Here comes a new PLoS ONE article describing one of the most authoritative analyses of the research impact - by none other than the Wellcome Trust. The research conducted by experts of the Trust summates that authoritative opinions about a published research finding constitute important benchmark of the quality of biomedical research. These data vindicate stand of the advocates of post publication peer review (and I am one humble volunteer) that modern day qualitative indicators are extremely necessary to judge the impact of biomedical research findings. Not only that this article supports and strengthens cause of the 'Faculty of 1000' but also that of PLoS ONE, although indirectly. The latter is no doubt the most successful forerunner of the idea of post-publication peer review and qualitative assessment while harnessing the web2.0 based semantic tools for such purposes. At this critical juncture, it is time for the concerned institutions to retrospect about their practices of evaluating research productivity of scientists based on bibliometric indices (such as the 'impact factor') alone.
Showing posts with label F1000. Show all posts
Showing posts with label F1000. Show all posts
Saturday, June 20, 2009
Wednesday, December 24, 2008
New PLoS ONE articles evaluated at F1000 Biology
It appears that the year 2008 is closing on a good note - in the last 6 days three important articles from PLoS ONE were evaluated by the F1000 Biology faculty. These articles were graded as significantly novel reports (see below).
Rapid SNP discovery and genetic mapping using sequenced RAD markers. Baird NA, Etter PD, …,
Evaluated by: Tony Long on December 23, 2008
F1000 Factor: 6.0 (Must Read)
If I were you: perceptual illusion of body swapping. Petkova VI, Ehrsson HH PLoS ONE 2008 3(12):e3832
Evaluated by: Aina Puce on December 19, 2008
F1000 Factor: 6.0 (Must Read)
The zinc transporter SLC39A13/ZIP13 is required for connective tissue development; its involvement in BMP/TGF-beta signaling pathways. Fukada T, Civic N, …, Superti-Furga A, Hirano T PLoS ONE 2008 3(11):e3642
Evaluated by Bruce Pitt on December 18, 2008
F1000 Factor: 9.0 (Exceptional)
All PLoS ONE content is freely available on the web and readers could themselves rate and evaluate the articles. However, those evaluated on F1000 are certainly the crème de la crème kind of material; at any given time about 4% of the PLoS ONE articles are evaluated at the F1000.
Friday, December 12, 2008
A PLoS ONE article that is hot favourite of F1000 Editors
Last month I evaluated on F1000 an article from PLoS ONE that addressed infection as a driving force for the extinction of rats native of Christmas Island. The importance of this timely study was also discussed on BLoG ONE. Apparently, it appears that the F1000 evaluation of this article has been taken on quite a good note. It just appeared in the latest issue of the F1000 update wherein the Editors of F1000 reinforce the opinion that the PLoS ONE paper indeed provides important evidence that infectious diseases are a potential cause of future extinctions of endangered mammalian species. The original article is freely available for anyone to read, rate and comment.
Thursday, July 17, 2008
100th PLoS ONE article evaluated at Faculty of 1000 Biology
As a part of its thematic focus for the month of July, PLoS ONE announced a call for papers addressing gene expression studies. It appears that the gene expression community has already embraced PLoS ONE in a great style - here appears the authoritative and insightful review [by Charles Auffray] of one of the gene expression articles published by PLoS ONE: ‘High throughput gene expression measurement with real time PCR in a microfluidic dynamic array’. Interestingly, Auffray’s is the 100th evaluation of PLoSONE articles at the Faculty of 1000 Biology.
Below is the simplified version of Charles Auffray’s evaluation of the article. Full evaluation can be read at F1000Biology website.
‘The novel microfluidic device described in this paper transforms real-time quantitative PCR into a much higher throughput technology for gene expression measurement. The authors have used a dynamic array of microfluidic channels, valves and nanoliter reaction chambers to perform simultaneously 2304 real-time qPCR assays, monitoring expression of 45 human genes in 18 tissues with very high sensitivity (down to <10 RNA molecules). The results presented compare very well with those obtained with conventional microliter RT-PCR, outperforming DNA microarrays. Miniaturization and parallelization result in faster delivery of results with much less reagents and handling. This technological advance should prove useful for validation of expression profile signatures obtained with microarrays, and their extensive use for diagnosis and prognosis. In order to compete directly with microarrays for transcriptome analysis, the number of genes that can be assayed in parallel would have to be increased by at least two orders of magnitude’.
