organisation), is live. This month's featured article is Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli, by Robert Schuetz, Lars Kuepfer & Uwe Sauer (Molecular Systems Biology 3, 119; 2007), with an accompanying News and Views article by Jens Nielsen (Molecular Systems Biology 3, 126; 2007). See the journal's home page for more research papers, News and Views, Perspectives and Editorials, as well as links to systems biology papers published in the Nature journals.

Posted by Maxine Clarke on July 25, 2007
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Open Access as a model for the future? So writes Evelyn Harvey in a news report at Nature Network. Is open access publishing an unstoppable force? Does it face immovable objects in the shape of publication costs, quality control and copyright? These were questions addressed by the third Lonon open research conference last month.
The successes of open access were highlighted by some speakers: it makes research available without access barriers or subscription costs. BioMedCentral and others believe they have shown that it can be a strong publishing business model. There were also various demonstrations of personalised readership profiles that can be created using metrics such as number of times a paper is downloaded.
The problems include the removal of the main source of income for scientific societies, and a possible compromise in quality via self-publication and inadequate review.
Evelyn writes that most delegates agreed that open access is here to stay, but that big challenges lay ahead. As one researcher said when confronted with the copyright risks: “My problem isn’t plagiarism, it’s obscurity!”.
Nature's two extensive debates on access to the literature, including commissioned articles from a range of perspectives, can be read here (free access!).

Posted by Maxine Clarke on July 24, 2007
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More than 100 STM publishers, including Nature Publishing Group, and three UN organizations (WHO, FAO and UNEP) have announced the extension of programmes that provide free, or almost free, access to online peer-reviewed journals to several developing nations that lack access to information and training. Microsoft has also announced its support of technical assistance to enhance access to online research for scientists, policymakers, and librarians in these countries.
The three sister programmes – HINARI (research on health), AGORA (research on agriculture) and OARE (research in the environment) - provide online research access to more than one hundred of the world’s poorest countries. All three programmes have official commitment from their partners until 2015, marking the target for reaching the Millennium Development Goals.
In a World Health Organisation (WHO) survey conducted in 2000, researchers and academics in developing countries ranked access to subscription based journals as one of their most pressing problems. In countries with per capita income of less than $1000 per annum, 56 per cent of academic institutions surveyed had no current subscriptions to international journals. These three programmes aim to solve this problem and make research as easily accessible in countries such as Sierra Leone as it is in the United States.

Posted by Maxine Clarke on July 12, 2007
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In this post on Nascent, NPG's web publishing and science blog, Timo Hannay provides a draft of his recent article in STM news : Nascent: Foo and beyond. The whole section is worth reading (and there is a good graphic of the opportunities provided by the "scientific web"), but here is an excerpt:

"The idea that everyone can now do their own publishing, making publishers superfluous, is misguided. But publishers do need to adapt. Online communities don't just happen, they require initiators, motivators, organisers, moderators, summarisers and guides. They also need trust systems based on user identification and reputation. In many ways, these, too, are traditional publishing roles, but they require new skills. Writers and editors now need to double as moderators and hosts. Publishers need to become adept at mitigating gaming and spamming of their systems, and at monetizing web traffic rather than selling subscriptions. On top of that, they need to become better at cooperating — with each other and with other organisations outside the industry. This particularly applies to online interoperability (even horror of horrors, with competitors), which is a positive-sum game that can benefit all participants. CrossRef has blazed a trail in this area, and we should build in its success.
Above all, publishers need to be leading the online charge, not following the scientists we serve. We are the information dissemination experts, so if we aren't pushing the boundaries and testing what's possible in this new world then we're not merely missing out, we're also not doing our jobs. Cynics will point out that most apparent 'opportunities' are a long way from turning a profit, and many probably never will. They're right. Do any of the STM projects I've mentioned above make a lot of money? No. But are they representative of the future of scientific communication, and do they provide a platform on which to build information businesses of the future? You'd better believe it."

