PheDRS

Phenotype Detection Registry System (PheDRS) User Documentation

Overview

The Phenotype Detection Registry System (PheDRS) is a tool at UAB used to assist researchers and clinicians identify populations of interest at UAB matching clinical criteria from both structured data (billing codes, medications, labs) and unstructured documents using Natural Language Processing. The user documentation described here is intended for managers and users of the PheDRS system.

Additional documentation for PheDRS is found in the following locations:

1. Project specific information is found in the appropriate git repo wikis and markdown text

2. UAB specific developer documentation is found in the UAB_BioMedInformatics\PHEDRS Box directory

Installation / Setup

Currently this is very site specific and depends on various backend systems, EHR vendors, etc... UAB specific site setup can be found in the UAB_BioMedInformatics\PHEDRS Box directory

Roles

PheDRS supports the following user roles:

Manager

The manager of a registry. Full read and write access to the registry. Can add new users as registrars or managers to the registry.

Registrar

A user with read and write access to the registry.

Administrator

System administrator responsible for maintaining the entire PheDRS system including all registries.

Viewer

Read only access to the registry.

Inactive

Former registrars no longer active.

De-ID Viewer

Viewer allowed to view de-identified data (18 HIPAA Safe Harbor items removed) data.

Registry Configuration

The registry is configured by the registry manager, often in conjunction with the system administrator.

Registry Property Descriptions and Examples

Registry Configuration: Cvtermprop parameters

CV NAME	CV ID	Example of cvterm name for TYPE_ID	Meaning and Use of VALUE field for this type	Example of Value Field
UAB ICD-10-CM Codes	9	Panlobular emphysema	If patient has this billing code, assign as candidate to registry	UAB COPD Registry ICD-10-CM diagnosis criteria
UAB MS DRG Codes	12	COPD w CC	If patient has this DRG code, then add anchor cvterm property to this code	DRG Codes COPD Anchor Encounter criteria
		COPD w MCC	If patient has this DRG code, then add patient to the registry as "accepted"	UAB COPD Registry DRG Codes inclusion criteria
PHEDRS Data Loading Criteria	23	Default NLP Pipeline Collection	This is the ID# of the default pipeline for displaying documents in this registry. Unenforced Foreign Key to db_id=14	2
		Encounter Collection	Encounters matching the appended SQL criteria are added to the registry	AND (SRC_ADMIT_DT_TM >= (SYSDATE-730)) AND FORMATTED_MEDICAL_RECORD_NBR IN (SELECT FORMATTED_UAB_MRN FROM REGISTRY_PATIENT WHERE REGISTRY_ID=2861)
		Encounter Intervention	Encounters matching the appended SQL criteria are added to the registry AND candidate is flagged for review	AND SRC_ADMIT_DT_TM >= (SYSDATE-30) AND ( (reason_for_visit_txt LIKE '%COPD%') OR (UPPER(reason_for_visit_txt) LIKE '%BRONCHITIS%') OR (UPPER(reason_for_visit_txt) LIKE '%BRONCHIECTASIS%') OR (UPPER(reason_for_visit_txt) LIKE '%EMPHYSEMA%') )
PHEDRS MetaData CV	24	Patient Review Cutoff Date	Do not retrieve any data (codes, encounters, documents) from source system before this date	1/1/17
		Registry Application Title	Use this text here for the name of the registry	COPD Registry Control Panel
		Display Codes Database Identifier	DB_ID permissable to display in "Diagnoses and Drgs" Panel	8
PHEDRS Tab CV	25	REGISTRY_INPATIENT_REVIEW	Indicates that this tab should be displayed in this registry. Value indicates display order from LEFT to RIGHT (1 for leftmost tab)	1
Optum UAB APR DRG Codes 2017	26
UAB WH CLN REF Codeset 69	27

Developer Guide for Registry Configuration Properties

Developer Guide for Registry Configuration Properties

CRITERIA NAME	EVENT DESCRIPTION	Input Patient Registry Status	Input Patient Review Status	Input Required Registry Patient Cvterm/s	Outputput Patient Registry Status	Output Patient Review Status	Output Change to Registry Patient Cvterm/s	Action Description	Implementation Notes
Diagnosis (Code_Detection)	PATIENT_CODE entry that matches diagnosis criteria in CVTERMPROP	NULL	NULL	NULL	CANDIDATE	NEVER REVIEWED	ANY	Add candidate	CVTERMs corresponding to codes have a CVTERMPROP set on them of type registry_name (from cv_id 11) with a value containing text "diagnosis criteria"