Over the past year, researchers in a variety of disciplines have posted 475 documents and 180+ comments. Thousands of readers have signed up to comment, vote, and submit documents on the site, and we’ve seen steady growth in site traffic and posted documents. The Nature Precedings group on Nature Network has become a lively place with discussions on many topics including “findability” , posting negative results on Precedings and academic search engines.

In response to suggestions from you, our users and contributors, we’ve rolled out a number of new features, including comment notifications, an OAI-PMH interface, and many usability enhancements.

To all of our visitors and supporters, we’d like to say Thank you! for helping turn the past year into a strong start for the project. We know that the site relies upon your contributions for its success.

As we celebrate one year of Nature Precedings, look for new features to be released on the site in the upcoming weeks and additional announcements. We have a lot to share with you and look forward to the year ahead.

-The Nature Precedings Team

New Communication Channels for Biology

The workshop is scheduled for next week (Thurs-Fri, June 26 and 27th, 2008) at Calit2: California Institute for Telecommunications and Information Technology in La Jolla, CA (directions).

The workshop is open to the public (and free!) although they request that you register beforehand.

Here’s an analysis done by counting the number of abstracts returned in PubMed searches using authors’ full names. The result indicates that well-published authors are publishing in Nature Precedings.

The graphic result can be seen here.

• Manuscripts that covered subjects not covered by PubMed were excluded.

• Only first, second or last authors were considered.

• Author names were converted to the format ‘First_name Last_name’; middle names/initials were removed.

• Authors with names with only initials for first names, or those using non-English alphabet characters were not considered.

• Nature Precedings metadata was acquired using OAI-PMH. PHP code was used to generate the filtered list of authors and for querying PubMed using Entrez Programming Utilities.

— 236 manuscripts

— 1166 authors

— 1007 unique author names

— 528 unique first, second or last author names

— 16 author names returned more than 200 abstracts each, likely because names like ‘Wei Zhang’ are common. The sixteen does have names like ‘Nicholas White’ and ‘Robert Williams’ as well.

Exploiting the OAI-PMH-accessibility of Nature Precedings, I mined some data to chart its growth over the last year (some of the crude PHP code is available here).

The graphic result, with three charts, can be seen here.

As previously noted, after an initial spurt, the number of posters/presentations is barely growing now. The number of manuscripts has grown at a steady rate over the last year.

For manuscripts, bioinformatics leads subject-wise, mainly because of a jump during the early months. Growth has been steady for most of the other subjects, though neuroscience and chemistry have picked up growth in the last 5-6 months.

One of the chart plots article ID numbers against article publication time to throw possible insights on the mystery behind the article ID numbers.

(The time-axes start before June 2007, when Nature Precedings was started. It probably existed prior to that as a closed beta.)

In comment 50 or 60-something (ok-I didn’t count), Henry Gee poses the following hypothetical example:

Group X discovers something which they write down with a time stamp. Group Y makes the same discovery – by the time Group X gets wind of this and has mobilized its army of intellectual property droids, Group Y has published it and has gotten the credit. In the eyes of the world, Group Y has made the discovery and Group X is eating dirt.

Let’s modify this a bit: Say Group X posts a preprint of their manuscript on a preprint server like ArXiv, time-stamping it, but more importantly, making it easily available via Google. Even though Group Y publishes first, say they publish in a closed-access journal to which few universities have subscriptions (at the worst, say the journal doesn’t even make their articles available online—it’s print only). Now whenever someone is looking for articles on Z in Google, they tend to find Group X’s paper on ArXiv, but not the journal article. Group X’s article on ArXiv is cited a couple of times, while Group Y’s languishes behind a subscription wall, or, at the worst, in the university library’s stacks… So is “getting credit” getting the first publication, or getting one’s work consistently cited and used as a reference point?

Now, most journals have been moving towards making their content available online, and many universities have extensive journal subscriptions, so this might be an extreme example. Most people will cite a peer-reviewed article when given the choice of either citing a preprint or a peer-reviewed article. But people will almost always cite articles that they can find and read, over those that they can’t. (Isn’t it a breach of ethics to cite documents one hasn’t read?) Most publishers realize this, and are working to increase the “findability” of these articles, but sometimes they don’t do the best that they can. Sometimes sites like also Google rank papers on ArXiv higher than those on journal sites (though the question of the role of page rank in literature reviews might best be left for another day.)

