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= Phenotype Detection Registry System =
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= Phenotype Detection Registry System (PheDRS) User Documentation =
  
 
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. This documentation is intended for managers and users of the PheDRS system.
 
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. This documentation is intended for managers and users of the PheDRS system.
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== Installation / Setup ==
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=== Software Dependency List ===
  
 
== Roles ==
 
== Roles ==
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== Installation / Setup ==
 
  
 
== Back End Workflow / Architecture ==
 
== Back End Workflow / Architecture ==
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=== UDAS ===
 
=== UDAS ===
  
== Software Dependency List ==
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== Paper References ==
 
== Paper References ==

Revision as of 11:39, 18 January 2019

Contents

Phenotype Detection Registry System (PheDRS) User Documentation

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. This documentation is intended for managers and users of the PheDRS system.

Installation / Setup

Software Dependency List

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 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


Back End Workflow / Architecture

Web Service Documentation

RegistryWS

UDAS

Paper References