Saturday, June 27, 2009

Failures of citation based rating - new analysis

Ramy Aziz, one of the most enthusiastic members of the PLoS ONE Editorial Board has very nicely commented on a recently published PLoS ONE article which highlights the failures of the so called 'impact factor' based rating of the value of science journals. The journal impact factors were released last week itself and thus the analysis presented in the article is very timely, indeed. Below are Ramy's comments to which I agree 100%:

"The presented results pertain to what we believe to be the largest and most thorough survey of usage- and citation based measures of scientific impact."

I agree with the above statement and I definitely like this thorough comparison of a large number of "impact measures." The article is also informative and has introduced in detail many methods for evaluation of scientific literature with which I was not familiar.

However, on reading the article, I had the following concerns regarding its reliability:

1) Most of the readers will only read the abstract, especially because the article is full of statistical and technical terms. The conclusion of the abstract is not so informative and poorly represents the insightful discussion at the end of the article.
In particular, I would have preferred a positive than a negative conclusion. I would have preferred a recommendation of which measures correlate better with each of the multiple dimensions of scientific attributes (e.g., quality, prestige, impact, immediacy, etc.) rather than the--rather obsolete--conclusion that JIF is not optimal and should be "used with caution." I have read more than 20 articles and editorials (including those in Science, JBC, JCI, PLoS) written in the past two years and stating that JIF should be used with caution.

2) I agree with the authors that JIF is misused; however, a value cannot be blamed for what it does not stand for. I believe the authors have given more importance to JIF (probably because of its "impact" on the scientific community), and I think that this has affected the objectiveness of the paper.

3) As the authors state in the introduction, until now I'm not sure whether how "scientific impact" is defined. Is it "journal impact", "article impact", or "scientist impact"? And which of these matters more? However, the authors seem to have committed the same unfair comparison that JIF and SJR do: measuring articles, scientists, and even "science" itself by the journals rather than by the articles. Journal-level metrics simply mean that an article is evaluated mostly prior to its publication. Once a scientist "makes it to Science or Nature," he or she celebrates even if the article will never be cited again!

4) Once more I declare my agreement with the authors that JIF is neither the most accurate nor the fairest way to measure scientists, articles, or even journals. However, this "conclusion" is clearly stated in the introduction (quoted below). Why the analysis then?

"The JIF is now commonly used to measure the impact of journals and by extension the impact of the articles they have published, and by even further extension the authors of these articles, their departments, their universities and even entire countries. However, the JIF has a number of undesirable properties which have been extensively discussed in the literature [2], [3], [4], [5], [6]. This had led to a situation in which most experts agree that the JIF is a far from perfect measure of scientific impact but it is still generally used because of the lack of accepted alternative"

5) One final concern/question.
Citation-based metrics take into consideration journals that are technologically behind (for many "non-science-related" reasons, including funding problems, poor management, being published in a developing country, etc.) and thus do not have well established web sites but are still citable and cited. Do the "usage-based metrics" just ignore those journals?

Saturday, June 20, 2009

Need for qualitative assessment of biomedical research

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.

Friday, June 19, 2009

New genome article added to 'PLoS ONE prokaryotic genome collection'

The article presents most important observations such as those related to the presence of several novel virulence determinants of non-mycobacterial origins and that these were perhaps acquired from other environmental organisms and pathogens including Rhodococcus sp., Streptomyces sp., pseudomonads and Burkholderia cepacia.

Standards for genome data reporting: should we go about it?

Within my overview article that accompanies the PLoS ONE Prokaryotic Genome Collection, one thing that I did not touch base with was the standards for genome data reporting. The Genome Standards Consortium (GSC) is now already in place (and I am one proud member of the same!) and they strongly advocate that certain standards be introduced (at the least) at the level of genome meta data. The consortium has recently published aims and objectives, prospective guidelines and envisaged benefits of such 'would be' mandatory standards (http://www.pubmedcentral....).

As a next critical step, the GSC are now starting to ask journals to require that new genome/metagenome publications be accompanied by completed 'Minumum Information about a Genome Sequence (MIGS/MIMS)' reports.

This sounds a wonderful proposition and I guess PLoS journals in this connection could lead headway as they already insist for adherence to certain other standards such as MIAME for reporting microarray data). Until this point, it is all OK. But some people feel that 'monopolizing' standards could be a kind of 'suffocation'. However, I am sure this will not lead to the kind of 'suffocating monopoly' created by certain 'nomenclature commissions' and their 'mouthpiece journals' in the area of taxonomy and systematics.

I discussed this with one of my friend, a genomic/bioinformatics expert and he says ".. my problem with standards is also not only the monopoly, but that it is also really hard to set a minimal role of meta data that need to be entered per genome. I suffer from the lack of organized meta data; but once the entry is enforced, people will just start putting anything to fill the tables and get their data out, which will lead to the opposite of what standards are supposed to achieve".

Given above, it is clear that some discussion and brainstorming is nevertheless required before journals start insisting for the MIGS/MIMS reports. I can not find a better place than PLoS ONE (sandbox) to discuss and resolve such issues.

