PMIDigest: Interactive Review of Large Collections of PubMed Entries to Distill Relevant Information

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 fac...

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Veröffentlicht in:Genes Jg. 14; H. 4; S. 942
Hauptverfasser: Novoa, Jorge, Chagoyen, Mónica, Benito, Carlos, Moreno, F. Javier, Pazos, Florencio
Format: Journal Article
Sprache:Englisch
Veröffentlicht: Switzerland MDPI AG 19.04.2023
MDPI
Schlagworte:
Bibliometrics
Breast cancer
Citations
color
Databases, Factual
Datasets
Documentation
face
genes
Humans
Keywords
Microorganisms
porous media
PubMed
Visualization
literature digest
citation databases
data mining
scientific literature
ISSN:2073-4425, 2073-4425
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Zusammenfassung: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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SourceType-Scholarly Journals-1
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ISSN:2073-4425
2073-4425
DOI:10.3390/genes14040942