{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,17]],"date-time":"2026-02-17T13:27:37Z","timestamp":1771334857489,"version":"3.50.1"},"reference-count":40,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,4,10]],"date-time":"2024-04-10T00:00:00Z","timestamp":1712707200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Integrated Infrastructure for Social Mining and Big Data Analytics"},{"name":"NextGenerationEU\u2014National Recovery and Resilience Plan"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The rapid increase of bio-medical literature makes it harder and harder for scientists to keep pace with the discoveries on which they build their studies. Therefore, computational tools have become more widespread, among which network analysis plays a crucial role in several life-science contexts. Nevertheless, building correct and complete networks about some user-defined biomedical topics on top of the available literature is still challenging.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We introduce NetMe 2.0, a web-based platform that automatically extracts relevant biomedical entities and their relations from a set of input texts\u2014i.e. in the form of full-text or abstract of PubMed Central\u2019s papers, free texts, or PDFs uploaded by users\u2014and models them as a BioMedical Knowledge Graph (BKG). NetMe 2.0 also implements an innovative Retrieval Augmented Generation module (Graph-RAG) that works on top of the relationships modeled by the BKG and allows the distilling of well-formed sentences that explain their content. The experimental results show that NetMe 2.0 can infer comprehensive and reliable biological networks with significant Precision\u2013Recall metrics when compared to state-of-the-art approaches.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/netme.click\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae194","type":"journal-article","created":{"date-parts":[[2024,4,8]],"date-time":"2024-04-08T17:25:24Z","timestamp":1712597124000},"source":"Crossref","is-referenced-by-count":6,"title":["NetMe 2.0: a web-based platform for extracting and modeling knowledge from biomedical literature as a labeled graph"],"prefix":"10.1093","volume":"40","author":[{"given":"Antonio","family":"Di Maria","sequence":"first","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Catania , Catania, 95125, Italy"}]},{"given":"Lorenzo","family":"Bellomo","sequence":"additional","affiliation":[{"name":"Scuola Normale Superiore , Pisa, 56126 , Italy"}]},{"given":"Fabrizio","family":"Billeci","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Catania , Catania, 95125, Italy"}]},{"given":"Alfio","family":"Cardillo","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Catania , Catania, 95125, Italy"}]},{"given":"Salvatore","family":"Alaimo","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Catania , Catania, 95125, Italy"}]},{"given":"Paolo","family":"Ferragina","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Pisa , Pisa, 56126 , Italy"}]},{"given":"Alfredo","family":"Ferro","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Catania , Catania, 95125, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9764-0295","authenticated-orcid":false,"given":"Alfredo","family":"Pulvirenti","sequence":"additional","affiliation":[{"name":"Department of Clinical and Experimental Medicine, University of Catania , Catania, 95125, Italy"}]}],"member":"286","published-online":{"date-parts":[[2024,4,10]]},"reference":[{"key":"2024050702561552100_btae194-B1","doi-asserted-by":"crossref","first-page":"3570","DOI":"10.1038\/s41467-023-39301-y","article-title":"Biomedical knowledge graph learning for drug repurposing by extending guilt-by-association to multiple layers","volume":"14","author":"Bang","year":"2023","journal-title":"Nat 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