Being new to the whole subject of Science 2.0 and online social networking communities for scientists, I am taking a look today at Nature Precedings. But that brings up the matter of classification of such things.

Maybe this isn’t a social network for scientists at all, for it says on its site, “What is Nature Precedings? Nature Precedings is a permanent, citable archive for pre-publication research and preliminary findings. It is a place for researchers to share documents, including presentations, posters, white papers, technical papers, supplementary findings, and non-peer-reviewed manuscripts. It provides a rapid way to share preliminary findings, disseminate emerging results, solicit community feedback, and claim priority over discoveries. It also makes such material easy to archive, share and cite.”

And, “Nature Precedings includes materials from biology, medicine (except clinical trials), chemistry and the earth sciences … We do not include submissions in physics because there is already a service (arXiv.org) for the physical sciences.”

And, “Nature Precedings includes manuscripts, posters, and presentations, submitted in PDF, Word or PowerPoint format.”

And, “We will post submissions in all areas of chemistry, the earth sciences, and biomedicine except for clinical medicine. In particular, we cannot accept submissions describing the results of clinical trials or those making specific therapeutic claims. (More general claims, for example that a certain line of basic research may have clinical potential, are usually acceptable.)”

Whew, that was a lot of copying and pasting! But we might as well get that all established before I commence the actual writing of my own opinions in the rest of this piece.

Like most people, I tend not to linger over the terms and conditions of a site before signing up but given the wording noted above, “Nature Precedings is a permanent, citable archive …” I might just note that the terms and conditions say, “We do not undertake to keep or make available any material that you or anyone else has contributed to this website for any length or time, and you are advised to make a copy of any material that you wish to keep. We may delete, archive, make unavailable, or comment on any material, and close or suspend any discussion topic without notice.” So much for the permanent part, or am I missing something here?

Aha. Here is more on this issue:

Q: How can I be sure that anything I submit here will remain available and free-of charge?

A: Partly because we say so. But we realise that that won’t be good enough for everyone, so we are in discussions with governmental, academic and not-for-profit organisations about establishing mirror sites in order to guarantee free availability of this content in the long-term.

Okay, so if everyone is comfortable with “because we say so,” I will go ahead and register. But first, given that more and more scientists and other researchers are also bloggers, this is rather important and interesting:

Q: I posted my document on my personal website / blog. Can I also submit it to Nature Precedings?

A: Yes. We suggest that you use the form at the bottom of the document page on Nature Precedings to submit a link to the version on your personal website or blog so that readers can see comments or other additional information provided there.

Q: I posted my document on Nature Precedings. Can I also post it on my personal website / blog?

A: Yes. When authors submit documents to Nature Precedings, they retain copyright and agree to license the document under a Creative Commons Attribution 2.5 or 3.0 License. Authors are free to (re-) distribute the document as they wish. If you do post your document on your personal website or blog, we suggest that you submit a link to the version on your site.

I find this particularly interesting given that I have been recently investigating the differences between Science Commons and Creative Commons and it takes a certain amount of close reading to figure out how the various forms of the Creative Commons system work. And I was a bit befuddled because the links that Nature Precedings given here both seem to be to 2.5:

Q: I posted my document on Nature Precedings. Can I also post it on my personal website / blog?

A: Yes. When authors submit documents to Nature Precedings, they retain copyright and agree to license the document under a Creative Commons Attribution 2.5 or 3.0 License. Authors are free to (re-) distribute the document as they wish. If you do post your document on your personal website or blog, we suggest that you submit a link to the version on your site.

All this makes me makes me a little doubtful about the curatorial expertise at Nature Precedings and I would not want to rely on it as an archive — too much jocularity on important matters and sloppiness with links about copyright matters. One expects better things from such a prestige publishing house as Nature Publishing Group (NPG).

But kudos for NPG for setting up such a handsome, useful service. I will now go get registered.

Okay — that was a piece of cake. Good sign.

The homepage is quite elegant and there seems to be plenty of intriguing stuff to check out:

I checked out the process of submitting a document — very straightforward. A dropdown offers the option of manuscript, poster or presentation. We are told, “All submissions are lightly screened.”

