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This abstract introduces GPDMiner(Gene, Protein, and Disease Miner), a platform designed for the biomedical domain, addressing the challenges posed by the growing volume of academic papers.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>GPDMiner is a text mining platform that utilizes advanced information retrieval techniques. It operates by searching PubMed for specific queries, extracting and analyzing information relevant to the biomedical field. This system is designed to discern and illustrate relationships between biomedical entities obtained from automated information extraction.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>The implementation of GPDMiner demonstrates its efficacy in navigating the extensive corpus of biomedical literature. It efficiently retrieves, extracts, and analyzes information, highlighting significant connections between genes, proteins, and diseases. The platform also allows users to save their analytical outcomes in various formats, including Excel and images.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>GPDMiner offers a notable additional functionality among the array of text mining tools available for the biomedical field. This tool presents an effective solution for researchers to navigate and extract relevant information from the vast unstructured texts found in biomedical literature, thereby providing distinctive capabilities that set it apart from existing methodologies. Its application is expected to greatly benefit researchers in this domain, enhancing their capacity for knowledge discovery and data management.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12859-024-05710-z","type":"journal-article","created":{"date-parts":[[2024,3,6]],"date-time":"2024-03-06T12:02:26Z","timestamp":1709726546000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["GPDminer: a tool for extracting named entities and analyzing relations in biological literature"],"prefix":"10.1186","volume":"25","author":[{"given":"Yeon-Ji","family":"Park","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Geun-Je","family":"Yang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chae-Bong","family":"Sohn","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soo Jun","family":"Park","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,3,6]]},"reference":[{"key":"5710_CR1","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1002\/aris.1440370106","volume":"37","author":"K B\u00f6rner","year":"2003","unstructured":"B\u00f6rner K, Chen C, Boyack KW. 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