. Author manuscript; available in PMC: 2013 Jun 23.

Published in final edited form as: Sci Transl Med. 2011 Apr 20;3(79):79re1. doi: 10.1126/scitranslmed.3001807

Table 2.

Data categories for defining a clinical gold standard, an EMR-derived phenotype, and covariates and exclusion criteria.

Primary Phenotype	Data Categories			Phenotyping Methods
Primary Phenotype	Clinical gold standard	EMR-derived phenotype	Phenotype cohort (e.g. covariates, exclusion criteria)	Phenotyping Methods
Dementia	Demographics, Clinical notes (clinician documentation of mental status and histopathological examination data)	Diagnoses, medications	Demographics, laboratory tests, radiology reports	Structured data extraction, Free-text searches, Manual chart review
Cataracts	Clinical notes (Ophthalmologic examination)	Diagnoses, procedure codes	Demographics, medications	Structured data extraction, NLP, Intelligent Character Recognition
Peripheral Arterial Disease	Radiology test results (ankle-brachial index or arteriography)	Diagnoses, procedure codes, medications, radiology test results	Demographics	Structured data extraction, NLP
Type 2 Diabetes	Laboratory Tests	Diagnoses, laboratory tests, medications	Demographics, Laboratory tests, height, weight, family history, smoking history	Structured data extraction, Free-text searches
Cardiac Conduction	ECG measurements	ECG report results	Demographics, diagnoses, procedure codes, medications, laboratory tests	Structured data extraction, NLP