I decided to check out what had recently been uploaded under the rubric, “Latest Manuscripts” and was impressed by the fact that there was a least one article that been received and posted on the same day, August 28, 2009. Two days seems to be the average turnaround and there were quite a few papers. This is a well-trafficked site certainly in comparison to Elsevier’s 2collab, which seems wan and blah when set side by side to Nature Precedings. It is truly odd that Elsevier just doesn’t get Science 2.0 to the extent that its far more nimble rivals NPG and Springer do. It isn’t like Elsevier doesn’t have the money or the brainpower to get into the Science 2.0 ring better. They do seem to be inviting in some brilliant experts to bring them up to speed, like Cameron Neylon.

But getting back to Nature Precedings, I browsed through the latest manuscripts. Again, all seemed handsome and a model of sleek Web design:

Nice screenshot of the papers with votes for each visible (three votes seemed a good day for each author). I clicked around and decided to check out the paper, “Jellyfish as vectors of bacterial disease for farmed fish.” Seemed like something at about my intellectual grasp as opposed to more arcane subjects such as, “Hematopoietic Cell Types: Prototype for a Revised Cell Ontology.”

Vis-a-vis the jellyfish article, it was by, “Hugh W. Ferguson et al.” I wanted to know more about Hugh W. Ferguson so clicked on his name, assuming that would take me to a profile page of him or a list of his other articles. But no, I was presented with a page highlighting the jellyfish article:

That was useful, but not what I was hoping for or expecting. Thus, Nature Precedings really does serve as an archive and repository and not so much as a social network for scientists the way Nature Networkdoes.

But let me waffle on that. Nature Precedings is a quasi social network in that when I clicked on the link for the paper up popped a beautifully arranged page showing the institutional affiliations of the authors, an email link to the main author, a PDF of the paper and so on. This is Science 2.0 at its finest.

Just think of the trouble academic librarians have in cajoling science faculty to deposit papers in institutional archives. Part of the problem for these long-suffering librarians is that researchers may (a) not see the value of archiving vis-a-vis their personal reputation and influence, (b) may not want to go to the trouble of mastering clunky software systems like Dspace (and I know some librarians will swear that it is user-friendly and all that, but I didn’t find it so), and (c) not want to have to go through library staff to archive and so don’t archive at all.

Uploading papers to Nature Precedings is as easy as pie and the results are not branded to the academic’s own institutional archive — and let’s face it would you rather have your paper on a site under the aegis of NPG or sitting in an obscure institutional repository in the middle of nowhere as far as the panjandrums that hold sway in the sciences are concerned and to which you would have to direct potential readers and the pathways of which they would have to master? Everything is so much easier on Nature Precedings.

But then again, institutional repositories are primarily for finished products, not pre-publication research and preliminary findings, which is what Nature Precedings is for. That is the problem librarians face in selling faculty on institutional repositories. Institutional repositories don’t have the immediacy and up to the minute timeliness of something like Nature Precedings and by the time the paper is finished, various versions of it may have already have made the rounds to the faculty’s peers elsewhere, thus de-incentivizing the act of archiving in institutional repositories. These are the kinds of issues that Science 2.0 brings up for the library profession.

One feature of Nature Precedings that I found really useful and slick and that anyone organizing an academic conference and who wants to ensure optimal dissemination of the resulting papers should know about is that you can create a collection that enables visitors to browse those papers. This is an ideal way to apprise those have not yet heard of your professional organization and its conferences to pique their interest in them.

For instance, I saw on the homepage of Nature Precedings that one of the highlighted collections was the International Conference on Biomedical Ontology University at Buffalo, NY. July 24-26, 2009. I clicked on that and read about the conference, was able to link out to the site of the conference itself and found this passage both edifying and a good example of effective marketing in the biomedical sciences, “… as ontologies become more commonly used, the problems involved in achieving coordination in ontology development become ever more urgent. To address these problems there is a need for an overarching conference which brings together representatives of all major communities involved in the development and application of ontologies in biomedicine and related areas. ICBO is designed to meet this need.”