One might also argue that no one uses Google to search for research, though trends suggest that this is changing, especially with the current crop of undergraduates. [1], [2]

If the published version is difficult to find, but one is able to read the preprint and finds it useful, then I suspect that one is more likely to ferret out a copy of the published version (even in the university stacks) for citation purposes. One is more likely to spend the time and effort trying to get a copy of an article that one already knows will be useful over an article that may or may not be. (This might explain why papers with posted preprints tend to get more citations than those without available preprints [3], [4] and why open access articles tend to have higher citation rates [5]).

There are many stories of disputes over claims of inventions (the modern computer, photography, the radio, the telephone, the steam engine…) A recent article from the NY Times’s Week in Review discusses Thomas Edison’s invention of the phonograph, noting that 17 years prior to Edison’s patent, a Parisian inventor had already created a device to make visual recordings of songs. Who was he? Who knows? The article goes on to note that Edison was perhaps not the first to invent the lightbulb, and was only credited as doing so when the Supreme Court ruled that the prior inventor’s patent was too broad. Did you know this? I didn’t.

The Times article suggests that credit for inventions is often correlated with who is able to make theirs accessible to the public, and not necessarily with who was first, even in the filing of patent documents. The author also notes the importance of timing: “Great ideas, while perhaps not novel, are delivered to us…just as we’re hungry for them.” Perhaps being the first to publication isn’t always the key to receiving credit, just as being the first to patent doesn’t mean that you won’t be eating dirt later.

¹ Student Searching Behavior and the Web: Use of Academic Resources and Google

² Information Illiterate or Lazy: How College Students Use the Web for Research *Disclosure: I didn’t read this article because I don’t have access, so I’m citing the abstract.

³ The Citation Impact of Digital Preprint Archives for Solar Physics Papers
Preprint version

⁴ E-prints and Journal Articles in Astronomy: a Productive Co-existence
Preprint version

⁵ Citation Advantage of Open Access Articles

The latest identifying numbers have crossed 1,800. However, there are only around 400 Nature Precedings articles online as of now. What explains the difference? Rejected submissions?

PS: The BASE academic search engine states that it currently covers around 1,200 Nature Precedings articles. Another mismatch, but explanable as BASE counts every version as a separate document?

Coverage by indexing services and search engines is a must for repositories to succeed.

I wonder if the site development team has considered the feasibility and merits of using the iPaper platform of Scribd.

If an author declares during the article submission process that the article is preprinted elsewhere, would the manuscript be rejected by Nature Precedings?

And what is the policy for cases in which duplicate preprinting at another location is discovered post-acceptance?

Preprinting at multiple locations may be a good thing as it increases the visibility and accessibility of articles. However, it can complicate citation-tracking. Some might also deem it unethical, wasteful of resources, etc.

One factor to keep in mind when pondering this is the proportion of worthy preprints that nevertheless remain unpublished (in traditional journals).

ROUGH ANALYSIS OF ‘Nature Precedings’ ARTICLES IN CATEGORY ‘bioinformatics’ AS ON March 16, 2008, 3:17 pm EST

ARTICLES

• All: 99
• Manuscripts: 65
• Other (posters/presentations): 34

DAYS

• Total: 273
• Avg. (all): 2.8
• Avg. (manuscript): 4.2
• Avg. (other): 8
• Avg. (range) between submission and acceptance (all): 3.5 (0-35)
• Avg. (range) between submission and acceptance (manuscript): 4.1 (0-35)
• Avg. (range) between submission and acceptance (other): 2.1 (0-8)