In a similar vein, Alex Palazzo of The Daily Transcript blog wrote about Nature Publishing Group's "game plan" as he calls it, regarding science publishing and web "2.0" (the social, interactive web). The post arose from Alex's attendance at Nature Network Boston's pub night. This post, and the lively set of comments accompanying it, range over the the topic of the value of publishing in a journal, "open access" publication, and whether the unit of publication will become the paper itself rather than the journal in which it is published.

Posted by Maxine Clarke on July 02, 2007
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In which I contemplate the unsung scientific record - Mind the Gap - Jennifer Rohn's blog on Nature Network

There is a very chatty conversaton happening at the above post on MInd the Gap, Jennifer Rohn's Nature Network blog. Jennifer's post is about the plea In Nature by Sydney Brenner and Richard Roberts to scientists to save their notebooks and correspondence and donate them to historians.

Jennifer writes: "Of course I agree that such materials should be preserved, which is probably why I can’t bring myself to throw away the two boxes of gently moulding lab notebooks, spanning thirteen years of research, stashed up in the loft. I’m sure these are not the papers that Brenner and Roberts had in mind, though – they want to preserve the detritus of the Watsons and Cricks of this world, not of ordinary research folk like me.
But then I got to wondering. Why not? My lab notebooks might make pretty compelling reading to some future historian starved for scraps of how 99.9% of (non-celebrity) researchers spent their days and nights in the lab. Why not document the parade of meaningless or ambiguous data that make up most researchers’ records? The ‘non-Eureka moments’, if you will? "

Join in the conversation here or at the Mind the Gap post's comments section, which has taken some fascinating tracks along avenues of clear communication and the virtue of electronic notebooks as well as the importance of a good cup of coffee.

Posted by Maxine Clarke on June 25, 2007
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Web inventor Tim Berners-Lee Unplugged: Semantic Web better than APIs for data access

Via Berlind's Testbed blog, Sir Tim Berners-Lee, inventor of the world-wide web, received the 2007 lifetime achievement award of the Massachusetts Innovation and Technology Exchange in Boston on 5 June. After the reception to honour his achievement, "Sir Tim" (as David Berlind calls him) answered questions about the semantic web, data access and standards. The session is captured on video at the link above.

Posted by Maxine Clarke on June 08, 2007
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Publisher Digitisation Service
The British Library has just launched its Publisher Digitisation Service (see link above), which, it says, is the first fully integrated journals digitization service on the market. One of the greatest challenges for a publisher undertaking a digitization of its archives is finding content -- one publisher had to locate 75% of the content for its programme from third parties. The British Library has an unrivalled collection of serial content and is aiming to save publishers time and money in locating material and providing it in online, searchable format. At the webpage linked to above are more details of the service, and a link to a downloadable PDF of the white paper 'Journal backfiles in scientific publishing.'
All the Nature journals have searchable online archives back to issue 1 available via each journal's website, except for the oldest, Nature. Nature's online, searchable archive currently extends back to 1950 but will be complete to issue 1 (4 November 1869) by the end of this year. In the meantime, the first issue of the journal is available online at the "about the journal" page of the Nature website.

Posted by Maxine Clarke on June 08, 2007
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In its June Editorial, which is freely available, Nature Chemical Biology (3, 297;2007) reports on new online features to enhance interdisciplinary communication and to increase the accessibility of chemical information for readers.

Most published chemical content is traditionally contained in the schemes, figures and tables of scientific papers. Authors also use abbreviations, acronyms or numbering schemes to identify specific molecules. Though these shorthand notations simplify the presentation of chemical information, they tend to make chemical papers less accessible to the general reader. This is a concern for chemical biology articles, which are intended to attract an interdisciplinary audience. Moreover, since the advent of the Internet, the way by which scientists acquire scientific information has changed. Though some scientists continue to read journal articles in print, most turn to the online HTML and PDF versions of published manuscripts. This expanded use of electronic resources offers an excellent opportunity to make chemical information more accessible and user-friendly to readers of scientific papers.

