Namespaces

Variants
Actions
Personal tools

PheDRS

From UABgrid Documentation

(Difference between revisions)
Jump to: navigation, search
(Developer Guide for Registry Configuration Properties)
(Developer Guide for Registry Configuration Properties)
Line 159: Line 159:
  
 
{| class="wikitable"
 
{| class="wikitable"
! Criteria Name !! Event Description !!  Input Patient Registry Status !! Input Patient Review Status !! Input REGISTRY_PATIENT _CVTERM !!  Output Patient Registry Status !! Output Patient Review Status !! Output REGISTRY_PATIENT_CVTERM !! Action Description !! Implementation Notes
+
! Criteria Name !! Event Description !!  Input Patient Registry Status !! Input Patient Review Status !! Input REGISTRY_PATIENT _CVTERM !!  Output Patient Registry Status !! Output Patient Review Status !! Output REGISTRY_PATIENT _CVTERM !! Action Description !! Implementation Notes
 
|-
 
|-
| Diagnosis (Code_Detection) ||  PATIENT_CODE entry || NULL || NULL || NULL || CANDIDATE || NEVER REVIEWED || ANY || Add candidate that matches diagnosis criteria in CVTERMPROP || 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"
+
| Diagnosis (Code_Detection) ||  PATIENT_CODE entry hat matches diagnosis criteria in CVTERMPROP || NULL || NULL || NULL || CANDIDATE || NEVER REVIEWED || ANY || Add candidate t || 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"
 
|-
 
|-
 
|  ||  || Rejected|Provisional || ANY || ANY || NO CHANGE || NEEDS REVIEW || ANY || Flag rejected and provisional candidates for review || Plan is to swap CVTERMs such that CVTERM_ID is the registry and the TYPE_ID is the code
 
|  ||  || Rejected|Provisional || ANY || ANY || NO CHANGE || NEEDS REVIEW || ANY || Flag rejected and provisional candidates for review || Plan is to swap CVTERMs such that CVTERM_ID is the registry and the TYPE_ID is the code
Line 175: Line 175:
 
|  || || Accepted|Candidate || ANY || ANY || NO CHANGE || NO CHANGE || ANY || Ignore detection criteria on accepted patients || Multiple CUIs are supported as additional rows in CVTERMPROP. Contextual CUIs are supported via commas
 
|  || || Accepted|Candidate || ANY || ANY || NO CHANGE || NO CHANGE || ANY || Ignore detection criteria on accepted patients || Multiple CUIs are supported as additional rows in CVTERMPROP. Contextual CUIs are supported via commas
 
|-
 
|-
|  ||  ||  ||  ||  ||  ||  ||  ||  ||  ||  
+
|  ||  ||  ||  ||  ||  ||  ||  ||  ||  
 
|-
 
|-
| NLP_Intervention || None || NLP_HITS_EXTENDED || ANY || ANY || Requires Intervention || NO CHANGE (CANDIDATE IF NULL) || NO CHANGE || NO CHANGE ||  || CVTERMS corresponding to registries have a CVTERMPROP set on them with cvterm_id (registry_id), type_id (cvterm in NLP Pipeline Parameter Ontology) with value containing a UMLS CUI
+
| NLP_Intervention || NLP_HITS_EXTENDED || ANY || ANY || Requires Intervention || NO CHANGE (CANDIDATE IF NULL) || NO CHANGE || NO CHANGE ||  || CVTERMS corresponding to registries have a CVTERMPROP set on them with cvterm_id (registry_id), type_id (cvterm in NLP Pipeline Parameter Ontology) with value containing a UMLS CUI
 
|-
 
|-
|  ||  || contains CUI with || ANY || ANY || Intervention Complete < Encounter Date || NO CHANGE (CANDIDATE IF NULL) || NO CHANGE || Requires Intervention ||  || Value Field Example: nlp_intervention|C98764323,C0012345,C0654321
+
|  || contains CUI with || ANY || ANY || Intervention Complete < Encounter Date || NO CHANGE (CANDIDATE IF NULL) || NO CHANGE || Requires Intervention ||  || Value Field Example: nlp_intervention|C98764323,C0012345,C0654321
 
|-
 
|-
|  ||  || intervention criteria || ANY || ANY || Any other current valid cvterms || NO CHANGE (CANDIDATE IF NULL) || NO CHANGE || Requires Intervention ||  || Multiple CUIs are supported as additional rows in CVTERMPROP. Contextual CUIs are supported via commas
+
|  || intervention criteria || ANY || ANY || Any other current valid cvterms || NO CHANGE (CANDIDATE IF NULL) || NO CHANGE || Requires Intervention ||  || Multiple CUIs are supported as additional rows in CVTERMPROP. Contextual CUIs are supported via commas
 
