Organizing training workshops on gene literature retrieval, profiling, and visualization for early career researchers

Fatima Al Ali, Alexandra K. Marr, Zohreh Tatari-Calderone, Mohamed Alfaki, Mohammed Toufiq, Jessica Roelands, Basirudeen Syed Ahamed Kabeer, Davide Bedognetti, Nico Marr, Mathieu Garand, Darawan Rinchai, Damien Chaussabel

Research output: Contribution to journalArticlepeer-review


Early-career researchers must acquire the skills necessary to effectively search and extract information from biomedical literature. This ability is for instance crucial for evaluating the novelty of experimental results, and assessing potential publishing opportunities. Given the rapidly growing 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. In this context, we present a hands-on training curriculum aimed at retrieval, profiling, and visualization of literature associated with a given topic. The curriculum was implemented in a workshop in January 2021. Here we provide supporting material and step-by-step implementation guidelines with the ISG15 gene literature serving as an illustrative use case. Workshop participants can learn several skills, including: 1) building and troubleshoot PubMed queries in order to retrieve the literature associated with a gene of interest; 2) identifying key concepts relevant to given themes (such as cell types, diseases, and biological processes); 3) measuring the prevalence of these concepts in the gene literature; 4) extracting key information from relevant articles, and 5) developing 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.

Original languageEnglish
Article number275
StatePublished - 2023


  • Concept extraction
  • Data visualization
  • Literature profiling
  • Science education


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