So I browed through the papers in that collection, came across this quite interesting one, learned about a project and consortium that I had not heard of, and made a mental note that the International Conference on Biomedical Ontology seemed like a gathering of smart cookies in the world of e-science and big data:

The goal of OBI is to enable a formal representation of biomedical investigations that captures the experimental evidence on which their findings are based. The scope of OBI includes: materials made in and produced for investigations, research objectives, experimental protocols, roles of people in investigations and processing and publication of data gathered in investigations. Use of OBI will allow comparison of experimental data from the wide array of scientific disciplines represented by domain experts in the OBI consortium. OBI follows the principles laid out by the OBO foundry, and integrates tightly with other foundry candidate ontologies, such as GO (www.geneontology.org) and ChEBI (www.ebi.ac.uk/chebi/) whose terms are used to describe biological reality. The use of OBI by the scientific community to represent or annotate their investigations within electronic data resources will facilitate interdisciplinary data synthesis, enable access to their data on the semantic web and improve third-party understanding of information related to life-science and clinical investigations.

And the paper was in PDF — the better to send it to others who would find it interesting.

The voting process was interesting in that there is no vetting of the expertise of the voters. You just have to be a registered user of Nature Precedings. For instance, I just clicked to vote for this presentation:

… even though I did so simply because it looked interesting and not because I have any background in epidemiology or bioinformatics. But hey that’s okay given that we are told, “Voting is intended to be an informal way of showing support for a researcher’s work.”

I decided to try the “Browse by subject” feature and chose “Neuroscience.” Quite a few of the papers were interesting. One was this quite fascinating bit of medical history, “The History, Development and Impact of Computed Imaging in Neurological Diagnosis and Neurosurgery: CT, MRI, and DTI.”

Rather touching that the author, Aaron G. Filler, seems to be an incredibly busy and productive neuroscientist who takes the time to contribute worthily and interesting to the history of medicine. That is the nice thing about such things as Nature Precedings. It enables scientists to share articles on subjects in which they are intellectually engaged that may not meet the stringent requirements of traditional journals.

And even though Nature Precedings might seem at first glance a rather dry collection of papers in some instances, it redounds to the credit of NPG that it features in the unlikely venue of the comments section of the paper, “Small critical RNAs in the scrapie agent” a lively discussion of the mores of online peer review that includes such biting comments as these:

Peer-review is not primarily meant to be a hassle for scientists eager to publish their findings. It is also a mean of protecting authors, e.g. by pointing out logical flaws, missing controls, alternative interpretations, etc. Not only does the process improve the quality of published science, but it also helps authors avoiding potential embarassment.

This paper appears to represent a good case in point. A plausible interpretation is that the traces of infectivity detected by the authors represent residual contamination stemming from the 263K inoculum. There would be valid ways to test for that, however no such efforts were undertaken. Experienced referees would have advised the authors to perform these tests before going public.

Time will tell whether the bypassing of the peer-review process, in this case, will have done any good to science at large and to the authors specifically …

The comment was responded to that very day by an NPG staffer:

Hilary Spencer on 19 June 2009 21:06 UTC

(Disclosure: I am the Product Manager for Nature Precedings). Nature Precedings is not designed to bypass the peer-review process, but to act as a complement. The ability of preprint servers to complement the traditional peer review and editorial process has already been demonstrated with the use of the preprint server arXiv in the physical sciences. Many of the articles later peer-reviewed and published in Nature Physics are first posted on arXiv prior to (or concurrently with) journal submission. We believe that the use of arXiv benefits the physics community at large and helps to accelerate the research cycle, and many authors believe feedback they receive from the service benefits their research. Nature Precedings is intended to bring the same benefits to the biomedical community.

One of the benefits is that authors are able to receive (hopefully) helpful comments from others who may not have participated in the traditional peer-review process, thereby leading to more robust (and open) research.

Thus, Nature Precedings is very much worth looking at by librarians, working scientists, those in the biomedical industry (many bright minds here, pharmaceutical industry headhunters) and even social scientists and those in the information sciences interested in how online communities are changing the way scientists interact and convey their findings to an ever wider audience. This is Science 2.0, Open Science, Research 2.0 and social networking all rolled into one.

And good for Science Commons for being one of the partners along with the British Library (which should drop the silly upside down thing-not the way to convey professionalism to have a dumb icon), the Wellcome Trust among other fine institutions:

On the down side, Nature Precedings doesn’t have much multimedia stuff and the RSS feeds don’t seem to work.

But I was very impressed. This is one A-number one product and a model of the latest and greatest in modes of scientific communication.

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