Nascent

Last night we published a special one-off podcast on stem cells. Some of our listeners requested longer and more in depth podcasts to complement the weekly magazine show, the Nature Podcast, so this is in part a response to those requests. The show runs to an hour, and features interviews with authors from the Insight on stem cells, published in this week's issue of Nature, but also a roundtable discussion and interviews from last week's ESHRE conference in Prague. It's presented by Gareth Mitchell in the Uk and Allan Coukell in Boston, BBC and NPR, respectively.

Have a listen and let us know what you think. We'll be doing more of these one-off shows in the future, so feedback is always appreciated.

Posted by Adam Rutherford at 06:20 AM | Permalink | Comments (0)

This week's contributions to Nature's Peer Review Debate include a thought-provoking piece by Richard Akerman about the effects of information technology on peer review. It follows on nicely from Chris Anderson's article last week. Richard also has a follow-up post on his blog and a collection of related links in Connotea.

Another contribution is from our own Brenda Riley, who works on the Molecule Pages, a free information resource about the proteins involved in cellular signalling. Technically it's a database, but it's also peer-reviewed like a journal (in a process run by editors like Brenda). There are some unique challenges to this approach, which she describes.

Speaking of debate, there seems to be a lot of it going on at the Nature Newsblog, especially in response to stories about Stephen Hawking's latest theory, earthquakes in California, and the economics of open-access publishing. The latter — which has also sparked some discussion on Declan Butler's own blog and a response on the PLoS blog — is perhaps the only one that comes even vaguely within my field of expertise. I may post on it before long because there does seem to be an awful lot of nonsense being said on the topic... so why shouldn't I add to it? ;)

Posted by Timo Hannay at 06:11 PM | Permalink | Comments (0)

This week's contributions to Nature's peer review debate include a piece by Chris Anderson (of Wired and Long Tail fame) about the wisdom of crowds. It's well worth a read.

Chris himself has blogged about this here.

Posted by Timo Hannay at 06:33 PM | Permalink | Comments (0)

A few weeks ago we floated OTMI as a suggested way of opening up subscriber-only articles to text mining research.

We received a lot of very useful feedback from that initial proposal, so we decided to update the demo, incorporating some of your suggested changes and additions.

As before, each of the articles in the 23rd March 2006 issue of Nature on the Future of Scientific Computing has some code embedded in the HTML:

<link rel="OTMI" type="application/atom+xml" href="../otmi/otmi-nature04614.xml" />

Those OTMI files have now been updated a little bit. In particular, we've made the following changes or additions:

Modified the method for extracting 'snippets'

Snippets are now a slightly better approximation to sentences, but they're still not perfect. The regular expression used to split the text into snippets is given in the OTMI file, as before.

Split the text into sections

OTMI files can now label snippets, word vectors, and the other text formats we've added by the section of the article that they came from. Currently this labeling uses a controlled list of names: abstract, standfirst, body, firstpara, methods, and other. These labels can be nested (so, for example, a snippet can be in both the methods section and the body), and most of the current example files have just one section that is labeled body and other.

Added raw text and reduced text options

As well as offering the text digested as word vectors or snippets, OTMI files now include two extra text formats. The first, raw text, is the full text of an article or section with all mark-up removed. The second, reduced text, is the raw text with all stop words removed. There is obviously some redundancy between these different digests, but we are offering all of them to increase the range of options for publishers. In our example files, the abstract, standfirst and first paragraph sections contain all forms, and other sections just give the word vectors and snippet forms.

Added information about figures

As well as sections, the new OTMI files also contain a list of the titles and captions for all the figures in an article. In our example files these are given as raw text, but the ability to use any of the other text forms is available too.

Included references

Each OTMI file now has a list of DOIs for the article's references. There's also an 'and n others' element in case a reference doesn't have a DOI.

Separated stoplist

The stoplist of common words is no longer included in every file, but pointed to from the file. The stoplist is still somewhat limited, and is there mostly to illustrate the concept.

Added rights element

Each article now has basic copyright information given in the Atom entry section of the OTMI file.

Thanks go to everyone who made contributions that led to these enhancements. Our plan now is to look for further feedback on this latest suggestion, and then move on to formalising a specification and rolling out the demonstration more widely.

Please have a look at the latest version and then leave feedback, either in the comments here or via b dot lund at nature dot com.

Posted by Ben Lund at 12:54 PM | Permalink | Comments (0)

Nature.com has just released a new public link interface (resolver base URL is http://www.nature.com/openurl?) into its content using the ANSI/NISO standard “OpenURL Framework”. This now allows its users to build Web links using familiar citation-based metadata elements which complements the existing support for Web linking using the DOI, or Digital Object Identifier – a persistent and managed identifier. It allows users freedom from any proprietary link syntax. Here’s how it works.

An OpenURL link is a simple URL with a familiar querystring which is conformant to open and public specifications and provides a description of the object requested using either known identifiers (such as DOIs or PubMed identifiers, etc.) or metadata fields (from registered vocabularies). This differs from most URLs which either provide an internally hard-coded database key, or else a proprietary service structure, and thus must generally be considered to be “opaque”, i.e. they are not open to further scrutiny, other than to blind guesswork (which can be a hazardous undertaking and is also subject to change at no notice). An OpenURL, on the other hand, is defined by standards documents, and so is a reliable – and moreover “provable” – information structure.

An OpenURL can be built by a third party and targeted at one service provider, or repointed at will at another service provider. If both service providers support the OpenURL standard then both links will be successful. There is no longer any requirement to learn each and every service provider’s own proprietary API (or application programming interface). OpenURL is thus one of the great levellers within the Web information space – a veritable “glue” technology – and is being actively deployed by the digital library and scholarly publishing communities as they begin to ramp up their interoperability initiatives in support of academic and professional information sharing. (For an excellent recent review, see "Why OpenURL?" in last month’s D-Lib Magazine.)