Of its 2600 articles in PubMED, one hundred (4%) articles have been already evaluated and commented upon by F1000 Members. For a broad based and high volume journal such as PLoS ONE, the F1000 evaluations constitute important quality indexes for individual articles apart from hundreds of articles already reviewed through PLoS ONE’s unique rating and discussion tools and journal clubs which are fully compliant to the cutting edge concepts of Science 2.0. Such 'article level metrics' are especially relevant when the significance of a popular bibliometric index, the 'impact factor' is increasingly being questioned.
Conflict of interest: I volunteer as Section Editor of PLoS ONE and as a Faculty Member at F1000 Biology and F1000 Medicine.
Below is the simplified version of Charles Auffray’s evaluation of the article. Full evaluation can be read at F1000Biology website.
‘The novel microfluidic device described in this paper transforms real-time quantitative PCR into a much higher throughput technology for gene expression measurement. The authors have used a dynamic array of microfluidic channels, valves and nanoliter reaction chambers to perform simultaneously 2304 real-time qPCR assays, monitoring expression of 45 human genes in 18 tissues with very high sensitivity (down to <10 RNA molecules). The results presented compare very well with those obtained with conventional microliter RT-PCR, outperforming DNA microarrays. Miniaturization and parallelization result in faster delivery of results with much less reagents and handling. This technological advance should prove useful for validation of expression profile signatures obtained with microarrays, and their extensive use for diagnosis and prognosis. In order to compete directly with microarrays for transcriptome analysis, the number of genes that can be assayed in parallel would have to be increased by at least two orders of magnitude’.
Of its 2600 articles in PubMED, one hundred (4%) articles have been already evaluated and commented upon by F1000 Members. For a broad based and high volume journal such as PLoS ONE, the F1000 evaluations constitute important quality indexes for individual articles apart from hundreds of articles already reviewed through PLoS ONE’s unique rating and discussion tools and journal clubs which are fully compliant to the cutting edge concepts of Science 2.0. Such 'article level metrics' are especially relevant when the significance of a popular bibliometric index, the 'impact factor' is increasingly being questioned.
Conflict of interest: I volunteer as Section Editor of PLoS ONE and as a Faculty Member at F1000 Biology and F1000 Medicine.
Friday, June 13, 2008
Soothing rains, soothing papers
My month long summer holidays just ended with the first rains after a very hot season (42 ℃) here in Hyderabad. Within the last 2 days the rejoice of Monsoon intensified also with the recent PLoS ONE evaluations at the F1000 Biology!! It appears that the Faculty Members of F1000 are now regularly picking up papers from PLoS series. Whereas this article Adaptation and mal-adaptation to ambient hypoxia; Andean, Ethiopian and Himalayan patterns. Xing G, Qualls C, .., Verma A, Appenzeller O, PLoS ONE 2008 3(6):e2342- [abstract on PubMed] [related articles] [free full text], by Xing and colleagues was rated as exceptional, the other two papers 1) Imaging cyclic AMP changes in pancreatic islets of transgenic reporter mice. Kim JW, Roberts CD, .., Roper SD, Chaudhari N, PLoS ONE 2008 3(5):e2127- [abstract on PubMed] [related articles] [free full text] and 2) East learns from West: Asiatic honeybees can understand dance language of European honeybees. Su S, Cai F, .., Tautz J, Chen S, PLoS ONE 2008 3(6):e2365- [abstract on PubMed] [related articles] [free full text] were tagged significant and with novel findings.
Roughly about 4-5% of PLoSONE articles are evaluated on the Faculty of 1000 at a given time, which coincides to fourth position in terms of number of evaluations, after Science (~17% of the published articles evaluated), Nature (~15% of the published articles evaluated) and PNAS (~15% of the published articles evaluated). For a broad based and high volume journal such as PLoS ONE, the F1000 evaluations constitute important quality indexes for individual articles especially when a much controversial bibliometric index such as 'impact factor' is becoming increasingly redundant.
