=== '''Objective''' ===
A new release of OpenRIMS always contains changes in the software codes and, very often, in the database structure. To install a new release, it is necessary to replace the software codes and implement the database structure changes, if ones.

The implementation of the database structure changes will keep all data, however, will allow the use of the new release of the software.

Despite it being possible to use this feature for the production databases, it is recommended only for test and demo systems.

Here are the steps to perform an upgrade from any version of OpenRIMS to latest version.

# Connect to destination server UI or CLI
# Backup Database
# Download the new MySQL model file
# Stop the OpenRIMS service
# Rename old Application file
# Download the new Application file (<nowiki>https://github.com/MSH/OpenRIMS/raw/main/bin/pharmadex2-0.0.1.jar</nowiki>)
# Change Permissions on the .jar file to make it executable: sudo chmod -x pharmadex2-0.0.1.jar
# Use Workbench to upgrade db structure based on the model - see below
# Start the OpenRIMS service

=== '''Tool''' ===
The tool is the latest version of MySQL Workbench.

For current, the latest stable release of the database is in pdx2demo.ddanet.org. To upgrade the database in any other server, or, even, in the localhost it is possible to use the feature “Model – Synchronize with any source” (<nowiki>https://dev.mysql.com/doc/workbench/en/wb-database-synchronization.html</nowiki>) provided by the MySQL Workbench.

This feature:

# reads the latest and the current database structures,
# compares them
# creates a script to upgrade the current database to the latest database structure
# executes this script

The result is the equal data structures for the latest and the current database. The data is still the same as was before.

=== '''Pre-requisites''' ===
You should have full access rights to your database and add the connection to the latest database depicted below. Ask for a password by email to alex.kurasoff@gmail.com.

Figure 1. The connection to the latest database

=== '''Process steps''' ===
Suppose you need to update the database structure of a database on the localhost.

Figure 2. Create a '''new''' model

Figure 3. Run the feature

Figure 4. The representation of the feature is a "wizard"

Figure 5. Tap the radio buttons

Figure 6. The latest database is on pdx2demo.ddanet.org. It is the source of the changes

Figure 7. Suppose the database going to be updated is in the localhost. It is the target of the changes

Figure 8. Extract the list of all sources and all target databases.

Figure 9. Select the source database. The target database is at the bottom of the screen. By default, the names of the target and the source should be the same

Figure 10. Compare the source and the target

Figure 11. Revise the changes.

Figure 12. The result DDA SQL script. There are no changes

=== '''Linux particularities''' ===
The MySQL database usage in Windows and Linux servers is slightly different. In the Linux server, the names of tables are cases sensitive, on Windows – no. There is any problem if the source server is under Linux, and the target server is under Windows. Otherwise, the tables SPRING_SESSION and SPRING_SESSION attributes should be ignored while synchronization. There are special tables that are in use by third-party software.

OpenRIMS-RPM - Upgrade Part 1

2024-06-28T16:52:45Z

Khoppenworth: Blanked the page

OpenRIMS-RPM - Configuration Part 1

2024-01-29T20:38:42Z

Khoppenworth:

OpenRIMS-RPM - Configuration Part 1

2024-01-29T20:34:55Z

Khoppenworth: New Page

This section describes how to use the WHO ATC/DDD standard in OpenRIMS-RPM.

In the Anatomical Therapeutic Chemical (ATC) classification system, the active substances are divided into different groups according to the organ or system on which they act and their therapeutic, pharmacological, and chemical properties. Drugs are classified at five different levels.

Details and tutorials can be found here <nowiki>https://www.who.int/tools/atc-ddd-toolkit/atc-classification</nowiki>.

WHO provides a free online actual electronic list of internationally recognized ATC here <nowiki>https://www.whocc.no/atc_ddd_index/</nowiki>.

In addition, <nowiki>https://www.whocc.no/atc_ddd_index_and_guidelines/order/</nowiki> the ATC data can be ordered in MS Excel format. This order is for money.

Along with ATC codes and active substances, the ATC list contains Defined Daily Dosage (DDD) for active substances. The DDD provides Units of Measurement (UOM) and Routes of Administration dictionaries.

Thus, the electronic list from WHO provides to Pharmadex 2:

· Active ingredients, recognized by WHO and grouped by ATC codes (who.atc.human)

· WHO Dosage units dictionary (dictionary.who.uom)

· WHO route of administration dictionary (dictionary.who.adminroute)

This manual intends for Pharmadex 2 supervisor user that is responsible for data maintenance.

= Source Data =
The data supported by WHO can be ordered here <nowiki>https://www.whocc.no/atc_ddd_index_and_guidelines/order/</nowiki>. This data contains English and Spanish versions of actual ATC/DDD registered in WHO. The data is in MS Excel (xlsx) format. The layout of the data seems as stable.

= Import data =

Figure 1 Import the WHO ATC-DDD file

1. Download the non-official MS Excel file of WHO online data for 2021-12-03 only if you do have not the official data <nowiki>https://www.whocc.no/atc_ddd_index_and_guidelines/order/</nowiki>.

2. Upload the MS Excel file to import

3. Press “Save” to start the import. The import process will be run in the background. It is possible to do another job, however, the content of the ATC component will be locked.

4. Press “Reload” to check the status – how many imported, how many are left

5. Intermediate and final statuses will be found under the “dataimport_result”

6. The result of the importing will be available here (Figure 2)

Figure 2 The result of the importing

In addition, such dictionaries will be created:

· dictionary.who.uom – Units of measures

· dictionary.who.adminroute – administrate routes

The values of these dictionaries are from DDD columns in the Excel file. These values are abbreviations that are not clear for a plain user. After the import, it will be recommended to add descriptions of them manually using the official WHO sources <nowiki>https://www.whocc.no/atc_ddd_index/</nowiki>.

= Re-import =
The complete data file should be used for re-import. Follow the same procedure as for the initial import. The re-import procedure:

1. Makes unusable all ATC records that are not present in the Excel file

2. Add new ATC records to the database that is present in the Excel file, but not present in the database

The e-import software determines the ATC record in the Excel file and the database as the same when all the following conditions will occur:

· ATC codes are equals

· DDD, UoM, and Admin Route are equal or empty in the both

For dictionaries dictionary.who.uom and dictionary.who.adminroute:

· The existing data will not be re-written

· The new abbreviations will be added

= Country specific data =
It is possible when a country uses active ingredients, UoMs, and routes of administration, that are not listed in the WHO data. In this case, this data should be added manually.

· For the active ingredients, country-specific records should be added to the end of the WHO data. The coding and description should follow rules for a particular country.

· UOMs should be added to the dictionary.who.uom

· Route of Administration should be added to the dictionary.who.adminroute

= Languages =
For current, it is no way to determine ATC and active ingredient data in the national language. This feature will be added soon.

For dictionary.who.uom and dictionary.who.adminroute it is possible to add data in the national language like to any other dictionary.

= Usage =

== Component “ATC” ==
The “ATC” component is dedicated to selecting ATC codes. Details can be found here <nowiki>http://redmine.inka.in.ua/documents/129</nowiki>. From November 2022 this component will be deprecated in favor of the “links” component.

Figure 3 ATC component

Figure 4 ATC component configuration

== Component “links” ==
The “links” is a universal component that allows adding references to the:

· Application's data

· Imported legacy data

· Imported ATC codes

Details can be found here <nowiki>http://redmine.inka.in.ua/documents/129</nowiki>. The usage of this component is strongly recommended instead of the ATC component.

Figure 5 Usage of component "links" for active ingredient references

Figure 6 The configuration of the component above

The value of the field “Name” is “Yes, thus the selection will be copied to literals:

· prefLabel - selected ingredient

· description - selected ingredient along with ATC, DDD, and notes

· atc - ATC code

OpenRIMS-RPM - Installation Part 1

2024-01-25T16:23:59Z

Khoppenworth:

== Purpose ==
This document describes deployment of OpenRIMS software on a default server.

The audience of it is IT persons that are responsible to install and maintain the OpenRIMS software.

You should have the ability to install and configure programs and components/services in the selected operating system.

Additionally you need experience on MySQL.

!'''PLEASE READ THE FULL DOCUMENT BEFORE PROCEDING WITH THE INSTALLATION!'''

== Overview of Server Requirements ==
Regardless of deployment configuration selected, the following pre-conditions should be fulfilled:

=== Hardware Requirements ===
{| class="wikitable"
|+Recommendation
|
|'''Initial Configuration and Testing Server'''
|'''Production Server'''
|-
|CPU
|1-2 cores
|8 cores
|-
|Memory
|At least 2 GB of free RAM
|At least 16 GB of free RAM
|-
|Harddrive
|At least 10GB of free SDD/HDD
|At least 10GB of free SDD/HDD
|-
|Internet connection
|Should align with minimal requirements for Google Mail
|Should align with minimal requirements for Google Mail
|}

=== Software Requirements ===
{| class="wikitable"
|Operating System
|Linux, released after 2018. Tested on Ubuntu 18.04.4 LTS and above
OR

Windows Server 2016 and above
|
|-
|Database:
|MySQL : Server 5.7 and Workbench 8.0
|
|-
|Java:
|Oracle Java JDK 1.8
OR

OpenJDK 1.8

''(OpenJDK 1.8 has been tested on Linux Ubuntu, but not Windows)''
|
|-
|OpenRIMS application & database:
|OpenRIMS Java application binary
AND

OpenRIMS demo database

(<nowiki>https://github.com/MSH/Pharmadex2/tree/main/database</nowiki>[1])

''(Please refer to the README.md file)''
|
|-
|Google Oauth ID & Secret
|A Google Mail account for OAuth Login SSO
|
|}

== The OpenRIMS Installation Procedure ==

=== Prepare to install ===
1. Install the following using the respective vendor’s deployment manuals:

1.1. MySQL 5.7 : Server 5.7 and Workbench 8.0

1.2. Java JDK 1.8

2. Restore the main database INCLUDING stored procedures to MySQL using MySQL Workbench or the command line. Name it '''pdx2'''. Verify that the stored procedures have been imported!

''Ubuntu MySQL CLI hint (<code>CREATE DATABASE pdx2</code>. And restore it: $ <code>mysql -u username -p pdx2 < DumpPdx2.sql</code>)''

3. Copy the binary application <code>pharmadex2-0.0.1.jar</code> and <code>application.properties</code> to a dedicated user folder, e.g. /home/{username}/applications/openrims

== Post-Installation OpenRIMS Configurations ==

=== Local TCP/IP port ===
Adjust the application.properties file for initial configuration as described below.

When initial configuration is concluded you should disable Variables Edit and Cloning of Workflows.

==== Database ====
In the application.properties file edit the values marked bold:

<code>spring.datasource.url = jdbc:mysql://localhost/'''openrimsre'''?useSSL=false&useUnicode=yes&characterEncoding=UTF-8&characterSetResults=UTF-8&'''serverTimezone=Europe/Kiev'''</code>

<code>spring.datasource.username = '''username'''</code>

<code>spring.datasource.password = '''password'''</code>

==== Logs ====
In the application.properties file edit the values marked bold:

<code>logging.file.path=/'''home/user/openrimsre/log'''</code>

<code>Recommended setting: '''logging.file.path= ./log/'''</code>

After configuration it will be necessary to copy Client ID and Client secret to the application.properties

==== OATH2 ====
<code>spring.security.oauth2.client.registration.google.client-id=client_id</code>

<code>spring.security.oauth2.client.registration.google.client-secret=client_secret</code>

==== '''SMTP Configuration''' ====
<nowiki>#</nowiki> SMPT Outgoing email settings

<code>spring.mail.username=NRAemail@gmail.com</code>

<code>spring.mail.password=MyPassword</code>

==== '''Allow System Edits for initial workflow configuration''' ====
<nowiki>##</nowiki> Developer Mode Status

<code>variables.properties.edit=true</code>

==== '''Allow Cloning of Workflows for initial workflow configuration''' ====
<code>pharmadex.allow.process.import=true</code>

== Install OpenRIMS as a service ==
Examples of the configurations are in the binary distributive on/from GitHub. The folders are “Windows” and “Linux”.

'''Linux'''

The official guide is here https://docs.spring.io/spring-boot/docs/current/reference/html/deployment.html#deployment.installing.nix-services.system-d

Here are detailed steps for Ubuntu 22.04:

# Copy file .service to /etc/systemd/system: <code>sudo cp openrims.service /etc/systemd/system</code>
# Edit file .service and change Username '''and''' Execstart path.
# Start the service: <code>systemctl enable openrims.service</code>
# Change Owner of the java application to your user: <code>sudo chmod a+rwx /home/ubuntu/applications/pharmadex2/pharmadex2-0.0.1.jar</code> OR <code>sudo cdmod 500 pharmadex2-0.0.1.jar</code>

For reference here is a sample service file:<blockquote><code>[Unit]</code>

<code>Description=Pharmadex 2 UAT version (madagascar)</code>

<code>After=pharmadex.service</code>

<code>[Service]</code>

<code>User=ubuntu</code>

<code>ExecStart=/home/{username}/applications/openrims/pharmadex2-0.0.1.jar</code>

<code>SuccessExitStatus=143</code>

<code>[Install]</code>

<code>WantedBy=multi-user.target</code></blockquote>
'''For Windows'''

The official guide is here https://docs.spring.io/spring-boot/docs/current/reference/html/deployment.html#deployment.installing.windows-services

== Provide access from the Internet ==
To provide access from the Internet it will be a good idea to establish a proxy gateway like Nginx or Apache2.

The example of virtual server configuration for Apache 2 is in the binary distributive folder named “Linux” on GitHub.

For Ubuntu 22.04 and Apache2 here are the steps:

# Copy pharmadex.conf to apache folder e.g. /etc/apache2/sites-available
# Enable the site a2ensite pharmadex
Here is another sample Apache conf file with https enabled by [https://www.digitalocean.com/community/tutorials/how-to-use-certbot-standalone-mode-to-retrieve-let-s-encrypt-ssl-certificates-on-ubuntu-20-04 Letsencrypt]:<blockquote><VirtualHost *:80>

ServerName openrims.yourdomain.com

Redirect permanent / <nowiki>https://openrims.yourdomain.com/</nowiki>

</VirtualHost>

<VirtualHost *:443>

ServerName openrims.yourdomain.com

SSLEngine On

SSLCertificateFile C:\Certbot\live\openrims.yourdomain.com\fullchain.pem

SSLCertificateKeyFile C:\Certbot\live\openrims.yourdomain.com\privkey.pem

SSLProtocol all -SSLv3 -TLSv1 -TLSv1.1

SSLCipherSuite ECDHE-ECDSA-AES256-GCM-SHA384:ECDHE-RSA-AES256-GCM-SHA384:ECDHE-ECDSA-CHACHA20-POLY1305:ECDHE-RSA-CHACHA20-POLY1305:ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-RSA-AES128-GCM-SHA256

SSLHonorCipherOrder on

SSLCompression off

SSLSessionTickets off

SSLSessionCacheTimeout 300

ProxyPreserveHost On

<Location />

ProxyPass <nowiki>http://192.168.1.10:8084/</nowiki>

ProxyPassReverse <nowiki>http://192.168.1.10:8084/</nowiki>

</Location>

</VirtualHost>"</blockquote>

== Configuring Google Authentication ==
LINK: See [[OpenRIMS - Installation Part 2]]

== Special Configuration ==
LINK: See '''[[Installation part 3|IIS as a gateway for Spring Boot application]]'''
----[1] For current, available only to MSH staff

OpenRIMS-RPM - Installation Part 1

2024-01-25T16:08:29Z

Khoppenworth: /* Post-Installation OpenRIMS Configurations */

== Purpose ==
This document describes deployment of OpenRIMS software on a default server.

The audience of it is IT persons that are responsible to install and maintain the OpenRIMS software.

You should have the ability to install and configure programs and components/services in the selected operating system.

Additionally you need experience on MySQL.

!'''PLEASE READ THE FULL DOCUMENT BEFORE PROCEDING WITH THE INSTALLATION!'''

== Overview of Server Requirements ==
Regardless of deployment configuration selected, the following pre-conditions should be fulfilled:

=== Hardware Requirements ===
{| class="wikitable"
|+Recommendation
|
|'''Initial Configuration and Testing Server'''
|'''Production Server'''
|-
|CPU
|1-2 cores
|8 cores
|-
|Memory
|At least 2 GB of free RAM
|At least 16 GB of free RAM
|-
|Harddrive
|At least 10GB of free SDD/HDD
|At least 10GB of free SDD/HDD
|-
|Internet connection
|Should align with minimal requirements for Google Mail
|Should align with minimal requirements for Google Mail
|}

=== Software Requirements ===
{| class="wikitable"
|Operating System
|Linux, released after 2018. Tested on Ubuntu 18.04.4 LTS and above
OR

Windows Server 2016 and above
|
|-
|Database:
|MySQL : Server 5.7 and Workbench 8.0
|
|-
|Java:
|Oracle Java JDK 1.8
OR

OpenJDK 1.8

''(OpenJDK 1.8 has been tested on Linux Ubuntu, but not Windows)''
|
|-
|OpenRIMS application & database:
|OpenRIMS Java application binary
AND

OpenRIMS demo database

(<nowiki>https://github.com/MSH/Pharmadex2/tree/main/database</nowiki>[1])

''(Please refer to the README.md file)''
|
|-
|Google Oauth ID & Secret
|A Google Mail account for OAuth Login SSO
|
|}

== The OpenRIMS Installation Procedure ==

=== Prepare to install ===
1. Install the following using the respective vendor’s deployment manuals:

1.1. MySQL 5.7 : Server 5.7 and Workbench 8.0

1.2. Java JDK 1.8

2. Restore the main database INCLUDING stored procedures to MySQL using MySQL Workbench or the command line. Name it '''pdx2'''. Verify that the stored procedures have been imported!

''Ubuntu MySQL CLI hint (<code>CREATE DATABASE pdx2</code>. And restore it: $ <code>mysql -u username -p pdx2 < DumpPdx2.sql</code>)''

3. Copy the binary application <code>pharmadex2-0.0.1.jar</code> and <code>application.properties</code> to a dedicated user folder, e.g. /home/{username}/applications/openrims

== Post-Installation OpenRIMS Configurations ==

=== Local TCP/IP port ===
Adjust the application.properties file for initial configuration as described below.

When initial configuration is concluded you should disable Variables Edit and Cloning of Workflows.

==== Database ====
In the application.properties file edit the values marked bold:

<code>spring.datasource.url = jdbc:mysql://localhost/'''openrimsre'''?useSSL=false&useUnicode=yes&characterEncoding=UTF-8&characterSetResults=UTF-8&'''serverTimezone=Europe/Kiev'''</code>

<code>spring.datasource.username = '''username'''</code>

<code>spring.datasource.password = '''password'''</code>

==== Logs ====
In the application.properties file edit the values marked bold:

<code>logging.file.path=/'''home/user/openrimsre/log'''</code>

<code>Recommended setting: '''logging.file.path= ./log/'''</code>

After configuration it will be necessary to copy Client ID and Client secret to the application.properties

==== OATH2 ====
<code>spring.security.oauth2.client.registration.google.client-id=client_id</code>

<code>spring.security.oauth2.client.registration.google.client-secret=client_secret</code>

'''SMTP Configuration'''

<nowiki>#</nowiki> SMPT Outgoing email settings

<code>spring.mail.username=NRAemail@gmail.com</code>

<code>spring.mail.password=MyPassword</code>

'''Allow System Edits for initial workflow configuration'''

<nowiki>##</nowiki> Developer Mode Status

<code>variables.properties.edit=true</code>

'''Allow Cloning of Workflows for initial workflow configuration'''

<code>pharmadex.allow.process.import=true</code>

== Install OpenRIMS as a service ==
Examples of the configurations are in the binary distributive on/from GitHub. The folders are “Windows” and “Linux”.

'''Linux'''

The official guide is here https://docs.spring.io/spring-boot/docs/current/reference/html/deployment.html#deployment.installing.nix-services.system-d

Here are detailed steps for Ubuntu 22.04:

# Copy file .service to /etc/systemd/system: <code>sudo cp openrims.service /etc/systemd/system</code>
# Edit file .service and change Username '''and''' Execstart path.
# Start the service: <code>systemctl enable openrims.service</code>
# Change Owner of the java application to your user: <code>sudo chmod a+rwx /home/ubuntu/applications/pharmadex2/pharmadex2-0.0.1.jar</code> OR <code>sudo cdmod 500 pharmadex2-0.0.1.jar</code>

For reference here is a sample service file:<blockquote><code>[Unit]</code>

<code>Description=Pharmadex 2 UAT version (madagascar)</code>

<code>After=pharmadex.service</code>

<code>[Service]</code>

<code>User=ubuntu</code>

<code>ExecStart=/home/{username}/applications/openrims/pharmadex2-0.0.1.jar</code>

<code>SuccessExitStatus=143</code>

<code>[Install]</code>

<code>WantedBy=multi-user.target</code></blockquote>
'''For Windows'''

The official guide is here https://docs.spring.io/spring-boot/docs/current/reference/html/deployment.html#deployment.installing.windows-services

== Provide access from the Internet ==
To provide access from the Internet it will be a good idea to establish a proxy gateway like Nginx or Apache2.

The example of virtual server configuration for Apache 2 is in the binary distributive folder named “Linux” on GitHub.

