chorus-ai / IVe

IVe

Integrated Viewer (IVe) webapp is to develop the proposed to support visualization and interrogation of the CHoRUS dataset that will include structured EHR (OMOP), extracted concepts from clinical notes, physiological vital signs/alarms/waveform, and image data. We decompose this task into subtasks, each of which either targets a specific key feature or workflow. The development will take place first at Emory University using an equivalent local dataset, in parallel to the development of proposed CHoRUS data platform and effort of data acquisition at other sites. Throughout the development process, alpha and beta versions of IVe will be made available to at least one additional CHoRUS site for further testing. In addition, frequent demonstrations will be offered to solicit feedback and inform details of various features from the whole CHoRUS team.

Table of Contents

• Installation
• Usage
• Features
• Tasks
• Contributing
• License
• Acknowledgements
• Contact

Installation

Provide instructions on how to install and set up your project. Include any dependencies or prerequisites that need to be installed.

# Clone the repository
git clone https://github.com/chorus-ai/IVe.git

# Install dependencies
npm install

Usage

# Run the server, listen PORT=8080
node server.js 

# Run the client, listen PORT=3000
npm start

DB Schema

Features

Based on the provided description, here's a breakdown of the features for the integrated viewer (IVe):

1. Data Visualization:

   • Support for visualizing structured EHR (OMOP) data.
   • Display of extracted concepts from clinical notes.
   • Visualization of physiological vital signs, alarms, and waveform data.
   • Image data viewer with zoom, pan, and other interactive features.

2. Interrogation Tools:

   • Search and filter functionality to quickly locate specific data points or trends.
   • Interactive tools to probe and analyze the displayed data.
   • Annotation and note-taking capabilities for users to mark important findings.
   • Share finginds with other users

3. Widget Development:

   • Support for widget layout configuration management.
   • Independent development modules to allow parallel work on different features.

4. Local Dataset Integration:

   • Ability to integrate and work with an equivalent local dataset from Emory University.
   • Compatibility with the CHoRUS data platform and other datasets.

5. Version Releases:

   • Alpha and beta version releases for preliminary testing.
   • Update and patch mechanisms to incorporate feedback and improvements.

6. User Authentication and Authorization:

   • User registration and login
   • Password recovery
   • Role-based access control

7. Performance and Optimization:

   • Fast page load times
   • Image and waveform optimization
   • In-memory caching

8. Security Features:

   • SSL certificate implementation
   • Data validation and sanitization
   • Regular security audits
   • Secure login and SSO authentication mechanisms.
   • Data encryption and privacy controls.
   • Audit trails for tracking user actions and changes.

9. Data Management and Storage:

   • Database integration
   • Data backup and recovery
   • Data encryption and security

10. Integration and API Features:

    • RESTful API endpoints

11. User Management and Roles:

    • Different user roles (e.g., Administrator, User) with specific permissions.
    • User profiles with details, activity logs, and project assignments.
    • A system for inviting new users to the platform or specific projects.

12. Reporting and Analytics:

    • Detailed reports on adjudication and annotation outcomes.
    • Visualization tools for data patterns and annotations.
    • Export functionality for reports and data.

13. Help and Documentation:

    • Detailed documentation on using the platform and its features.
    • FAQ section and support ticketing system.

14. Responsive Design:

    • The application should adapt to most common browsers and different screen sizes, ensuring usability on desktops, and tablets.

15. Customization and Settings:

    • Theme customization to align with the branding of CHoRUS or specific projects.
    • User-specific settings for notifications, display preferences(light or dark) .