|-
 
|-
|  ||  ||  || ANY || ANY || Intervention Complete > Encounter Date || NO CHANGE (CANDIDATE IF NULL) || NO CHANGE || NO CHANGE ||  || Compare date of code/encounter with the end(if not null) or start_date of the REGISTRY_PATIENT_CVTERM entry
+
|  ||  || ANY || ANY || Intervention Complete > Encounter Date || NO CHANGE (CANDIDATE IF NULL) || NO CHANGE || NO CHANGE ||  || Compare date of code/encounter with the end(if not null) or start_date of the REGISTRY_PATIENT_CVTERM entry
 
|-
 
|-
|  ||  ||  ||  ||  ||  ||  ||  ||  ||  ||  
+
|  ||  ||  ||  ||  ||  ||  ||  ||  ||  
 
|-
 
|-
| Inclusion (Code Inclusion) || COPD || PATIENT_CODE entry || All except Accepted || ANY || ANY || ACCEPTED || NEEDS REVIEW ||  || DRG Codes generate automatic registry inclusion ||  
+
| Inclusion (Code Inclusion) || PATIENT_CODE entry that matches inclusion criteria in CVTERMPROP|| All except Accepted || ANY || ANY || ACCEPTED || NEEDS REVIEW ||  || DRG Codes generate automatic registry inclusion ||  
 
|-
 
|-
|  ||  || that matches inclusion || Accepted || ANY || ANY || NO CHANGE || NEEDS REVIEW ||  ||  ||  
+
|  ||  || Accepted || ANY || ANY || NO CHANGE || NEEDS REVIEW ||  ||  ||  
 
|-
 
|-
|  ||  || criteria in CVTERMPROP ||  ||  ||  ||  ||  ||  ||  ||  
+
|  ||  ||  ||  ||  ||  ||  ||  ||  ||  
 
|-
 
|-
|  || ||  ||  ||  ||  ||  ||  ||  ||  ||  
+
|  || ||  ||  ||  ||  ||  ||  ||  ||  
 
|-
 
|-
| Eligibility || CRCP || Custom || ANY || ANY || ANY || NO CHANGE || NO CHANGE || NO CHANGE || Machine learning of patient eligibility || Custom registry specific implementation that should result in a publication… :)
+
| Eligibility || Custom || ANY || ANY || ANY || NO CHANGE || NO CHANGE || NO CHANGE || Machine learning of patient eligibility || Custom registry specific implementation that should result in a publication… :)
 
|-
 
|-
|  ||  ||  ||  ||  ||  ||  ||  ||  || MACHINE_ACCEPTANCE_SCORE in REGISTRY_PATIENT ||  
+
|  ||  ||  ||  ||  ||  ||  ||  || MACHINE_ACCEPTANCE_SCORE in REGISTRY_PATIENT ||  
 
|-
 
|-
|  ||  ||  ||  ||  ||  ||  ||  ||  || is set to a non-zero value ||  
+
|  ||  ||  ||  ||  ||  ||  ||  || is set to a non-zero value ||  
 
|-
 
|-
|  || ||  ||  ||  ||  ||  ||  ||  ||  ||  
+
|  ||   ||  ||  ||  ||  ||  ||  ||  ||  
 
|-
 
|-
| Code_Collection || CRCP, MM || None (daily) || Rejected|Candidate || ANY || ANY || NO CHANGE || NO CHANGE || NO CHANGE || Specify data to collect for the registry || CVTERMPROP has cvterm_id (registry_id) and type_id (data source) and value which is a regular expression specifying code_values to collect from REGISTRY_PATIENT_CODES
+
| Code_Collection || None (daily) || Rejected|Candidate || ANY || ANY || NO CHANGE || NO CHANGE || NO CHANGE || Specify data to collect for the registry || CVTERMPROP has cvterm_id (registry_id) and type_id (data source) and value which is a regular expression specifying code_values to collect from REGISTRY_PATIENT_CODES
 
|-
 
|-
|  || ||  || Provisional|Accepted || ANY || ANY || NO CHANGE || NO CHANGE || NO CHANGE || Do not collect data unless patient is in registry ||  
+
|  || || Provisional|Accepted || ANY || ANY || NO CHANGE || NO CHANGE || NO CHANGE || Do not collect data unless patient is in registry ||  
 
|-
 
|-
|  || ||  ||  ||  ||  ||  ||  ||  ||  ||  
+
|  || ||  ||  ||  ||  ||  ||  ||  ||  
 
|-
 
|-
 
| Encounter Collection || COPD,CRCP(?) || None (daily) || Rejected|Candidate || ANY || ANY || NO CHANGE || NO CHANGE || NO CHANGE || Collect specified encounter data for people in the registry || CVTERMPROP has cvterm_id (registry_id) and type_id (sourcesystem_cd) and value in the format below
 
| Encounter Collection || COPD,CRCP(?) || None (daily) || Rejected|Candidate || ANY || ANY || NO CHANGE || NO CHANGE || NO CHANGE || Collect specified encounter data for people in the registry || CVTERMPROP has cvterm_id (registry_id) and type_id (sourcesystem_cd) and value in the format below

Revision as of 13:38, 18 January 2019

Contents

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"