For Ubuntu 22.04 and Apache2 here are the steps:

# Copy pharmadex.conf to apache folder e.g. /etc/apache2/sites-available
# Enable the site a2ensite pharmadex
Here is another sample Apache conf file with https enabled by [https://www.digitalocean.com/community/tutorials/how-to-use-certbot-standalone-mode-to-retrieve-let-s-encrypt-ssl-certificates-on-ubuntu-20-04 Letsencrypt]:<blockquote><VirtualHost *:80>

ServerName openrims.yourdomain.com

Redirect permanent / <nowiki>https://openrims.yourdomain.com/</nowiki>

</VirtualHost>

<VirtualHost *:443>

ServerName openrims.yourdomain.com

SSLEngine On

SSLCertificateFile C:\Certbot\live\openrims.yourdomain.com\fullchain.pem

SSLCertificateKeyFile C:\Certbot\live\openrims.yourdomain.com\privkey.pem

SSLProtocol all -SSLv3 -TLSv1 -TLSv1.1

SSLCipherSuite ECDHE-ECDSA-AES256-GCM-SHA384:ECDHE-RSA-AES256-GCM-SHA384:ECDHE-ECDSA-CHACHA20-POLY1305:ECDHE-RSA-CHACHA20-POLY1305:ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-RSA-AES128-GCM-SHA256

SSLHonorCipherOrder on

SSLCompression off

SSLSessionTickets off

SSLSessionCacheTimeout 300

ProxyPreserveHost On

<Location />

ProxyPass <nowiki>http://192.168.1.10:8084/</nowiki>

ProxyPassReverse <nowiki>http://192.168.1.10:8084/</nowiki>

</Location>

</VirtualHost>"</blockquote>

== Configuring Google Authentication ==
LINK: See [[OpenRIMS - Installation Part 2]]

== Special Configuration ==
LINK: See '''[[Installation part 3|IIS as a gateway for Spring Boot application]]'''
----[1] For current, available only to MSH staff

OpenRIMS-RPM - Installation Part 1

2024-01-25T16:06:28Z

Khoppenworth: /* Post-Installation OpenRIMS Configurations */

== Purpose ==
This document describes deployment of OpenRIMS software on a default server.

The audience of it is IT persons that are responsible to install and maintain the OpenRIMS software.

You should have the ability to install and configure programs and components/services in the selected operating system.

Additionally you need experience on MySQL.

!'''PLEASE READ THE FULL DOCUMENT BEFORE PROCEDING WITH THE INSTALLATION!'''

== Overview of Server Requirements ==
Regardless of deployment configuration selected, the following pre-conditions should be fulfilled:

=== Hardware Requirements ===
{| class="wikitable"
|+Recommendation
|
|'''Initial Configuration and Testing Server'''
|'''Production Server'''
|-
|CPU
|1-2 cores
|8 cores
|-
|Memory
|At least 2 GB of free RAM
|At least 16 GB of free RAM
|-
|Harddrive
|At least 10GB of free SDD/HDD
|At least 10GB of free SDD/HDD
|-
|Internet connection
|Should align with minimal requirements for Google Mail
|Should align with minimal requirements for Google Mail
|}

=== Software Requirements ===
{| class="wikitable"
|Operating System
|Linux, released after 2018. Tested on Ubuntu 18.04.4 LTS and above
OR

Windows Server 2016 and above
|
|-
|Database:
|MySQL : Server 5.7 and Workbench 8.0
|
|-
|Java:
|Oracle Java JDK 1.8
OR

OpenJDK 1.8

''(OpenJDK 1.8 has been tested on Linux Ubuntu, but not Windows)''
|
|-
|OpenRIMS application & database:
|OpenRIMS Java application binary
AND

OpenRIMS demo database

(<nowiki>https://github.com/MSH/Pharmadex2/tree/main/database</nowiki>[1])

''(Please refer to the README.md file)''
|
|-
|Google Oauth ID & Secret
|A Google Mail account for OAuth Login SSO
|
|}

== The OpenRIMS Installation Procedure ==

=== Prepare to install ===
1. Install the following using the respective vendor’s deployment manuals:

1.1. MySQL 5.7 : Server 5.7 and Workbench 8.0

1.2. Java JDK 1.8

2. Restore the main database INCLUDING stored procedures to MySQL using MySQL Workbench or the command line. Name it '''pdx2'''. Verify that the stored procedures have been imported!

''Ubuntu MySQL CLI hint (<code>CREATE DATABASE pdx2</code>. And restore it: $ <code>mysql -u username -p pdx2 < DumpPdx2.sql</code>)''

3. Copy the binary application <code>pharmadex2-0.0.1.jar</code> and <code>application.properties</code> to a dedicated user folder, e.g. /home/{username}/applications/openrims

== Post-Installation OpenRIMS Configurations ==

=== Local TCP/IP port ===
In the application.properties file edit the values marked bold (if it will be necessary):

==== Database ====
In the application.properties file edit the values marked bold:

<code>spring.datasource.url = jdbc:mysql://localhost/pdx2?useSSL=false&useUnicode=yes&characterEncoding=UTF-8&characterSetResults=UTF-8&'''serverTimezone=Europe/Kiev'''</code>

<code>spring.datasource.username = '''username'''</code>

<code>spring.datasource.password = '''password'''</code>

==== Logs ====
In the application.properties file edit the values marked bold:

<code>logging.file.path=/'''home/user/pharmadex/log'''</code>

<code>Recommended setting: '''logging.file.path= ./log/'''</code>

After configuration it will be necessary to copy Client ID and Client secret to the application.properties

==== OATH2 ====
<code>spring.security.oauth2.client.registration.google.client-id=client_id</code>

<code>spring.security.oauth2.client.registration.google.client-secret=client_secret</code>

'''SMTP Configuration'''

<nowiki>#</nowiki> SMPT Outgoing email settings

<code>spring.mail.username=NRAemail@gmail.com</code>

<code>spring.mail.password=MyPassword</code>

'''Allow System Edits for initial workflow configuration'''

<nowiki>##</nowiki> Developer Mode Status

<code>variables.properties.edit=true</code>

'''Allow Cloning of Workflows for initial workflow configuration'''

<code>pharmadex.allow.process.import=true</code>

== Install OpenRIMS as a service ==
Examples of the configurations are in the binary distributive on/from GitHub. The folders are “Windows” and “Linux”.

'''Linux'''

The official guide is here https://docs.spring.io/spring-boot/docs/current/reference/html/deployment.html#deployment.installing.nix-services.system-d

Here are detailed steps for Ubuntu 22.04:

# Copy file .service to /etc/systemd/system: <code>sudo cp openrims.service /etc/systemd/system</code>
# Edit file .service and change Username '''and''' Execstart path.
# Start the service: <code>systemctl enable openrims.service</code>
# Change Owner of the java application to your user: <code>sudo chmod a+rwx /home/ubuntu/applications/pharmadex2/pharmadex2-0.0.1.jar</code> OR <code>sudo cdmod 500 pharmadex2-0.0.1.jar</code>

For reference here is a sample service file:<blockquote><code>[Unit]</code>

<code>Description=Pharmadex 2 UAT version (madagascar)</code>

<code>After=pharmadex.service</code>

<code>[Service]</code>

<code>User=ubuntu</code>

<code>ExecStart=/home/{username}/applications/openrims/pharmadex2-0.0.1.jar</code>

<code>SuccessExitStatus=143</code>

<code>[Install]</code>

<code>WantedBy=multi-user.target</code></blockquote>
'''For Windows'''

The official guide is here https://docs.spring.io/spring-boot/docs/current/reference/html/deployment.html#deployment.installing.windows-services

== Provide access from the Internet ==
To provide access from the Internet it will be a good idea to establish a proxy gateway like Nginx or Apache2.

The example of virtual server configuration for Apache 2 is in the binary distributive folder named “Linux” on GitHub.

For Ubuntu 22.04 and Apache2 here are the steps:

# Copy pharmadex.conf to apache folder e.g. /etc/apache2/sites-available
# Enable the site a2ensite pharmadex
Here is another sample Apache conf file with https enabled by [https://www.digitalocean.com/community/tutorials/how-to-use-certbot-standalone-mode-to-retrieve-let-s-encrypt-ssl-certificates-on-ubuntu-20-04 Letsencrypt]:<blockquote><VirtualHost *:80>

ServerName openrims.yourdomain.com

Redirect permanent / <nowiki>https://openrims.yourdomain.com/</nowiki>

</VirtualHost>

<VirtualHost *:443>

ServerName openrims.yourdomain.com

SSLEngine On

SSLCertificateFile C:\Certbot\live\openrims.yourdomain.com\fullchain.pem

SSLCertificateKeyFile C:\Certbot\live\openrims.yourdomain.com\privkey.pem

SSLProtocol all -SSLv3 -TLSv1 -TLSv1.1

SSLCipherSuite ECDHE-ECDSA-AES256-GCM-SHA384:ECDHE-RSA-AES256-GCM-SHA384:ECDHE-ECDSA-CHACHA20-POLY1305:ECDHE-RSA-CHACHA20-POLY1305:ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-RSA-AES128-GCM-SHA256

SSLHonorCipherOrder on

SSLCompression off

SSLSessionTickets off

SSLSessionCacheTimeout 300

ProxyPreserveHost On

<Location />

ProxyPass <nowiki>http://192.168.1.10:8084/</nowiki>

ProxyPassReverse <nowiki>http://192.168.1.10:8084/</nowiki>

</Location>

</VirtualHost>"</blockquote>

== Configuring Google Authentication ==
LINK: See [[OpenRIMS - Installation Part 2]]

== Special Configuration ==
LINK: See '''[[Installation part 3|IIS as a gateway for Spring Boot application]]'''
----[1] For current, available only to MSH staff

OpenRIMS-RPM - Implementation Kickstart Guide Part 1

2023-12-19T17:19:56Z

Khoppenworth: New Page

== Background ==
Several aspects must be considered before diving into use of OpenRIMS at a Regulatory Authority.

This article will highlight the main aspects and provide links to further information needed to make a good project plan.

== Roles and Responsibilities ==
First and foremost - OpenRIMS depend on solid, verified and approved Standard Operating Procedures. This cannot be emphasized enough.

These SOPs are controlled by the '''Process Owners'''.

To automate and configure these SOPs in OpenRIMS we have designated '''System Owners'''. They are trained on setting up the Workflows according to the SOPs.

Expectation management

Which functions? Which budget is available?

external dependencies

OpenRIMS-RPM - Base Configuration Part 1

2023-11-15T17:36:07Z

Khoppenworth: New Page

The Pharmadex 2 provides true multi-language features. It means that:

1. The user interface (UI) may be represented in the language selected by a user

2. A user may use the selected language to fill out on-screen data forms as well as to get documents, reports, etc.

The Pharmadex 2 distribution software allows US English and a national language.

This manual intends for IT experts to help replace the national language provided in the distribution software with the language of a particular country.

To perform this job following IT skills will be needed:

1. Operation Systems – start and stop Pharmadex 2 service

2. MySQL database:

3. Ability to use MySQL Workbench, relation database, and SQL knowledge

4. MS Excel – ability to use

The roadmap chapter contains a particular example to replace the Nepali language with the Portuguese language. It is possible to define many languages, however, the reasonable choice is two languages. Many languages will slow down Pharmadex 2 and hard to maintain.

Refer to Annex 1 for the troubleshooting.

Annex 2 contains technical data that may be useful to understand how it works “under the stage”.

Annex 3 contains directions on how to maintain labels and messages in the actual state

= 1 Pre-request =
· Direct access to Pharmadex 2 server computer console with administrative privileges

· Supervisor’s access rights to Pharmadex 2

· The MySQL Workbench is installed and a connection to the Pharmadex 2 database is defined. The rights should be at least query/update

· The MS Excel released after 2017 is installed

· The MySQL for Excel plugin is installed, see <nowiki>https://downloads.mysql.com/archives/excel/</nowiki>[1]

= 2 The roadmap =
1. Stop Pharmadex 2 server

2. Create a backup copy of the database

3. Determine languages that are in use

4. Upload to MS Excel messages for English US language and translate them

5. Add a new language:

5.1. Register a new language in the database

5.2. Remove an excess language

5.3. Insert messages in the new language into the database

5.4. Replace the language tag in the demo examples

6. Start Pharmadex 2 and test the new language

7. Replace logos

8. Fine-tune tiles

== 2.1 Stop Pharmadex 2 server ==
For MS Windows installation stop the Pharmadex 2 service using the Services tool. Refer to MS Windows documentation for details. The most used tool is “services.msc”.

For Linux installation stop the Pharmadex 2 service. Refer to the appropriate Linux documentation for details. The most used tool is “systemctl”.

== 2.2 Create a backup copy of the database ==
Use MySQL Workbench to create a backup copy of the database. Refer to the MySQL workbench manual for details.

Figure 1 Backup dump creation

== 2.3 Determine languages that are in use ==
Use MySQL Workbench connection to Pharmadex 2 database to execute a query

SELECT ID, `locale`, `displayname` FROM pdx2.resource_bundle;

Figure 2 Nepali and English US are in use

'''In this particular example, the Nepali language should be removed. The Portuguese language should be added.'''

== 2.4 Upload to MS Excel messages in English US and translate them ==
As we determine above (3), the English US language ID is 3. Use MySQL Workbench connection to Pharmadex 2 database to select all messages in English

Query is SELECT * FROM pdx2.resource_message where key_bundle=3

Figure 3 Select all messages in English US (key_bundle=3)

Figure 4 Select all records from the result

Figure 5. Insert records to MS Excel sheet

Figure 6 Translate them (e.g., to Portuguese)

== 2.5 Add a new language ==

=== 2.5.1 Register a new language in the database ===
Prepare image of countries flag as SVG file.

Use MySQL Workbench to add a new record into table pdx2.resource_bundle. Fields NmraLogo, and UsaidLogo should be filled with space, not NULL

Figure 7 The Portuguese language has been registered

=== 2.5.2 Remove an excess language ===
Use MySQL Workbench to remove the Nepali language registration record from the database. All messages in the Nepali language will be removed as well.

Figure 8 Nepali language bundle is going to be removed

=== 2.5.3 Insert messages in the new language into the database ===
Open the Excel file prepared in 4 and fill out the rightmost column (D) by the ID of the new registered language - 4

Figure 9 Fill out the column D for key_bundle with the key bundle for a new language (4)

Figure 10 Use MySQL for Excel plugin to insert messages, refer to the plugin’s manual

Figure 11 Define column mapping

Figure 12 Append them

=== 2.5.4 Replace language tag in existing workflow configurations ===
The distribution database contains demonstration workflows. Their configurations are defined in the old language. Use MySQL workbench to replace language tags in the configuration.

The script below will replace the language tag “ne_NP” with “pt_BR”. Modify it for the actual languages

UPDATE `pdx2`.`concept` c SET `Identifier` = 'pt_BR'

where c.Identifier='ne_NP'

= 3 Start Pharmadex 2 and test the new language =
For MS Windows installation start the Pharmadex 2 service using the Services tool. Refer to MS Windows documentation for details. The most used tool is “services.msc”.

For Linux installation start the Pharmadex 2 service. Refer to appropriative Linux documentation for details. The most used tool is “systemctl”.

Figure 13 New language is available

= 4 Replace logos =
Figure 14 Feature Administrate-Configurations-Resources allows uploading logos. Use language switch to upload logos for any given language separately.

= 5 Fine-tune tiles =
Figure 15 Administrate, Configuration, Tiles, tick-up on the tile group in the table

Figure 16 Administrate page tiles as an example. Click on “Administrate” in the left table for the next screen

Figure 17 Elements available for internationalization

1. Select the language using the language switch

2. Fill out this information using the language selected

3. It is possible to select another picture from a tile

4. This label should be in the language selected

= 6 Annex 1 Troubleshooting =

== 6.1 The new language doesn’t appear in the language selector ==
Check table resource_bundle. If the new language is present, restart Pharmadex 2 server. Otherwise, add new language exactly as described in the Roadmap chapter.

== 6.2 The labels in new languages appear improperly ==
The messages on the selected language appears improperly like 'new_chemical_entity', or 'UserType.TIPC'.

The messages for the language selected are not defined. Suppose it is Portuguese. To check it:

Execute SELECT * FROM pdx2.resource_bundle;

Figure 18 The Portuguese language is registered. ID is 4

Execute SELECT * FROM pdx2.resource_message where key_bundle=4

Figure 19 For the Portuguese language messages are not defined

Insert messages from MS Excel as described in 4.3

== 6.3 The labels for the new language appear in the old language ==
The ID field in table resource_bundle does not match the ID in resource_message.

To check it, execute SQL queries from 8.2. The resource_message table should contain messages in the wrong language

Figure 20 Messages in English, despite the Portuguese language

To fix it restore the database from backup and repeat the new language definition. Step, described in chapter 4, may be omitted.

== 6.4 The SVG logo or flag in the language selector doesn’t appear ==
Open the SVG file locally by browser or lnkscape (<nowiki>https://inkscape.org/</nowiki>). If the file is consistent, re-import it to the database using the “value editor” feature.

Figure 21 Right-click and Open Value in Editor

Figure 22 The SVG file is a text. Insert it into the Value Editor

= 7 Annex 2 Technical implementation =
The internationalization of the user interfaces is grounded on Java i18N approach[2].

Textual labels and messages are available directly in the database tables:

1. resource_bundle – keeps languages definitions.

2. resource_message – keeps textual labels and messages

Each row in the resource_bundle represents a language. Columns are:
{| class="wikitable"
|'''Column'''
|'''Purpose'''
|'''Example'''
|-
|Id
|Unique key for a language definition
|1
|-
|sortOrder
|Order to use in the user interface. The 0 is the highest priority, the rest are the lowest. For more details see chapter “Language by default” below
|0 – the default language
|-
|basename
|For compatibility with the previous release. Should be unique for a language
|English
|-
|locale
|Locale ID for a language. Please, put attention to _ (underscore), instead of – (dash) usage. It is to be compatible with java.util.Locale.toString[3]
|en_US
|-
|displayName
|Human-readable name of the language
|לשון עבר
|-
|svgFlag
|Flag to represent the language in the user interface. Must be defined.
|<?XML version="1.0" encoding="iso-8859-1"?>

<!-- Generator: Adobe Illustrator…
|-
|updatedDate
|Not used in Pharmadex 2
|
|-
|createdDate
|Not used in Pharmadex 2
|
|-
|UsaidLogo
|Not used in Pharmadex 2
|
|-
|NmraLogo
|Not used in Pharmadex 2
|
|}

Each row in resource_message table represents a text on the language as key-value pair:
{| class="wikitable"
|'''Column'''
|'''Purpose'''
|'''Example'''
|-
|id
|Unique key for a text in a language
|5376
|-
|message_key
|Unique language - independent key for a text
|global_cancel
|-
|message_value
|Value in a language
|Cancel
|-
|key_bundle
|Id in resource_bundle to link to the language
|3
|}

The Pharmadex 2 database allows defining multi-language classifiers (dictionaries) as well as files to upload (resources). When a user selects a language, the Pharmadex 2 switches the language of the user interface, dictionaries, and resources. Thus, a user can fill out the application electronic form in the language selected.

When a user fills application electronic form, Pharmadex 2 stores user input for each language separately. Suppose the form in Portuguese

'''Fator de forma''': [Caixa Cinza]

When a user will switch to English it will be:

'''Form factor:''' [Caixa Cinza]

It is possible to change the data in the English form

'''Form factor:''' [Gray Box]

The Portuguese form will still keep

'''Fator de forma''': [Caixa Cinza]

The English form will keep:

'''Form factor:''' [Gray Box]

The true multi-language is a powerful, however costly feature:

· The database should keep and process more data.

· The data in the database is complex, because of the necessity to keep language for any data element

· The initial input and maintenance of multi-language dictionaries and resources are costly

The two languages are the optimal choice.

= 8 Annex 3 Maintenance and language by default =
Figure 23 Feature Administrate-Configurations-Messages allows changing initial uploaded labels and messages as well as adding missed ones

When a user enters Pharmadex first time, the system proposed a language that is defined in the file “application.properties” under the key spring.web.locale, e.g., “spring.web.locale=en_US”. It is recommended not re-define this key to the local language because some browsers will not accept the local language, thus Pharmadex 2 will be inaccessible.

When a user selects a language, this selection will be stored in the file cookie on the user’s computer. All follow-up calls will set the selected language. The time to live the selection is a year or until a user will switch to another language.

----[1] This plugin is out of support for now. Despite this it is available yet. The MS Excel export-import features will be implemented in Pharmadex 2 ASAP.

[2] <nowiki>https://docs.oracle.com/javase/8/docs/technotes/guides/intl/index.html</nowiki>

[3] <nowiki>https://docs.oracle.com/javase/8/docs/api/java/util/Locale.html#toString()</nowiki>

Main Page

2023-10-26T20:22:27Z

Khoppenworth: /* Welcome! */

== '''Welcome!''' ==
This site supports the installation, deployment and full documentation of OpenRIMS modules for Registration Process Management (RPM) and Pharmacovigilance Management (PVM).

Information on this site is provided under Creative Commons standards: https://creativecommons.org/licenses/by/4.0/

=== '''Navigation & Language''' ===
Please click here to see an index of all content of this Wiki: https://wiki.openrims.org/index.php/Special:AllPages

To change language please open this website in Google Chrome and then Right Click to select Translate to select a different language. The Wiki use Google Translate which might not always be 100% accurate.

=== '''What is a RIMS?''' ===
The purpose of a Regulatory Information Management System (RIMS) is to automate and digitalize the processes and work routines at a National Medicines Regulatory Authority (NMRA).

OpenRIMS serves that purpose and is built on [[Common Standards for RIMS]].

=== Localization ===
OpenRIMS is Free and Open Source Software (FOSS) and can from the browser be localized to country procedures and needs like language.

