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Background  Although electronic health records (EHRs) have been widely used in secondary assessments, clinical documents are relatively less utilized owing to the lack of standardized clinical text frameworks across different institutions.    Objective  This study aimed to develop a framework for processing unstructured clinical documents of EHRs and integration with standardized structured data.    Methods  We developed a framework known as Staged Optimization of Curation, Regularization, and Annotation of clinical text (SOCRATex). SOCRATex has the following four aspects: (1) extracting clinical notes for the target population and preprocessing the data, (2) defining the annotation schema with a hierarchical structure, (3) performing document-level hierarchical annotation using the annotation schema, and (4) indexing annotations for a search engine system. To test the usability of the proposed framework, proof-of-concept studies were performed on EHRs. We defined three distinctive patient groups and extracted their clinical documents (ie, pathology reports, radiology reports, and admission notes). The documents were annotated and integrated into the Observational Medical Outcomes Partnership (OMOP)-common data model (CDM) database. The annotations were used for creating Cox proportional hazard models with different settings of clinical analyses to measure (1) all-cause mortality, (2) thyroid cancer recurrence, and (3) 30-day hospital readmission.    Results  Overall, 1055 clinical documents of 953 patients were extracted and annotated using the defined annotation schemas. The generated annotations were indexed into an unstructured textual data repository. Using the annotations of pathology reports, we identified that node metastasis and lymphovascular tumor invasion were associated with all-cause mortality among colon and rectum cancer patients (both  P =.02). The other analyses involving measuring thyroid cancer recurrence using radiology reports and 30-day hospital readmission using admission notes in depressive disorder patients also showed results consistent with previous findings.    Conclusions  We propose a framework for hierarchical annotation of textual data and integration into a standardized OMOP-CDM medical database. The proof-of-concept studies demonstrated that our framework can effectively process and integrate diverse clinical documents with standardized structured data for clinical research.

jmir medical informatics

A Framework (SOCRATex) for Hierarchical Annotation of Unstructured Electronic Health Records and Integration Into a Standardized Medical Database: Development and Usability Study