The Editorial provides details of the resources now available to authors and readers, and asks for your evaluation of what has been done so far, and your 'wish list' for new chemical or biological functionality that will foster communication and collaboration between researchers at the interface of chemistry and biology.

Posted by Maxine Clarke on May 30, 2007
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Microsoft's scholarly search engine, Live Search Academic, has been available in a beta (trial) version for more than a year. Launched 18 months after Google Scholar, it has a lot of catching up to do in order to make researchers aware of it and want to use it in preference to other search services. To this end, it has expanded the range of articles in its index from computing and physics only, to all disciplines. When it launched in 2006, it contained around 7 million articles; now it contains about 40 million.
Unlike Google Scholar, Live Search Academic content is not scraped remotely from the web, but uses feeds from CrossRef, HighWire, JSTOR, PubMed and others, making it part of the network of connected scholarly information. By so doing, it hopes to have better relevancy in search query returns, because the engine is indexing a regularly updated feed, is flexible and able to adapt immediately to new citation links and taxonomies. Microsoft is also aware that, as the amount of web content grows ever larger, there is a danger that services like Google Scholar will get bogged down with the sheer quantity of information that needs to be signposted. Google Scholar brings academic researchers more results, but Microsoft´s hope is that Live Search Academic results will be more relevant to users.

Posted by Maxine Clarke on May 25, 2007
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The HINARI Access to Research Initiative of the World Health Organisation has announced the registration of the 2,500th institution to access free or low-cost online medical journals and databases. These publicly funded and non-profit institutions include universities, medical schools, hospitals and research institutes drawn from 109 developing countries. Through HINARI, they are able to access 3,750 journals online from 100 different publishers covering medicine, nursing and related health and social sciences -- including Nature, the Nature journals and all journals published by Nature Publishing Group.
HINARI facilitates teaching, research and the delivery of health care in the developing world while helping researchers in these countries to get their work published and made available to a wider international audience. Access is free for institutions in countries with a GNP of less than $1000 per year while there is a small charge for countries with a GNP of $1000-$3000. The income generated is used for local training initiatives.
Launched in January 2002, HINARI Access to Research Initiative is managed by the World Health Organisation in partnership with The International Association of Scientific, Technical and Medical publishers, 100 publishers and Yale University Library. The HINARI website is the main port of call for thousands of librarians, scientists, students, medics and healthcare researchers in the world's poorest countries. They benefit from free access to the leading international biomedical peer-reviewed journals and other information resources.
There are similar initatives for agricultural research (AGORA); and climate and environmental research (OARE). Nature and all Nature Publishing Group journals are included in these programmes.

Posted by Maxine Clarke on May 25, 2007
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The Geological Society of London, one of the world's oldest national scientific and professional societies for earth scientists, is opening up its archive of published material free to anyone for four weeks from 17 May to 18 June.
The Lyell Collection represents the digitized content of the society's extensive range of publications, covering journal and book articles from the mid 1800s to the present. The Lyell Collection was created to mark the Geological Society of London's 200th anniversary, and is one of the largest integrated collections of online earth science literature.
Although a subscription will be required for full access from June 18, many aspects of the service will remain entirely free for public use. This includes a sophisticated search functionality, access to summaries and abstracts and e-mail alerts about new content as it is added.