=== '''Getting Started''' ===
* [[OpenRIMS-RPM - Installation Part 1|OpenRIMS-RPM Installation/Deployment Part 1]]
* [[OpenRIMS - Installation Part 2|OpenRIMS-RPM Installation/Deployment Part 2]]
* [[OpenRIMS - User Management|OpenRIMS User Management]]
* [[OpenRIMS - Workflows Part 1|OpenRIMS Workflow Configuration]]
* [[OpenRIMS - Reporting Google Part 1|OpenRIMS and Google Looker Studio]]

=== '''The Common Regulatory Function Examples''' ===
* OpenRIMS-RPM - M2 - Marketing Authorization - Coming Soon!
* OpenRIMS-PVM - M3 - Pharmacovigilance - Coming Soon!
* OpenRIMS-RPM - M4 - Import/Export Certificates - Coming Soon!
* OpenRIMS-RPM - M5 - Premises and People Registration - Coming Soon!
* OpenRIMS-RPM - M6 - Inspection - Coming Soon!
* OpenRIMS-RPM - M8 - Clinical Trial Approval - Coming Soon!
<blockquote>
=== '''Making content contributions - Currently Not Available!!''' ===
'''PLEASE NOTE!'''

Use the following syntax to name the pages:

''"System name"_"Page/Subject Title"_"Part Number"''

Example:

'''OpenRIMS_Cleaning the Database_Part 1'''

All new content is subject to review and approval.

OpenRIMS reserves the right to edit or delete content or pages as appropriate if the content is not relevant for Regulatory Information Management Systems.</blockquote>

OpenRIMS-RPM - Installation Part 1

2023-09-26T13:45:32Z

Khoppenworth: /* Hardware Requirements */

== Purpose ==
This document describes deployment of OpenRIMS software on a default server.

The audience of it is IT persons that are responsible to install and maintain the OpenRIMS software.

You should have the ability to install and configure programs and components/services in the selected operating system.

Additionally you need experience on MySQL.

!'''PLEASE READ THE FULL DOCUMENT BEFORE PROCEDING WITH THE INSTALLATION!'''

== Overview of Server Requirements ==
Regardless of deployment configuration selected, the following pre-conditions should be fulfilled:

=== Hardware Requirements ===
{| class="wikitable"
|+Recommendation
|
|'''Initial Configuration and Testing Server'''
|'''Production Server'''
|-
|CPU
|1-2 cores
|8 cores
|-
|Memory
|At least 2 GB of free RAM
|At least 16 GB of free RAM
|-
|Harddrive
|At least 10GB of free SDD/HDD
|At least 10GB of free SDD/HDD
|-
|Internet connection
|Should align with minimal requirements for Google Mail
|Should align with minimal requirements for Google Mail
|}

=== Software Requirements ===
{| class="wikitable"
|Operating System
|Linux, released after 2018. Tested on Ubuntu 18.04.4 LTS and above
OR

Windows Server 2016 and above
|
|-
|Database:
|MySQL : Server 5.7 and Workbench 8.0
|
|-
|Java:
|Oracle Java JDK 1.8
OR

OpenJDK 1.8

''(OpenJDK 1.8 has been tested on Linux Ubuntu, but not Windows)''
|
|-
|OpenRIMS application & database:
|OpenRIMS Java application binary
AND

OpenRIMS demo database

(<nowiki>https://github.com/MSH/Pharmadex2/tree/main/database</nowiki>[1])

''(Please refer to the README.md file)''
|
|-
|Google Oauth ID & Secret
|A Google Mail account for OAuth Login SSO
|
|}

== The OpenRIMS Installation Procedure ==

=== Prepare to install ===
1. Install the following using the respective vendor’s deployment manuals:

1.1. MySQL 5.7 : Server 5.7 and Workbench 8.0

1.2. Java JDK 1.8

2. Restore the main database INCLUDING stored procedures to MySQL using MySQL Workbench or the command line. Name it '''pdx2'''. Verify that the stored procedures have been imported!

''Ubuntu MySQL CLI hint (<code>CREATE DATABASE pdx2</code>. And restore it: $ <code>mysql -u username -p pdx2 < DumpPdx2.sql</code>)''

3. Copy the binary application <code>pharmadex2-0.0.1.jar</code> and <code>application.properties</code> to a dedicated user folder, e.g. /home/{username}/applications/openrims

== Post-Installation OpenRIMS Configurations ==

=== Local TCP/IP port ===
In the application.properties file edit the values marked bold (if it will be necessary):

==== Database ====
In the application.properties file edit the values marked bold:

<code>spring.datasource.url = jdbc:mysql://localhost/pdx2?useSSL=false&useUnicode=yes&characterEncoding=UTF-8&characterSetResults=UTF-8&'''serverTimezone=Europe/Kiev'''</code>

<code>spring.datasource.username = '''username'''</code>

<code>spring.datasource.password = '''password'''</code>

==== Logs ====
In the application.properties file edit the values marked bold:

<code>logging.file.path=/'''home/user/pharmadex/log'''</code>

<code>Recommended setting: '''logging.file.path= ./log/'''</code>

After configuration it will be necessary to copy Client ID and Client secret to the application.properties

==== OATH2 ====
<code>spring.security.oauth2.client.registration.google.client-id=client_id</code>

<code>spring.security.oauth2.client.registration.google.client-secret=client_secret</code>

== Install OpenRIMS as a service ==
Examples of the configurations are in the binary distributive on/from GitHub. The folders are “Windows” and “Linux”.

'''Linux'''

The official guide is here https://docs.spring.io/spring-boot/docs/current/reference/html/deployment.html#deployment.installing.nix-services.system-d

Here are detailed steps for Ubuntu 22.04:

# Copy file .service to /etc/systemd/system: <code>sudo cp openrims.service /etc/systemd/system</code>
# Edit file .service and change Username '''and''' Execstart path.
# Start the service: <code>systemctl enable openrims.service</code>
# Change Owner of the java application to your user: <code>sudo chmod a+rwx /home/ubuntu/applications/pharmadex2/pharmadex2-0.0.1.jar</code> OR <code>sudo cdmod 500 pharmadex2-0.0.1.jar</code>

For reference here is a sample service file:<blockquote><code>[Unit]</code>

<code>Description=Pharmadex 2 UAT version (madagascar)</code>

<code>After=pharmadex.service</code>

<code>[Service]</code>

<code>User=ubuntu</code>

<code>ExecStart=/home/{username}/applications/openrims/pharmadex2-0.0.1.jar</code>

<code>SuccessExitStatus=143</code>

<code>[Install]</code>

<code>WantedBy=multi-user.target</code></blockquote>
'''For Windows'''

The official guide is here https://docs.spring.io/spring-boot/docs/current/reference/html/deployment.html#deployment.installing.windows-services

== Provide access from the Internet ==
To provide access from the Internet it will be a good idea to establish a proxy gateway like Nginx or Apache2.

The example of virtual server configuration for Apache 2 is in the binary distributive folder named “Linux” on GitHub.

For Ubuntu 22.04 and Apache2 here are the steps:

# Copy pharmadex.conf to apache folder e.g. /etc/apache2/sites-available
# Enable the site a2ensite pharmadex
Here is another sample Apache conf file with https enabled by [https://www.digitalocean.com/community/tutorials/how-to-use-certbot-standalone-mode-to-retrieve-let-s-encrypt-ssl-certificates-on-ubuntu-20-04 Letsencrypt]:<blockquote><VirtualHost *:80>

ServerName openrims.yourdomain.com

Redirect permanent / <nowiki>https://openrims.yourdomain.com/</nowiki>

</VirtualHost>

<VirtualHost *:443>

ServerName openrims.yourdomain.com

SSLEngine On

SSLCertificateFile C:\Certbot\live\openrims.yourdomain.com\fullchain.pem

SSLCertificateKeyFile C:\Certbot\live\openrims.yourdomain.com\privkey.pem

SSLProtocol all -SSLv3 -TLSv1 -TLSv1.1

SSLCipherSuite ECDHE-ECDSA-AES256-GCM-SHA384:ECDHE-RSA-AES256-GCM-SHA384:ECDHE-ECDSA-CHACHA20-POLY1305:ECDHE-RSA-CHACHA20-POLY1305:ECDHE-ECDSA-AES128-GCM-SHA256:ECDHE-RSA-AES128-GCM-SHA256

SSLHonorCipherOrder on

SSLCompression off

SSLSessionTickets off

SSLSessionCacheTimeout 300

ProxyPreserveHost On

<Location />

ProxyPass <nowiki>http://192.168.1.10:8084/</nowiki>

ProxyPassReverse <nowiki>http://192.168.1.10:8084/</nowiki>

</Location>

</VirtualHost>"</blockquote>

== Configuring Google Authentication ==
LINK: See [[OpenRIMS - Installation Part 2]]

== Special Configuration ==
LINK: See '''[[Installation part 3|IIS as a gateway for Spring Boot application]]'''
----[1] For current, available only to MSH staff

OpenRIMS-PVM - User Manual Chapter 5

2023-09-12T15:51:42Z

Khoppenworth: /* 1.8.4 Downloading a Dataset for Further Analysis */

= Analytical Portal =
At the '''Home Page''' of the Analytical Portal''',''' you will be presented with the following options:

● Spontaneous and Active Reports

● Spontaneous and Active Analyzer

{| class="wikitable"
|The analytical portal is the centralized hub for causative drug assessment using traditional recognized rating scales, standardized terminology, and risk detection with exposed versus non-exposed risk ratios.

'''Note''': the following roles have access to the analytical portal:

· '''Administrator.''' The administrator has FULL permissions to the analytical portal.

· '''Analyst.''' An analytics user is able to assign terminology, set causality and run analysis on collected data.
|}

{| class="wikitable"
|Click on the user profile menu option which appears when clicking on the profile icon to view roles and facilities you currently have access to.

|}

== Spontaneous Reporting ==
Spontaneous reports are termed spontaneous as they take place during the clinician’s normal diagnostic appraisal of a patient, when the clinician is drawing the conclusion that the drug may be implicated in the causality of the event.

Spontaneous reporting system relies on vigilant physicians, other healthcare professionals, and patients who not only generate a suspicion of an ADR, but also report it.

It is an important source of regulatory actions such as taking a drug off the market or a label change due to safety problems. Spontaneous reporting is the core data-generating system of international pharmacovigilance, relying on healthcare professionals (and, in some countries, consumers) to identify and report any adverse events to their national pharmacovigilance center.

Spontaneous reports are, by definition, submitted voluntarily.

PViMS facilitates a public facing interface that allows clinicians or the public itself to spontaneously report on adverse event related data. See chapter 8 for more information.

== Active Reporting ==
Active surveillance for monitoring the safety and effectiveness of medical products is increasingly recognized as a complement to spontaneous reporting commonly used by pharmacovigilance systems. Integrated mechanisms and processes for monitoring the safety of medicines are essential to a well-functioning pharmaceutical sector. A positive benefit-to-risk balance should precede access to market; however, most regulatory decisions take place early in the product lifecycle and are based on limited data from clinical trials that may be of relatively short duration with limited numbers and types of subjects.

It is critical, therefore, that medicines continue to be monitored for safety and effectiveness once they enter the market under real-life conditions. For some medicines, issues will only emerge under real-world conditions as a result of prolonged use, use in specific subpopulations or in patients with multiple comorbidities, or use in combination with other medicines. In some cases, rare adverse effects only emerge after a product is used for many years, by large numbers of patients, or both.

Active surveillance is particularly important to support the introduction of new essential medicines in LMICs whose regulatory systems are being developed and are in need of support. In resource-limited settings, active surveillance can help determine the real-life frequency, risk factors, and impact of clinically significant adverse medicine events on treatment outcomes.

== Pharmacovigilance Activities ==
{| class="wikitable"
|This section describes the common processes adopted by the pharmacovigilance unit in responding to both spontaneous and active reports submitted through PViMS.

'''PLEASE NOTE:''' In relation to spontaneous reports, the patient identified in the report does '''NOT''' form part of the active reporting patient dataset. Therefore, spontaneous reports do not form part of any analysis conducted through the analyzer.

The following activities are facilitated in the Analytical portal:

· Verify quality of report data

· Set terminology for adverse drug reaction (MedDRA)

· Set causality per drug (Naranjo or WHO)

· Create and update E2B files (Export to XML)

· Generate a patient summary
|}

==== Terminology ====
'''Causality Assessment Scale or Terms.''' The assessment scales or terms were developed to help standardize assessment of causality for all adverse drug reactions. The result is determined by an algorithm designed by Naranjo or WHO for determining the likelihood of whether an adverse drug event is actually due to the drug rather than the result of other factors. Probability is assigned via a score termed definite, probable, possible or doubtful (Naranjo) or certain, probable/likely, possible, unlikely, conditional, unassessable or unclassified (WHO). Values obtained from this algorithm are sometimes used in peer reviews to verify the validity of author's conclusions regarding adverse drug reactions.

'''MedDRA Terminology'''. MedDRA or Medical Dictionary for Regulatory Activities is a clinically validated international medical terminology dictionary by regulatory authorities in the pharmaceutical industry during the regulatory process, from pre-marketing to post-marketing activities, and for data entry, retrieval, evaluation, and presentation. In addition, it is the adverse event classification dictionary endorsed by the International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH).

'''E2B'''. The international standard for transmitting medicine adverse event reports specified by the ICH.

==== 1.3.2 Process Flow ====
{| class="wikitable"
|'''Activity: Start of Process'''

Clinician adds a new adverse event to the patient record.

Reporter adds a new spontaneous report.

System generates a new report for the PV unit to action:

* Report has a unique identifier
* Report has a default activity of '''Confirm Report Data'''
* Report has a sub status of '''UNCONFIRMED'''
|'''Confirm Report Data'''

The purpose of this activity is to facilitate the checking, vetting, and updating of the clinical data collected for the adverse event logged. The PV unit will be unable to perform any causality or terminology configurations until the data is confirmed as accurate and comprehensive.

The PV specialist has the following options:

* Delete Report
* Confirm Report
|-
| colspan="2" |'''Activity: Confirm Report Data'''

'''Step 1:''' PV specialist and clinician/reporter update clinical data until there is sufficient information to perform causality and terminology configurations.

For active reporting the patient record is modified through the clinical portal.

For spontaneous reporting the report is modified directly in the analytical portal.

'''Step 2:''' Once data has been confirmed, the PV specialist will confirm the report is ready for assessment by selecting the Confirm report option.

'''Step 3:''' The report is moved into a new activity: Set MedDRA and Causality.
|-
|'''Activity: Set MedDRA and Causality'''

'''Step 1:''' PV specialist sets the terminology for the adverse event. This will be the terminology used for analysis purposes.

'''Step 2:''' PV specialist then sets the causality per medication that was in use at the onset date of the adverse event.

''Please note: the specialist'' ''is unable to set causality until the MedDRA term has been selected.''

'''Step 3:''' On completion, the PV specialist confirms causality has been set.

'''Step 4:''' The report is moved into a new activity: Extract E2B.
|'''Set MedDRA and Causality'''

The purpose of this activity is to facilitate the setting of the MedDRA terminology for the event and to set causality per medication using either the Naranjo or WHO causality scales.

The PV specialist has the following options:

* Set Terminology
* WHO Causality
* Naranjo Causality
* Confirm Causality Set
|-
|'''Activity: Extract E2B'''

'''Step 1:''' PV technician creates an E2B XML file for submission.

''Please note: a patient summary is stored at the time of generating the E2B XML to allow for data verification.''

'''Step 2:''' PV technician then confirms that the E2B XML file has been submitted to WHO.

* A receipt code and time can be noted here

''Please note: submission to WHO UMC is a manual process.''
|'''Extract E2B'''

The purpose of this activity is to facilitate sharing of E2B adverse drug reactions with the WHO Uppsala Monitoring Centre using the ICH ICSR E2B specification.

The PV specialist has the following options:

* Create E2B
* Confirm E2B submission

|-
| colspan="2" |'''PROCESS COMPLETED'''
|}

=== 1.3.3 Identifying New Reports ===
It is possible to identify new active or spontaneous reports using the notification panel in the main system header. A number next to the notification icon indicates you either have a new adverse event report requiring analysis or new terminology has been defined for an existing report.

The number of new reports registered within a pre-defined period of time is displayed as a value in the notification list of menu items.
{| class="wikitable"
|
|This alert will vary in count depending on the '''ReportInstanceNewAlertCount''' configuration. Please speak to your system administrator to confirm what this value is set to in days.
|}

=== 1.3.4 Search for a Report ===
In the '''Reports''' function for Spontaneous and Active Reporting, you can '''Search''' for new reports that have been created. The '''Reports''' function can be accessed either through the Spontaneous or Active menu.

There are three ways to search for a report. You can search by:

● Activity (what stage of analysis the report is currently in)

● Report date range

● By a search term

==== 1.3.4.1 Search by Active Work ====
Searching by activity allows you to search for all incomplete reports by the current stage a report may be in or by listing all new reports that have been identified as per the '''ReportInstanceNewAlertCount''' configuration'''.'''

· Select the '''New Reports''' button to view a list of new reports within the system

· Or select the current activity stage if you would like to filter reports based on the stage they are currently in
{| class="wikitable"
|
|'''Confirm Report Data Stage:''' Search on all reports that are newly submitted and are not yet VERIFIED.

'''Set MedDRA and Causality:''' Search on all reports that have been VERIFIED and are in the process of being defined through terminology.

'''Extract E2B:''' Search on all reports that have all terminology defined and are ready to extract information for submission to the WHO Uppsala Monitoring Centre.
|}

The system will display a list of reports according to the filter selected, please note the Unique Identifier of the report in column 2.

==== 1.3.4.2 Search for all Reports within a Date Range ====
Search by date range searches for all complete and incomplete reports within a given date range.

· Enter the '''Search From''' and '''Search To date fields''' for the date range to search.

· Click the '''Search''' button.

The system will display a list of reports according to the filter selected, please note the Unique Identifier of the report in column 2.

==== 1.3.4.3 Search Reports by Term ====
The '''Search by term''' tab allows the user to search for all reports using the following criteria:

· Patient name

· MedDRA term as set by the clinician and technician

· Report identifier

· Medications

The search function uses a partial term to search all reports on the terms noted above. For instance, searching for the term Accelerated returns all reports that have that partial term in the MedDRA term for the report.

The columns in the report table are described below:
{| class="wikitable"
|Created
|The date and time the report was registered in the analytical portal
|
|-
|Identifier
|Unique identifier for the report (system generated)
|
|-
|Patient
|Patient name
|
|-
|Medication Summary
|Overview of all medications associated with the patient at the time of the event, including the WHO or Naranjo causality assessment outcome once that has been set
|
|-
|Adverse Event
|The adverse event experienced by the patient
|
|-
|MedDRA Terminology
| colspan="2" |The unique and internationally recognized MedDRA term defined for the event
|-
|Status
|Current status of the report
|
|-
|Actions
|'''Confirm Report Data Stage'''

View Activity History

Confirm or Delete Report

View Patient (Active Only)

View SAE Report or Patient Summary

Update Report (Spontaneous Only)

'''Set MedDRA and Causality Stage'''

View Activity History

Set Terminology (MedDRA), Naranjo or WHO Causality Term

Confirm Causality Set

View Patient (Active Only)

View SAE Report or Patient Summary

Update Report (Spontaneous Only)

'''Extract E2B Stage'''

View Activity History

Create or Update an E2B file

Prepare or Confirm E2B file for submission

Download XML file

View Patient (Active Only)

View SAE Report or Patient Summary

Update Report (Spontaneous Only)
|
|}

== 1.4 Pharmacovigilance Activities - General ==

=== 1.4.1 Viewing Activity History for Report ===
Irrespective of the stage the report is currently in, you will be able to view a comprehensive history for the report detailing all actions that have occurred, who effected the action, and any additional comments.

Once you have searched for a report, click on the '''View activity history''' menu for the associated report you would like to view.

The system will navigate you to the '''View activity history''' page.

The columns in the activity history table are described below:

{| class="wikitable"
|Activity
|The primary activity stage performed by the analyst
|
|-
|Execution event
|The primary activity performed by the analyst. Activities are dependent on the stage the report is in.
|
|-
|Execution date
|The date and time the user executed the activity
|
|-
|Comments
|Any comments noted by the user at the point of completing the activity
|
|-
|Receipt date
| colspan="2" |Particular to the E2B Extract Stage. Confirmation an E2B extract has been received by UMC and this is the associated receipt date
|-
|Receipt code
|Particular to the E2B Extract Stage. Confirmation an E2B extract has been received by UMC and this is the associated receipt code that may be supplied by UMC
|
|-
|Action
|Download summary

Download extract

Download E2B file
|
|}

=== 1.4.2 Viewing a Patient Record ===
The '''View patient''' menu allows the user to navigate to the Patient View for the patient so that the analyst may gather additional information to the adverse event.

Once you have searched for a report, click on the '''View patient''' menu for the associated report you would like to view.

The system will navigate you to the '''Patient View''' page in the Clinical Portal.
{| class="wikitable"
|
|This menu item will only be made available under the following circumstances:

· Active reports only

· If the user has the Registration Clerk, Data Capture or Clinician role assigned to their user profile
|}

=== 1.4.3 Extracting a Patient Summary ===
The '''Download summary''' menu allows the user to generate an overall summary of the patient clinical record in MS Word format. This is the preferred method of granting access to the clinical record for the analyst.

Once you have searched for a report, click on the '''Download Summary''' menu for the associated report you would like to view.

The system generates an extract of the patient summary:

.
{| class="wikitable"
|
|If the event is defined as serious, the system will include additional information that explains the seriousness of the report. The heading of the extract will be changed to '''Serious Adverse Event.'''
|}

=== 1.4.4 Updating a Spontaneous Report ===
The '''Update report''' menu allows the user to navigate to the spontaneous report for the patient and allow the analyst the ability to amend the report.

Once you have searched for a report, click on the '''Update report''' menu for the associated report you would like to amend.