Saturday, June 13, 2009

New F1000 Evaluation of a PLoS ONE article

Yet another PLoS ONE article was evaluated by F1000 Biology, making the total number of evaluated articles to 180. At any given time, about 3-4% of PLoS ONE articles are evaluated at F1000. Below is a simplified version of the evaluation of the article by Myers et al. The article was evaluated by Felix Viana of the UMH Instituto de Neurociencias, Spain.
Evolution of thermal response properties in a cold-activated TRP channel.
Myers BR, Sigal YM, Julius D
PLoS ONE 2009 4(5):e5741 [
abstract on PubMed] [citations on Google Scholar] [related articles] [FREE full text]
"This is an interesting study, comparing functional properties of ortholog thermosensitive TRPM8 channels in frogs and rats. It suggests that intrinsic thermosensitivity is tuned to the normal operating range of body temperature. Animals populate different ecological niches. Survival in these environments is strongly dependent on properly tuned sensory systems that allow the rapid detection of food and the avoidance of dangerous situations, like predators or exposure to extreme temperatures. TRPM8 is a transient receptor potential activated by cold temperatures and cooling compounds like menthol {1, 2}. In mice, TRPM8 is critical for the detection of mild cold temperatures, and perhaps for unpleasant or noxious cold. In this paper, the authors cloned and characterized the functional properties of frog, specifically Xenopus laevis and Xenopus tropicalis, TRPM8. These aquatic frogs are poikilotherms, their core body temperature fluctuates with environmental temperature, in a range clearly below the core body temperature of mammals and birds. While various properties (i.e. menthol sensitivity and voltage-dependence) of frog TRPM8 were similar to those described for rat and mice, there was a clear shift in the thermal response of the channel towards temperatures below their "normal" core temperature. The amino acid sequence of Xenopus TRPM8 displays 75% identity to the rat sequence. This result suggests that this thermo TRP is under strong evolutionary pressure, likely reflecting an important role in temperature sensing in species other than mammals. Besides the intrinsic interest of this novel information for thermosensory biology in general, a careful analysis of the differences in sequence between different species, and the construction of chimeras, may provide additional insights into the mechanism of temperature gating of TRPs, an important unsolved question".

References: {1} McKemy et al. Nature 2002, 416:52-8 [PMID:11882888]. {2} Peier et al. Cell 2002, 108:705-15 [PMID:11893340].

Wednesday, June 10, 2009

Single Cell Genomics: New PLoS ONE article evaluated at Faculty of 1000

I recently handled an interesting article at PLoS ONE [Assembling the marine metagenome, one cell at a time. Woyke T, et al., PLoS ONE 2009 4(4):e5299].
As for the other high ranking PLoS ONE articles, this article too was evaluated at the Faculty of 1000 Biology and was rated with a F1000 Factor of 6.0 (Must Read). A redacted version of the evaluation by Douglas Bartlett is here: 
'This work details the use of single cell genomics from two uncultured marine Flavobacteria to recruit considerable sequence data from the Global Ocean Survey (GOS) compared to genome sequences from cultured Flavobacteria isolates. The genome reconstruction and stringent quality control of the two SAGs (single amplified genomes) are well handled, considering contamination and chimeras associated with the amplification process. The analyses of the two SAGs indicate unique metabolic features such as hydrogen oxidation, proteorhodopsin photometabolism, and biopolymer hydrolysis. Also of interest is the genome streamlining in the ...' ..... Full evaluation of the article is available here (

BLoG ONE has moved to Word Press

A mirror of BLoG ONE now operates from WordPress. All contents from this site will be mirrored from there.

PLoS ONE Prokaryotic Genome Collection - now launched

I am excited to tell you of the latest collection of some of the high-impact articles, the PLoS ONE Prokaryotic Genome Collection. Liz Allen of PLoS, has some more things to say …read her full blog post here.

There is an editorial overview that accompanies the new collection; it’s written by me. Comments related to the collection and the ‘overview’ have started to trickle in, such as this one by Dr Ramy Aziz:

“This article lists very interesting challenges and questions that will be answered in the next decade of this millennium. With the revolution stirred by next-gen sequencing machines, sequencing/resequencing steps have become quick and cheap. Thus, data generation is the least part to worry about. However, as the article appropriately discusses, the problem is what to sequence and then how to make sense out of the piles.

We will very soon have 5,000 fully sequenced prokaryotic genomes, but, as quick annotation tools are being developed, we realize very well that more genomes annotated = more errors propagated.

In addition to high-speed and high-performance …”
Read more here.

Wednesday, June 3, 2009

Evidence of Leprosy in Ancient India

In a recent PLoS ONE article, Gwen Robbins and colleagues reported analysis of a 4000-year-old skeleton from India, which represents both the earliest archaeological evidence for human infection with Mycobacterium leprae in the world and the first evidence for the disease in prehistoric India. I think the authors need to have clear definitions of 'ancient origins' and 'historic presence'. Leprosy has clear origins from Africa as for tubeculosis (TB). After spreading from Africa the disease may have assumed endemic potentials in certain countries such as India. Therefore, the findings here should be consistent with our own research, published back in 2006 about TB, wherein we suggested that India was a historic cradle for mycobacterial infections and that she served as an ancient corridor for an early worldwide spread of TB. The authors did not cite our work; may be an oversight! But, I am more concerned that they as well forgot to refer to an important PLoS ONE paper which recently attempted to characterize about 9000 year old skeletons from submerged, ancient burials in Israel using paleopathology and DNA based evidence.