{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T11:13:50Z","timestamp":1780485230507,"version":"3.54.1"},"reference-count":119,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2024,4,12]],"date-time":"2024-04-12T00:00:00Z","timestamp":1712880000000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100009122","name":"Ministry of Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009122","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007225","name":"Ministry of Science and Technology","doi-asserted-by":"publisher","award":["MOST 108-2319-B-400-001"],"award-info":[{"award-number":["MOST 108-2319-B-400-001"]}],"id":[{"id":"10.13039\/100007225","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Bioinformatics Core Facility for Biotechnology and Pharmaceuticals","award":["MOST 111-2740-B-400-002"],"award-info":[{"award-number":["MOST 111-2740-B-400-002"]}]},{"name":"Bioinformatics Core Facility for Biotechnology and Pharmaceuticals","award":["NSTC 112-2740-B-400-005"],"award-info":[{"award-number":["NSTC 112-2740-B-400-005"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Natural language processing (NLP) has become an essential technique in various fields, offering a wide range of possibilities for analyzing data and developing diverse NLP tasks. In the biomedical domain, understanding the complex relationships between compounds and proteins is critical, especially in the context of signal transduction and biochemical pathways. Among these relationships, protein\u2013protein interactions (PPIs) are of particular interest, given their potential to trigger a variety of biological reactions. To improve the ability to predict PPI events, we propose the protein event detection dataset (PEDD), which comprises 6823 abstracts, 39\u2009488 sentences and 182\u2009937 gene pairs. Our PEDD dataset has been utilized in the AI CUP Biomedical Paper Analysis competition, where systems are challenged to predict 12 different relation types. In this paper, we review the state-of-the-art relation extraction research and provide an overview of the PEDD\u2019s compilation process. Furthermore, we present the results of the PPI extraction competition and evaluate several language models\u2019 performances on the PEDD. This paper\u2019s outcomes will provide a valuable roadmap for future studies on protein event detection in NLP. By addressing this critical challenge, we hope to enable breakthroughs in drug discovery and enhance our understanding of the molecular mechanisms underlying various diseases.<\/jats:p>","DOI":"10.1093\/bib\/bbae132","type":"journal-article","created":{"date-parts":[[2024,4,13]],"date-time":"2024-04-13T01:12:14Z","timestamp":1712970734000},"source":"Crossref","is-referenced-by-count":14,"title":["Surveying biomedical relation extraction: a critical examination of current datasets and the proposal of a new resource"],"prefix":"10.1093","volume":"25","author":[{"given":"Ming-Siang","family":"Huang","sequence":"first","affiliation":[{"name":"Intelligent Agent Systems Laboratory , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan"},{"name":"Asia University , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan"},{"name":"National Institute of Cancer Research, National Health Research Institutes , Tainan , Taiwan"},{"name":"Department of Computer Science and Information Engineering , College of Information and Electrical Engineering, , Taichung , Taiwan"},{"name":"Asia University , College of Information and Electrical Engineering, , Taichung , Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jen-Chieh","family":"Han","sequence":"additional","affiliation":[{"name":"Intelligent Information Service Research Laboratory , Department of Computer Science and Information Engineering, , Taoyuan , Taiwan"},{"name":"National Central University , Department of Computer Science and Information Engineering, , Taoyuan , Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pei-Yen","family":"Lin","sequence":"additional","affiliation":[{"name":"Intelligent Agent Systems Laboratory , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan"},{"name":"Asia University , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-Ting","family":"You","sequence":"additional","affiliation":[{"name":"Intelligent Agent Systems Laboratory , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan"},{"name":"Asia University , Department of Computer Science and Information Engineering, , New Taipei City , Taiwan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0513-107X","authenticated-orcid":false,"given":"Richard Tzong-Han","family":"Tsai","sequence":"additional","affiliation":[{"name":"Intelligent Information Service Research Laboratory , Department of Computer Science and Information Engineering, , Taoyuan , Taiwan"},{"name":"National Central University , Department of Computer Science and Information Engineering, , Taoyuan , Taiwan"},{"name":"Center for Geographic Information Science, Research Center for Humanities and Social Sciences, Academia 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