PheDRS
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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.
Documentation for PheDRS is found in the following locations:
1. User documentation including this documentation is publicly available and found in https://docs.uabgrid.uab.edu/wiki/PheDRS 2. Project specific information is found in the appropriate git repo wikis and markdown text 3. UAB specific developer documentation is found inthe UAB_BioMedInformatics\PHEDRS Box directory
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Former registrars no longer active.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.
| 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 |