Posted by Maxine Clarke on May 21, 2007
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Expand free journal project so poor countries can share their valuable climate data : Article : Nature

Julian Hunt, of the Department of Earth Sciences, University College London, Gower Street, London WC1E 6BT, and House of Lords, London SW1A 0PW, UK, writes in Nature's Correspondence section this week:

I warmly approve your Editorial 'Millennium development holes' (Nature 446, 347; 2007) about the lack of weather data from African and other developing countries. A further problem is that when measurements have been taken they are often not disseminated to interested organizations within their own country, let alone beyond it.
Both aspects became very apparent at the second international conference on coastal zones in sub-Saharan Africa held in Ghana in 2005 . Excellent data taken by Ghana's meteorological service along the coast, showing steadily rising temperatures and decling rainfall over 20 years, are not widely known even at the African Centre of Meteorological Application for Development at Niamey in Niger. I found a similar situation in the West Indies. These local time series show the seriousness of the problem of climate change for these countries.
There is currently no financial or other incentive to share these data. African colleagues complain that, even if they send the data to international centres, they cannot benefit, as they do not receive current issues of the journals and bulletins where the results are published.
One way forward, which I have been pursuing by lobbying UK ministers and others, is to ensure that the latest publications of such literature are sent, at no cost, to the regional and national meteorological services that are providing data in developing countries. The UN Food and Agricultural Organisation is already providing current literature to some agricultural centres in the world's poorest countries, through its AGORA programme. The OARE programme, launched last November, has similar arrangements for the environmental-science literature, including weather and climate journals — and more countries are being included in the programme next year.

These are suitable projects for extension to more countries, and for further donations from environmental and other charities. The media organizations that focus on ghoulish pictures of climatic devastation around the world might also contribute.

Nature adds: Primary research papers and other content in Nature and all Nature Publishing Group journals are made freely available online to readers in countries that are members of AGORA, OARE or HINARI, which covers health. These provide information in a timely fashion to people who might not otherwise be able to obtain it or obtain it promptly. See the author and reviewers' website for more details.

Posted by Maxine Clarke on May 18, 2007
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Copyright Clearance Center Launches Enhanced Copyright.com Site - Copyright.com

DANVERS, Mass., May 14, 2007—Copyright Clearance Center, Inc. (CCC), the world's largest provider of text-licensing solutions, today released a complete redesign and significant enhancements to its widely used web site, copyright.com. Copyright.com is the largest licensing platform on the Web for text content, with more than 1 million visits per year by corporate and academic content users. The site offers rights to millions of copyrighted works.The new site can be found here , and the changes and improvements are described here.
See here for the CCC's author pages.

Note added, 18 May. Pedro Belatro has added a comment to this post which I am also pasting-in here, for information:
Maybe it would be good to remind readers that the Copyright Clearance Center handles copyright licensing for Nature [and Nature Publishing Group] titles.
For bloggers: I had a quick look and for Nature, the licensing of up to three pictures for a non-commercial website is still free:
"This reuse request is free of charge although you are required to obtain a license through Rightslink and comply with the license terms and conditions. You will not be charged for this order."

Thank you, Pedro.

Posted by Maxine Clarke on May 17, 2007
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Three Correspondence letters in this week's Nature (447, 142; 2007) all concern information on the web, in rather different ways.
Mark Gerstein and colleagues raise the oft-discussed question of structured abstracts in journal articles: that is, an abstract that contains bold headings to introduce the text. The difference here, though, is that the structured abstract is for digital publication, and would use a web standard such as XML or OWL, to allow automated literature mining.
In another letter, Douglas Crawford highlights the Human RefSeq database as a standard for genes that have more than one name: a common occurrence. Associations between genes can only be made accurately when the gene and all its synonyms can be correctly identified. If genes in a publication were identified via RefSeq, genomic analysis would be more likely to identify genes of common interest
Finally for this week, Quentin Wheeler and Frank Krell comment on a Commentary in Nature's Linnaeus special issue. They say that mandatory online registration of taxonomic names should accompany any new species description, to ensure true accessibility and knowledge.

