{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,8,7]],"date-time":"2024-08-07T14:07:59Z","timestamp":1723039679801},"reference-count":0,"publisher":"IOS Press","isbn-type":[{"type":"print","value":"9781643682907"},{"type":"electronic","value":"9781643682914"}],"license":[{"start":{"date-parts":[[2022,6,29]],"date-time":"2022-06-29T00:00:00Z","timestamp":1656460800000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,29]]},"abstract":"<jats:p>The accelerating impact of genomic data in clinical decision-making has generated a paradigm shift from treatment based on the anatomic origin of the tumor to the incorporation of key genomic features to guide therapy. Assessing the clinical validity and utility of the genomic background of a patient\u2019s cancer represents one of the emerging challenges in oncology practice, demanding the development of automated platforms for extracting clinically relevant genomic information from medical texts. We developed PubMiner, a natural language processing tool to extract and interpret cancer type, therapy, and genomic information from biomedical abstracts. Our initial focus has been the retrieval of gene names, variants, and negations, where PubMiner performed highly in terms of total recall (91.7%) with a precision of 79.7%. Our next steps include developing a web-based interface to promote personalized treatment based on each tumor\u2019s unique genomic fingerprints.<\/jats:p>","DOI":"10.3233\/shti220735","type":"book-chapter","created":{"date-parts":[[2022,6,30]],"date-time":"2022-06-30T07:34:07Z","timestamp":1656574447000},"source":"Crossref","is-referenced-by-count":1,"title":["Natural Language Processing Approaches for Retrieval of Clinically Relevant Genomic Information in Cancer"],"prefix":"10.3233","author":[{"given":"Taxiarchis","family":"Botsis","sequence":"first","affiliation":[{"name":"The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA"}]},{"name":"the Johns Hopkins Molecular Tumor Board Investigators","sequence":"additional","affiliation":[]},{"given":"Joseph","family":"Murray","sequence":"additional","affiliation":[{"name":"The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA"}]},{"given":"Alessandro","family":"Leal","sequence":"additional","affiliation":[{"name":"The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA"}]},{"given":"Doreen","family":"Palsgrove","sequence":"additional","affiliation":[{"name":"The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA"}]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[{"name":"The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA"}]},{"given":"James R.","family":"White","sequence":"additional","affiliation":[{"name":"The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA"}]},{"given":"Victor E.","family":"Velculescu","sequence":"additional","affiliation":[{"name":"The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA"}]},{"given":"Valsamo","family":"Anagnostou","sequence":"additional","affiliation":[{"name":"The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA"}]}],"member":"7437","container-title":["Studies in Health Technology and Informatics","Advances in Informatics, Management and Technology in Healthcare"],"original-title":[],"link":[{"URL":"https:\/\/ebooks.iospress.nl\/pdf\/doi\/10.3233\/SHTI220735","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,30]],"date-time":"2022-06-30T07:34:08Z","timestamp":1656574448000},"score":1,"resource":{"primary":{"URL":"https:\/\/ebooks.iospress.nl\/doi\/10.3233\/SHTI220735"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,6,29]]},"ISBN":["9781643682907","9781643682914"],"references-count":0,"URL":"https:\/\/doi.org\/10.3233\/shti220735","relation":{},"ISSN":["0926-9630","1879-8365"],"issn-type":[{"type":"print","value":"0926-9630"},{"type":"electronic","value":"1879-8365"}],"subject":[],"published":{"date-parts":[[2022,6,29]]}}}