Laskin J, Jones S, Aparicio S, Chia S, Ch’ng C, Deyell R, et al. Precision oncology: origins, optimism, and potential. Differential diagnosis between classic Hodgkin’s lymphoma, T-cell-rich B-cell lymphoma, and paragranuloma by paraffin immunohistochemistry. Rüdiger T, Ott G, Ott MM, Müller-Deubert SM, Müller-Hermelink HK. Breast cancer subtypes based on ER/PR and Her2 expression: comparison of clinicopathologic features and survival. Onitilo AA, Engel JM, Greenlee RT, Mukesh BN. Ĭancer biomarkers Information extraction Machine learning Precision oncology Text mining. The CIViCmine knowledgebase is available at. All data is publically available and distributed with a Creative Commons Zero license. Through integration with CIVIC, we provide a prioritized list of curatable clinically relevant cancer biomarkers as well as a resource that is valuable to other knowledgebases and precision cancer analysts in general. CIViCmine contains over 87,412 biomarkers associated with 8035 genes, 337 drugs, and 572 cancer types, representing 25,818 abstracts and 39,795 full-text publications. We extracted 121,589 relevant sentences from PubMed abstracts and PubMed Central Open Access full-text papers. We then used a supervised learning approach to construct the CIViCmine knowledgebase. To this end, a group of cancer genomics experts annotated sentences that discussed biomarkers with their clinical associations and achieved good inter-annotator agreement. To aid in this curation and provide the greatest coverage for these databases, particularly CIViC, we propose the use of text mining approaches to extract these clinically relevant biomarkers from all available published literature. These databases rely on time-consuming manual curation from skilled experts who read and interpret the relevant biomedical literature. These include the open-access Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. Several knowledgebases have been created by different groups to collate evidence for these associations. To improve patient care, knowledge of diagnostic, prognostic, predisposing, and drug response markers is essential. oncology involves analysis of individual cancer samples to understand the genes and pathways involved in the development and progression of a cancer. 15 Simon Fraser University, Burnaby, BC, Canada. 14 University of British Columbia, Vancouver, BC, Canada. 13 Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada. 12 Department of Genetics, Washington University School of Medicine, St. 11 Division of Oncology, Department of Medicine, Washington University School of Medicine, St. 10 Siteman Cancer Center, Washington University School of Medicine, St. 9 McDonnell Genome Institute, Washington University School of Medicine, St. 8 Department of Genetics, Washington University School of Medicine, St. 7 Division of Oncology, Department of Medicine, Washington University School of Medicine, St. 6 Siteman Cancer Center, Washington University School of Medicine, St. 5 McDonnell Genome Institute, Washington University School of Medicine, St. 4 Siteman Cancer Center, Washington University School of Medicine, St.3 McDonnell Genome Institute, Washington University School of Medicine, St.2 University of British Columbia, Vancouver, BC, Canada.1 Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada.
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