PMIDigest: Interactive review of large collections of PubMed entries to distill relevant information

Novoa, Jorge; Chagoyen, Mónica; Benito, Carlos; Moreno, F. Javier; Pazos, Florencio; European Food Safety Authority; Chagoyen, Mónica [0000-0001-6911-1591]; Moreno, F. Javier [0000-0002-7637-9542]

PMIDigest: Interactive review of large collections of PubMed entries to distill relevant information

2023

Scientific knowledge is being accumulated in the biomedical literature at an unprecedented pace. The most widely used database with biomedicine-related article abstracts, PubMed, currently contains more than 36 million entries. Users performing searches in this database for a subject of interest face thousands of entries (articles) that are difficult to process manually. In this work, we present an interactive tool for automatically digesting large sets of PubMed articles: PMIDigest (PubMed IDs digester). The system allows for classification/sorting of articles according to different criteria, including the type of article and different citation-related figures. It also calculates the distribution of MeSH (medical subject headings) terms for categories of interest, providing in a picture of the themes addressed in the set. These MeSH terms are highlighted in the article abstracts in different colors depending on the category. An interactive representation of the interarticle citation network is also presented in order to easily locate article “clusters” related to particular subjects, as well as their corresponding “hub” articles. In addition to PubMed articles, the system can also process a set of Scopus or Web of Science entries. In summary, with this system, the user can have a “bird’s eye view” of a large set of articles and their main thematic tendencies and obtain additional information not evident in a plain list of abstracts.

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This research was funded by the European Food Safety Authority (grant number GP/EFSA/ENCO/2020/02-1).

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Peer reviewed

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