Posted by Maxine Clarke on May 10, 2007
Categories: Access, Author benefits, Publications | Permalink | Comments (2)

Euan Adie, on his Nature Network blog FnL, posts about Shelley Batts' Retrospectacle review of a paper about treating fruit with natural volatile compounds to make it last longer, in which she included a figure and chart from the paper (the source was cited). An editorial assistant at the Journal of the Science of Food and Agriculture – where the paper was published – threatened her with legal action unless she removed the images immediately. The blogosphere reacted with predictable speed and free-expresssion, documented in Euan's FnL post.
Euan goes on to ask whether the reaction is, in the cold light of a couple of days later, reasonable, looking at the incident both from the point of view of the publisher concerned as well as the blogger. As he puts it: "Storm in a teacup or dark conspiracy?" There is a good debate in the comments to the FnL post, so if you are interested in weighing up these pros and cons, and would like to add your take, please take a look.

Posted by Maxine Clarke on May 02, 2007
Categories: Access, Policies, Public and media, Publishing | Permalink | Comments (1)

Save your notes, drafts and printouts: today's work is tomorrow's history : Article : Nature

Sydney Brenner of the Salk Institute for Biological Studies, PO Box 85800, San Diego, California 92186, USA; and Richard Roberts of New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, USA, write in Correspondence in Nature 446, 725 (12 April 2007) | doi:10.1038/446725a:

Science is one of the greatest cultural achievements of humankind. And yet — although we assiduously preserve the preparatory sketches of artists, the drafts of novelists and the manuscript scores of composers — there is little systematic preservation of the workings of scientists. This is certainly regrettable for historical studies of modern experimental biology. Since the discovery of the double helix in 1953, biological research has flourished at an ever-increasing pace and many basic insights continue to emerge. Our knowledge of the workings of organisms from all branches of life is increasing at an unprecedented rate, making it imperative that we document the history of these discoveries.

Continue reading "Save your notes, drafts and printouts" »

Posted by Maxine Clarke on April 13, 2007
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Goals for Public Policy - Scholarly Communications Statement of Principles | RIN

The UK's Research Information Network (RIN) has brought together research institutions, publishers, funders and libraries, who have reached agreement on a statement of "the principles and goals at the heart of the scholarly communications process". The signatories so far include:
Association of Learned and Professional Society Publishers (ALPSP)
The British Library
The Consortium of Research Libraries in the British Isles (CURL)
The International Association of Scientific, Technical and Medical Publishers
The Joint Information Systems Committee (JISC)
The Publishers Association
Research Councils UK (RCUK)
The Research Information Network (RIN)
The Society of College, National and University Libraries (SCONUL)
The Wellcome Trust.

The statement can be downloaded as a PDF (8 pages). The organizations have signed up to seven principles, including the aims and quality of research; recognition and reward; dissemination, publication and access; and preservation of printed and digital output.

According to an article in Research Information, "Michael Jubb, director of RIN, admitted that ‘at one level, the statement states the blindingly obvious’, but he was keen to point out that this is the first time that all the major players have agreed on what the goals of scholarly publishing are. ‘The next step is for us all to discuss how best to achieve these goals,’ said Jubb."

Posted by Maxine Clarke on April 12, 2007
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The United Kingdom Serials Group (UKSG), in association with the online usage metrics organisation COUNTER, is funding a study to explore how online journal usage statistics might form the basis of a new metric of journal quality, the "Usage Factor". The first stage of this project involved a series of interviews with various stakeholders, and the second, current stage involves a web-based survey designed to obtain the views of many more librarians and authors than was possible for the interview stage.

If you are an author of a publication in any of the Nature or Nature Publishing Group journals, we hope you can spare a few minutes to complete this important survey, which you can do by clicking on this link. The survey aims to:

* Discover what you think about the measures that are currently used to assess the value of scholarly journals (notably impact factors);
* Gauge the potential for usage-based measures;
* Provide an opportunity for you to suggest possible different, additional measures.

See here for the author survey. It will take less than 5 minutes to do; because it is due to close by 30 March (though it may be extended for a few days), please do visit the survey site now if you are interested in contributing your views and experience.

