Back to Search
Start Over
Extracting tumour prognostic factors from a diverse electronic record dataset in genito-urinary oncology
- Source :
- International Journal of Medical Informatics. 121:53-57
- Publication Year :
- 2019
- Publisher :
- Elsevier BV, 2019.
-
Abstract
- Objectives To implement a system for unsupervised extraction of tumor stage and prognostic data in patients with genitourinary cancers using clinicopathological and radiology text. Methods A corpus of 1054 electronic notes (clinician notes, radiology reports and pathology reports) was annotated for tumor stage, prostate specific antigen (PSA) and Gleason grade. Annotations from five clinicians were reconciled to form a gold standard dataset. A training dataset of 386 documents was sequestered. The Medtex algorithm was adapted using the training dataset. Results Adapted Medtex equaled or exceeded human performance in most annotations, except for implicit M stage (F-measure of 0.69 vs 0.84) and PSA (0.92 vs 0.96). Overall Medtex performed with an F-measure of 0.86 compared to human annotations of 0.92. There was significant inter-observer variability when comparing human annotators to the gold standard. Conclusions The Medtex algorithm performed similarly to human annotators for extracting stage and prognostic data from varied clinical texts.
- Subjects :
- Oncology
medicine.medical_specialty
020205 medical informatics
Urinary system
Information Storage and Retrieval
Health Informatics
02 engineering and technology
Gleason grade
03 medical and health sciences
Prostate cancer
0302 clinical medicine
Text mining
Internal medicine
0202 electrical engineering, electronic engineering, information engineering
medicine
Data Mining
Electronic Health Records
Humans
030212 general & internal medicine
Stage (cooking)
Natural Language Processing
Observer Variation
business.industry
Gold standard (test)
Prognosis
medicine.disease
Prostate-specific antigen
business
Urogenital Neoplasms
Genitourinary Cancers
Subjects
Details
- ISSN :
- 13865056
- Volume :
- 121
- Database :
- OpenAIRE
- Journal :
- International Journal of Medical Informatics
- Accession number :
- edsair.doi.dedup.....adb026ab20f7447c4ccb49408f0acba9