= BRU Data Flows

== Onyx

=== Leicester BRICCS

==== Data Collection: Nearly Complete

No new patients are being entered into Onyx at Leicester.  However, there are still some patients whose data is not yet complete, as they have not had their medical notes checked.

==== i2b2 Extract

- **Status**: Working
- **Improvements Required**: Needs replacing
- **Source**: Onyx
- **Destination**: i2b2
- **Technology**: [[i2b2 - Onyx import]]
- **Description**: This requires the {{{Next Patient Number}}}.

==== CiviCRM Import

- **Status**: Deprecated when data collection complete
- **Source**: Onyx
- **Destination**: CiviCRM
- **Technology**: Drupal Cron Job
- **Description**: Pulls data out of Onyx database and creates a patient record and BRICCS study enrolment in CiviCRM. 

==== CiviCRM Extract

- **Status**: Not yet written
- **Source**: CiviCRM
- **Destination**: i2b2
- **Technology**: Mapped Data Importer
- **Description**: Pulls data out of Onyx database and creates a patient record and BRICCS study enrolment in CiviCRM. 

=== Northampton BRICCS

==== Data Collection: Ongoing

New patients continue to be entered into Onyx at Northampton.

==== i2b2 Extract

- **Status**: Working
- **Improvements Required**: Needs replacing
- **Source**: Onyx
- **Destination**: i2b2
- **Technology**: Drupal Cron Job
- **Description**: This requires the {{{Next Patient Number}}}.

==== CiviCRM Extract

- **Status**: Not Required

=== Test BRICCS

==== Data Collection: Complete

==== i2b2 Extract

- **Status**: Working
- **Improvements Required**: Needs replacing
- **Source**: Onyx
- **Destination**: i2b2
- **Technology**: [[i2b2 - Onyx import]]
- **Description**: This requires the {{{Next Patient Number}}}.

==== i2b2 Extract (Version 2)

- **Status**: Working
- **Improvements Required**: Needs replacing
- **Source**: Onyx
- **Destination**: i2b2
- **Technology**: [[i2b2 - Mapped Importer]]
- **Description**: 

== REDCap

=== SCAD (university Internet server)

==== Data Collection: Ongoing

Participants still register for the SCAD study and existing participants continue to complete additional questionnaires.

==== CiviCRM Extract

- **Status**: Working
- **Improvements Required**: OK for now
- **Source**: REDCap
- **Destination**: CiviCRM
- **Technology**: Manual
- **Description**: Spreadsheets are downloaded from REDCap and loaded into CiviCRM.

=== BRICCS Leicester (hospital internal server)

==== Data Collection: Ongoing

==== CiviCRM Extract

- **Status**: Required
- **Improvements Required**:
- **Source**: REDCap
- **Destination**: CiviCRM
- **Technology**: Drupal cron job
- **Description**: Load status of REDCap questionnaire into CiviCRM BRICCS enrolment.

==== i2b2 Extract

- **Status**: Written
- **Improvements Required**:
 - Add more fields as needs arise
 - No interview date, so no start date for observations
 - Needs Scheduling [[ToDo]]
- **Source**: REDCap
- **Destination**: i2b2
- **Technology**: [[i2b2 - Mapped Importer]]
- **Description**: Load questionnaire data into i2b2.

=== BRICCS External Sites (hospital N3 server)

==== Sites

- Kettering: recruiting
- Doncaster: recruiting
- Sheffield: recruiting
- Lincoln: recruiting
- Grantham: recruiting
- Chesterfield: recruiting
- Northampton: planned
- Royal Free Hospital: planned (might be DREAM)

==== CiviCRM Extract

- **Status**: Not Required

==== i2b2 Extract

- **Status**: Planned when completed for BRICCS Leicester
- **Improvements Required**:
- **Source**: REDCap
- **Destination**: i2b2
- **Technology**: [[i2b2 - Mapped Importer]]
- **Description**: Load questionnaire data.

== CiviCRM

=== Common

==== HSCIC Practice Import

- **Status**: Working
- **Improvements Required**: None
- **Source**: HSCIC practice details files
- **Destination**: CiviCRM practice details
- **Technology**: Drupal cron job

=== GENVASC

==== Data Collection: Ongoing

Recruitment ongoing.  Will need to be able to continue amending participants records after recruitment is complete to track withdrawals.

==== ICE Message Import

- **Status**: Working
- **Improvements Required**: Amend the processing of ICE messages to require fewer manual amendments by the administrators.
- **Source**: Server: UHLSQLPRIME01\UHLBRICCSDB Database: genvasc-ice
- **Destination**: CiviCRM
- **Technology**: PHP MS SQL Server connection

==== i2b2 Extract Available Patients

- **Status**: Working
- **Improvements Required**: None
- **Source**: CiviCRM
- **Destination**: i2b2
- **Technology**: [[i2b2 - Mapped Importer]]
- **Description**: Load participant and consent information.