Posted by Maxine Clarke on March 28, 2007
Categories: Access, Citation analysis, Quality measures | Permalink | Comments (0)

There is a post on Cosmic Blog about journals' embargo policies, specifically those of the journals Nature and Science. Donald Kennedy, Editor-in-Chief of Science, is quoted from a talk he gave at a conference "Best practices: covering science in cyberspace" earlier this month. Dr Kennedy suggested that print versions of papers in future might be much shorter and "user-friendly", with the full account, complete with multimedia, appearing online only.

"It's going to create a problem for the people who try to manage science news," Kennedy said. "My guess is that the embargo system will either be abandoned, in which case it'll be a free-for-all ... [or] it's certainly likely that embargoes will be shortened, and the distribution of news to mainstream news media - which used to happen in clumps so that embargoes for an entire clump could be organized - is going to happen in driblets. So there will have to be a more confusing embargo environment."

Nature's embargo policy can be found here, and an article about how its press office operates is here.

Posted by Maxine Clarke on March 26, 2007
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Nature Publishing Group is one of several publishers whose policy on picture copyright is examined on the blog Public Rambling. The verdict on us?

"In their page on rights and permission they write:

"Permission can be obtained for re-use of portions of material - ranging from a single figure to a whole paper - in books, journals/magazines, newsletters, theses/dissertations, classroom materials/academic course packs, academic conference materials, training materials (including continuing medical education), promotional materials, and web sites. Some permission requests can be granted free of charge, others carry a fee."

So it is possible to get permission to use their content but it has to be obtained on a case by case basis and it might cost money. I tried getting permissions to use pictures from a Nature Biotech paper for a educational website and it cost nothing for 1 to 3 pictures. Above that it starts costing 150 dollars. It also costs nothing to get permission to include less than 400 words but above that we have to pay. The procedure is very straightforward and can be done in a minute."

Posted by Maxine Clarke on March 13, 2007
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Despite the inroads into publishing made by the open-access journals highlighted by the News articles in Nature (445, pp 347 and 351; 2007), there is one domain where traditional for-profit publishers still reign supreme: the academic edited book containing a set of chapters written by individual authors. Such books continue to be valuable to the scientific community. Many provide a collection of works on a single topic by authors with different perspectives, all guided by an editor who is one of the leading experts in the field. Today, publishers still churn them out, but increasingly books suffer in comparison to electronic journals. By the time all the authors send in their chapters and the book is typeset, printed, and purchased by libraries and individuals, the content is likely to be out of date. Unfortunately, the academic edited book is also usually expensive and not as widely available as most journals.

To save the academic edited book, it could be reinvented as an online open-access web resource. Speedy publication would result, publication costs would be low, and the "chapters" would be free to all. The only critical losses might be that of the promotion provided by the traditional publisher and the publisher's imprint, which certifies quality. But these roles could easily be taken on by open-access publishers or professional societies. By promoting the book in their publications and website, and lending their imprimatur to the website of the book, the society or publisher would signal that they were satisfied that the editor and authors met the standard of an academic book. Furthermore, online reader annotation tools could allow the book's value to grow with time rather than dwindle.

A possible objection to this scheme is that some open-access journals publish special issues, which already provide a collection of related articles, like the chapters of an edited book. But a special issue is a somewhat different animal, because for that the journal's editors expect the same peer review process and criteria as for the normal issues of the journal. The online edited "book" - a collection of invited manuscripts - would allow the book's editor and authors to better realize their vision, with a far greater audience than with a traditional book.
Alex O. Holcombe, PhD
School of Psychology
University of Sydney
Brennan MacCallum Building (A18)
Sydney NSW 2006
Australia

Posted by Maxine Clarke on February 20, 2007
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Jim Giles reports in Nature's news pages this week about a collaborative wiki approach for sharing biological information. From the article: "Barend Mons's first objective would be ambitious enough for most people: to meld some of the most important biomedical databases into a single information resource. But that's just the beginning. Mons, a bioinformatician at the Erasmus Medical Centre in Rotterdam, the Netherlands, also wants to apply the Wikipedia philosophy. He's inviting the whole research community to help update a vast store of interlinked data. If he and his colleagues can pull it off — and even the project's advocates are not sure they can — they could transform the databases that are central to the work of many life scientists.
A test version of the project, provisionally dubbed Wiki for Professionals , is due to launch in the next month."
The rest of the story is at the news @ nature.com site, where readers can add their comments online.