The system will navigate you to the '''Spontaneous View''' pop up form for the report.
{| class="wikitable"
|
|This menu item will only be available for spontaneous reports.

|}

== 1.5 Pharmacovigilance Activities – Confirm Report Data ==

=== 1.5.1 Deleting a Report ===
The '''Confirm Report Data''' stage enforces a process whereby the analyst ensures the necessary clinical data is of sufficient quality to allow terminology and causality to be completed. In the event a report is deemed to be insufficient, inaccurate, or erroneous, a report may be deleted, which will effectively remove it from analysis.

Once you have searched for a report, click on the '''Delete report''' menu for the associated report you would like to delete.

The system will navigate you to the '''Add Activity''' page.

Specify the reason for deleting the record and click '''Save''' to confirm the deletion or '''Cancel''' to cancel the action and return to the previous page.

The system will update the status of the report accordingly.
{| class="wikitable"
|
|Once a report is deleted, it is not possible to re-include the report for analysis. Please ensure you are correct in deleting the report before committing the action.

|}

=== 1.5.2 Confirming a Report ===
The '''Confirm Report Data''' stage enforces a process whereby the analyst ensures the necessary clinical data is of sufficient quality to allow terminology and causality to be completed. When a report is deemed to be sufficient and accurate, the report should be confirmed, which will effectively allow terminology definition to commence.

Once you have searched for a report, click on the '''Confirm Report''' menu for the associated report you would like to confirm.

The system will navigate you to the '''Add Activity''' page.

Specify any additional comments for confirming the record and click '''Save''' to confirm the deletion or '''Cancel''' to cancel the action and return to the previous page.

The system will update the status of the report accordingly.

{| class="wikitable"
|
|Confirming a report will move the report into the next stage: '''Set MedDRA and Causality.'''

|}

== 1.6 Pharmacovigilance Activities – Set MedDRA and Causality ==

=== 1.6.1 Set MedDRA Terminology ===
The '''Set MedDRA and Causality''' stage facilitates the process of confirming the final MedDRA term for the adverse event and allows assignment of causality per relevant medication using either the World Health Organization or the Naranjo Causality Scale.

Once you have searched for a report, click on the '''Set Terminology''' menu for the associated report you would like to set terminology for.

The system will pop up a '''MedDRA Terminology''' form.

The '''MedDRA Terminology''' form displays the adverse event as reported by the clinician and/or reporter.

MedDRA terms can be searched in the following ways:

• Search by MedDRA Term

• Search by MedDRA Code

• Search by MedDRA List

==== 1.6.1.1 Search by MedDRA Term ====
Searching by a MedDRA term allows you the ability to filter through MedDRA using a partial or fully defined term.

In the '''Term type''' field, select the level of specificity for the search (SOC, HLTG, HLT, PT, or LLT).

In the '''Find by term''' field, enter the term you are searching for.
{| class="wikitable"
|
|It is possible to complete a partial search by entering as few as 3 characters that form part of the overall term.

|}

Click the '''Select''' icon next to the term you would like to assign or click the '''Cancel''' button to cancel the action and return to the previous page. The report will be updated with the new term accordingly.

==== 1.6.1.2 Search by MedDRA Code ====

Searching by a MedDRA code allows you the ability to filter through MedDRA using an associated code which can be fully defined or partial in nature.

In the '''Find by code''' field, enter the code you are searching for.
{| class="wikitable"
|
|It is possible to complete a partial search by entering as few as 4 numerical characters that form part of the overall code.

|}
Click the '''Select''' icon next to the term you would like to assign or click the '''Cancel''' button to cancel the action and return to the previous page. The report will be updated with the new term accordingly.

==== 1.6.1.3 Search for MedDRA Term by List ====
The list search function allows the user to navigate the MedDRA dictionary using the hierarchical structure of the dictionary. Select the System Organ Class field to select a SOC.

Continue selecting through the hierarchy (HLGT, HLT, PT) until you have selected the Low-Level Term that matches the adverse event.

Click the '''Select''' icon next to the term you would like to assign or click the '''Cancel''' button to cancel the action and return to the previous page. The report will be updated with the new term accordingly.

=== 1.6.2 Causality Assessment using the WHO Scale ===
The '''Set MedDRA and Causality''' stage facilitates the process of confirming the final MedDRA term for the adverse event and allows assignment of causality per relevant medication using either the World Health Organization or the Naranjo Causality Scale.

Once the MedDRA terminology for the event has been set, the report will be updated accordingly.

Setting the terminology will further allow the setting of causality per medication. Click on the '''WHO Causality''' menu option for the associated report you would like to set causality for.

The system will open up the '''WHO Causality Assessment''' pop up form.

The '''WHO Causality Assessment''' form displays the adverse event as reported by the clinician and/or reporter and the MedDRA Terminology that has been set for the event.

The '''WHO Causality Assessment''' form also displays the list of medications that the patient was exposed to at the onset of the adverse event.

The analyst can perform the following actions against each medication the patient was exposed to:

· Ignore the medication (the medication is definitely not responsible for the adverse event)

· Set causality for the medication

==== 1.6.2.1 Ignoring the Medication ====
Ignoring the medication means that a causality assessment need not be set for that medication.

To ignore assigning a WHO causality assessment for this medication, click the '''Ignore Medication''' icon. The system will assign '''Ignored''' as the causality term.

==== 1.6.2.2 Set Causality ====
By clicking the '''Set Causality''' icon, the system will enable you to set causality for this medication.

The system displays a series of questions for assigning the WHO causality term.

Click the appropriate response (Yes or No) for question 1 and continue to respond to the first five questions.

If responses to all five questions are '''Yes,''' the system will assign '''Certain''' as the causality term.

Click the '''Set causality icon''' next to the causality assessment and the system will assign the term as Certain in the system.

Click the '''Close''' button at any time to undo the action and return to the list reports.

If any of the questions in the Certain category have a response of '''No''' the system will display questions for the Probable/Likely category.

Continue this process until you have answered '''Yes''' to all questions in a specific category. This will result in the classification for that medication being set to that category.

In the event you reach the '''Unassessable/Unclassified''' category, if one of the two questions asked in that category is answered as '''No,''' the system will trigger an alert.

Once the term has been assigned click the '''Close''' button to continue.

=== 1.6.3 Causality Assessment using the Naranjo Scale ===
The '''Set MedDRA and Causality''' stage facilitates the process of confirming the final MedDRA term for the adverse event and allows assignment of causality per relevant medication using either the World Health Organization or the Naranjo Causality Scale.

Once the MedDRA terminology for the event has been set, the report will be updated accordingly.

Setting the terminology will further allow the setting of causality per medication. Click on the '''Naranjo Causality''' menu for the associated report you would like to set causality for.

The system will open up the '''Naranjo Causality Assessment''' pop up form.

The '''Naranjo Causality Assessment''' form displays the adverse event as reported by the clinician and/or reporter and the MedDRA Terminology set.

The '''Naranjo Causality Assessment''' form also displays the list of medications that the patient was exposed to at the onset of the adverse event.

The analyst can perform the following actions against each medication the patient was exposed to:

· Ignore the medication (the medication is definitely not responsible for the adverse event)

· Set causality for the medication

==== 1.6.3.1 Ignoring the Medication ====

Ignoring the medication means that a causality assessment need not be set for that medication.

To ignore assigning a Naranjo causality assessment for this medication, click the '''Ignore Medication''' icon. The system will assign '''Ignored''' as the causality term.

==== 1.6.3.2 Set Causality ====

By clicking the '''Set Causality''' icon, the system will enable you to set causality for this medication.

The system displays a series of questions for calculating the Naranjo causality score.

Click the appropriate response (Yes or No) for question 1 and continue to respond to all remaining questions. Once all responses have been selected, the system will automatically calculate the causality assessment.

Click the '''Set causality icon''' next to the causality assessment and the system will assign the term as per the calculation in the system.

Click the '''Close''' button at any time to undo the action and return to the list reports.

=== 1.6.4 Confirming Causality Set ===
The '''Set MedDRA and Causality''' stage facilitates the process of confirming the final MedDRA term for the adverse event and allows assignment of causality per relevant medication using either the World Health Organization or the Naranjo Causality Scale.

Once causality for all medications has been set, the report will be updated accordingly.

Click on the '''Confirm Causality Set''' menu for the associated report you would like to confirm causality set for.

The system will navigate you to the '''Confirm Causality Set''' form.

Specify any comment if necessary and click '''Save''' to confirm the setting of the causality or '''Cancel''' to cancel the action and return to the previous page.

The system will update the status of the report accordingly. Please note the report will now be located in the Extract E2B tab.

== 1.7 Pharmacovigilance Activities – Extract E2B ==

=== 1.7.1 Create E2B ===
{| class="wikitable"
|'''BUZZWORDS'''

'''ICH E2B:''' An E2B dataset facilitates the Electronic Transmission of Individual Case Safety Reports (ICSRs) and can be used to submit such reports to WHO. The E2B dataset within PViMS is implemented using the standard adopted by the ICH1 for electronic transmission of ICSRs according to the ICH E2B(R3) message standard.
|}

The '''Extract E2B''' stage generates an E2B extract for submission to the World Health Organization Uppsala Monitoring Centre.
{| class="wikitable"
|
|<nowiki>By clicking this menu item, the system generates an E2B dataset that is populated with clinical information from the source form. This E2B dataset can be amended by you to reflect additional clinical information pertinent to WHO. This menu item is only available for forms that are in the Extract E2B | NOTGENERATED stage.</nowiki>

|}
Once you have searched for a report, click on the '''Create E2B''' menu for the associated report you would like to create E2B for.

Once the system has created the E2B dataset, the status of the report will be updated to E2BINITIATED to indicate the dataset has been created.

The E2B dataset is constructed with the following sections (these sections are based on R2 of the E2B ICH definition):

· Message Header

· Safety Report

· Primary Source

· Sender

· Receiver

· Patient

· Medical History Episode

· Past Drug Therapy

· Patient Death

· Reaction

· Test

· Drug

· Summary

{| class="wikitable"
|'''ICH E2B:''' Please see the electronic Transmission of Individual Case Safety Reports Message Specification for detail specifications on the above categories. This specification can be found on

<nowiki>https://admin.ich.org/sites/default/files/inline-files/ICH_ICSR_Specification_V2-3.pdf</nowiki>
|}

=== 1.7.2 Adding Information to and Updating an E2B File ===
Once an E2B file is created, the '''Update E2B''' menu allows the user to add information to or updating existing information populated in an E2B file.

Once you have searched for a report, click on the '''Update E2B''' menu for the associated file you would like to amend.

The system will pop up a '''E2B ICH Report''' form for the file.

Once you completed making amendments, click on the '''Save''' button to save the changes or the '''Cancel''' button to cancel the action and return to the previous page.
{| class="wikitable"
|
|
|}

=== 1.7.3 Preparing a Report for E2B Submission ===
The '''Extract E2B''' stage facilitates the process of generating an E2B extract for submission to the World Health Organization Uppsala Monitoring Centre.

Once you have created an E2B file and searched for the report, click on the '''Prepare Report for E2B Submission''' menu for the associated report you would like to prepare.

The system will navigate you to the '''Prepare report for E2B submission''' pop up form.

Specify any additional comments for preparing the record and click '''Save''' to confirm the preparation or '''Cancel''' to cancel the action and return to the previous page.

The system will update the status of the report accordingly.
{| class="wikitable"
|
|It is during this stage that PViMS prepares the XML file for submission. It also prepares an associated patient summary and patient extract that correspond to the clinical data at the point of generating the submission.

|}

=== 1.7.4 Viewing the E2B XML File ===
Once you have prepared the E2B file for submission and searched for the report, click on the '''View Activity History''' menu for the associated report you would like to view the XML file for.

The system will navigate you to the '''Activities''' page where you will be able to view a comprehensive history of activities by the analyst against this adverse event.

Locate the '''E2BGENERATED''' execution event for the report, click the menu for that event, and select the '''Download E2B File''' menu.

The system will automatically generate the XML file for the E2B submission to WHO. Save the file on your local computer for referral when sending to WHO.

The extract below is the XML generated for the Message Header section of the XML file.

=== 1.7.5 Viewing the Clinical Data Associated to the E2B XML File ===
Once you have prepared the E2B file for submission and searched for the report, click on the '''View Activity History''' menu for the associated report you would like to view the XML file for.

The system will navigate you to the '''Activities''' page where you will be able to view a comprehensive history of activities by the analyst against this adverse event.

Locate the '''E2BGENERATED''' execution event for the report, click the action menu, and select the '''Download summary or Download extract''' menu.

If you select the '''Download summary''' menu, the system will generate a MS Word extract of the associated clinical data. See Extracting a Patient Summary.

If you select the '''Download extract''' menu, the system will generate an MS Excel extract of the associated clinical data.
{| class="wikitable"
|
|In both the Patient Extract and Summary above, these files are stored along with the XML file as a reference to the clinical data associated with the XML file at the point the XML file was generated.

|}

=== 1.7.6 Confirming a Report for E2B Submission ===
Once you have prepared the E2B file for submission and searched for the report, click on the '''Confirm E2B Submission''' menu for the associated report you would like to submit.

The system will navigate you to the '''Confirm E2B Submission''' pop up form.

Specify any additional comments for confirming the submission and click '''Save''' to confirm the submission or '''Cancel''' to cancel the action and return to the previous page.
{| class="wikitable"
|
|The receipt date and code can be used to note correspondence with WHO on the receipt of the E2B XML submission file.

|}
The system will update the status of the report accordingly. Please note that the report is removed from the Extract E2B tab as work for this report is now classified as finished. Use the S'''earch by date''' or '''Search by term''' tabs to locate this report again.

== 1.8 Analyser ==
{| class="wikitable"
|This section is used to generate the relative risk for a specified adverse drug reaction based on an exposed and non-exposed population set over a defined period of time.

The analyser user can access the following functionality within the analytical portal:

· Define population set (cohort or condition group)

· Define reporting period

· Specify additional risk factors

· View risk ratios per exposed drug

· Download dataset for further analysis
|}
'''2 '''

2.1 ''' '''

2.2 ''' '''

2.3 ''' '''

2.4 ''' '''

2.5 ''' '''

2.6 ''' '''

2.7 ''' '''

2.8 ''' '''

=== 2.8.1 Methodology ===
The following formulas, calculations and definitions are used in the calculation of the relative risk for a specific medication and adverse reaction.

==== 1.8.1.1 Incidence Rate ====
The incidence rate is the number of new cases per population in a given time period
{| class="wikitable"
|IR = (ADR / Population) * 1000

'''Where'''

IR = Incidence Rate

ADR = Number of adverse drug reactions *

Population = Total patient years in reporting period **

'''Note'''

<nowiki>*</nowiki> Where causality is set to possible, probably/likely or Certain for WHO assessments and where causality is set to possible, probable or definite for Naranjo assessments

<nowiki>**</nowiki> Population is represented in patient years. For example, if the reporting period is 30 days, and 10 patients were on treatment for all 30 days, the total patient years is 300 /365.25 which is 0.82.

'''Example'''

Cases = 11

Non-Cases = 170

Population = 181 (11 + 170)

Incidence Rate = 11/181 * 1000 = '''60.77'''
|}

==== 1.8.1.2 Relative Risk ====
Relative risk is defined as the incidence in the exposed over incidence in the non-exposed.
{| class="wikitable"
|RR= IR1 / IR2

'''Where'''

RR = Relative Risk

IR1 = Incidence Rate for exposed population. The exposed population is defined as the patient population that have been exposed to a medication in the reporting period.

IR2 = Incidence Rate for non-exposed population. The exposed population is defined as the patient population that have NOT been exposed to a medication in the reporting period.

'''Example'''

Incidence Rate Exposed = 60.77

Incidence Rate Non-Exposed = 45.12

RR = '''1.35'''
|}

==== 1.8.1.3 Confidence Interval ====
A confidence interval is a range of values so defined that there is a specified probability that the value of a parameter lies within it. Most commonly, the 95% confidence interval is used.
{| class="wikitable"
|

'''Where'''

''z''<sub>α</sub> is the standard score for the chosen level of significance and SE the standard error.
|}

=== 1.8.2 Generating Unadjusted Relative Risk Ratios ===
To implement the methodology for generating an '''Unadjusted Relative Risk Ratio,''' the following parameters will need to be specified:

· The population target (condition group or Cohort)

· The date range for the analysis

The '''Analyser''' function can be accessed through the main menu.

==== 1.8.2.1 Specifying the Population Group ====
Ensure the '''Analysis Criteria''' tab is selected to allow the selection of the patient population.

By selecting a '''Condition Group''' or '''Cohort''', you are effectively able to target a specific set of patients for analysis.

To specify a '''Condition Group,''' click the Primary Condition Group Risk Factor field and select the primary condition you would like to run analysis against. If this option is selected, all patients that belong to the corresponding Condition Group will be included in the analysis.

To specify a '''Cohort,''' click the Cohort field and select the primary cohort you would like to run analysis against. If this option is selected, all patients that belong to the corresponding Cohort will be included in the analysis.

==== 1.8.2.2 Specifying the Date Range for the Analysis ====
By selecting a '''Date Range''', the system will determine which patients should be included into the analysis from the Patient Population specified in the previous step. Patients that have been actively exposed to medication within that range will be included.

==== 1.8.2.3 Running the Analysis ====
Once the '''Patient Population''' and '''Date Range''' parameters have been selected, click on the '''Analyse''' button to execute the analysis.

The system will conduct an initial analysis that will identify what Adverse Drug Reactions have been identified over the reporting period. All results are included in the '''Analysis Results''' tab. Please note that only adverse drug reactions where a MedDRA term has been selected by the PV technician will be selected.

Select the '''Adverse Drug Reaction''' that you would like to detect signals for by clicking on the tab for that reaction. The selected tab will turn a dark blue to signify that it has been selected.

Please note that selecting the Adverse Drug Reaction will enable the Dashboard and Patients tab.

You are able to now view a 2 by 2 table illustrating relative risk and 95% Confidence Interval for the selected reaction.

· Incidence Rate for exposed group

· Incidence Rate for non-exposed group

· Relative Risk for the associated medication

· 95% Confidence Interval for the associated medication

==== 1.8.2.4 Viewing the Contributing Patient List ====
Once analysis has been executed, it is possible to view the list of patients that have contributed to the analysis population set through the '''Patients''' tab.

The columns in the patient list table are described below:
{| class="wikitable"
|Patient name
|The name of the patient contributing to the patient population
|-
|Medication
|The drug the patient was exposed to during the period of analysis
|-
|Days contributed
|The number of days the patient contributed to the patient population
|-
|Reaction
|Did the patient suffer a reaction during the period of analysis
|-
|Risk Factor
|Which risk factor does the patient match
|}

==== 1.8.2.5 Resetting Criteria ====
If at any point you would like to alter the patient population or date range, click the '''Reset criteria''' tab alongside the list of Adverse Drug Reactions to reset analysis. Selecting this tab will remove existing analysis and reopen the Analysis Criteria tab for modification.

=== 1.8.3 Generating Adjusted Relative Risk Ratios ===
To implement the methodology for generating an '''Adjusted Relative Risk Ratio,''' the following parameters will need to be specified:

· The population target (condition group or Cohort)

· The date range for the analysis

· The risk factors to be applied

The '''Analyser''' function can be accessed through the main menu.

==== 1.8.3.1 Specifying the Population Group ====
Ensure the '''Analysis Criteria''' tab is selected to allow the selection of the patient population.

By selecting a '''Condition Group''' or '''Cohort''', you are effectively able to target a specific set of patients for analysis.

To specify a '''Condition Group,''' click the Primary Condition Group Risk Factor field and select the primary condition you would like to run analysis against. If this option is selected, all patients that belong to the corresponding Condition Group will be included in the analysis.

To specify a '''Cohort,''' click the Cohort field and select the primary cohort you would like to run analysis against. If this option is selected, all patients that belong to the corresponding Cohort will be included in the analysis.

==== 1.8.3.2 Specifying the Date Range for the Analysis ====
By selecting a '''Date Range''', the system will determine which patients should be included into the analysis from the Patient Population specified in the previous step. Patients that have been actively exposed to medication within that range will be included.
==== 1.8.3.3 Specifying Risk Factors for the Analysis ====

To specify a '''Risk Factor,''' click the Risk factor field and select the risk factor you would like to include into the analysis. Once you have selected the risk factor, select the appropriate option associated to that risk factor and click the '''add''' icon to add the risk factor to the selected list.

You are able to add as many risk factors as you would like to include into the analysis by repeating the above process.

By including '''Risk Factors''' into the analysis, the system will determine which patients match the criteria stipulated by the set of risk factors and the corresponding '''Relative Risk Ratio''' will be adjusted based on the new population set.

==== 1.8.3.4 Running the Analysis ====
Once the '''Patient Population, Date Range, and Risk Factor''' parameters have been selected, click on the '''Analyse''' button to execute the analysis.

The system will conduct an initial analysis that will identify what Adverse Drug Reactions have been identified over the reporting period. All results are included in the '''Analysis Results''' tab. Please note that only adverse drug reactions where a MedDRA term has been selected by the PV technician will be selected.

Select the '''Adverse Drug Reaction''' that you would like to detect signals for by clicking on the tab for that reaction. The selected tab will turn a dark blue to signify that it has been selected.

Please note that selecting the Adverse Drug Reaction will enable the Dashboard and Patients tab.

You are able to now view a 2 by 2 table illustrating relative risk and 95% Confidence Interval for the selected reaction.

· Incidence Rate for exposed group

· Incidence Rate for non-exposed group

· Relative Risk for the associated medication

· 95% Confidence Interval for the associated medication
=== 1.8.4 Downloading a Dataset for Further Analysis ===
Select the '''Download Data''' tab and then click the '''Download Dataset''' button to able to download a comprehensive dataset of patient clinical data in XLSX Excel format for importation into a third-party statistical tool.