While OpenURL is not defined as a network wire protocol – e.g. there is no prescribed response from a given link server – typically it has been used within library contexts to address the so-called “appropriate copy” problem, whereby a library with multiple subscriptions to online services could find itself (and its users) badly caught out if it did not have a subscription for a given link provider (i.e. the one issuing the link). (See this D-Lib paper for a review of the “appropriate copy” problem.) OpenURL technology instead allows for the downstream communication of an object description which an institution’s link server can then mediate (or broker) and provide the best links for its own local users using local knowledge of subscription entitlements. This is a truly remarkable – if not astonishing – development of a cooperation between publishers and their customers, which does nothing less than allow the customer to determine the final destination of network endpoints, i.e. the customer chooses what it is that is “published”.

There are two strains of OpenURL available: an early de facto “SFX” specification which is a very simple hardwired set of URL querystring keys, and the full-blown ANSI/NISO information standard Z39.88-2004: "The OpenURL Framework for Context-Sensitive Services". The Nature.com link server can handle either form, and more interestingly can handle a combination of both since there is no possibility of key collisions between the two forms so they can both co-exist on the same URL.

The Nature.com link server (resolver base URL is http://www.nature.com/openurl?) aims to link its users directly with content hosted on its platform. The recently developed CrossRef link server also has this same aim. Institutional link servers, meanwhile, may choose to “maximize” the links made available to end users – and this is something that Nature.com could pursue at some later date. OpenURL is further supported by Connotea – Nature.com’s well-known online reference management utility – which allows its users to register their own favoured link servers and so, where possible, Connotea will build outward-bound links to these link servers.

OpenURL is very definitely a technology on the move. Watch this space.

(Ooh, and, by way of being my first post here and all of that, my name is Tony Hammond and I work in Nature’s New Technology team. A strange fascination with identifiers and metadata, a long association with other climes – hot and cold, and a peculiar conviction that England might at least make the quarter-finals. It could be.)

Posted by Tony Hammond at 09:56 AM | Permalink | Comments (0)

Science is a close knit community, but often this is between small groups of people in a similar field. What if you wanted to collaborate with people in a related area? A way of finding collaborators would be good and it'd be great if they were nearby. Face to face meetings are good at getting projects started.

Well to that end, Nature has released Nature Network Boston. It is a social networking website for scientists, aimed at researchers in the Boston area, though it is not just for Bostonians. Locality lets us offer a solid events listing service to which anyone can add events. We also cover news from the Boston area, home to both MIT, Harvard, Mass General and dozens of biotech companies.

Some of the key features of the site are the groups, which allow individual communities to have their own spaces within NNB. Each user has a public profile, which tracks their activity on the site and each user has a corresponding page to track the activity of people in their social network. So you can get an at a glance with of what is happening on Nature Network Boston with hooks to explore more. Tagging is a core feature, virtually everything can be tagged and this allows for discovery of new content and bookmarking of existing content.

The application is built in Ruby on Rails, it is from the ground up, all new. We did look at a range of technologies and products, but wanted to build something tightly integrated with nature.com identity and incorporating tagging at a high level. We found Rails to be very much as advertised, using a small team we went rapidly from wireframes of site functionality to implemented, test backed code.

Giving scientists a persistent public profile, which lets them find their own voice, we hope, will raise the visibility of individual scientists and encourage early collaboration and information sharing. Nature Network Boston is a first release and we have plans for the future, more features to add and other Nature Networks to build.

Posted by Gavin Bell at 04:13 PM | Permalink | Comments (0)

If you want to see a nice concise list of Nature's funkier web projects — including the new Nature Network Boston site that Gavin's just blogged — then check out our new Launch Pad page.

As ever, this blog will continue to provide you with the latest updates on those and other web projects at Nature.

Posted by Timo Hannay at 12:20 PM | Permalink | Comments (0)

Through all the discussion in recent years about the most appropriate business models for disseminating scientific information (reader pays, authors pays, wealthy benefactor pays, and so on), at least one of science publishing's sacred cows has been left largely undisturbed. Peer review is much more central to scientific communication than any particular economic model. That might mean it's safer from disruption by the transformative effects of the web — or might mean that it represents an even more profound revolution yet to take place. Frankly, I don't know.

Which is why I'm so pleased that Nature has just launched an online debate on the topic of peer review. The first batch of contributions covers a range of perspectives and opinions (and you can post your own comments here). Readers of this blog might be most interested in the piece from Herbert Van de Sompel, who, with his colleagues at LANL, is doing some fascinating work on unbundling the process of scientific communication and automating the process of peer review.

Simultaneously, and just as importantly, Nature is conducting a peer review trial of its own. From today, submitters to the journal are being offered the option of having their manuscripts posted on a preprint server to solicit public comments. At the same time, their work will go through the usual anonymous peer review process, and both sets of comments will be considered by the editors in making their decisions.

At the end of the trial, which will last for about three months, Nature editorial staff will assess the overall value of comments from self-selected public contributors versus those from invited anonymous reviewers. At the risk of over-simplifying a bit, I think this could turn out to be an interesting test of Wisdom of Crowds theory versus Madness of Crowds theory. It will also be fascinating to see what the take-up is among submitters, not least because it constitutes something of a test of openness among scientists. I expect the proportion to vary greatly by discipline, but let's see.

It all begins here.

Posted by Timo Hannay at 05:28 PM | Permalink | Comments (10)