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Updated: Jun 14, 2026
A Metadata Extraction Approach for Clinical Case Reports to Enable Advanced Understanding of Biomedical Concepts
Published on: September 20, 2018
Using a statistical natural language Parser augmented with the UMLS specialist lexicon to assign SNOMED CT codes to
Henry J Lowe1, Yang Huang, Donald P Regula
1Center for Clinical Informatics, Stanford University, Stanford, CA, USA.
Abstract:
To address the problem of extracting structured information from pathology reports for research purposes in the STRIDE Clinical Data Warehouse, we adapted the ChartIndex Medical Language Processing system to automatically identify and map anatomic and diagnostic noun phrases found in full-text pathology reports to SNOMED CT concept descriptors. An evaluation of the system's performance showed a positive predictive value for anatomic concepts of 92.3% and positive predictive value for diagnostic concepts of 84.4%. The experiment also suggested strategies for improving ChartIndex's performance coding pathology reports.
