Organizing gene literature retrieval, profiling, and visualization training workshops for early career researchers [version 1; peer review: 1 approved, 1 not approved]

• Published in: F1000 research Vol. 10; p. 275
• Main Authors: Al Ali, Fatima, Marr, Alexandra K, Tatari-Calderone, Zohreh, Alfaki, Mohamed, Toufiq, Mohammed, Roelands, Jessica, Syed Ahamed Kabeer, Basirudeen, Bedognetti, Davide, Marr, Nico, Garand, Mathieu, Rinchai, Darawan, Chaussabel, Damien
• Format: Journal Article
• Language: English
• Published: 2021
• Subjects: Science education; Literature profiling; Data visualization; Concept extraction
• ISSN: 2046-1402; 2046-1402
• DOI: 10.12688/f1000research.36395.1

Developing the skills needed to effectively search and extract information from biomedical literature is essential for early-career researchers. It is, for instance, on this basis that the novelty of experimental results, and therefore publishing opportunities, can be evaluated. Given the unprecedented volume of publications in the field of biomedical research, new systematic approaches need to be devised and adopted for the retrieval and curation of literature relevant to a specific theme. Here we describe a hands-on training curriculum aimed at retrieval, profiling, and visualization of literature associated with a given topic. This curriculum was implemented in a workshop in January 2021. We provide supporting material and step-by-step implementation guidelines with the ISG15 gene literature serving as an illustrative use case. Through participation in such a workshop, trainees can learn: 1) to build and troubleshoot PubMed queries in order to retrieve the literature associated with a gene of interest; 2) to identify key concepts relevant to given themes (such as cell types, diseases, and biological processes); 3) to measure the prevalence of these concepts in the gene literature; 4) to extract key information from relevant articles, and 5) to develop a background section or summary on the basis of this information. Finally, trainees can learn to consolidate the structured information captured through this process for presentation via an interactive web application.