Criteria Name Event Description Input Patient Registry Status Input Patient Review Status Input REGISTRY_PATIENT _CVTERM Output Patient Registry Status Output Patient Review Status Output REGISTRY_PATIENT _CVTERM Action Description Implementation Notes
Diagnosis (Code_Detection) PATIENT_CODE entry hat matches diagnosis criteria in CVTERMPROP NULL NULL NULL CANDIDATE NEVER REVIEWED ANY Add candidate t 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"
Provisional ANY ANY NO CHANGE NEEDS REVIEW ANY Flag rejected and provisional candidates for review Plan is to swap CVTERMs such that CVTERM_ID is the registry and the TYPE_ID is the code
Candidate ANY ANY NO CHANGE NO CHANGE ANY Ignore diagnosis criteria on accepted patients
NLP_Detection NLP_HITS_EXTENDED contains CUI with detection criteria NULL NULL NULL CANDIDATE NEVER REVIEWED ANY Add candidate CVTERMS corresponding to registries have a CVTERMPROP set on them with cvterm_id (registry_id), type_id (cvterm in NLP Pipeline Parameter Ontology) with value containing a UMLS CUI
Provisional ANY ANY NO CHANGE NEEDS REVIEW ANY Flag rejected and provisional candidates for review C98764323,C0012345,C0654321
Candidate ANY ANY NO CHANGE NO CHANGE ANY Ignore detection criteria on accepted patients Multiple CUIs are supported as additional rows in CVTERMPROP. Contextual CUIs are supported via commas
NLP_Intervention NLP_HITS_EXTENDED ANY ANY Requires Intervention NO CHANGE (CANDIDATE IF NULL) NO CHANGE NO CHANGE CVTERMS corresponding to registries have a CVTERMPROP set on them with cvterm_id (registry_id), type_id (cvterm in NLP Pipeline Parameter Ontology) with value containing a UMLS CUI
contains CUI with ANY ANY Intervention Complete < Encounter Date NO CHANGE (CANDIDATE IF NULL) NO CHANGE Requires Intervention C98764323,C0012345,C0654321
intervention criteria ANY ANY Any other current valid cvterms NO CHANGE (CANDIDATE IF NULL) NO CHANGE Requires Intervention Multiple CUIs are supported as additional rows in CVTERMPROP. Contextual CUIs are supported via commas
ANY ANY Intervention Complete > Encounter Date NO CHANGE (CANDIDATE IF NULL) NO CHANGE NO CHANGE Compare date of code/encounter with the end(if not null) or start_date of the REGISTRY_PATIENT_CVTERM entry
Inclusion (Code Inclusion) PATIENT_CODE entry that matches inclusion criteria in CVTERMPROP All except Accepted ANY ANY ACCEPTED NEEDS REVIEW DRG Codes generate automatic registry inclusion
Accepted ANY ANY NO CHANGE NEEDS REVIEW
Eligibility Custom ANY ANY ANY NO CHANGE NO CHANGE NO CHANGE Machine learning of patient eligibility Custom registry specific implementation that should result in a publication… :)
MACHINE_ACCEPTANCE_SCORE in REGISTRY_PATIENT
is set to a non-zero value
Code_Collection None (daily) Candidate ANY ANY NO CHANGE NO CHANGE NO CHANGE Specify data to collect for the registry CVTERMPROP has cvterm_id (registry_id) and type_id (data source) and value which is a regular expression specifying code_values to collect from REGISTRY_PATIENT_CODES
Accepted ANY ANY NO CHANGE NO CHANGE NO CHANGE Do not collect data unless patient is in registry
Encounter Collection COPD,CRCP(?) None (daily) Candidate ANY ANY NO CHANGE NO CHANGE NO CHANGE Collect specified encounter data for people in the registry CVTERMPROP has cvterm_id (registry_id) and type_id (sourcesystem_cd) and value in the format below
Accepted ANY ANY NO CHANGE NO CHANGE NO CHANGE REGEX REGEX….
Encounter Intervention COPD Encounter ANY ANY Requires Intervention NO CHANGE (CANDIDATE IF NULL) NO CHANGE NO CHANGE Encounters matching criteria specified in CVTERM_PROP CVTERMPROP has cvterm_id (registry_id) and type_id (sourcesystem_cd) and value in SQL format
ANY ANY Intervention Complete < Encounter Date NO CHANGE (CANDIDATE IF NULL) NO CHANGE Requires Intervention (which contains WHERE clause SQL) are loaded into
ANY ANY Any other current valid cvterms NO CHANGE (CANDIDATE IF NULL) NO CHANGE Requires Intervention REGISTRY_ENCOUNTERS
ANY ANY Intervention Complete > Encounter Date NO CHANGE (CANDIDATE IF NULL) NO CHANGE NO CHANGE Flag patients for intervention
Encounter Detection None Encounter
Document Loading COPD Exisitence of documents Accepted ANY ANY NO CHANGE NO CHANGE NO CHANGE Load NLP_DOCS from source systems for registry patients Should be a default analysis type that is used for CVTERMPROP

Back End Workflow / Architecture

Web Service Documentation

RegistryWS

UDAS

Paper References