Another soothing observation was that the Viking DNA paper from Jørgen Dissing’s group, Evidence of Authentic DNA from Danish Viking Age Skeletons Untouched by Humans for 1,000 Years, which I handled recently was very well taken by the popular and science press. The paper was Slashdotted and subsequently received several thousand hits within the space of a couple of days as also reported in PLoS Blog by Rebecca Walton. Some of the coverage of this article is listed below:
Live Science – DNA Retrieved from 1000-year-old Vikings; Wired – Researchers Recover Thousand-Year-Old Viking DNA; People's Daily, China Impossible! Scientists retrieve ancient Viking DNA; Zee News (India) DNA from 1000 yr old skeletons!; Malaysia Sun Viking DNA retrieved from 1000-year-old skeletons; Newsweek – Bring Back the Vikings: Ancient DNA; Discover Magazine – Hide the Women and Children! Researchers Dig up Viking DNA Scientist Live, UK – Authentic Viking DNA; Huffington Post – Viking DNA Recovered From Ten 1,000-Year-Old Skeletons: Report; Anthropology.net – Recovering 1,000 Year Old Viking mtDNA; Science a Gogo Viking DNA Retrieved etc.
Friday, April 11, 2008
PLoS ONE’s strides at the Faculty-of-1000-Biology
The emergence of Open Access Publishing has brought into practice the long envisioned model of post publication peer review. The success of such models is largely spearheaded by the new technologies based on Web 2.0. For example, the multidisciplinary journal, PLoS ONE, launched in late 2006 has been successfully strengthening the spirit and mission of Open Access while harnessing the power of web technology; at the same time its hosted on a powerful TOPAZ platform for community based review, evaluation and dialogue. It makes a terrific resource when an open access journal combines the power of rating and evaluation in real time.
Another revolution of our time is the authoritative, post-publication benchmarking and rating of most impacting articles through services such as the Faculty of 1000. Faculty of 1000 Biology is a web based, authoritative, next generation literature awareness tool. Run by the Medicine reports Limited (UK), it is a revolutionary online research service that comprehensively and systematically highlights and reviews path-breaking papers based on the recommendations of a faculty of well over 2300 selected leading researchers ("Faculty Members"). This service is run by scientists for scientists and provides ‘a rapidly updated consensus map of the important papers and trends across biology’. F1000Medicine is the sister concern of F1000Biology run by medical academics and clinicians and is rapidly gaining popularity among medical doctors and paramedics.
I consider myself fortunate to have published in Open Access journals in both PLoSONE and BMC and to be associated in editorial capacities with PLoS ONE, F1000Medicine, F1000Biology and the BMC led journals, Annals of Clinical Microbiol Antimicrobials, Infect Agents Cancer, Acta Vet Scand and Gut Pathogens (to be launched soon). I must say that I am thoroughly enjoying open access publishing and witnessing the success and impact of the revolutionary evaluating services.
Since a few weeks I have been associated with PLoS ONE in a more dedicated capacity of a Section Editor (Microbiology and Genomics) and therefore, got further opportunity to look into how this journal is going from strength to strength in such a short time of not even two years? Well that was evident from the number of articles published and their quality. However, I was keen in seeing this from the lenses of giants! I did some analyses involving tools at F1000Biology to know how inclined are the opinion leaders in biological sciences about PLoSONE articles given that the Faculty Members of F1000 have been traditionally ‘jumping’ to articles from a few top tier journals such as Nature or Cell. Good to say, the trend is reversing, although slow. Here is how - I was very much pleased to note PLoS ONE’s visible impact; 55 of the1241 articles (4.4%) published in PLoS ONE in 2007 have been evaluated and recommended by the experts at F1000Biology. What this means in terms of impact? As a comparison I modeled PLoS ONE statistics alongside one highly established journal, Nature (the only journal with which PLoS ONE can be compared due to its multidisciplinary nature). A total of 349 articles out of 2892 (12%) published by Nature in 2007 were evaluated at F1000Biology. Seemingly, the difference in terms of number of articles evaluated looks large. However, as I mentioned, if we consider the current visible bias of F1000 faculty towards Nature journals and the publishing criteria (at Nature) linked to space (huge rejection rates due to subjective criteria), PLoS ONE stands distinctly tall given the fact that it is just born. Performances of all other titles were nowhere near. Other 66 Open Access titles (all BMC series + Genome Biology put together) from Biomed Central (4740 articles in 2007) could yield only 47 evaluations at F1000Biology (0.9%) during 2007. Given that BMC titles are also freely available, it is intriguing to know what makes PLoSONE so successful at F1000? In my perception - it is the high quality of the articles plus the ease with which they can be judged on face - PLoSONE sandbox makes it extremely simple for the evaluators to quickly pick the articles based on notes, referee’s comments, ratings, reader responses and community feedback etc.
