DeepPhe: A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records

Cancer Research
Guergana K SavovaRebecca S Jacobson

Abstract

Precise phenotype information is needed to understand the effects of genetic and epigenetic changes on tumor behavior and responsiveness. Extraction and representation of cancer phenotypes is currently mostly performed manually, making it difficult to correlate phenotypic data to genomic data. In addition, genomic data are being produced at an increasingly faster pace, exacerbating the problem. The DeepPhe software enables automated extraction of detailed phenotype information from electronic medical records of cancer patients. The system implements advanced Natural Language Processing and knowledge engineering methods within a flexible modular architecture, and was evaluated using a manually annotated dataset of the University of Pittsburgh Medical Center breast cancer patients. The resulting platform provides critical and missing computational methods for computational phenotyping. Working in tandem with advanced analysis of high-throughput sequencing, these approaches will further accelerate the transition to precision cancer treatment. Cancer Res; 77(21); e115-8. ©2017 AACR.

References

Feb 3, 2005·Journal of the American Medical Informatics Association : JAMIA·George Hripcsak, Adam S Rothschild
Sep 8, 2010·Journal of the American Medical Informatics Association : JAMIA·Guergana K SavovaChristopher G Chute
Jan 5, 2013·Journal of Biomedical Semantics·Stephen T WuChristopher G Chute
Sep 16, 2016·BMC Medical Informatics and Decision Making·Harry HochheiserRebecca S Jacobson

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Citations

Dec 6, 2018·Journal of the American Medical Informatics Association : JAMIA·Ronilda LacsonRamin Khorasani
Sep 22, 2018·JCO Clinical Cancer Informatics·Andrew M MaltyJeremy L Warner
May 10, 2020·JCO Clinical Cancer Informatics·Zhou YuanHarry Hochheiser
Aug 22, 2020·Yearbook of Medical Informatics·Ashley C GriffinArlene E Chung
Mar 14, 2020·Journal of Pathology Informatics·Pericles S GiannarisDmitriy Shin
Aug 17, 2020·Journal of Medical Internet Research·Sally L BaxterMichael Hogarth
Aug 28, 2020·Nature Reviews. Clinical Oncology·Elizabeth HuynhRaymond H Mak
Dec 6, 2019·BMC Medical Informatics and Decision Making·Liwei WangHongfang Liu
Jan 8, 2021·JCO Clinical Cancer Informatics·Rimma BelenkayaChristian Reich
Feb 6, 2021·International Journal of Radiation Oncology, Biology, Physics·Danielle S BittermanGuergana K Savova
Oct 28, 2019·Cancer radiothérapie : journal de la Société française de radiothérapie oncologique·A Burgun
Oct 26, 2021·JCO Clinical Cancer Informatics·Sajjad AbedianThomas R Campion

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