Are you struggling to keep on top of the literature in your field? Because I know I was, using keyword searches and alerts for tables of contents. In the first week of June 2022 32,294 entries were added to PubMed – an enormous amount of information is being made available every week and is increasing all the time. This makes it hard for researchers, like me, to keep up with the latest information being published in their field of interest. Searching and table of contents alerts have been the traditional way to keep up with publications, but these may not cover all relevant publications or provide off-topic results. This has been addressed by the development of some smart search tools, many of which I have tried, with varying amounts of success.
I have been struggling to do this for my interest in mitochondria and the diversity of areas that mitochondria impact on. I have tried numerous tools and ways to help focus my PubMed search, but nothing seemed to work as I wanted.
During a chance meeting with Thomas Krichel, a digital librarian, in 2017, he proposed building a system based on PubMed that would be better. I know it beggars belief to think he could succeed, as an individual, when all these other companies failed. During a walk in New York’s Central Park he bombarded me with his arguments, first, impressing me with a system he had built and maintained since 1998 call “NEP: New Economics Papers”. Secondly, the approach he proposed is completely different; instead of searching the literature anew, he would apply machine learning.
I decided to take up his offer to test this approach. Then he offered me the chance to lead the project. After some soul-searching we came up with the name “Bims: Biomed News” and I am running a report “bims-cytox1. Here is how it works.
Each week I am sent a list of abstracts that are ranked by relevance to my area of interest. These rankings are based on the abstracts I select in previous weeks. Therefore, this list provides me with potential papers of interest, but also a functionality where I decide whether to include or exclude an abstract. These selections are the basis of the machine learning model. It only takes about 15 minutes for me to complete an issue, therefore making my literature alert system quick and efficient.
Since the first report we have attracted over 70 users who curate a weekly report on a variety of topics. Our current topic selectors are free to share their weekly results in any way they please – everything is free and open for sharing and reuse. We do not yet? cover the breadth of what is contained in PubMed, and that is why we are looking for more people to start reports on their topic of interest. This will give you the ability to keep up with the literature, contribute to your discipline, and potentially gain some recognition. Our testimonials highlight how some of our users have found using Biomed News, so my initial hunch, after speaking to Thomas, is something that has also been experienced by others. So, if you are looking for a way to keep up with the biomedical literature, give Biomed News a try. You can get in touch directly with Gavin using any of the links below with questions or a proposed report topic.
Liverpool John Moores University
Gavin has studied mitochondria and cell death for the past 20 years in institutions in the UK and USA. He is a senior lecturer at Liverpool John Moores University in the School of Pharmacy and Biomolecular Sciences.