{| class="wikitable"
|
|If you are unable to locate this function, please liaise with your system administrator as the ability to download a dataset for external consumption will need to be assigned to your user profile.

|}
The Excel file password is: rcAHtHx&pN6cE3kL

OpenRIMS-PVM - User Manual Chapter 5

2023-09-12T15:41:37Z

Khoppenworth: /* 1.8.4 Downloading a Dataset for Further Analysis */

= Analytical Portal =
At the '''Home Page''' of the Analytical Portal''',''' you will be presented with the following options:

● Spontaneous and Active Reports

● Spontaneous and Active Analyzer

{| class="wikitable"
|The analytical portal is the centralized hub for causative drug assessment using traditional recognized rating scales, standardized terminology, and risk detection with exposed versus non-exposed risk ratios.

'''Note''': the following roles have access to the analytical portal:

· '''Administrator.''' The administrator has FULL permissions to the analytical portal.

· '''Analyst.''' An analytics user is able to assign terminology, set causality and run analysis on collected data.
|}

{| class="wikitable"
|Click on the user profile menu option which appears when clicking on the profile icon to view roles and facilities you currently have access to.

|}

== Spontaneous Reporting ==
Spontaneous reports are termed spontaneous as they take place during the clinician’s normal diagnostic appraisal of a patient, when the clinician is drawing the conclusion that the drug may be implicated in the causality of the event.

Spontaneous reporting system relies on vigilant physicians, other healthcare professionals, and patients who not only generate a suspicion of an ADR, but also report it.

It is an important source of regulatory actions such as taking a drug off the market or a label change due to safety problems. Spontaneous reporting is the core data-generating system of international pharmacovigilance, relying on healthcare professionals (and, in some countries, consumers) to identify and report any adverse events to their national pharmacovigilance center.

Spontaneous reports are, by definition, submitted voluntarily.

PViMS facilitates a public facing interface that allows clinicians or the public itself to spontaneously report on adverse event related data. See chapter 8 for more information.

== Active Reporting ==
Active surveillance for monitoring the safety and effectiveness of medical products is increasingly recognized as a complement to spontaneous reporting commonly used by pharmacovigilance systems. Integrated mechanisms and processes for monitoring the safety of medicines are essential to a well-functioning pharmaceutical sector. A positive benefit-to-risk balance should precede access to market; however, most regulatory decisions take place early in the product lifecycle and are based on limited data from clinical trials that may be of relatively short duration with limited numbers and types of subjects.

It is critical, therefore, that medicines continue to be monitored for safety and effectiveness once they enter the market under real-life conditions. For some medicines, issues will only emerge under real-world conditions as a result of prolonged use, use in specific subpopulations or in patients with multiple comorbidities, or use in combination with other medicines. In some cases, rare adverse effects only emerge after a product is used for many years, by large numbers of patients, or both.

Active surveillance is particularly important to support the introduction of new essential medicines in LMICs whose regulatory systems are being developed and are in need of support. In resource-limited settings, active surveillance can help determine the real-life frequency, risk factors, and impact of clinically significant adverse medicine events on treatment outcomes.

== Pharmacovigilance Activities ==
{| class="wikitable"
|This section describes the common processes adopted by the pharmacovigilance unit in responding to both spontaneous and active reports submitted through PViMS.

'''PLEASE NOTE:''' In relation to spontaneous reports, the patient identified in the report does '''NOT''' form part of the active reporting patient dataset. Therefore, spontaneous reports do not form part of any analysis conducted through the analyzer.

The following activities are facilitated in the Analytical portal:

· Verify quality of report data

· Set terminology for adverse drug reaction (MedDRA)

· Set causality per drug (Naranjo or WHO)

· Create and update E2B files (Export to XML)

· Generate a patient summary
|}

==== Terminology ====
'''Causality Assessment Scale or Terms.''' The assessment scales or terms were developed to help standardize assessment of causality for all adverse drug reactions. The result is determined by an algorithm designed by Naranjo or WHO for determining the likelihood of whether an adverse drug event is actually due to the drug rather than the result of other factors. Probability is assigned via a score termed definite, probable, possible or doubtful (Naranjo) or certain, probable/likely, possible, unlikely, conditional, unassessable or unclassified (WHO). Values obtained from this algorithm are sometimes used in peer reviews to verify the validity of author's conclusions regarding adverse drug reactions.

'''MedDRA Terminology'''. MedDRA or Medical Dictionary for Regulatory Activities is a clinically validated international medical terminology dictionary by regulatory authorities in the pharmaceutical industry during the regulatory process, from pre-marketing to post-marketing activities, and for data entry, retrieval, evaluation, and presentation. In addition, it is the adverse event classification dictionary endorsed by the International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH).

'''E2B'''. The international standard for transmitting medicine adverse event reports specified by the ICH.

==== 1.3.2 Process Flow ====
{| class="wikitable"
|'''Activity: Start of Process'''

Clinician adds a new adverse event to the patient record.

Reporter adds a new spontaneous report.

System generates a new report for the PV unit to action:

* Report has a unique identifier
* Report has a default activity of '''Confirm Report Data'''
* Report has a sub status of '''UNCONFIRMED'''
|'''Confirm Report Data'''

The purpose of this activity is to facilitate the checking, vetting, and updating of the clinical data collected for the adverse event logged. The PV unit will be unable to perform any causality or terminology configurations until the data is confirmed as accurate and comprehensive.

The PV specialist has the following options:

* Delete Report
* Confirm Report
|-
| colspan="2" |'''Activity: Confirm Report Data'''

'''Step 1:''' PV specialist and clinician/reporter update clinical data until there is sufficient information to perform causality and terminology configurations.

For active reporting the patient record is modified through the clinical portal.

For spontaneous reporting the report is modified directly in the analytical portal.

'''Step 2:''' Once data has been confirmed, the PV specialist will confirm the report is ready for assessment by selecting the Confirm report option.

'''Step 3:''' The report is moved into a new activity: Set MedDRA and Causality.
|-
|'''Activity: Set MedDRA and Causality'''

'''Step 1:''' PV specialist sets the terminology for the adverse event. This will be the terminology used for analysis purposes.

'''Step 2:''' PV specialist then sets the causality per medication that was in use at the onset date of the adverse event.

''Please note: the specialist'' ''is unable to set causality until the MedDRA term has been selected.''

'''Step 3:''' On completion, the PV specialist confirms causality has been set.

'''Step 4:''' The report is moved into a new activity: Extract E2B.
|'''Set MedDRA and Causality'''

The purpose of this activity is to facilitate the setting of the MedDRA terminology for the event and to set causality per medication using either the Naranjo or WHO causality scales.

The PV specialist has the following options:

* Set Terminology
* WHO Causality
* Naranjo Causality
* Confirm Causality Set
|-
|'''Activity: Extract E2B'''

'''Step 1:''' PV technician creates an E2B XML file for submission.

''Please note: a patient summary is stored at the time of generating the E2B XML to allow for data verification.''

'''Step 2:''' PV technician then confirms that the E2B XML file has been submitted to WHO.

* A receipt code and time can be noted here

''Please note: submission to WHO UMC is a manual process.''
|'''Extract E2B'''

The purpose of this activity is to facilitate sharing of E2B adverse drug reactions with the WHO Uppsala Monitoring Centre using the ICH ICSR E2B specification.

The PV specialist has the following options:

* Create E2B
* Confirm E2B submission

|-
| colspan="2" |'''PROCESS COMPLETED'''
|}

=== 1.3.3 Identifying New Reports ===
It is possible to identify new active or spontaneous reports using the notification panel in the main system header. A number next to the notification icon indicates you either have a new adverse event report requiring analysis or new terminology has been defined for an existing report.

The number of new reports registered within a pre-defined period of time is displayed as a value in the notification list of menu items.
{| class="wikitable"
|
|This alert will vary in count depending on the '''ReportInstanceNewAlertCount''' configuration. Please speak to your system administrator to confirm what this value is set to in days.
|}

=== 1.3.4 Search for a Report ===
In the '''Reports''' function for Spontaneous and Active Reporting, you can '''Search''' for new reports that have been created. The '''Reports''' function can be accessed either through the Spontaneous or Active menu.

There are three ways to search for a report. You can search by:

● Activity (what stage of analysis the report is currently in)

● Report date range

● By a search term

==== 1.3.4.1 Search by Active Work ====
Searching by activity allows you to search for all incomplete reports by the current stage a report may be in or by listing all new reports that have been identified as per the '''ReportInstanceNewAlertCount''' configuration'''.'''

· Select the '''New Reports''' button to view a list of new reports within the system

· Or select the current activity stage if you would like to filter reports based on the stage they are currently in
{| class="wikitable"
|
|'''Confirm Report Data Stage:''' Search on all reports that are newly submitted and are not yet VERIFIED.

'''Set MedDRA and Causality:''' Search on all reports that have been VERIFIED and are in the process of being defined through terminology.

'''Extract E2B:''' Search on all reports that have all terminology defined and are ready to extract information for submission to the WHO Uppsala Monitoring Centre.
|}

The system will display a list of reports according to the filter selected, please note the Unique Identifier of the report in column 2.

==== 1.3.4.2 Search for all Reports within a Date Range ====
Search by date range searches for all complete and incomplete reports within a given date range.

· Enter the '''Search From''' and '''Search To date fields''' for the date range to search.

· Click the '''Search''' button.

The system will display a list of reports according to the filter selected, please note the Unique Identifier of the report in column 2.

==== 1.3.4.3 Search Reports by Term ====
The '''Search by term''' tab allows the user to search for all reports using the following criteria:

· Patient name

· MedDRA term as set by the clinician and technician

· Report identifier

· Medications

The search function uses a partial term to search all reports on the terms noted above. For instance, searching for the term Accelerated returns all reports that have that partial term in the MedDRA term for the report.

The columns in the report table are described below:
{| class="wikitable"
|Created
|The date and time the report was registered in the analytical portal
|
|-
|Identifier
|Unique identifier for the report (system generated)
|
|-
|Patient
|Patient name
|
|-
|Medication Summary
|Overview of all medications associated with the patient at the time of the event, including the WHO or Naranjo causality assessment outcome once that has been set
|
|-
|Adverse Event
|The adverse event experienced by the patient
|
|-
|MedDRA Terminology
| colspan="2" |The unique and internationally recognized MedDRA term defined for the event
|-
|Status
|Current status of the report
|
|-
|Actions
|'''Confirm Report Data Stage'''

View Activity History

Confirm or Delete Report

View Patient (Active Only)

View SAE Report or Patient Summary

Update Report (Spontaneous Only)

'''Set MedDRA and Causality Stage'''

View Activity History

Set Terminology (MedDRA), Naranjo or WHO Causality Term

Confirm Causality Set

View Patient (Active Only)

View SAE Report or Patient Summary

Update Report (Spontaneous Only)

'''Extract E2B Stage'''

View Activity History

Create or Update an E2B file

Prepare or Confirm E2B file for submission

Download XML file

View Patient (Active Only)

View SAE Report or Patient Summary

Update Report (Spontaneous Only)
|
|}

== 1.4 Pharmacovigilance Activities - General ==

=== 1.4.1 Viewing Activity History for Report ===
Irrespective of the stage the report is currently in, you will be able to view a comprehensive history for the report detailing all actions that have occurred, who effected the action, and any additional comments.

Once you have searched for a report, click on the '''View activity history''' menu for the associated report you would like to view.

The system will navigate you to the '''View activity history''' page.

The columns in the activity history table are described below:

{| class="wikitable"
|Activity
|The primary activity stage performed by the analyst
|
|-
|Execution event
|The primary activity performed by the analyst. Activities are dependent on the stage the report is in.
|
|-
|Execution date
|The date and time the user executed the activity
|
|-
|Comments
|Any comments noted by the user at the point of completing the activity
|
|-
|Receipt date
| colspan="2" |Particular to the E2B Extract Stage. Confirmation an E2B extract has been received by UMC and this is the associated receipt date
|-
|Receipt code
|Particular to the E2B Extract Stage. Confirmation an E2B extract has been received by UMC and this is the associated receipt code that may be supplied by UMC
|
|-
|Action
|Download summary

Download extract

Download E2B file
|
|}

=== 1.4.2 Viewing a Patient Record ===
The '''View patient''' menu allows the user to navigate to the Patient View for the patient so that the analyst may gather additional information to the adverse event.

Once you have searched for a report, click on the '''View patient''' menu for the associated report you would like to view.

The system will navigate you to the '''Patient View''' page in the Clinical Portal.
{| class="wikitable"
|
|This menu item will only be made available under the following circumstances:

· Active reports only

· If the user has the Registration Clerk, Data Capture or Clinician role assigned to their user profile
|}

=== 1.4.3 Extracting a Patient Summary ===
The '''Download summary''' menu allows the user to generate an overall summary of the patient clinical record in MS Word format. This is the preferred method of granting access to the clinical record for the analyst.

Once you have searched for a report, click on the '''Download Summary''' menu for the associated report you would like to view.

The system generates an extract of the patient summary:

.
{| class="wikitable"
|
|If the event is defined as serious, the system will include additional information that explains the seriousness of the report. The heading of the extract will be changed to '''Serious Adverse Event.'''
|}

=== 1.4.4 Updating a Spontaneous Report ===
The '''Update report''' menu allows the user to navigate to the spontaneous report for the patient and allow the analyst the ability to amend the report.

Once you have searched for a report, click on the '''Update report''' menu for the associated report you would like to amend.

The system will navigate you to the '''Spontaneous View''' pop up form for the report.
{| class="wikitable"
|
|This menu item will only be available for spontaneous reports.

|}

== 1.5 Pharmacovigilance Activities – Confirm Report Data ==

=== 1.5.1 Deleting a Report ===
The '''Confirm Report Data''' stage enforces a process whereby the analyst ensures the necessary clinical data is of sufficient quality to allow terminology and causality to be completed. In the event a report is deemed to be insufficient, inaccurate, or erroneous, a report may be deleted, which will effectively remove it from analysis.

Once you have searched for a report, click on the '''Delete report''' menu for the associated report you would like to delete.

The system will navigate you to the '''Add Activity''' page.

Specify the reason for deleting the record and click '''Save''' to confirm the deletion or '''Cancel''' to cancel the action and return to the previous page.

The system will update the status of the report accordingly.
{| class="wikitable"
|
|Once a report is deleted, it is not possible to re-include the report for analysis. Please ensure you are correct in deleting the report before committing the action.

|}

=== 1.5.2 Confirming a Report ===
The '''Confirm Report Data''' stage enforces a process whereby the analyst ensures the necessary clinical data is of sufficient quality to allow terminology and causality to be completed. When a report is deemed to be sufficient and accurate, the report should be confirmed, which will effectively allow terminology definition to commence.

Once you have searched for a report, click on the '''Confirm Report''' menu for the associated report you would like to confirm.

The system will navigate you to the '''Add Activity''' page.

Specify any additional comments for confirming the record and click '''Save''' to confirm the deletion or '''Cancel''' to cancel the action and return to the previous page.

The system will update the status of the report accordingly.

{| class="wikitable"
|
|Confirming a report will move the report into the next stage: '''Set MedDRA and Causality.'''

|}

== 1.6 Pharmacovigilance Activities – Set MedDRA and Causality ==

=== 1.6.1 Set MedDRA Terminology ===
The '''Set MedDRA and Causality''' stage facilitates the process of confirming the final MedDRA term for the adverse event and allows assignment of causality per relevant medication using either the World Health Organization or the Naranjo Causality Scale.

Once you have searched for a report, click on the '''Set Terminology''' menu for the associated report you would like to set terminology for.

The system will pop up a '''MedDRA Terminology''' form.

The '''MedDRA Terminology''' form displays the adverse event as reported by the clinician and/or reporter.

MedDRA terms can be searched in the following ways:

• Search by MedDRA Term

• Search by MedDRA Code

• Search by MedDRA List

==== 1.6.1.1 Search by MedDRA Term ====
Searching by a MedDRA term allows you the ability to filter through MedDRA using a partial or fully defined term.

In the '''Term type''' field, select the level of specificity for the search (SOC, HLTG, HLT, PT, or LLT).

In the '''Find by term''' field, enter the term you are searching for.
{| class="wikitable"
|
|It is possible to complete a partial search by entering as few as 3 characters that form part of the overall term.

|}

Click the '''Select''' icon next to the term you would like to assign or click the '''Cancel''' button to cancel the action and return to the previous page. The report will be updated with the new term accordingly.

==== 1.6.1.2 Search by MedDRA Code ====

Searching by a MedDRA code allows you the ability to filter through MedDRA using an associated code which can be fully defined or partial in nature.

In the '''Find by code''' field, enter the code you are searching for.
{| class="wikitable"
|
|It is possible to complete a partial search by entering as few as 4 numerical characters that form part of the overall code.

|}
Click the '''Select''' icon next to the term you would like to assign or click the '''Cancel''' button to cancel the action and return to the previous page. The report will be updated with the new term accordingly.

==== 1.6.1.3 Search for MedDRA Term by List ====
The list search function allows the user to navigate the MedDRA dictionary using the hierarchical structure of the dictionary. Select the System Organ Class field to select a SOC.

Continue selecting through the hierarchy (HLGT, HLT, PT) until you have selected the Low-Level Term that matches the adverse event.

Click the '''Select''' icon next to the term you would like to assign or click the '''Cancel''' button to cancel the action and return to the previous page. The report will be updated with the new term accordingly.

=== 1.6.2 Causality Assessment using the WHO Scale ===
The '''Set MedDRA and Causality''' stage facilitates the process of confirming the final MedDRA term for the adverse event and allows assignment of causality per relevant medication using either the World Health Organization or the Naranjo Causality Scale.

Once the MedDRA terminology for the event has been set, the report will be updated accordingly.

Setting the terminology will further allow the setting of causality per medication. Click on the '''WHO Causality''' menu option for the associated report you would like to set causality for.

The system will open up the '''WHO Causality Assessment''' pop up form.

The '''WHO Causality Assessment''' form displays the adverse event as reported by the clinician and/or reporter and the MedDRA Terminology that has been set for the event.

The '''WHO Causality Assessment''' form also displays the list of medications that the patient was exposed to at the onset of the adverse event.

The analyst can perform the following actions against each medication the patient was exposed to:

· Ignore the medication (the medication is definitely not responsible for the adverse event)

· Set causality for the medication

==== 1.6.2.1 Ignoring the Medication ====
Ignoring the medication means that a causality assessment need not be set for that medication.

To ignore assigning a WHO causality assessment for this medication, click the '''Ignore Medication''' icon. The system will assign '''Ignored''' as the causality term.

==== 1.6.2.2 Set Causality ====
By clicking the '''Set Causality''' icon, the system will enable you to set causality for this medication.

The system displays a series of questions for assigning the WHO causality term.

Click the appropriate response (Yes or No) for question 1 and continue to respond to the first five questions.

If responses to all five questions are '''Yes,''' the system will assign '''Certain''' as the causality term.

Click the '''Set causality icon''' next to the causality assessment and the system will assign the term as Certain in the system.

Click the '''Close''' button at any time to undo the action and return to the list reports.

If any of the questions in the Certain category have a response of '''No''' the system will display questions for the Probable/Likely category.

Continue this process until you have answered '''Yes''' to all questions in a specific category. This will result in the classification for that medication being set to that category.

In the event you reach the '''Unassessable/Unclassified''' category, if one of the two questions asked in that category is answered as '''No,''' the system will trigger an alert.

Once the term has been assigned click the '''Close''' button to continue.

=== 1.6.3 Causality Assessment using the Naranjo Scale ===
The '''Set MedDRA and Causality''' stage facilitates the process of confirming the final MedDRA term for the adverse event and allows assignment of causality per relevant medication using either the World Health Organization or the Naranjo Causality Scale.

Once the MedDRA terminology for the event has been set, the report will be updated accordingly.

Setting the terminology will further allow the setting of causality per medication. Click on the '''Naranjo Causality''' menu for the associated report you would like to set causality for.

The system will open up the '''Naranjo Causality Assessment''' pop up form.

The '''Naranjo Causality Assessment''' form displays the adverse event as reported by the clinician and/or reporter and the MedDRA Terminology set.

The '''Naranjo Causality Assessment''' form also displays the list of medications that the patient was exposed to at the onset of the adverse event.

The analyst can perform the following actions against each medication the patient was exposed to:

· Ignore the medication (the medication is definitely not responsible for the adverse event)

· Set causality for the medication

==== 1.6.3.1 Ignoring the Medication ====

Ignoring the medication means that a causality assessment need not be set for that medication.

To ignore assigning a Naranjo causality assessment for this medication, click the '''Ignore Medication''' icon. The system will assign '''Ignored''' as the causality term.

==== 1.6.3.2 Set Causality ====

By clicking the '''Set Causality''' icon, the system will enable you to set causality for this medication.

The system displays a series of questions for calculating the Naranjo causality score.

Click the appropriate response (Yes or No) for question 1 and continue to respond to all remaining questions. Once all responses have been selected, the system will automatically calculate the causality assessment.

Click the '''Set causality icon''' next to the causality assessment and the system will assign the term as per the calculation in the system.

Click the '''Close''' button at any time to undo the action and return to the list reports.

=== 1.6.4 Confirming Causality Set ===
The '''Set MedDRA and Causality''' stage facilitates the process of confirming the final MedDRA term for the adverse event and allows assignment of causality per relevant medication using either the World Health Organization or the Naranjo Causality Scale.

Once causality for all medications has been set, the report will be updated accordingly.

Click on the '''Confirm Causality Set''' menu for the associated report you would like to confirm causality set for.

The system will navigate you to the '''Confirm Causality Set''' form.

Specify any comment if necessary and click '''Save''' to confirm the setting of the causality or '''Cancel''' to cancel the action and return to the previous page.

The system will update the status of the report accordingly. Please note the report will now be located in the Extract E2B tab.

