{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:36:49Z","timestamp":1772138209191,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2023,11,4]],"date-time":"2023-11-04T00:00:00Z","timestamp":1699056000000},"content-version":"vor","delay-in-days":307,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771466 92259101"],"award-info":[{"award-number":["31771466 92259101"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Strategic Priority Research Program of the Chinese Academy of Sciences, China","award":["XDB38040100"],"award-info":[{"award-number":["XDB38040100"]}]},{"name":"the Cancer Genome Atlas of China (CGAC) project","award":["YCZYPT [2018]06"],"award-info":[{"award-number":["YCZYPT [2018]06"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771466 92259101"],"award-info":[{"award-number":["31771466 92259101"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Strategic Priority Research Program of the Chinese Academy of Sciences, China","award":["XDB38040100"],"award-info":[{"award-number":["XDB38040100"]}]},{"name":"the Cancer Genome Atlas of China (CGAC) project","award":["YCZYPT [2018]06"],"award-info":[{"award-number":["YCZYPT [2018]06"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,11,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>By establishing omics sequencing of patient tumors as a crucial element in cancer treatment, the extensive implementation of precision oncology necessitates effective and prompt execution of clinical studies for approving molecular-targeted therapies. However, the substantial volume of patient sequencing data, combined with strict clinical trial criteria, increasingly complicates the process of matching patients to precision oncology studies. To streamline enrollment in these studies, we developed OncoCTMiner, an automated pre-screening platform for molecular cancer clinical trials. Through manual tagging of eligibility criteria for 2227 oncology trials, we identified key bio-concepts such as cancer types, genes, alterations, drugs, biomarkers and therapies. Utilizing this manually annotated corpus along with open-source biomedical natural language processing tools, we trained multiple named entity recognition models specifically designed for precision oncology trials. These models analyzed 460\u2009952 clinical trials, revealing 8.15 million precision medicine concepts, 9.32 million entity-criteria-trial triplets and a comprehensive precision oncology eligibility criteria database. Most significantly, we developed a patient-trial matching system based on cancer patients\u2019 clinical and genetic profiles, which can seamlessly integrate with the omics data analysis platform. This system expedites the pre-screening process for potentially suitable precision oncology trials, offering patients swifter access to promising treatment options.<\/jats:p>\n                  <jats:p>Database URL \u00a0https:\/\/oncoctminer.chosenmedinfo.com<\/jats:p>","DOI":"10.1093\/database\/baad077","type":"journal-article","created":{"date-parts":[[2023,10,21]],"date-time":"2023-10-21T08:01:39Z","timestamp":1697875299000},"source":"Crossref","is-referenced-by-count":4,"title":["OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis"],"prefix":"10.1093","volume":"2023","author":[{"given":"Quan","family":"Xu","sequence":"first","affiliation":[{"name":"Department of Bioinformatics, Beijing ChosenMed Clinical Laboratory Co. Ltd. , Jinghai Industrial Park, 156 Jinghai 4th Road, Economic and Technological Development Area, Beijing 100176, China"},{"name":"Research and Development Center, ChosenMed Technology (Zhejiang) Co. Ltd. , Room 101, Building 8, Jincheng International Science and Technology City, No. 26 Zhenxing East Road, Linping District, Hangzhou, 311103, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yueyue","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Beijing ChosenMed Clinical Laboratory Co. Ltd. , Jinghai Industrial Park, 156 Jinghai 4th Road, Economic and Technological Development Area, Beijing 100176, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dawei","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Beijing ChosenMed Clinical Laboratory Co. Ltd. , Jinghai Industrial Park, 156 Jinghai 4th Road, Economic and Technological Development Area, Beijing 100176, China"},{"name":"Research and Development Center, ChosenMed Technology (Zhejiang) Co. Ltd. , Room 101, Building 8, Jincheng International Science and Technology City, No. 26 Zhenxing East Road, Linping District, Hangzhou, 311103, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoqian","family":"Huang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Beijing ChosenMed Clinical Laboratory Co. Ltd. , Jinghai Industrial Park, 156 Jinghai 4th Road, Economic and Technological Development Area, Beijing 100176, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Feihong","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Beijing ChosenMed Clinical Laboratory Co. Ltd. , Jinghai Industrial Park, 156 Jinghai 4th Road, Economic and Technological Development Area, Beijing 100176, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"JinCheng","family":"Zhai","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Beijing ChosenMed Clinical Laboratory Co. Ltd. , Jinghai Industrial Park, 156 Jinghai 4th Road, Economic and Technological Development Area, Beijing 100176, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yang","family":"Li","sequence":"additional","affiliation":[{"name":"Beijing International Center for Mathematical Research, Peking University , No. 5 Yiheyuan Road Haidian District, Beijing 100871, China"},{"name":"Chongqing Research Institute of Big Data, Peking University , Chongqing 401333, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qiming","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Beijing ChosenMed Clinical Laboratory Co. Ltd. , Jinghai Industrial Park, 156 Jinghai 4th Road, Economic and Technological Development Area, Beijing 100176, China"},{"name":"Research and Development Center, ChosenMed Technology (Zhejiang) Co. Ltd. , Room 101, Building 8, Jincheng International Science and Technology City, No. 26 Zhenxing East Road, Linping District, Hangzhou, 311103, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niansong","family":"Qian","sequence":"additional","affiliation":[{"name":"Department of Oncology, Senior Department of Respiratory and Critical Care Medicine, The Eighth Medical Center of Chinese PLA General Hospital , No.17 A Heishanhu Road, Haidian District, Beijing 100853, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7448-7793","authenticated-orcid":false,"given":"Beifang","family":"Niu","sequence":"additional","affiliation":[{"name":"Computer Network Information Center, Chinese Academy of Sciences , Beijing 100190, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100190, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2023,11,4]]},"reference":[{"key":"2023110804335602400_R1","doi-asserted-by":"crossref","first-page":"1452","DOI":"10.1001\/jamaoncol.2016.2129","article-title":"Association of\u00a0biomarker-based treatment strategies with response rates and\u00a0progression-free survival in\u00a0refractory malignant neoplasms: a meta-analysis","volume":"2","author":"Schwaederle","year":"2016","journal-title":"JAMA Oncol"},{"key":"2023110804335602400_R2","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1093\/jamia\/ocw030","article-title":"Automated identification of\u00a0molecular effects of\u00a0drugs (AIMED)","volume":"23","author":"Fathiamini","year":"2016","journal-title":"J Am Med Inform Assoc"},{"key":"2023110804335602400_R3","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1093\/jnci\/djy221","article-title":"Systematic review and\u00a0meta-analysis of\u00a0the magnitude of\u00a0structural, clinical, and\u00a0physician and\u00a0patient barriers to cancer clinical trial participation","volume":"111","author":"Unger","year":"2019","journal-title":"JNCI:J Natl Cancer Inst"},{"key":"2023110804335602400_R4","doi-asserted-by":"crossref","first-page":"231","DOI":"10.1200\/CCI.20.00142","article-title":"Learnings from precision clinical trial matching for\u00a0oncology patients who received NGS testing","volume":"5","author":"Jain","year":"2021","journal-title":"JCO Clin Cancer Inform"},{"key":"2023110804335602400_R5","doi-asserted-by":"crossref","first-page":"2753","DOI":"10.1200\/JCO.2014.60.4165","article-title":"Feasibility of\u00a0large-scale genomic testing to facilitate enrollment onto genomically matched clinical trials","volume":"33","author":"Meric-Bernstam","year":"2015","journal-title":"J Clin 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