Literature DB >> 17238518

Automated extraction of free-text from pathology reports.

Anne-Marie Currie1, Travis Fricke, Agnes Gawne, Ric Johnston, John Liu, Barbara Stein.   

Abstract

Manually populating a cancer registry from free-text pathology reports is labor intensive and costly. This poster describes a method of automated text extraction to improve the efficiency of this process and reduce cost. FineTooth, a software company, provides an automated service to the Fred Hutchinson Cancer Research Center (FHCRC) to help populate their breast and prostate cancer clinical research database by electronically abstracting over 80 data fields from pathology text reports.

Entities:  

Mesh：

Year:  2006        PMID： 17238518      PMCID： PMC1839446     

Source DB:  PubMed          Journal:  AMIA Annu Symp Proc        ISSN： 1559-4076


  13 in total

1.  Using a statistical natural language Parser augmented with the UMLS specialist lexicon to assign SNOMED CT codes to anatomic sites and pathologic diagnoses in full text pathology reports.

Authors:  Henry J Lowe; Yang Huang; Donald P Regula
Journal:  AMIA Annu Symp Proc       Date:  2009-11-14

2.  Evaluation of an Automated Information Extraction Tool for Imaging Data Elements to Populate a Breast Cancer Screening Registry.

Authors:  Ronilda Lacson; Kimberly Harris; Phyllis Brawarsky; Tor D Tosteson; Tracy Onega; Anna N A Tosteson; Abby Kaye; Irina Gonzalez; Robyn Birdwell; Jennifer S Haas
Journal:  J Digit Imaging       Date:  2015-10       Impact factor: 4.056

3.  Extracting data from electronic medical records: validation of a natural language processing program to assess prostate biopsy results.

Authors:  Anil A Thomas; Chengyi Zheng; Howard Jung; Allen Chang; Brian Kim; Joy Gelfond; Jeff Slezak; Kim Porter; Steven J Jacobsen; Gary W Chien
Journal:  World J Urol       Date:  2013-02-17       Impact factor: 4.226

4.  Age at diagnosis predicts local recurrence in women treated with breast-conserving surgery and postoperative radiation therapy for ductal carcinoma in situ: a population-based outcomes analysis.

Authors:  I Kong; S A Narod; C Taylor; L Paszat; R Saskin; S Nofech-Moses; D Thiruchelvam; W Hanna; J P Pignol; S Sengupta; L Elavathil; P A Jani; S J Done; S Metcalfe; E Rakovitch
Journal:  Curr Oncol       Date:  2014-02       Impact factor: 3.677

5.  Assessing the Utility of Automatic Cancer Registry Notifications Data Extraction from Free-Text Pathology Reports.

Authors:  Anthony N Nguyen; Julie Moore; John O'Dwyer; Shoni Philpot
Journal:  AMIA Annu Symp Proc       Date:  2015-11-05

6.  Close or positive resection margins are not associated with an increased risk of chest wall recurrence in women with DCIS treated by mastectomy: a population-based analysis.

Authors:  Jonathan Klein; Iwa Kong; Lawrence Paszat; Sharon Nofech-Mozes; Wedad Hanna; Deva Thiruchelvam; Steven A Narod; Refik Saskin; Susan J Done; Naomi Miller; Bruce Youngson; Alan Tuck; Sandip Sengupta; Leela Elavathil; Prashant A Jani; Elzbieta Slodkowska; Michel Bonin; Eileen Rakovitch
Journal:  Springerplus       Date:  2015-07-10

7.  Automated extraction of precise protein expression patterns in lymphoma by text mining abstracts of immunohistochemical studies.

Authors:  Jia-Fu Chang; Mihail Popescu; Gerald L Arthur
Journal:  J Pathol Inform       Date:  2013-07-31

8.  Machine learning for syndromic surveillance using veterinary necropsy reports.

Authors:  Nathan Bollig; Lorelei Clarke; Elizabeth Elsmo; Mark Craven
Journal:  PLoS One       Date:  2020-02-05       Impact factor: 3.240

9.  Generating high-quality data abstractions from scanned clinical records: text-mining-assisted extraction of endometrial carcinoma pathology features as proof of principle.

Authors:  Anthony Nguyen; John O'Dwyer; Thanh Vu; Penelope M Webb; Sharon E Johnatty; Amanda B Spurdle
Journal:  BMJ Open       Date:  2020-06-11       Impact factor: 2.692

10.  Web Application for the Automated Extraction of Diagnosis and Site From Pathology Reports for Keratinocyte Cancers.

Authors:  Bridie S Thompson; Sam Hardy; Nirmala Pandeya; Jean Claude Dusingize; Adele C Green; Athon Millane; Daniel Bourke; Ronald Grande; Cameron D Bean; Catherine M Olsen; David C Whiteman
Journal:  JCO Clin Cancer Inform       Date:  2020-08
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