== 1.7 Pharmacovigilance Activities – Extract E2B ==

=== 1.7.1 Create E2B ===
{| class="wikitable"
|'''BUZZWORDS'''

'''ICH E2B:''' An E2B dataset facilitates the Electronic Transmission of Individual Case Safety Reports (ICSRs) and can be used to submit such reports to WHO. The E2B dataset within PViMS is implemented using the standard adopted by the ICH1 for electronic transmission of ICSRs according to the ICH E2B(R3) message standard.
|}

The '''Extract E2B''' stage generates an E2B extract for submission to the World Health Organization Uppsala Monitoring Centre.
{| class="wikitable"
|
|<nowiki>By clicking this menu item, the system generates an E2B dataset that is populated with clinical information from the source form. This E2B dataset can be amended by you to reflect additional clinical information pertinent to WHO. This menu item is only available for forms that are in the Extract E2B | NOTGENERATED stage.</nowiki>

|}
Once you have searched for a report, click on the '''Create E2B''' menu for the associated report you would like to create E2B for.

Once the system has created the E2B dataset, the status of the report will be updated to E2BINITIATED to indicate the dataset has been created.

The E2B dataset is constructed with the following sections (these sections are based on R2 of the E2B ICH definition):

· Message Header

· Safety Report

· Primary Source

· Sender

· Receiver

· Patient

· Medical History Episode

· Past Drug Therapy

· Patient Death

· Reaction

· Test

· Drug

· Summary

{| class="wikitable"
|'''ICH E2B:''' Please see the electronic Transmission of Individual Case Safety Reports Message Specification for detail specifications on the above categories. This specification can be found on

<nowiki>https://admin.ich.org/sites/default/files/inline-files/ICH_ICSR_Specification_V2-3.pdf</nowiki>
|}

=== 1.7.2 Adding Information to and Updating an E2B File ===
Once an E2B file is created, the '''Update E2B''' menu allows the user to add information to or updating existing information populated in an E2B file.

Once you have searched for a report, click on the '''Update E2B''' menu for the associated file you would like to amend.

The system will pop up a '''E2B ICH Report''' form for the file.

Once you completed making amendments, click on the '''Save''' button to save the changes or the '''Cancel''' button to cancel the action and return to the previous page.
{| class="wikitable"
|
|
|}

=== 1.7.3 Preparing a Report for E2B Submission ===
The '''Extract E2B''' stage facilitates the process of generating an E2B extract for submission to the World Health Organization Uppsala Monitoring Centre.

Once you have created an E2B file and searched for the report, click on the '''Prepare Report for E2B Submission''' menu for the associated report you would like to prepare.

The system will navigate you to the '''Prepare report for E2B submission''' pop up form.

Specify any additional comments for preparing the record and click '''Save''' to confirm the preparation or '''Cancel''' to cancel the action and return to the previous page.

The system will update the status of the report accordingly.
{| class="wikitable"
|
|It is during this stage that PViMS prepares the XML file for submission. It also prepares an associated patient summary and patient extract that correspond to the clinical data at the point of generating the submission.

|}

=== 1.7.4 Viewing the E2B XML File ===
Once you have prepared the E2B file for submission and searched for the report, click on the '''View Activity History''' menu for the associated report you would like to view the XML file for.

The system will navigate you to the '''Activities''' page where you will be able to view a comprehensive history of activities by the analyst against this adverse event.

Locate the '''E2BGENERATED''' execution event for the report, click the menu for that event, and select the '''Download E2B File''' menu.

The system will automatically generate the XML file for the E2B submission to WHO. Save the file on your local computer for referral when sending to WHO.

The extract below is the XML generated for the Message Header section of the XML file.

=== 1.7.5 Viewing the Clinical Data Associated to the E2B XML File ===
Once you have prepared the E2B file for submission and searched for the report, click on the '''View Activity History''' menu for the associated report you would like to view the XML file for.

The system will navigate you to the '''Activities''' page where you will be able to view a comprehensive history of activities by the analyst against this adverse event.

Locate the '''E2BGENERATED''' execution event for the report, click the action menu, and select the '''Download summary or Download extract''' menu.

If you select the '''Download summary''' menu, the system will generate a MS Word extract of the associated clinical data. See Extracting a Patient Summary.

If you select the '''Download extract''' menu, the system will generate an MS Excel extract of the associated clinical data.
{| class="wikitable"
|
|In both the Patient Extract and Summary above, these files are stored along with the XML file as a reference to the clinical data associated with the XML file at the point the XML file was generated.

|}

=== 1.7.6 Confirming a Report for E2B Submission ===
Once you have prepared the E2B file for submission and searched for the report, click on the '''Confirm E2B Submission''' menu for the associated report you would like to submit.

The system will navigate you to the '''Confirm E2B Submission''' pop up form.

Specify any additional comments for confirming the submission and click '''Save''' to confirm the submission or '''Cancel''' to cancel the action and return to the previous page.
{| class="wikitable"
|
|The receipt date and code can be used to note correspondence with WHO on the receipt of the E2B XML submission file.

|}
The system will update the status of the report accordingly. Please note that the report is removed from the Extract E2B tab as work for this report is now classified as finished. Use the S'''earch by date''' or '''Search by term''' tabs to locate this report again.

== 1.8 Analyser ==
{| class="wikitable"
|This section is used to generate the relative risk for a specified adverse drug reaction based on an exposed and non-exposed population set over a defined period of time.

The analyser user can access the following functionality within the analytical portal:

· Define population set (cohort or condition group)

· Define reporting period

· Specify additional risk factors

· View risk ratios per exposed drug

· Download dataset for further analysis
|}
'''2 '''

2.1 ''' '''

2.2 ''' '''

2.3 ''' '''

2.4 ''' '''

2.5 ''' '''

2.6 ''' '''

2.7 ''' '''

2.8 ''' '''

=== 2.8.1 Methodology ===
The following formulas, calculations and definitions are used in the calculation of the relative risk for a specific medication and adverse reaction.

==== 1.8.1.1 Incidence Rate ====
The incidence rate is the number of new cases per population in a given time period
{| class="wikitable"
|IR = (ADR / Population) * 1000

'''Where'''

IR = Incidence Rate

ADR = Number of adverse drug reactions *

Population = Total patient years in reporting period **

'''Note'''

<nowiki>*</nowiki> Where causality is set to possible, probably/likely or Certain for WHO assessments and where causality is set to possible, probable or definite for Naranjo assessments

<nowiki>**</nowiki> Population is represented in patient years. For example, if the reporting period is 30 days, and 10 patients were on treatment for all 30 days, the total patient years is 300 /365.25 which is 0.82.

'''Example'''

Cases = 11

Non-Cases = 170

Population = 181 (11 + 170)

Incidence Rate = 11/181 * 1000 = '''60.77'''
|}

==== 1.8.1.2 Relative Risk ====
Relative risk is defined as the incidence in the exposed over incidence in the non-exposed.
{| class="wikitable"
|RR= IR1 / IR2

'''Where'''

RR = Relative Risk

IR1 = Incidence Rate for exposed population. The exposed population is defined as the patient population that have been exposed to a medication in the reporting period.

IR2 = Incidence Rate for non-exposed population. The exposed population is defined as the patient population that have NOT been exposed to a medication in the reporting period.

'''Example'''

Incidence Rate Exposed = 60.77

Incidence Rate Non-Exposed = 45.12

RR = '''1.35'''
|}

==== 1.8.1.3 Confidence Interval ====
A confidence interval is a range of values so defined that there is a specified probability that the value of a parameter lies within it. Most commonly, the 95% confidence interval is used.
{| class="wikitable"
|

'''Where'''

''z''<sub>α</sub> is the standard score for the chosen level of significance and SE the standard error.
|}

=== 1.8.2 Generating Unadjusted Relative Risk Ratios ===
To implement the methodology for generating an '''Unadjusted Relative Risk Ratio,''' the following parameters will need to be specified:

· The population target (condition group or Cohort)

· The date range for the analysis

The '''Analyser''' function can be accessed through the main menu.

==== 1.8.2.1 Specifying the Population Group ====
Ensure the '''Analysis Criteria''' tab is selected to allow the selection of the patient population.

By selecting a '''Condition Group''' or '''Cohort''', you are effectively able to target a specific set of patients for analysis.

To specify a '''Condition Group,''' click the Primary Condition Group Risk Factor field and select the primary condition you would like to run analysis against. If this option is selected, all patients that belong to the corresponding Condition Group will be included in the analysis.

To specify a '''Cohort,''' click the Cohort field and select the primary cohort you would like to run analysis against. If this option is selected, all patients that belong to the corresponding Cohort will be included in the analysis.

==== 1.8.2.2 Specifying the Date Range for the Analysis ====
By selecting a '''Date Range''', the system will determine which patients should be included into the analysis from the Patient Population specified in the previous step. Patients that have been actively exposed to medication within that range will be included.

==== 1.8.2.3 Running the Analysis ====
Once the '''Patient Population''' and '''Date Range''' parameters have been selected, click on the '''Analyse''' button to execute the analysis.

The system will conduct an initial analysis that will identify what Adverse Drug Reactions have been identified over the reporting period. All results are included in the '''Analysis Results''' tab. Please note that only adverse drug reactions where a MedDRA term has been selected by the PV technician will be selected.

Select the '''Adverse Drug Reaction''' that you would like to detect signals for by clicking on the tab for that reaction. The selected tab will turn a dark blue to signify that it has been selected.

Please note that selecting the Adverse Drug Reaction will enable the Dashboard and Patients tab.

You are able to now view a 2 by 2 table illustrating relative risk and 95% Confidence Interval for the selected reaction.

· Incidence Rate for exposed group

· Incidence Rate for non-exposed group

· Relative Risk for the associated medication

· 95% Confidence Interval for the associated medication

==== 1.8.2.4 Viewing the Contributing Patient List ====
Once analysis has been executed, it is possible to view the list of patients that have contributed to the analysis population set through the '''Patients''' tab.

The columns in the patient list table are described below:
{| class="wikitable"
|Patient name
|The name of the patient contributing to the patient population
|-
|Medication
|The drug the patient was exposed to during the period of analysis
|-
|Days contributed
|The number of days the patient contributed to the patient population
|-
|Reaction
|Did the patient suffer a reaction during the period of analysis
|-
|Risk Factor
|Which risk factor does the patient match
|}

==== 1.8.2.5 Resetting Criteria ====
If at any point you would like to alter the patient population or date range, click the '''Reset criteria''' tab alongside the list of Adverse Drug Reactions to reset analysis. Selecting this tab will remove existing analysis and reopen the Analysis Criteria tab for modification.

=== 1.8.3 Generating Adjusted Relative Risk Ratios ===
To implement the methodology for generating an '''Adjusted Relative Risk Ratio,''' the following parameters will need to be specified:

· The population target (condition group or Cohort)

· The date range for the analysis

· The risk factors to be applied

The '''Analyser''' function can be accessed through the main menu.

==== 1.8.3.1 Specifying the Population Group ====
Ensure the '''Analysis Criteria''' tab is selected to allow the selection of the patient population.

By selecting a '''Condition Group''' or '''Cohort''', you are effectively able to target a specific set of patients for analysis.

To specify a '''Condition Group,''' click the Primary Condition Group Risk Factor field and select the primary condition you would like to run analysis against. If this option is selected, all patients that belong to the corresponding Condition Group will be included in the analysis.

To specify a '''Cohort,''' click the Cohort field and select the primary cohort you would like to run analysis against. If this option is selected, all patients that belong to the corresponding Cohort will be included in the analysis.

==== 1.8.3.2 Specifying the Date Range for the Analysis ====
By selecting a '''Date Range''', the system will determine which patients should be included into the analysis from the Patient Population specified in the previous step. Patients that have been actively exposed to medication within that range will be included.
==== 1.8.3.3 Specifying Risk Factors for the Analysis ====

To specify a '''Risk Factor,''' click the Risk factor field and select the risk factor you would like to include into the analysis. Once you have selected the risk factor, select the appropriate option associated to that risk factor and click the '''add''' icon to add the risk factor to the selected list.

You are able to add as many risk factors as you would like to include into the analysis by repeating the above process.

By including '''Risk Factors''' into the analysis, the system will determine which patients match the criteria stipulated by the set of risk factors and the corresponding '''Relative Risk Ratio''' will be adjusted based on the new population set.

==== 1.8.3.4 Running the Analysis ====
Once the '''Patient Population, Date Range, and Risk Factor''' parameters have been selected, click on the '''Analyse''' button to execute the analysis.

The system will conduct an initial analysis that will identify what Adverse Drug Reactions have been identified over the reporting period. All results are included in the '''Analysis Results''' tab. Please note that only adverse drug reactions where a MedDRA term has been selected by the PV technician will be selected.

Select the '''Adverse Drug Reaction''' that you would like to detect signals for by clicking on the tab for that reaction. The selected tab will turn a dark blue to signify that it has been selected.

Please note that selecting the Adverse Drug Reaction will enable the Dashboard and Patients tab.

You are able to now view a 2 by 2 table illustrating relative risk and 95% Confidence Interval for the selected reaction.

· Incidence Rate for exposed group

· Incidence Rate for non-exposed group

· Relative Risk for the associated medication

· 95% Confidence Interval for the associated medication
=== 1.8.4 Downloading a Dataset for Further Analysis ===
Select the '''Download Data''' tab and then click the '''Download Dataset''' button to able to download a comprehensive dataset of patient clinical data in XLSX format for importation into a third-party statistical tool.

{| class="wikitable"
|
|If you are unable to locate this function, please liaise with your system administrator as the ability to download a dataset for external consumption will need to be assigned to your user profile.

|}

OpenRIMS-RPM - Upgrade Part 1

2023-08-31T18:44:19Z

Khoppenworth:

= Objective =
A new release of OpenRIMS always contains changes in the software codes and, very often, in the database structure. To install a new release, it is necessary to replace the software codes and implement the database structure changes, if ones.

The implementation of the database structure changes will keep all data, however, will allow the use of the new release of the software.

Despite it being possible to use this feature for the production databases, it is recommended only for test and demo systems.

Here are the steps to perform an upgrade from any version of OpenRIMS to latest version.

# Connect to destination server UI or CLI
# Backup Database
# Download the new MySQL model file
# Stop the OpenRIMS service
# Rename old Application file
# Download the new Application file (https://github.com/MSH/OpenRIMS/raw/main/bin/pharmadex2-0.0.1.jar)
# Change Permissions on the .jar file to make it executable: sudo chmod -x pharmadex2-0.0.1.jar
# Use Workbench to upgrade db structure based on the model - see below
# Start the OpenRIMS service

= Tool =
   The tool is the latest version of MySQL Workbench.

   For current, the latest stable release of the database is in pdx2demo.ddanet.org. To upgrade the database in any other server, or, even, in the localhost it is possible to use the feature “Model – Synchronize with any source” (<nowiki>https://dev.mysql.com/doc/workbench/en/wb-database-synchronization.html</nowiki>) provided by the MySQL Workbench.

   This feature:

1. reads the latest and the current database structures,

2. compares them

3. creates a script to upgrade the current database to the latest database structure

4. executes this script

   The result is the equal data structures for the latest and the current database. The data is still the same as was before.

= Pre-condition =
   You should have full access rights to your database and add the connection to the latest database depicted below. Ask for a password by email to alex.kurasoff@gmail.com.

Figure 1. The connection to the latest database

= The sequence of steps =
   Suppose you need to update the database structure of a database on the localhost.

Figure 2. Create a '''new''' model

Figure 3. Run the feature

Figure 4. The representation of the feature is a "wizard"

Figure 5. Tap the radio buttons

Figure 6. The latest database is on pdx2demo.ddanet.org. It is the source of the changes

Figure 7. Suppose the database going to be updated is in the localhost. It is the target of the changes

Figure 8. Extract the list of all sources and all target databases.

Figure 9. Select the source database. The target database is at the bottom of the screen. By default, the names of the target and the source should be the same

Figure 10. Compare the source and the target

Figure 11. Revise the changes.

Figure 12. The result DDA SQL script. There are no changes

= Linux particularities =
   The MySQL database usage in Windows and Linux servers is slightly different. In the Linux server, the names of tables are cases sensitive, on Windows – no. There is any problem if the source server is under Linux, and the target server is under Windows. Otherwise, the tables SPRING_SESSION and SPRING_SESSION attributes should be ignored while synchronization. There are special tables that are in use by third-party software.

OpenRIMS-RPM - Upgrade Part 1

2023-08-31T16:04:33Z

Khoppenworth: New Page

= Objective =
A new release of OpenRIMS always contains changes in the software codes and, very often, in the database structure. To install a new release, it is necessary to replace the software codes and implement the database structure changes, if ones.

The implementation of the database structure changes will keep all data, however, will allow the use of the new release of the software.

Despite it being possible to use this feature for the production databases, it is recommended only for test and demo systems.

Here are the steps to perform an upgrade from any version of OpenRIMS to latest version.

# Connect to destination server UI or CLI
# Backup Database
# Download the new MySQL model file
# Stop the OpenRIMS service
# Rename old Application file
# Download the new Application file (https://github.com/MSH/OpenRIMS/raw/main/bin/pharmadex2-0.0.1.jar)
# Change Permissions on the .jar file to make it executable
# Use Workbench to upgrade db structure based on the model - see below
# Start the OpenRIMS service

= Tool =
   The tool is the latest version of MySQL Workbench.

   For current, the latest stable release of the database is in pdx2demo.ddanet.org. To upgrade the database in any other server, or, even, in the localhost it is possible to use the feature “Model – Synchronize with any source” (<nowiki>https://dev.mysql.com/doc/workbench/en/wb-database-synchronization.html</nowiki>) provided by the MySQL Workbench.

   This feature:

1. reads the latest and the current database structures,

2. compares them

3. creates a script to upgrade the current database to the latest database structure

4. executes this script

   The result is the equal data structures for the latest and the current database. The data is still the same as was before.

= Pre-condition =
   You should have full access rights to your database and add the connection to the latest database depicted below. Ask for a password by email to alex.kurasoff@gmail.com.

Figure 1. The connection to the latest database

= The sequence of steps =
   Suppose you need to update the database structure of a database on the localhost.

Figure 2. Create a '''new''' model

Figure 3. Run the feature

Figure 4. The representation of the feature is a "wizard"

Figure 5. Tap the radio buttons

Figure 6. The latest database is on pdx2demo.ddanet.org. It is the source of the changes

Figure 7. Suppose the database going to be updated is in the localhost. It is the target of the changes

Figure 8. Extract the list of all sources and all target databases.

Figure 9. Select the source database. The target database is at the bottom of the screen. By default, the names of the target and the source should be the same

Figure 10. Compare the source and the target

Figure 11. Revise the changes.

Figure 12. The result DDA SQL script. There are no changes

= Linux particularities =
   The MySQL database usage in Windows and Linux servers is slightly different. In the Linux server, the names of tables are cases sensitive, on Windows – no. There is any problem if the source server is under Linux, and the target server is under Windows. Otherwise, the tables SPRING_SESSION and SPRING_SESSION attributes should be ignored while synchronization. There are special tables that are in use by third-party software.

OpenRIMS-PVM - Upgrade Chapter 1

2023-08-24T19:33:12Z

Khoppenworth: New page

New versions will be released on GitHub: https://github.com/msh/openrims-pvm

To upgrade to the latest version you must follow these steps:

# Backup the database
# Stop the service
# Copy APP and API folders to a backup destination
# With that in place you can now:
## Download the new APP and API files
## Extract
## Copy to the web server folder; typically /var/www/html/'''api''' and /var/www/html/'''app'''

---End of document---

OpenRIMS-PVM - Installation Chapter 1

2023-08-21T18:59:13Z

Khoppenworth:

This guide describes the deployment for a '''MySQL''' Linux server i.e. Ubuntu for the below instructions.

Please click this link for an MSSQL deployment.

== Pre-Requisites ==
You need a server to install on. Local or Cloud.

In this example we are deploying on an Oracle OCI server.

The server is accessed using SSH.