AUTHORS

• Total: 287
• Avg. (range) (all): 3.7 (1-51)
• Avg. (range) (manuscript): 4.2 (1-51)
• Avg. (range) (other): 2.9 (1-14)
• With >1 article (all): Diego Mauricio Riaño-Pachón, 3; Konrad U. Foerstner, 3; Cameron Neylon, 2; Wei Zhang, 2; Jean-Claude Bradley, 2; Ravi Iyengar, 3; Michael Hucka, 4; Sarah M. Keating, 2; Jayapal J. Manikandan, 4; Alirio Jose Melendez, 2; Peter Natesan Pushparaj, 3; Bernd Mueller-Roeber, 2; Marie Loh, 2; Adrian Mondry, 2; Roderic Page, 3; Henry L. Niman, 4; Magdi D. Saad, 2; Jeffery Tjaden, 2; Kenneth C. Earhart, 2; Marshall R. Monteville, 2; Mona M. Aly, 2; Moustafa M. Mansour, 2; Bruce R. Boynton, 3; Kailash C. Upadhyaya, 2; Sebastian Bassi, 2; Heather A. Piwowar, 2; Ilya Shmulevich, 2; Avi Ma’ayan, 2; Pedro Beltrao, 3; James C. Paulson, 2;

AFFILIATIONS

• Total: 166
• Avg. (range) (all): 2 (1-23)
• Avg. (range) (manuscript): 2.3 (1-23)
• Avg. (range) (other): 1.3 (1-5)
• Avg. no. of authors (all): 1.7
• With >1 article (all): European Molecular Biology Laboratory, Heidelberg, Germany, 3; Stanford University, 2; STFC Rutherford Appleton Laboratory, 2; Drexel University, 2; Mount Sinai School of Medicine, 2; Department of Physiology, National University of Singapore, 4; Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, 2; Oxford Radcliffe Hospitals NHS Trust, Oxford, United Kingdom, 2; DEEB, IBLS, University of Glasgow, 3; Recombinomics, Inc, 3; Central Laboratory for Veterinary Quality Control, Giza, 2; Ministry of Health, Arabic Republic of Egypt, 2; Jawaharlal Nehru University, New Delhi-67, 2; Universidad Nacional de Quilmes, 2; University of Pittsburgh, 2; Institute for Systems Biology, 2; EMBL-Heidelberg, 3; Mount Sinai School of Medicine, New York, NY, 2; BNMC, California Institute of Technology, 3; The Scripps Research Instiute, 3;

TAGS

• Total: 330
• Avg. (range) (all): 4.3 (1-11)
• Avg. (range) (manuscript): 4.4 (1-11)
• Avg. (range) (other): 4.1 (1-10)
• With >1 article (all): NMR, 2; database, 3; Plants, 3; open access, 3; open science, 5; open source, 2; proposal, 3; p18, 2; This document has not been tagged., 2; malaria, 2; epidemiology, 2; Open data, 2; data, 2; protein interactions, 2; phylogenetics, 2; prediction, 3; Semantic Web, 2; DNA, 2; networks, 4; modeling, 3; transcription factor regulation, 2; microarray, 4; BioPax, 2; statistics, 2; docking, 2; systems biology, 6; SBML, 6; pathway, 2; transcription factors, 3; chemoinformatics, 2; databases, 3; mast cells, 2; gene expression profile, 2; oligonucleotide microarray, 2; neuroinformatics, 2; phylogeny, 2; algorithm, 2; Recombination, 4; Vaccine, 2; Evolution, 5; Polymorphisms, 2; Influenza, 4; Genetics, 3; H5N1, 3; Cicer arietinum, 2; bioinformatics, 3; sharing, 2; microarrays, 2; XML, 5; graph theory, 2; structured data formats, 3; standards, 3; modelling, 4; glycomics, 3; CFG, 2;

SUBJECTS

• Total: 13
• Avg. (range) (all): 2.5 (1-6)
• Avg. (range) (manuscript): 2.6 (1-6)
• Avg. (range) (other): 2.3 (1-5)
• Other than bioinformatics with >10 articles: Biotechnology, 27; Chemistry, 10; Genetics, 20; Molecular Cell Biology, 24; Evolution and Ecology, 21; Pharmacology, 10;

SIZE (MB)

• Avg. (range) (all): 1.5 (0.011-13.7)
• Avg. (range) (manuscript): 0.8 (0.011-10.6)
• Avg. (range) (other): 2.8 (0.049-13.7)