The future is even brighter – more and more F1000 members are inclined to using open access articles for their benchmarking. It makes life easy. I remember, I once had almost begged for a reprint from an author of a beautiful review article on genome duplications (many authors do not respond to reprint requests in a reasonable time frame). I wanted to have it evaluated at F1000Medicine and the closed access article was costing me USD 60.00 (in India, this equals to a monthly rent for a 2 bedroom house!!) – how shame!
Finally, I do not know how useful will be these initial statistics on F1000 ratings; but, I am sure this could mean a good indicator for the prospective authors at PLoSONE (especially in the absence of any bibliometric index such as Impact Factor) to foresee its reputation and peer-acceptance that the journal has earned in a short time.
Another revolution of our time is the authoritative, post-publication benchmarking and rating of most impacting articles through services such as the Faculty of 1000. Faculty of 1000 Biology is a web based, authoritative, next generation literature awareness tool. Run by the Medicine reports Limited (UK), it is a revolutionary online research service that comprehensively and systematically highlights and reviews path-breaking papers based on the recommendations of a faculty of well over 2300 selected leading researchers ("Faculty Members"). This service is run by scientists for scientists and provides ‘a rapidly updated consensus map of the important papers and trends across biology’. F1000Medicine is the sister concern of F1000Biology run by medical academics and clinicians and is rapidly gaining popularity among medical doctors and paramedics.
I consider myself fortunate to have published in Open Access journals in both PLoSONE and BMC and to be associated in editorial capacities with PLoS ONE, F1000Medicine, F1000Biology and the BMC led journals, Annals of Clinical Microbiol Antimicrobials, Infect Agents Cancer, Acta Vet Scand and Gut Pathogens (to be launched soon). I must say that I am thoroughly enjoying open access publishing and witnessing the success and impact of the revolutionary evaluating services.
Since a few weeks I have been associated with PLoS ONE in a more dedicated capacity of a Section Editor (Microbiology and Genomics) and therefore, got further opportunity to look into how this journal is going from strength to strength in such a short time of not even two years? Well that was evident from the number of articles published and their quality. However, I was keen in seeing this from the lenses of giants! I did some analyses involving tools at F1000Biology to know how inclined are the opinion leaders in biological sciences about PLoSONE articles given that the Faculty Members of F1000 have been traditionally ‘jumping’ to articles from a few top tier journals such as Nature or Cell. Good to say, the trend is reversing, although slow. Here is how - I was very much pleased to note PLoS ONE’s visible impact; 55 of the1241 articles (4.4%) published in PLoS ONE in 2007 have been evaluated and recommended by the experts at F1000Biology. What this means in terms of impact? As a comparison I modeled PLoS ONE statistics alongside one highly established journal, Nature (the only journal with which PLoS ONE can be compared due to its multidisciplinary nature). A total of 349 articles out of 2892 (12%) published by Nature in 2007 were evaluated at F1000Biology. Seemingly, the difference in terms of number of articles evaluated looks large. However, as I mentioned, if we consider the current visible bias of F1000 faculty towards Nature journals and the publishing criteria (at Nature) linked to space (huge rejection rates due to subjective criteria), PLoS ONE stands distinctly tall given the fact that it is just born. Performances of all other titles were nowhere near. Other 66 Open Access titles (all BMC series + Genome Biology put together) from Biomed Central (4740 articles in 2007) could yield only 47 evaluations at F1000Biology (0.9%) during 2007. Given that BMC titles are also freely available, it is intriguing to know what makes PLoSONE so successful at F1000? In my perception - it is the high quality of the articles plus the ease with which they can be judged on face - PLoSONE sandbox makes it extremely simple for the evaluators to quickly pick the articles based on notes, referee’s comments, ratings, reader responses and community feedback etc.
The future is even brighter – more and more F1000 members are inclined to using open access articles for their benchmarking. It makes life easy. I remember, I once had almost begged for a reprint from an author of a beautiful review article on genome duplications (many authors do not respond to reprint requests in a reasonable time frame). I wanted to have it evaluated at F1000Medicine and the closed access article was costing me USD 60.00 (in India, this equals to a monthly rent for a 2 bedroom house!!) – how shame!
Finally, I do not know how useful will be these initial statistics on F1000 ratings; but, I am sure this could mean a good indicator for the prospective authors at PLoSONE (especially in the absence of any bibliometric index such as Impact Factor) to foresee its reputation and peer-acceptance that the journal has earned in a short time.
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