== Basic Web Server Setup ==
sudo apt update

sudo apt install apache2
Then enable Proxy which will be used for the .Net api:
a2enmod proxy proxy_http proxy_html

sudo systemctl restart apache2
Oracle OCI specific:
sudo iptables -I INPUT 6 -m state --state NEW -p tcp --dport 80 -j ACCEPT

sudo iptables -I INPUT 6 -m state --state NEW -p tcp --dport 443 -j ACCEPT

sudo iptables -I INPUT 6 -m state --state NEW -p tcp --dport 3306 -j ACCEPT

sudo netfilter-persistent save

== '''Basic MySQL Setup''' ==
sudo apt install mysql-server

sudo mysql
Configure root user password:
ALTER USER 'root'@'localhost' IDENTIFIED WITH mysql_native_password BY 'password';
Create database user named ''openrimspvm'' with your ''password'' of choice:
CREATE USER 'openrimspvm'@'%' IDENTIFIED BY 'password';
Give the user access to the database with the name you have chosen/defined (in appsettings.json - see later section):
GRANT PRIVILEGE ON pvims TO 'openrimspvm'@'%';
Or full access to database (only if remote access is disabled for better security):
GRANT ALL PRIVILEGES ON *.* TO 'sammy'@'localhost' WITH GRANT OPTION;

FLUSH PRIVILEGES;

== '''.NET Core 6 Runtime''' ==
curl -SL -o dotnet.tar.gz <nowiki>https://download.visualstudio.microsoft.com/download/pr/33c6e1e3-e81f-44e8-9de8-91934fba3c94/9105f95a9e37cda6bd0c33651be2b90a/dotnet-sdk-6.0.201-linux-arm64.tar.gz</nowiki>

sudo mkdir -p /usr/share/dotnet

sudo tar -zxf dotnet.tar.gz -C /usr/share/dotnet

sudo ln -s /usr/share/dotnet/dotnet /usr/bin/dotnet

== '''APP and API''' ==
Please send an email to info@openrims.org to download the required files.<blockquote>TIP - Install Midnight Commander for easy file navigation in the Linux commandline:

sudo apt install mc (Install midnight commander for file management and permissions)</blockquote>wget zip files for each app and api (from openrims.org/GitHub)

Unzip to /var/www/html/app using mc

Unzip to /var/www/html/api using mc

Make dll application file in the API folder executable:
sudo chmod -x PViMS.API.dll
Edit appsettings.json connection string to MySQL with password:
sudo nano /var/www/html/api/appsettings.json
Test API with direct dotnet command:
dotnet PViMS.API.dll

* Check for red text errors in the CLI window e.g. wrong database connection
* Check that the database has been created in MySQL

Stop dotnet with Ctrl+C

== '''Configure the Service''' ==
We need auto start in case of reboot
cd /etc/systemd/system

sudo nano openrimspvm.service
The system file must contain something like: <blockquote>[Unit]

Description=Example .NET Web API App OpenRIMS-PVM running on Linux

[Service]

WorkingDirectory=/var/www/html/api

ExecStart=/usr/bin/dotnet /var/www/html/api/PViMS.API.dll

Restart=always

<nowiki>#</nowiki> Restart service after 10 seconds if the dotnet service crashes:

RestartSec=10

KillSignal=SIGINT

SyslogIdentifier=dotnet-example

User=www-data

Environment=ASPNETCORE_ENVIRONMENT=Production

Environment=DOTNET_PRINT_TELEMETRY_MESSAGE=false

[Install]

WantedBy=multi-user.target</blockquote>
sudo systemctl daemon-reload

sudo systemctl start openrimspvm.service

sudo systemctl restart apache2

== '''Secure The Website''' ==
sudo nano /etc/apache2/sites-enabled/000-default.conf

Sample content with app and api:

<VirtualHost *:80>

ServerName '''subdomain'''.openrims.org

DocumentRoot /var/www/html/app

ErrorLog ${APACHE_LOG_DIR}/error.log

CustomLog ${APACHE_LOG_DIR}/access.log combined

</VirtualHost>

<VirtualHost *:80>

ServerName '''subdomain-api'''.openrims.org

DocumentRoot /var/www/html/api

ErrorLog ${APACHE_LOG_DIR}/error.log

CustomLog ${APACHE_LOG_DIR}/access.log combined

</VirtualHost>

Then apply SSL:
sudo apt install certbot python3-certbot-apache

sudo certbot

== '''Webserver Config''' ==
We need to separate secure vhost: One for APP and one for API

Vhost on port 80 for redirect to APP

Vhost on 443 pointing to APP (Then API as <Location /> with reverse proxy?)

Vhost on port 80 for redirect API

This one is just a reverse proxy to port 5000 where Kestrel is running the dotnet PViMS.API.dll
sudo nano /etc/apache2/sites-enabled/000-default-le-ssl.conf
SAMPLE Apache .conf file:<blockquote><IfModule mod_ssl.c>

<VirtualHost *:443>

   '''ServerName pv.openrims.org'''

   DocumentRoot /var/www/html/app

   ErrorLog ${APACHE_LOG_DIR}/error.log

   CustomLog ${APACHE_LOG_DIR}/access.log combined

Include /etc/letsencrypt/options-ssl-apache.conf

SSLCertificateFile /etc/letsencrypt/live/pv-api.openrims.org/fullchain.pem

SSLCertificateKeyFile /etc/letsencrypt/live/pv-api.openrims.org/privkey.pem

</VirtualHost>

</IfModule>

<IfModule mod_ssl.c>

<VirtualHost *:443>

   '''ServerName''' '''pv-api.openrims.org'''

   ErrorLog ${APACHE_LOG_DIR}/error.log

   CustomLog ${APACHE_LOG_DIR}/access.log combined

   <Location />

ProxyPreserveHost On

ProxyPass <nowiki>http://0.0.0.0:5000/</nowiki>

ProxyPassReverse <nowiki>http://0.0.0.0:5000/</nowiki>

</Location>

Include /etc/letsencrypt/options-ssl-apache.conf

SSLCertificateFile /etc/letsencrypt/live/pv-api.openrims.org/fullchain.pem

SSLCertificateKeyFile /etc/letsencrypt/live/pv-api.openrims.org/privkey.pem

</VirtualHost>

</IfModule></blockquote>This Concludes the guide!

OpenRIMS-PVM - Causality & Terminology Chapter 1

2023-08-18T18:10:50Z

Khoppenworth: /* Outcome B: Setting Causality and Terminology for a Report */

== Outcome A: Confirming Quality of Report Data ==
Determining if the report has sufficient quality of data to enable setting causality and terminology by the PV team

=== '''Step 1: Identifying new adverse event reports that have been submitted by a facility''' ===
Reports that have been submitted within a specified timeframe will be designated as new and appear in the '''New Report''' tab. Reports will remain in this tab for a period of 2 days, irrespective if any updates have been applied to the report.
[[File:NewReportTab01.png.png|alt=NewReportTab01.png|frameless|500x500px]][[File:NewReportTab02.png.png|alt=NewReportTab02.png|'''Benefits of the New Reports tab'''This tab is useful to easily identify reports that have recently been submitted. It can be used to ensure there is sufficient resource to respond to each report and to initiate the process of event management between the PV team and the facility clinician who reported the event.

'''New Reports time frame'''

It is possible to confirm the period of what constitutes a new report in the administration section of PViMS. The default setting is 2 days from date of report submission.

|thumb|300x300px|none]]'''Step 2: View clinical details associated to the report'''

Once you have identified that a new report has been created in PViMS, the process of confirming if the report is of sufficient quality to allow the setting of causality and terminology can begin. Clinical details associated to the adverse event can be viewed using the '''View Details''' or '''Patient Summary''' menu options that appear alongside the corresponding report.

# Locate the report you would like to view in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select that item
# The system will either display details associated to the report within PViMS or download a patient summary MS Word Document
[[File:PatientSummaryTab01.png.png|alt=PatientSummaryTab01.png|thumb|'''Benefits of the Patient Summary.'''Producing a patient summary provides you with a physical file that can be emailed separately from within the system. This may allow you to share details of the report without designated recipients needing access to PViMS.|none|405x405px]]

'''Step 3: Generating tasks per issue of data quality'''

Data inconsistencies or lack of sufficient data invariably has a multi-faceted impact on the time taken to determine causality, the strength and accuracy of the causality determined and will ultimately negatively affect the ability of the national PV team to assist the clinician in the management of the event. The primary function of the '''Confirm Report Data''' stage is to expedite the process of assuring data quality and to ensure there is ongoing training and communication with the facility to improve clinical record keeping.

A key tool in the confirmation process is the ability to create data quality tasks for the associated report. To add a task,

# Locate the report you would like to add a '''Task''' for in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon[[File:Creating a Task.png|alt=Creating a Task|none|thumb|700x700px|Creating a Task]]
# Navigate to the corresponding menu and select that item
# The system will navigate you to a form that lists existing tasks that have been allocated to the report (Please note that if this is the first task for the report you will be notified of this)[[File:CreateTask02.png.png|alt=CreateTask02.png|none|thumb|684x684px|Create Task 2]]
# Select the '''Add Task''' button to add a new task.
# Enter details of the task noting that the form area is a generic area of the report where the data quality issue lies, and the type of task can be used to indicate if there is a data quality issue or a general follow up on the report required. Enter details of the issue or follow up in the details tab.
# Select the '''Save''' button to save the task for the adverse event report.[[File:CreateTask03.png.png|alt=CreateTask03.png|none|thumb|450x450px|Save the Task.]]
<blockquote>'''Using tasks to initiate follow up with the clinician'''

Generating a task will result in two notifications been sent. The first notification takes the form of an email that is sent to the reporting clinician containing details of the report and the task that has been created. The second notification takes the form of an internal PViMS notification that is sent to the system user that registered the report, this includes a system notification to EDRWeb.</blockquote>

=== '''Step 4: Tracking tasks using its status and adding comments to the task''' ===
The key to expediting the data quality assurance process is to improve the process of fixing data quality issues through improved communication between the facility clinician and the PV technician. The ability to track task the task becomes critical in this regard.

To change the status of a task:

# Locate the report you would like to ass a '''Task''' for in the '''Confirm Report Data''' table.
# Mouse over the menu item at the end of the report and select this icon.
# Navigate to the corresponding menu and select that item.[[File:Creating a Task.png|alt=Creating a Task.png|none|thumb|700x700px|Tracking a Task]]
# [[File:Tracking Tasks.png|alt=TrackingTasks02.png|none|thumb|450x450px|Tracking Tasks]]The system will navigate you to a form that lists existing tasks that have been allocated to the report.
# [[File:ChangeTaskStatus.png.png|alt=ChangeTaskStatus.png|none|thumb|450x450px|Changing Task Status]]Mouse over the menu item at the end of the task and select this icon.
# Navigate to the corresponding menu and select that item.
# [[File:ConfirmTaskChange.png.png|alt=ConfirmTaskChange.png|none|thumb|450x450px|Confirm Task Change]]The system will pop up a form where the status of a task can be changed.
# The following task statuses apply:

{| class="wikitable"
|Acknowledge Task
|The clinician can acknowledge that they have received the task
|-
|On Hold
|The Task has not been cancelled but can be put on hold
|-
|Cancel
|The task is cancelled and no follow up is required
|-
|Completed
|The task has been completed and addressed
|}
<blockquote>'''Using tasks to track efficiency of data quality processes'''

A task forms a fundamentally useful mechanism for determining efficacy of data quality processes centrally and at facility level. Useful metrics such as the number of tasks per report per facility allow us to determine if a facility needs additional intervention in the form of training or resources. Other metrics such as time taken to complete a task may also indicate a new for improved communication and resourcing.</blockquote>Comments can be used to facilitate ongoing communication between the PV technician and the reporting clinician. To add a comment to a report:

# Locate the report you would like to add a '''Task''' for in the '''Confirm Report Data''' table.
# Mouse over the menu item at the end of the report and select this icon.[[File:Creating a Task.png|alt=Open the Task screen|none|thumb|700x700px|Open the Task screen]]
# Navigate to the corresponding menu and select that item.
# The system will navigate you to a form that lists existing tasks that have been allocated to the report.
# Mouse over the menu item at the end of the task and select this icon.
# Navigate to the corresponding menu and select that item.
# The system will pop up a form where comments can be added to the report.
<blockquote>'''Using comments effectively to communicate between the PV team and the clinician'''

Comments are useful in that they facilitate communication between the PV team and the clinician. While comments should be used judiciously, they indicate there is activity on the task and forms an effective audit trail for activity on the task for all to see.</blockquote>

=== '''Step 5: Confirming report is of sufficient quality to proceed''' ===
A report may only move into the causality and terminology phase by confirming the report is of sufficient quality to proceed. It is very important to note that once a report is confirmed, it is expected that the report is of sufficient quality to proceed.

Confirmation that a report has successfully passed the '''Confirm Data''' stage can be achieved by,

# Locate the report you would like to ass a '''Task''' for in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select '''Confirm Report'''
# The system will pop up a form asking the user to confirm if the report is ready for confirmation
# Enter any comments if necessary and select the '''Save''' button to confirm the report
<blockquote>'''Confirm data for a report'''

Confirming the report will effectively move the report into the Causality and Terminology tab

'''Deleting a report'''

A report should only be deleted if it is determined to be a duplicate or was incorrectly captured in the clinical system</blockquote>

== Outcome B: Setting Causality and Terminology for a Report ==
Setting causality using either the MedDRA or Naranjo scale and determining the MedDRA term for the adverse event

=== '''Step 1: Identifying adverse event reports that are set for causality and terminology''' ===
Reports that have been confirmed will now appear in the '''Set MedDRA and Causality''' tab. Reports will remain in this tab until causality and terminology has been completed.

=== '''Step 2: Setting the MedDRA term for a report'''MedDRA is the Medical Dictionary for Regulatory Activities and is a clinically validated international medical terminology dictionary-thesaurus used by regulatory authorities and the biopharmaceutical industry during the regulatory process. ===
Once a report is moved into the Set MedDRA and Causality phase, the first step is to set the MedDRA term for the report. To set the term,

# Locate the report you would like to '''Set''' '''Terminology''' for in the '''Set MedDRA and Causality''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select '''Set Terminology'''
# The system will pop up a form where the MedDRA term can be set for the report
# It is possible to search for a MedDRA term using 3 different methods.
#* '''Method 1''' allows for searching for the at the corresponding level you select. For instance, you can search all Low-Level Terms which include the term you are searching for. This is the most efficient method for searching for a term.
#* '''Method 2''' allows for searching for the term by its associated code. This method is primarily useful if you know the code you are searching for.
#* '''Method 3''' allows for searching for the term using the hierarchical structure of MedDRA. This is the most precise way of searching through MedDRA but is also the most time consuming.
# Once you have located the term you have searched for, select the send icon next to the corresponding term. This will set the term for the report.
<blockquote>'''Benefits of allocating a MedDRA term to a report'''

By allocating a MedDRA term to the report, this endeavors to facilitate the exchange of clinical information through a single standardized international medical terminology that can be used for regulatory communication and evaluation of data pertaining to medicinal products for human use.</blockquote>

=== '''Step 3: Setting causality per medication''' ===
Causality assessment essentially means finding a causal association or relationship between a drug and a drug reaction. It is an evaluation of the likelihood that a particular treatment is the cause of an observed adverse event.

Once a report is moved into the Set MedDRA and Causality phase, after the MedDRA term for the report is set, the second step is to set causality per medication the patient has been exposed to. To set causality using the Naranjo scale,

# Locate the report you would like to '''Set''' '''Causality''' for in the '''Set MedDRA and Causality''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select '''Naranjo Causality'''
# The system will pop up a form where causality can be set per medication
# To set causality for a specific medication, select the blue send icon for the corresponding medication, after which you will be navigated to a form where you can set causality for the medication using the Naranjo scale
# Answer each question in turn and once all questions are answered, the user will be presented with the associated causality based on the answers provided
# Select the '''Save button''' to save causality for the medication
# You can view causality set per medication using the '''View Button'''
<blockquote>'''Benefits of setting causality per medication'''

Once causality has been set, PViMS is able to detect signals based on patient exposure rates per medication.</blockquote>

OpenRIMS-PVM - Causality & Terminology Chapter 1

2023-08-18T15:12:21Z

Khoppenworth: /* Step 5: Confirming report is of sufficient quality to proceed */

== Outcome A: Confirming Quality of Report Data ==
Determining if the report has sufficient quality of data to enable setting causality and terminology by the PV team

=== '''Step 1: Identifying new adverse event reports that have been submitted by a facility''' ===
Reports that have been submitted within a specified timeframe will be designated as new and appear in the '''New Report''' tab. Reports will remain in this tab for a period of 2 days, irrespective if any updates have been applied to the report.
[[File:NewReportTab01.png.png|alt=NewReportTab01.png|frameless|500x500px]][[File:NewReportTab02.png.png|alt=NewReportTab02.png|'''Benefits of the New Reports tab'''This tab is useful to easily identify reports that have recently been submitted. It can be used to ensure there is sufficient resource to respond to each report and to initiate the process of event management between the PV team and the facility clinician who reported the event.

'''New Reports time frame'''

It is possible to confirm the period of what constitutes a new report in the administration section of PViMS. The default setting is 2 days from date of report submission.

|thumb|300x300px|none]]'''Step 2: View clinical details associated to the report'''

Once you have identified that a new report has been created in PViMS, the process of confirming if the report is of sufficient quality to allow the setting of causality and terminology can begin. Clinical details associated to the adverse event can be viewed using the '''View Details''' or '''Patient Summary''' menu options that appear alongside the corresponding report.

# Locate the report you would like to view in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select that item
# The system will either display details associated to the report within PViMS or download a patient summary MS Word Document
[[File:PatientSummaryTab01.png.png|alt=PatientSummaryTab01.png|thumb|'''Benefits of the Patient Summary.'''Producing a patient summary provides you with a physical file that can be emailed separately from within the system. This may allow you to share details of the report without designated recipients needing access to PViMS.|none|405x405px]]

'''Step 3: Generating tasks per issue of data quality'''

Data inconsistencies or lack of sufficient data invariably has a multi-faceted impact on the time taken to determine causality, the strength and accuracy of the causality determined and will ultimately negatively affect the ability of the national PV team to assist the clinician in the management of the event. The primary function of the '''Confirm Report Data''' stage is to expedite the process of assuring data quality and to ensure there is ongoing training and communication with the facility to improve clinical record keeping.

A key tool in the confirmation process is the ability to create data quality tasks for the associated report. To add a task,

# Locate the report you would like to add a '''Task''' for in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon[[File:Creating a Task.png|alt=Creating a Task|none|thumb|700x700px|Creating a Task]]
# Navigate to the corresponding menu and select that item
# The system will navigate you to a form that lists existing tasks that have been allocated to the report (Please note that if this is the first task for the report you will be notified of this)[[File:CreateTask02.png.png|alt=CreateTask02.png|none|thumb|684x684px|Create Task 2]]
# Select the '''Add Task''' button to add a new task.
# Enter details of the task noting that the form area is a generic area of the report where the data quality issue lies, and the type of task can be used to indicate if there is a data quality issue or a general follow up on the report required. Enter details of the issue or follow up in the details tab.
# Select the '''Save''' button to save the task for the adverse event report.[[File:CreateTask03.png.png|alt=CreateTask03.png|none|thumb|450x450px|Save the Task.]]
<blockquote>'''Using tasks to initiate follow up with the clinician'''

Generating a task will result in two notifications been sent. The first notification takes the form of an email that is sent to the reporting clinician containing details of the report and the task that has been created. The second notification takes the form of an internal PViMS notification that is sent to the system user that registered the report, this includes a system notification to EDRWeb.</blockquote>

=== '''Step 4: Tracking tasks using its status and adding comments to the task''' ===
The key to expediting the data quality assurance process is to improve the process of fixing data quality issues through improved communication between the facility clinician and the PV technician. The ability to track task the task becomes critical in this regard.

To change the status of a task:

# Locate the report you would like to ass a '''Task''' for in the '''Confirm Report Data''' table.
# Mouse over the menu item at the end of the report and select this icon.
# Navigate to the corresponding menu and select that item.[[File:Creating a Task.png|alt=Creating a Task.png|none|thumb|700x700px|Tracking a Task]]
# [[File:Tracking Tasks.png|alt=TrackingTasks02.png|none|thumb|450x450px|Tracking Tasks]]The system will navigate you to a form that lists existing tasks that have been allocated to the report.
# [[File:ChangeTaskStatus.png.png|alt=ChangeTaskStatus.png|none|thumb|450x450px|Changing Task Status]]Mouse over the menu item at the end of the task and select this icon.
# Navigate to the corresponding menu and select that item.
# [[File:ConfirmTaskChange.png.png|alt=ConfirmTaskChange.png|none|thumb|700x700px|Confirm Task Change]]The system will pop up a form where the status of a task can be changed.
# The following task statuses apply:

{| class="wikitable"
|Acknowledge Task
|The clinician can acknowledge that they have received the task
|-
|On Hold
|The Task has not been cancelled but can be put on hold
|-
|Cancel
|The task is cancelled and no follow up is required
|-
|Completed
|The task has been completed and addressed
|}
<blockquote>'''Using tasks to track efficiency of data quality processes'''

A task forms a fundamentally useful mechanism for determining efficacy of data quality processes centrally and at facility level. Useful metrics such as the number of tasks per report per facility allow us to determine if a facility needs additional intervention in the form of training or resources. Other metrics such as time taken to complete a task may also indicate a new for improved communication and resourcing.</blockquote>Comments can be used to facilitate ongoing communication between the PV technician and the reporting clinician. To add a comment to a report:

# Locate the report you would like to add a '''Task''' for in the '''Confirm Report Data''' table.
# Mouse over the menu item at the end of the report and select this icon.
# Navigate to the corresponding menu and select that item.
# The system will navigate you to a form that lists existing tasks that have been allocated to the report.
# Mouse over the menu item at the end of the task and select this icon.
# Navigate to the corresponding menu and select that item.
# The system will pop up a form where comments can be added to the report.
<blockquote>'''Using comments effectively to communicate between the PV team and the clinician'''

Comments are useful in that they facilitate communication between the PV team and the clinician. While comments should be used judiciously, they indicate there is activity on the task and forms an effective audit trail for activity on the task for all to see.</blockquote>

=== '''Step 5: Confirming report is of sufficient quality to proceed''' ===
A report may only move into the causality and terminology phase by confirming the report is of sufficient quality to proceed. It is very important to note that once a report is confirmed, it is expected that the report is of sufficient quality to proceed.

Confirmation that a report has successfully passed the '''Confirm Data''' stage can be achieved by,

# Locate the report you would like to ass a '''Task''' for in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select '''Confirm Report'''
# The system will pop up a form asking the user to confirm if the report is ready for confirmation
# Enter any comments if necessary and select the '''Save''' button to confirm the report
<blockquote>'''Confirm data for a report'''

Confirming the report will effectively move the report into the Causality and Terminology tab

'''Deleting a report'''

A report should only be deleted if it is determined to be a duplicate or was incorrectly captured in the clinical system</blockquote>

== Outcome B: Setting Causality and Terminology for a Report ==
Setting causality using either the MedDRA or Naranjo scale and determining the MedDRA term for the adverse event

=== '''Step 1: Identifying adverse event reports that are set for causality and terminology''' ===
Reports that have been confirmed will now appear in the '''Set MedDRA and Causality''' tab. Reports will remain in this tab until causality and terminology has been completed.