==== i2b2 Delete Withdrawn Patients

- **Status**: Working
- **Improvements Required**: None
- **Source**: CiviCRM
- **Destination**: i2b2
- **Technology**: [[i2b2 - Mapped Importer]]
- **Description**: Delete participants who have withdrawn.

===== Improvements Required

Check that it also deletes excluded participants.

=== BRICCS

==== Data Collection: Ongoing

Recruitment ongoing.  Will need to be able to continue amending participants records after recruitment is complete to track withdrawals.

==== i2b2 Delete Withdrawn Patients

- **Status**: Required
- **Improvements Required**: None
- **Source**: CiviCRM
- **Destination**: i2b2
- **Technology**: [[i2b2 - Mapped Importer]]
- **Description**: Delete participants who have withdrawn.

=== NIHR Bio-Resource

==== Data Collection: Ongoing

Recruitment ongoing.  Will need to be able to continue amending participants records after recruitment is complete to track withdrawals.

==== i2b2 Extract Available Patients

- **Status**: Working
- **Improvements Required**: None
- **Source**: CiviCRM
- **Destination**: i2b2
- **Technology**: [[i2b2 - Mapped Importer]]
- **Description**: Load participant and consent information.

==== i2b2 Delete Withdrawn Patients

- **Status**: Required
- **Improvements Required**: None
- **Source**: CiviCRM
- **Destination**: i2b2
- **Technology**: [[i2b2 - Mapped Importer]]
- **Description**: Delete participants who have withdrawn.

== CaTissue

=== GENVASC

==== Data Collection: Ongoing

==== Participant Reconciliation

- **Status**: Required
- **Improvements Required**: None
- **Source**: CiviCRM & CaTissue
- **Destination**: Report
- **Technology**: Drupal cron job?
- **Description**: Reconcile the GPt numbers in CaTissue with those in CiviCRM to check that all samples have enrolments and all enrolments have samples.

=== BRICCS

==== Data Collection: Ongoing

==== Participant Reconciliation

- **Status**: Required
- **Improvements Required**: None
- **Source**: CiviCRM & CaTissue
- **Destination**: Report
- **Technology**: Drupal cron job?
- **Description**: Reconcile the BPt numbers in CaTissue with those in CiviCRM to check that all samples have enrolments and all enrolments have samples.

== i2b2

=== GENVASC

==== Data Collection: Ongoing

==== GEM Primary Care Data

- **Status**: Particially Written
- **Improvements Required**: Need meeting with GEM
- **Source**: GEM SystemOne and EMIS data warehouses
- **Destination**: i2b2
- **Technology**: SSIS
- **Description**: Import primary care data from GEM

==== PATS Data

- **Status**: Working
- **Improvements Required**: None
- **Source**: UHL data warehouses
- **Destination**: i2b2
- **Technology**: SSIS
- **Description**: Import hospital audit data

==== PMI Data

- **Status**: Working
- **Improvements Required**: None
- **Source**: UHL data warehouses
- **Destination**: i2b2
- **Technology**: SSIS
- **Description**: Import hospital PMI data

==== Hospital HES Data

- **Status**: Partially Written
- **Improvements Required**: None
- **Source**: UHL data warehouses
- **Destination**: i2b2
- **Technology**: SSIS
- **Description**: Import hospital HES data

==== Hospital Discharge Letters Data

- **Status**: Partially Written
- **Improvements Required**: None
- **Source**: UHL data warehouses
- **Destination**: i2b2
- **Technology**: SSIS
- **Description**: Import hospital discharge data

==== National HES Data

- **Status**: Required
- **Improvements Required**: None
- **Source**: HSCIC DARS
- **Destination**: i2b2
- **Technology**: ?
- **Description**: Import national HES data

==== National ONS Cause of Death Data

- **Status**: Required
- **Improvements Required**: None
- **Source**: HSCIC DARS
- **Destination**: i2b2
- **Technology**: ?
- **Description**: Import national ONS Cause of Death data

=== BRICCS

==== Data Collection: Ongoing

==== PATS Data

- **Status**: Working
- **Improvements Required**: None
- **Source**: UHL data warehouses
- **Destination**: i2b2
- **Technology**: SSIS
- **Description**: Import hospital audit data

==== PMI Data

- **Status**: Working
- **Improvements Required**: None
- **Source**: UHL data warehouses
- **Destination**: i2b2
- **Technology**: SSIS
- **Description**: Import hospital PMI data

==== Hospital HES Data

- **Status**: Partially Written
- **Improvements Required**: None
- **Source**: UHL data warehouses
- **Destination**: i2b2
- **Technology**: SSIS
- **Description**: Import hospital HES data

==== Hospital Discharge Letters Data

- **Status**: Partially Written
- **Improvements Required**: None
- **Source**: UHL data warehouses
- **Destination**: i2b2
- **Technology**: SSIS
- **Description**: Import hospital discharge data