VOTES

• Avg. (range) (all): 3.5 (0-35)
• Avg. (range) (manuscript): 4.1 (0-35)
• Avg. (range) (other): 2.1 (0-8)

COMMENTS

• Avg. (range) (all): 0.7 (0-8)
• Avg. (range) (manuscript): 0.8 (0-8)
• Avg. (range) (other): 0.5 (0-6)

OTHER Nature Precedings VERSIONS

• Avg. (range) (all): 0.1 (0-2)
• Avg. (range) (manuscript): 0.2 (0-2)
• Avg. (range) (other): 0.1 (0-2)
• Avg. (range) days between 1st and 2nd versions (all): 5.1 (1-168)
• Avg. (range) days between 1st and 2nd versions (manuscript): 7.7 (1-168)
• Avg. (range) days between 1st and 2nd versions (other): 0 (1-1)

NON-Nature Precedings VERSIONS

• Fraction (all): 0.1
• Fraction (manuscript): 0.1
• Fraction (other): 0.1

ROUGH ANALYSIS OF ‘Nature Precedings’ ARTICLES IN CATEGORY ‘molecular-cell-biology’ AS ON March 15, 2008, 10:30 pm EST

ARTICLES

• All: 69
• Manuscripts: 51
• Other (posters/presentations): 18

DAYS

• Total: 272
• Avg. (all): 3.9
• Avg. (manuscript): 5.3
• Avg. (other): 15.1
• Avg. (range) between submission and acceptance (all): 2.8 (0-11)
• Avg. (range) between submission and acceptance (manuscript): 2.9 (0-11)
• Avg. (range) between submission and acceptance (other): 2.4 (0-6)

AUTHORS

• Total: 242
• Avg. (range) (all): 4.6 (1-15)
• Avg. (range) (manuscript): 4.7 (1-15)
• Avg. (range) (other): 4.2 (1-14)

• With >1 article (all): Alessandra Pani, 3; Sandra Dessi, 2; Claudia Abete, 3; Claudia Mulas, 3; Claudia Norfo, 3; Marirosa Putzolu, 3; Alessandra Mocali, 2; Paolo La Colla, 3; Francesco Paoletti, 2; Jawed Iqbal, 2; Najmul Islam, 3; Irfan Ahmad Ansari, 2; Ravi Iyengar, 3; Sergio Laconi, 2; Jayapal J. Manikandan, 5; Alirio Jose Melendez, 2; Peter Natesan Pushparaj, 3; Alirio Jose A. J. Melendez, 2; Marie Loh, 2; Adrian Mondry, 2; Avi Ma’ayan, 2; James C. Paulson, 2;

AFFILIATIONS

• Total: 118
• Avg. (range) (all): 1.9 (1-6)
• Avg. (range) (manuscript): 2 (1-6)
• Avg. (range) (other): 1.7 (1-5)
• Avg. no. of authors (all): 2.1

• With >1 article (all): Shizuoka University, Faculty of Science, 2; University of Florence, Experimental Pathology and Oncology, 2; Department of Cell Biology and Genetics, Erasmus Medical Center, Rotterdam, The Netherlands, 2; Department of Biochemistry, Faculty of Medicine, J. N. Medical College, A.M.U., Aligarh 202002, U.P., India, 3; Mount Sinai School of Medicine, 2; Columbia University, 2; Department of Physiology, National University of Singapore, 5; Bioinformatics Institute, Agency for Science, Technology and Research, Singapore, 2; Oxford Radcliffe Hospitals NHS Trust, Oxford, United Kingdom, 2; Mount Sinai School of Medicine, New York, NY, 2; The Scripps Research Instiute, 3;

TAGS

• Total: 248
• Avg. (range) (all): 4.1 (1-7)
• Avg. (range) (manuscript): 4.1 (1-7)
• Avg. (range) (other): 4.1 (1-7)