=== '''Step 2: Setting the MedDRA term for a report'''MedDRA is the Medical Dictionary for Regulatory Activities and is a clinically validated international medical terminology dictionary-thesaurus used by regulatory authorities and the biopharmaceutical industry during the regulatory process. ===
Once a report is moved into the Set MedDRA and Causality phase, the first step is to set the MedDRA term for the report. To set the term,

# Locate the report you would like to '''Set''' '''Terminology''' for in the '''Set MedDRA and Causality''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select '''Set Terminology'''
# The system will pop up a form where the MedDRA term can be set for the report
# It is possible to search for a MedDRA term using 3 different methods.
#* '''Method 1''' allows for searching for the at the corresponding level you select. For instance, you can search all Low-Level Terms which include the term you are searching for. This is the most efficient method for searching for a term.
#* '''Method 2''' allows for searching for the term by its associated code. This method is primarily useful if you know the code you are searching for.
#* '''Method 3''' allows for searching for the term using the hierarchical structure of MedDRA. This is the most precise way of searching through MedDRA but is also the most time consuming.
# Once you have located the term you have searched for, select the send icon next to the corresponding term. This will set the term for the report.
<blockquote>'''Benefits of allocating a MedDRA term to a report'''

By allocating a MedDRA term to the report, this endeavors to facilitate the exchange of clinical information through a single standardized international medical terminology that can be used for regulatory communication and evaluation of data pertaining to medicinal products for human use.</blockquote>

=== '''Step 3: Setting causality per medication''' ===
Causality assessment essentially means finding a causal association or relationship between a drug and a drug reaction. It is an evaluation of the likelihood that a particular treatment is the cause of an observed adverse event.

Once a report is moved into the Set MedDRA and Causality phase, after the MedDRA term for the report is set, the second step is to set causality per medication the patient has been exposed to. To set causality using the Naranjo scale,

# Locate the report you would like to '''Set''' '''Causality''' for in the '''Set MedDRA and Causality''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select '''Naranjo Causality'''
# The system will pop up a form where causality can be set per medication
# To set causality for a specific medication, select the blue send icon for the corresponding medication, after which you will be navigated to a form where you can set causality for the medication using the Naranjo scale
# Answer each question in turn and once all questions are answered, the user will be presented with the associated causality based on the answers provided
# Select the '''Save button''' to save causality for the medication
# You can view causality set per medication using the '''View Button'''
<blockquote>'''Benefits of setting causality per medication'''

Once causality has been set, PViMS is able to detect signals based on patient exposure rates per medication.</blockquote>

OpenRIMS-PVM - Causality & Terminology Chapter 1

2023-08-18T15:03:43Z

Khoppenworth: /* Step 5: Confirming report is of sufficient quality to proceed */

== Outcome A: Confirming Quality of Report Data ==
Determining if the report has sufficient quality of data to enable setting causality and terminology by the PV team

=== '''Step 1: Identifying new adverse event reports that have been submitted by a facility''' ===
Reports that have been submitted within a specified timeframe will be designated as new and appear in the '''New Report''' tab. Reports will remain in this tab for a period of 2 days, irrespective if any updates have been applied to the report.
[[File:NewReportTab01.png.png|alt=NewReportTab01.png|frameless|500x500px]][[File:NewReportTab02.png.png|alt=NewReportTab02.png|'''Benefits of the New Reports tab'''This tab is useful to easily identify reports that have recently been submitted. It can be used to ensure there is sufficient resource to respond to each report and to initiate the process of event management between the PV team and the facility clinician who reported the event.

'''New Reports time frame'''

It is possible to confirm the period of what constitutes a new report in the administration section of PViMS. The default setting is 2 days from date of report submission.

|thumb|300x300px|none]]'''Step 2: View clinical details associated to the report'''

Once you have identified that a new report has been created in PViMS, the process of confirming if the report is of sufficient quality to allow the setting of causality and terminology can begin. Clinical details associated to the adverse event can be viewed using the '''View Details''' or '''Patient Summary''' menu options that appear alongside the corresponding report.

# Locate the report you would like to view in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select that item
# The system will either display details associated to the report within PViMS or download a patient summary MS Word Document
[[File:PatientSummaryTab01.png.png|alt=PatientSummaryTab01.png|thumb|'''Benefits of the Patient Summary.'''Producing a patient summary provides you with a physical file that can be emailed separately from within the system. This may allow you to share details of the report without designated recipients needing access to PViMS.|none|405x405px]]

'''Step 3: Generating tasks per issue of data quality'''

Data inconsistencies or lack of sufficient data invariably has a multi-faceted impact on the time taken to determine causality, the strength and accuracy of the causality determined and will ultimately negatively affect the ability of the national PV team to assist the clinician in the management of the event. The primary function of the '''Confirm Report Data''' stage is to expedite the process of assuring data quality and to ensure there is ongoing training and communication with the facility to improve clinical record keeping.

A key tool in the confirmation process is the ability to create data quality tasks for the associated report. To add a task,

# Locate the report you would like to add a '''Task''' for in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon[[File:Creating a Task.png|alt=Creating a Task|none|thumb|700x700px|Creating a Task]]
# Navigate to the corresponding menu and select that item
# The system will navigate you to a form that lists existing tasks that have been allocated to the report (Please note that if this is the first task for the report you will be notified of this)[[File:CreateTask02.png.png|alt=CreateTask02.png|none|thumb|684x684px|Create Task 2]]
# Select the '''Add Task''' button to add a new task.
# Enter details of the task noting that the form area is a generic area of the report where the data quality issue lies, and the type of task can be used to indicate if there is a data quality issue or a general follow up on the report required. Enter details of the issue or follow up in the details tab.
# Select the '''Save''' button to save the task for the adverse event report.[[File:CreateTask03.png.png|alt=CreateTask03.png|none|thumb|450x450px|Save the Task.]]
<blockquote>'''Using tasks to initiate follow up with the clinician'''

Generating a task will result in two notifications been sent. The first notification takes the form of an email that is sent to the reporting clinician containing details of the report and the task that has been created. The second notification takes the form of an internal PViMS notification that is sent to the system user that registered the report, this includes a system notification to EDRWeb.</blockquote>

=== '''Step 4: Tracking tasks using its status and adding comments to the task''' ===
The key to expediting the data quality assurance process is to improve the process of fixing data quality issues through improved communication between the facility clinician and the PV technician. The ability to track task the task becomes critical in this regard.

To change the status of a task:

# Locate the report you would like to ass a '''Task''' for in the '''Confirm Report Data''' table.
# Mouse over the menu item at the end of the report and select this icon.
# Navigate to the corresponding menu and select that item.[[File:Creating a Task.png|alt=Creating a Task.png|none|thumb|700x700px|Tracking a Task]]
# [[File:Tracking Tasks.png|alt=TrackingTasks02.png|none|thumb|450x450px|Tracking Tasks]]The system will navigate you to a form that lists existing tasks that have been allocated to the report.
# [[File:ChangeTaskStatus.png.png|alt=ChangeTaskStatus.png|none|thumb|450x450px|Changing Task Status]]Mouse over the menu item at the end of the task and select this icon.
# Navigate to the corresponding menu and select that item.
# [[File:ConfirmTaskChange.png.png|alt=ConfirmTaskChange.png|none|thumb|700x700px|Confirm Task Change]]The system will pop up a form where the status of a task can be changed.
# The following task statuses apply:

{| class="wikitable"
|Acknowledge Task
|The clinician can acknowledge that they have received the task
|-
|On Hold
|The Task has not been cancelled but can be put on hold
|-
|Cancel
|The task is cancelled and no follow up is required
|-
|Completed
|The task has been completed and addressed
|}
<blockquote>'''Using tasks to track efficiency of data quality processes'''

A task forms a fundamentally useful mechanism for determining efficacy of data quality processes centrally and at facility level. Useful metrics such as the number of tasks per report per facility allow us to determine if a facility needs additional intervention in the form of training or resources. Other metrics such as time taken to complete a task may also indicate a new for improved communication and resourcing.</blockquote>Comments can be used to facilitate ongoing communication between the PV technician and the reporting clinician. To add a comment to a report:

# Locate the report you would like to ass a '''Task''' for in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select that item
# The system will navigate you to a form that lists existing tasks that have been allocated to the report
# Mouse over the menu item at the end of the task and select this icon
# Navigate to the corresponding menu and select that item
# The system will pop up a form where comments can be added to the report

'''Using comments effectively to communicate between the PV team and the clinician'''

Comments are useful in that they facilitate communication between the PV team and the clinician. While comments should be used judiciously, they indicate there is activity on the task and forms an effective audit trail for activity on the task for all to see.

=== '''Step 5: Confirming report is of sufficient quality to proceed''' ===
A report may only move into the causality and terminology phase by confirming the report is of sufficient quality to proceed. It is very important to note that once a report is confirmed, it is expected that the report is of sufficient quality to proceed.

Confirmation that a report has successfully passed the '''Confirm Data''' stage can be achieved by,

# Locate the report you would like to ass a '''Task''' for in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select '''Confirm Report'''
# The system will pop up a form asking the user to confirm if the report is ready for confirmation
# Enter any comments if necessary and select the '''Save''' button to confirm the report

'''Confirm data for a report'''

Confirming the report will effectively move the report into the Causality and Terminology tab

'''Deleting a report'''

A report should only be deleted if it is determined to be a duplicate or was incorrectly captured in the clinical system

== Outcome B: Setting Causality and Terminology for a Report ==
Setting causality using either the MedDRA or Naranjo scale and determining the MedDRA term for the adverse event

=== '''Step 1: Identifying adverse event reports that are set for causality and terminology''' ===
Reports that have been confirmed will now appear in the '''Set MedDRA and Causality''' tab. Reports will remain in this tab until causality and terminology has been completed.

=== '''Step 2: Setting the MedDRA term for a report'''MedDRA is the Medical Dictionary for Regulatory Activities and is a clinically validated international medical terminology dictionary-thesaurus used by regulatory authorities and the biopharmaceutical industry during the regulatory process. ===
Once a report is moved into the Set MedDRA and Causality phase, the first step is to set the MedDRA term for the report. To set the term,

# Locate the report you would like to '''Set''' '''Terminology''' for in the '''Set MedDRA and Causality''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select '''Set Terminology'''
# The system will pop up a form where the MedDRA term can be set for the report
# It is possible to search for a MedDRA term using 3 different methods.
#* '''Method 1''' allows for searching for the at the corresponding level you select. For instance, you can search all Low-Level Terms which include the term you are searching for. This is the most efficient method for searching for a term.
#* '''Method 2''' allows for searching for the term by its associated code. This method is primarily useful if you know the code you are searching for.
#* '''Method 3''' allows for searching for the term using the hierarchical structure of MedDRA. This is the most precise way of searching through MedDRA but is also the most time consuming.
# Once you have located the term you have searched for, select the send icon next to the corresponding term. This will set the term for the report.

'''Benefits of allocating a MedDRA term to a report'''

By allocating a MedDRA term to the report, this endeavors to facilitate the exchange of clinical information through a single standardized international medical terminology that can be used for regulatory communication and evaluation of data pertaining to medicinal products for human use.

=== '''Step 3: Setting causality per medication''' ===
Causality assessment essentially means finding a causal association or relationship between a drug and a drug reaction. It is an evaluation of the likelihood that a particular treatment is the cause of an observed adverse event.

Once a report is moved into the Set MedDRA and Causality phase, after the MedDRA term for the report is set, the second step is to set causality per medication the patient has been exposed to. To set causality using the Naranjo scale,

# Locate the report you would like to '''Set''' '''Causality''' for in the '''Set MedDRA and Causality''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select '''Naranjo Causality'''
# The system will pop up a form where causality can be set per medication
# To set causality for a specific medication, select the blue send icon for the corresponding medication, after which you will be navigated to a form where you can set causality for the medication using the Naranjo scale
# Answer each question in turn and once all questions are answered, the user will be presented with the associated causality based on the answers provided
# Select the '''Save button''' to save causality for the medication
# You can view causality set per medication using the '''View Button'''

'''Benefits of setting causality per medication'''

Once causality has been set, PViMS is able to detect signals based on patient exposure rates per medication.

OpenRIMS-PVM - Causality & Terminology Chapter 1

2023-08-18T15:01:47Z

Khoppenworth: /* Step 5: Confirming report is of sufficient quality to proceed */

== Outcome A: Confirming Quality of Report Data ==
Determining if the report has sufficient quality of data to enable setting causality and terminology by the PV team

=== '''Step 1: Identifying new adverse event reports that have been submitted by a facility''' ===
Reports that have been submitted within a specified timeframe will be designated as new and appear in the '''New Report''' tab. Reports will remain in this tab for a period of 2 days, irrespective if any updates have been applied to the report.
[[File:NewReportTab01.png.png|alt=NewReportTab01.png|frameless|500x500px]][[File:NewReportTab02.png.png|alt=NewReportTab02.png|'''Benefits of the New Reports tab'''This tab is useful to easily identify reports that have recently been submitted. It can be used to ensure there is sufficient resource to respond to each report and to initiate the process of event management between the PV team and the facility clinician who reported the event.

'''New Reports time frame'''

It is possible to confirm the period of what constitutes a new report in the administration section of PViMS. The default setting is 2 days from date of report submission.

|thumb|300x300px|none]]'''Step 2: View clinical details associated to the report'''

Once you have identified that a new report has been created in PViMS, the process of confirming if the report is of sufficient quality to allow the setting of causality and terminology can begin. Clinical details associated to the adverse event can be viewed using the '''View Details''' or '''Patient Summary''' menu options that appear alongside the corresponding report.

# Locate the report you would like to view in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select that item
# The system will either display details associated to the report within PViMS or download a patient summary MS Word Document
[[File:PatientSummaryTab01.png.png|alt=PatientSummaryTab01.png|thumb|'''Benefits of the Patient Summary.'''Producing a patient summary provides you with a physical file that can be emailed separately from within the system. This may allow you to share details of the report without designated recipients needing access to PViMS.|none|405x405px]]

'''Step 3: Generating tasks per issue of data quality'''

Data inconsistencies or lack of sufficient data invariably has a multi-faceted impact on the time taken to determine causality, the strength and accuracy of the causality determined and will ultimately negatively affect the ability of the national PV team to assist the clinician in the management of the event. The primary function of the '''Confirm Report Data''' stage is to expedite the process of assuring data quality and to ensure there is ongoing training and communication with the facility to improve clinical record keeping.

A key tool in the confirmation process is the ability to create data quality tasks for the associated report. To add a task,

# Locate the report you would like to add a '''Task''' for in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon[[File:Creating a Task.png|alt=Creating a Task|none|thumb|700x700px|Creating a Task]]
# Navigate to the corresponding menu and select that item
# The system will navigate you to a form that lists existing tasks that have been allocated to the report (Please note that if this is the first task for the report you will be notified of this)[[File:CreateTask02.png.png|alt=CreateTask02.png|none|thumb|684x684px|Create Task 2]]
# Select the '''Add Task''' button to add a new task.
# Enter details of the task noting that the form area is a generic area of the report where the data quality issue lies, and the type of task can be used to indicate if there is a data quality issue or a general follow up on the report required. Enter details of the issue or follow up in the details tab.
# Select the '''Save''' button to save the task for the adverse event report.[[File:CreateTask03.png.png|alt=CreateTask03.png|none|thumb|450x450px|Save the Task.]]
<blockquote>'''Using tasks to initiate follow up with the clinician'''

Generating a task will result in two notifications been sent. The first notification takes the form of an email that is sent to the reporting clinician containing details of the report and the task that has been created. The second notification takes the form of an internal PViMS notification that is sent to the system user that registered the report, this includes a system notification to EDRWeb.</blockquote>

=== '''Step 4: Tracking tasks using its status and adding comments to the task''' ===
The key to expediting the data quality assurance process is to improve the process of fixing data quality issues through improved communication between the facility clinician and the PV technician. The ability to track task the task becomes critical in this regard.

To change the status of a task:

# Locate the report you would like to ass a '''Task''' for in the '''Confirm Report Data''' table.
# Mouse over the menu item at the end of the report and select this icon.
# Navigate to the corresponding menu and select that item.[[File:Creating a Task.png|alt=Creating a Task.png|none|thumb|700x700px|Tracking a Task]]
# [[File:Tracking Tasks.png|alt=TrackingTasks02.png|none|thumb|450x450px|Tracking Tasks]]The system will navigate you to a form that lists existing tasks that have been allocated to the report.
# [[File:ChangeTaskStatus.png.png|alt=ChangeTaskStatus.png|none|thumb|450x450px|Changing Task Status]]Mouse over the menu item at the end of the task and select this icon.
# Navigate to the corresponding menu and select that item.
# [[File:ConfirmTaskChange.png.png|alt=ConfirmTaskChange.png|none|thumb|700x700px|Confirm Task Change]]The system will pop up a form where the status of a task can be changed.
# The following task statuses apply:

{| class="wikitable"
|Acknowledge Task
|The clinician can acknowledge that they have received the task
|-
|On Hold
|The Task has not been cancelled but can be put on hold
|-
|Cancel
|The task is cancelled and no follow up is required
|-
|Completed
|The task has been completed and addressed
|}
'''Using tasks to track efficiency of data quality processes'''

A task forms a fundamentally useful mechanism for determining efficacy of data quality processes centrally and at facility level. Useful metrics such as the number of tasks per report per facility allow us to determine if a facility needs additional intervention in the form of training or resources. Other metrics such as time taken to complete a task may also indicate a new for improved communication and resourcing.Comments can be used to facilitate ongoing communication between the PV technician and the reporting clinician. To add a comment to a report,

# Locate the report you would like to ass a '''Task''' for in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select that item
# The system will navigate you to a form that lists existing tasks that have been allocated to the report
# Mouse over the menu item at the end of the task and select this icon
# Navigate to the corresponding menu and select that item
# The system will pop up a form where comments can be added to the report

'''Using comments effectively to communicate between the PV team and the clinician'''

Comments are useful in that they facilitate communication between the PV team and the clinician. While comments should be used judiciously, they indicate there is activity on the task and forms an effective audit trail for activity on the task for all to see.

=== '''Step 5: Confirming report is of sufficient quality to proceed''' ===
A report may only move into the causality and terminology phase by confirming the report is of sufficient quality to proceed. It is very important to note that once a report is confirmed, it is expected that the report is of sufficient quality to proceed.

Confirmation that a report has successfully passed the '''Confirm Data''' stage can be achieved by,

# Locate the report you would like to ass a '''Task''' for in the '''Confirm Report Data''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select '''Confirm Report'''
# The system will pop up a form asking the user to confirm if the report is ready for confirmation
# Enter any comments if necessary and select the '''Save''' button to confirm the report

'''Confirm data for a report'''

Confirming the report will effectively move the report into the Causality and Terminology tab

'''Deleting a report'''

A report should only be deleted if it is determined to be a duplicate or was incorrectly captured in the clinical system

== Outcome B: Setting Causality and Terminology for a Report ==
Setting causality using either the MedDRA or Naranjo scale and determining the MedDRA term for the adverse event

=== '''Step 1: Identifying adverse event reports that are set for causality and terminology''' ===
Reports that have been confirmed will now appear in the '''Set MedDRA and Causality''' tab. Reports will remain in this tab until causality and terminology has been completed.

=== '''Step 2: Setting the MedDRA term for a report'''MedDRA is the Medical Dictionary for Regulatory Activities and is a clinically validated international medical terminology dictionary-thesaurus used by regulatory authorities and the biopharmaceutical industry during the regulatory process. ===
Once a report is moved into the Set MedDRA and Causality phase, the first step is to set the MedDRA term for the report. To set the term,

# Locate the report you would like to '''Set''' '''Terminology''' for in the '''Set MedDRA and Causality''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select '''Set Terminology'''
# The system will pop up a form where the MedDRA term can be set for the report
# It is possible to search for a MedDRA term using 3 different methods.
#* '''Method 1''' allows for searching for the at the corresponding level you select. For instance, you can search all Low-Level Terms which include the term you are searching for. This is the most efficient method for searching for a term.
#* '''Method 2''' allows for searching for the term by its associated code. This method is primarily useful if you know the code you are searching for.
#* '''Method 3''' allows for searching for the term using the hierarchical structure of MedDRA. This is the most precise way of searching through MedDRA but is also the most time consuming.
# Once you have located the term you have searched for, select the send icon next to the corresponding term. This will set the term for the report.

'''Benefits of allocating a MedDRA term to a report'''

By allocating a MedDRA term to the report, this endeavors to facilitate the exchange of clinical information through a single standardized international medical terminology that can be used for regulatory communication and evaluation of data pertaining to medicinal products for human use.

=== '''Step 3: Setting causality per medication''' ===
Causality assessment essentially means finding a causal association or relationship between a drug and a drug reaction. It is an evaluation of the likelihood that a particular treatment is the cause of an observed adverse event.

Once a report is moved into the Set MedDRA and Causality phase, after the MedDRA term for the report is set, the second step is to set causality per medication the patient has been exposed to. To set causality using the Naranjo scale,

# Locate the report you would like to '''Set''' '''Causality''' for in the '''Set MedDRA and Causality''' table
# Mouse over the menu item at the end of the report and select this icon
# Navigate to the corresponding menu and select '''Naranjo Causality'''
# The system will pop up a form where causality can be set per medication
# To set causality for a specific medication, select the blue send icon for the corresponding medication, after which you will be navigated to a form where you can set causality for the medication using the Naranjo scale
# Answer each question in turn and once all questions are answered, the user will be presented with the associated causality based on the answers provided
# Select the '''Save button''' to save causality for the medication
# You can view causality set per medication using the '''View Button'''

'''Benefits of setting causality per medication'''

Once causality has been set, PViMS is able to detect signals based on patient exposure rates per medication.

File:ConfirmTaskChange.png.png

2023-08-18T15:00:24Z

Khoppenworth:

ConfirmTaskChange.png