{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:41:45Z","timestamp":1772138505490,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,24]],"date-time":"2023-05-24T00:00:00Z","timestamp":1684886400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"BMBF","doi-asserted-by":"publisher","award":["01ZX1402"],"award-info":[{"award-number":["01ZX1402"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Leibniz-HKI"},{"DOI":"10.13039\/501100002347","name":"BMBF","doi-asserted-by":"publisher","award":["01ZZ1803G"],"award-info":[{"award-number":["01ZZ1803G"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100004316","name":"IBM","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100004316","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>We present GePI, a novel Web server for large-scale text mining of molecular interactions from the scientific biomedical literature. GePI leverages natural language processing techniques to identify genes and related entities, interactions between those entities and biomolecular events involving them. GePI supports rapid retrieval of interactions based on powerful search options to contextualize queries targeting (lists of) genes of interest. Contextualization is enabled by full-text filters constraining the search for interactions to either sentences or paragraphs, with or without pre-defined gene lists. Our knowledge graph is updated several times a week ensuring the most recent information to be available at all times. The result page provides an overview of the outcome of a search, with accompanying interaction statistics and visualizations. A table (downloadable in Excel format) gives direct access to the retrieved interaction pairs, together with information about the molecular entities, the factual certainty of the interactions (as verbatim expressed by the authors), and a text snippet from the original document that verbalizes each interaction. In summary, our Web application offers free, easy-to-use, and up-to-date monitoring of gene and protein interaction information, in company with flexible query formulation and filtering options. GePI is available at https:\/\/gepi.coling.uni-jena.de\/.<\/jats:p>","DOI":"10.1093\/nar\/gkad445","type":"journal-article","created":{"date-parts":[[2023,5,24]],"date-time":"2023-05-24T16:27:04Z","timestamp":1684945624000},"page":"W237-W242","source":"Crossref","is-referenced-by-count":5,"title":["<scp>GePI<\/scp>\n                    : large-scale text mining, customized retrieval and flexible filtering of gene\/protein interactions"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1193-5103","authenticated-orcid":false,"given":"Erik","family":"Faessler","sequence":"first","affiliation":[{"name":"Jena University Language and Information Engineering (JULIE) Lab, Friedrich Schiller University Jena , F\u00fcrstengraben 30, 07743 Jena, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5052-0245","authenticated-orcid":false,"given":"Udo","family":"Hahn","sequence":"additional","affiliation":[{"name":"Jena University Language and Information Engineering (JULIE) Lab, Friedrich Schiller University Jena , F\u00fcrstengraben 30, 07743 Jena, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3862-6546","authenticated-orcid":false,"given":"Sascha","family":"Sch\u00e4uble","sequence":"additional","affiliation":[{"name":"Jena University Language and Information Engineering (JULIE) Lab, Friedrich Schiller University Jena , F\u00fcrstengraben 30, 07743 Jena, Germany"},{"name":"Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI) , 07745 Jena, Germany"}]}],"member":"286","published-online":{"date-parts":[[2023,5,24]]},"reference":[{"key":"2023070505033626000_B1","doi-asserted-by":"crossref","first-page":"767","DOI":"10.1093\/nar\/gkn892","article-title":"Human protein reference database - 2009 update","volume":"37","author":"Keshava\u00a0Prasad","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023070505033626000_B2","doi-asserted-by":"crossref","first-page":"D358","DOI":"10.1093\/nar\/gkt1115","article-title":"The MIntAct project: IntAct as a common curation platform for 11 molecular interaction databases","volume":"42","author":"Orchard","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2023070505033626000_B3","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1002\/pro.3978","article-title":"The BioGRID database: a comprehensive biomedical resource of curated protein, genetic, and chemical interactions","volume":"30","author":"Oughtred","year":"2021","journal-title":"Protein Sci."},{"key":"2023070505033626000_B4","doi-asserted-by":"crossref","first-page":"D638","DOI":"10.1093\/nar\/gkac1000","article-title":"The String database in 2023: protein-protein association networks and functional enrichment analyses for any sequenced genome of interest","volume":"51","author":"Szklarczyk","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"2023070505033626000_B5","doi-asserted-by":"crossref","first-page":"D605","DOI":"10.1093\/nar\/gkaa1074","article-title":"The String database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene\/measurement sets","volume":"49","author":"Szklarczyk","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"2023070505033626000_B6","doi-asserted-by":"crossref","first-page":"D808","DOI":"10.1093\/nar\/gks1094","article-title":"String v9.1 : protein-protein interaction networks, with increased coverage and integration","volume":"41","author":"Franceschini","year":"2013","journal-title":"Nucleic Acids Res."},{"key":"2023070505033626000_B7","doi-asserted-by":"crossref","first-page":"3442","DOI":"10.1093\/nar\/28.18.3442","article-title":"String : a Web-server to retrieve and display the repeatedly occurring neighbourhood of a gene","volume":"28","author":"Snel","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"2023070505033626000_B8","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1093\/bib\/bbv024","article-title":"Community challenges in biomedical text mining over 10 years: success, failure and the future","volume":"17","author":"Huang","year":"2016","journal-title":"Brief. 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