• With >1 article (all): Alzheimer, 2; DNA damage, 2; p18, 2; monocytes, 2; apoptosis, 2; This document has not been tagged., 3; translation initiation, 2; siRNA, 2; HIV, 2; mitochondria, 2; Signal transduction, 2; BioPax, 2; metabolism, 2; pathway, 2; HIV-1, 2; gene expression, 4; transcription, 4; type-I Allergy, 2; mast cells, 2; gene expression profile, 2; oligonucleotide microarray, 2; microarray, 3; cancer, 2; cytoskeleton, 2; systems biology, 2; graph theory, 2; glycomics, 3; CFG, 2;

SUBJECTS

• Total: 12
• Avg. (range) (all): 2.4 (1-6)
• Avg. (range) (manuscript): 2.3 (1-6)
• Avg. (range) (other): 2.9 (1-4)

• Other than mol. cell bio. with >10 articles: Bioinformatics, 24; Immunology, 12; Cancer, 10; Biotechnology, 13;

SIZE (MB)

• Avg. (range) (all): 1.8 (0.021-15.8)
• Avg. (range) (manuscript): 1.9 (0.035-15.8)
• Avg. (range) (other): 1.6 (0.021-13.7)

VOTES

• Avg. (range) (all): 2.8 (0-11)
• Avg. (range) (manuscript): 2.9 (0-11)
• Avg. (range) (other): 2.4 (0-6)

COMMENTS

• Avg. (range) (all): 0.3 (0-6)
• Avg. (range) (manuscript): 0.3 (0-6)
• Avg. (range) (other): 0.2 (0-2)

OTHER Nature Precedings VERSIONS

• Avg. (range) (all): 0.1 (0-1)
• Avg. (range) (manuscript): 0.1 (0-1)
• Avg. (range) (other): 0.1 (0-1)
• Avg. (range) days between 1st and 2nd versions (all): 2.5 (1-168)
• Avg. (range) days between 1st and 2nd versions (manuscript): 3.3 (1-168)
• Avg. (range) days between 1st and 2nd versions (other): 0.1 (1-1)

NON-Nature Precedings VERSIONS

• Fraction (all): 0.1
• Fraction (manuscript): 0.1
• Fraction (other): 0.1

PubMed does accept non-peer-reviewed publications.

With a little search I did find an article being mentioned in a news report in the Journal of the National Cancer Institute [Jan 2008; 100(2) 88-89]. Atleast one article has been mentioned in the traditional popular media (Fox News story).

A 2006 study identified a number of papers posted to the physics preprint server, ArXiv, which copied papers in ArXiv. In 2007, a minor scandal erupted over the discovery that about 30 papers published in low-profile peer-reviewed journals were heavily copied from other papers in ArXiv (see coverage in Nature). Had the original authors not posted their papers to the preprint server, this plagiarism might never have been detected.

However, there is a flip side to this argument, namely that posting one’s paper on a preprint server may facilitate the very plagiarism that it can help to later detect. For many authors, this is a legitimate fear in today’s cut-and-paste climate. Is the risk (of facilitating plagiarism) worth the benefit (of facilitating detection)?

One’s answer might be conditional on whether journals systematically check preprint servers for potential plagiarism. If one is confident that any plagiarism of one’s document is likely to be detected and exposed, then one would perhaps be more comfortable posting early versions of one’s work.

From the Wikipedia article on Nature Precedings:

55 preprints were posted in the first 15 days of Nature Precedings. Of these, 26 were submitted as manuscripts and 29 as posters/presentations. Corresponding numbers for the first 50 days are 89, 48 and 41, and for the first six months, 303, 227 and 76.

A few suggestions have been put forth in this forum to further improve the publication. E.g., here and here and here. One wonders if and when atleast some of the suggestions would get implemented.

Try it: hdl:10101/npre.2007.905.1

Bjoern

Most article authors do not provide links for references in their manuscripts. Having links this way therefore helps viewers. Also, it will aid in estimating the quality and content of articles before downloading them, and will facilitate software-based citation evaluations.

Nature Precedings can provide an extra form field for bibliography that authors can use to copy-paste their reference list in when submitting manuscripts. Alternately, it should not be difficult to have some software extract the bibliography from the article.

Because providing direct links (to abstracts or full-text content) for each reference may be too resource-intensive for the Nature Precedings team, indirect links that direct one to results from specialized search engines will suffice. The example page mentioned earlier has such indirect links (using ParaCite).