Posted by Maxine Clarke on February 16, 2007
Categories: Access, Data availability | Permalink | Comments (0)

Rebels hold their own in journal price war : Article : Nature (Subscription or site licence required.)

In a News story in the current issue of Nature, "Rebels hold their own in journal price war", Declan Butler looks at what has happened since last August, when the entire editorial board of the Elsevier journal Topology quit in a row over pricing. Now the board is setting up a non-profit competitor to be published by the London Mathematical Society. The Journal of Topology, announced last week, will launch next January and will cost US$570 per year, compared with Topology's $1,665.

Over the past eight years, continues the News story, around a dozen cheap or open-access journals have been created to compete directly with an expensive commercial journal, many by editorial boards that had quit the original publication in protest. (See the News story for a table of these journals.) But do the cheaper journals fare better than their rivals?

As far as scientific credibility is concerned, the answer is often yes — many of the challengers have obtained impact factors (a measure of the citations its papers receive) higher than their competitor. Nevertheless, the rebel journals often get poor support from libraries, with subscriptions being an uphill battle for them.

Source: Nature 445, 351 (25 January 2007) | doi:10.1038/445351a; Published online 24 January 2007.

Posted by Maxine Clarke on January 29, 2007
Categories: Access, Policies, Quality measures | Permalink | Comments (0)

Q. Dear Editor
My collaborators and I just submitted a paper to Nature. We would like to know whether we can send the present paper on the physics arxiv web site (see for example xxx.lanl.gov) or if -- to respect Nature policy-- we should wait for the editorial decision.

A. Dear Author

Thank you for your message. It would be fine for you to send your preprint to the arxiv site, or any other recognised community preprint server. Please provide the arxiv reference number to the editor handling your paper for his/her information, though.

Our policy is here:

"Contributions submitted to, in press with or published in Nature must not be posted on any web site, except for preprints posted on recognized preprint servers (such as ArXiv) where this is community practice. The server concerned must be identified to the editor in the cover letter accompanying submission of the paper, and the content of the paper must not be advertised to the media by virtue of being on the preprint server, as explained fully in Nature."

Best wishes
Nature.

Posted by Maxine Clarke on December 18, 2006
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Nature Publishing Group has joined with other leading science publishers to develop a web portal called OARE (online access to research in the environment). The project provides countries in the developing world with free or reduced cost access to the scholarly environmental record, and is modelled on the HINARI and AGORA projects for health and agricultural communities, respectively, in which NPG is already a partner.

The United Nations Environment Programme, the World Health Organization, the Food and Agriculture Organization , Cornell and Yale universities are developing the OARE portal with the publishers. Yale university, for example, is contributing grants of $500,000. Its OARE activities are directed by Oswald Schmitz, professor of population and community ecology and associate dean of academic affairs for the School of Forestry & Environmental Studies, and Ann Okerson, associate university librarian for collections and international programs. As with HINARI and AGORA, Yale University library will provide much of the infrastructure for the OARE portal, via its collection of journals

OARE will use information and communication technologies, digitized global scientific information, and a creative public-private partnership to fulfill the information needs of environmental scientists in the developing world.

Further information can be found in this article by Maurice Long, publisher coordinator of these three projects.

Posted by Maxine Clarke on December 13, 2006
Categories: Access, Partners | Permalink | Comments (0)