Posts Tagged ‘scientific publications’

A Revolution in Scientific Publication

 :: Posted by American Biotechnologist on 07-30-2014

Since we are talking about impact factors and Journal related stuff, (see When JIF Becomes a Dirty Word), I wanted to share with you a very cool concept that I saw recently in F1000 Research.

Aside from it’s move to the digital world, scientific publication, as we know it, has remained relatively constant for over four hundred years. Papers are written in a scientific method-based theme and broken down into bite size sections. Papers are very much there for scientists to communicate their findings with us and for the investigators to provide us with their personal interpretation of the data. While a sort of 2-way communication often happens via editorials and personal communication, the presentation of the data remains static and one dimensional. Results, which represent the heart of the researchar, often presented in tabular or pictorial format. Much of the effort and funding allocated to a research project can be distilled down to several figures and maximizing the communicative ability of these results is essential to successful publication. That is why the methodology used to publish a recent paper in the journal F1000 Research may, in fact, revolutionize the world of scientific publishing.

In the newly released article, German professor of neurogenetics, Bjorn Brembs, published a proof-of-concept figure allowing readers and reviewers to run the underlying code within the online article. Instead of presenting readers with a static figure that can only be interpreted by the author, Dr. Brembs submitted the figure’s underlying code to the journal, allowing readers and reviewers to render the figure in various formats giving them more control over interpretation of the original data.

According to Brembs, the ultimate goal is to set up all journal submissions in such a way that authors will no longer have to deal with figures. They will simply need to submit text with links to data and code, and the rest will be up to the reader.

The recent rise in retraction rates of scientific articles proves that attempts at reproducibility by other labs are crucial to cross-checking our understanding of science. With only one or two figures to choose from in the past, authors were incentivized to pick the view of the data that best demonstrated their conclusions. “The traditional method of publishing still used by most journals today means that as a referee or reader, the data cannot be reused nor can the analysis be checked to see if all agree with the reported conclusions”, said Brembs. “This slows down scientific discovery. We are pleased to be able to pioneer these two interactive figures with F1000Research, which will hopefully be the start of a big shift in the way journals treat their figures.”

Co-Founders of PLOS Discuss Open Access

 :: Posted by American Biotechnologist on 01-14-2014

A Journal Impact Factor Scandal

 :: Posted by American Biotechnologist on 08-29-2013

In a wildly popular post published several months ago, we took a controversial stance in discussing the ugly side of the journal impact factor. In that article we argued that the journal impact factor (JIF) is a useless tool for measuring the productivity of scientists and that it is being used unfairly to grant merit increases to scientists based solely on their JIF ranking. The article generated dozens of comments, with many readers avidly agreeing with our opinion and enthusiastically sharing their stories of colleagues who have been cheated out of deserved promotions due to their dearth of publications in journals with high JIF rankings.

In a rather ironic twist of fate, the journal Nature, (probably one of the highest ranking JIF journals around), broke a story on how several Brazilian scientific journals have been suspended from Thomson Reuters’ JIF service for inappropriately manipulating the journal’s content to falsely increase their JIF rating. The accused Brazilian journal editors encouraged scientists to cite other Brazilian journal articles in their publication in order to help increase the JIF ranking of the cited journal. In an even more egregious move, the editors created a Brazilian cartel and agreed to stack their publications with citations from their peer’s journals, falsely inflating the Brazilian journals’ JIF.

The editors defended their action by claiming that many Brazilian scientists are hesitant to publish in local journals due to the governmental policy of preferentially funding scientists that publish in high JIF journals. This has created a Pandora’s box for Brazilian journals looking to improve their JIF score since local scientists are unwilling to publish in the local journals, (which in the long-term would help increase the journal’s JIF), making it even more difficult for Brazilian journals to improve their ranking.

So as you see, not only are academic institutions using JIF the wrong way, governments are as well. Moral of the story, get rid of JIF and find a better way to evaluate scientific contribution!

The Ugly Side of the Journal Impact Factor

 :: Posted by American Biotechnologist on 05-16-2013

Are you obsessed with publishing in high ranking journals such as Cell or Science? Do you gloss over your works that have been published in low ranked journals when talking with colleagues or attending a job interview? If the answer is yes, you are not alone.

Since its invention approximately 60 years ago, the Journal Impact Factor (JIF) has been used to assess the quality of academic literature and the influence of scientific papers on the scientific community. The JIF was proposed by Eugene Garfield in the early 1950s and originally published by his Institute for Scientific Information (ISI) as a subscription buying tool for academic and medical librarians. The JIF assigns a score to scientific journals based on the average number of citations received in a year per paper published in the journal during the two preceding years. It has since become the authority on which journals are considered top tier publications are therefore premiere space for scientists wishing to best publicize their work and gain notoriety.

Unfortunately, the JIF has also become a tool used to ascertain a scientist’s worth and can often be a determining factor in the levels of funding they are to receive. This is an unfortunate turn of events since the JIF contains many deficiencies such as glossing over differences between fields, and lumping primary research articles in with much more easily cited review articles. As such, researchers that publish quality work in lower ranked journals are often at a disadvantage compared to those publishing secondary research in higher ranking journals.

In order to “protest” and counter this phenomenon, a group of publishers from both high impact and low impact journals have formed the Declaration on Research Assessment (DORA) which aims to lower the influence of the JIF on assessing scientific merit.

Dora has released 18 principles which are geared towards accomplishing these goals. Some of the recommendations that stand out the most include:

  • JIF should not be used to measure quality of individual articles or to asses an individual scientist’s contributions, or in hiring, promotion or funding decisions
  • Funding agencies should place more weight on the scientific content of a paper than its JIF
  • Scientific content of a paper should be considered a more important hiring decision than the JIF
  • A call for organizations to be open and transparent by providing data and methods used to calculate all metrics
  • Researchers should challenge research assessment practices that rely inappropriately on JIF

To download the full list of recommendations visit

Becoming a PubMed Expert

 :: Posted by American Biotechnologist on 06-14-2012

PubMed is probably the most important database used by scientists across the globe. Most researchers will routinely do a PubMed search to look for relevant literature on a monthly, if not weekly, basis. But how many of us really know how to use PubMed to its fullest extent? How much more efficient would our literature searches be if we just knew how to make the most out of PubMed? Luckily, NCBI, has put together a YouTube channel with detailed explanations on how to use many of their advanced products. Here is a video demonstrating how to use the PubMed Advanced Search Builder. Be sure to checkout the NCBI YouTube page for more great videos.