16. Maintenance and Support:

    • Bug fixes
    • Regular updates
    • Customer support

Tasks

15.1 Set up software development and local deployment environment at Emory

• 15.1.1 Set up the team mangement environment
• 15.1.2 Set up the development environment
• 15.1.3 Set up the production environment on Emory AWS Cloud
• 15.1.4 Set up the DNS and Firewall Rule Exception with Emory IT
• 15.1.1 Configure cloud environment
• 15.1.2 Launch Alpha testing and get feedbacks
• 15.1.3 Document APT with OpenAPI 3.0 Specification and authenticate AP routes

15.2 Design and develop IVe database architecture. This database will store patient data, data about users, data generated by users using IVe

• 15.2.1 Design and develop table schemes with future expansion in mind
• 15.2.2 Define relationships and constraints between the tables
• 15.2.1 Quick prototyping and feedback around clinical data component's user interface it widget-like tiles management

15.3 Design and develop user authentication and management module

• 15.3.1 Setup OAuth 2.0 to secure the REST APIs
• 15.3.2 Setup Single Sign-on (SSO)
• 15.3.3 Setup Security Assertion Markup Language (SAML)
• 15.3.4 Setup one-time codes delivered by email or SMS to handle broken password
• 15.3.1 Develop front-end UI
• 15.3.2 Develop back-end logic

15.4 Design and develop patient search/list module

• 15.4.1 Design a search logic, implement auto-suggest mechanism and ensure lazy-loading on results
• 15.4.2 Design and develop UI and corresponding filtering options
• 15.4.1 Develp front-end UI
• 15.4.2 Develp back-end logic

15.5 Design and develop patient timeline/navigator module

• 15.5.1 Implment back-end services to extract multi model data from database
• 15.5.2 Design and develop user roles and features
• 15.5.3 Design and develp UI according to the user role and features
• 15.5.1 Quick prototyping and feedback around patient search and resulting patient list
• 15.5.2 Patient search with search history preserved
• 15.5.3 Setup/develop caching logic in Cloud instance

15.6 Design and develop dashboard module

• 15.6.1 Design and develop independent compents to create, names, edited, persisted, deleted, and shared like widget style dashboard
• 15.6.2 Design and develop share snapshot of the dashboard to another user to review
• 15.6.1 Map OMOP alarm data to IVe alarm module and develop back-end services
• 15.6.2 Map OMOP lab tests data to IVe lab module and develop back-end services
• 15.6.3 Map OMOP vitals data to IVe vitals module and develop back-end serices

15.7 Design and develop laboratory test results module

• 15.7.1 Design and draft various wireframes
• 15.7.2 Select the design based on feedback from CHoRUS team
• 15.7.3 Design options and selection will be recorded on the JIRA page
• 15.7.4 Implement data retrieval APIs
• 15.7.5 Implement and release an alpha version
• 15.7.6 Implement and release a beta version
• 15.7.7 Implement and release 1.0 version
• 15.7.8 Maintain and feature expansion

15.8 Design and develop NLP-extracted concept module

• 15.8.1 Prepre clinical concepts form the raw clincial notes and design object relational model in the structured database
• 15.8.2 Develop notes component in the client and controller/model in teh server

15.9 Deploy IVe in the CHoRUS data platform

• 15.9.1 Add embedding in the CHoRUS data platform to redirect to IVe hosting server

15.10 Design and develop medication order/administration module

• 15.10.1 Perform data element mapping to follow OMOP Common Data Model convention on drug exposure
• 15.10.2 Perform ETL strategy as more data pouring in

15.11 Design and develop vital sign module

• 15.11.1 Perform data element mapping to follow OMOP Common Data Model convention using measurement object
• 15.11.2 Perform ETL strategy as more ata pouringorm ETL strategy as more data pouring in

15.12 Design and develop physiological waveform patient monitor

• 15.12.1 Perform data element mapping to follow OMOP Common Data Model convention using observation object
• 15.12.2 Perform ETL strategy as more data pouring in

15.13 Design and develop image module

• 15.13.1 Custom image table will be designed and developed in the OMOP Common Data Mode
• 15.13.2 Perform data element mapping to follow OMOP Common data Model convention in the usom image object

Contributing

1. Fork the repository
2. Create a new branch: git checkout -b feature-branch
3. Make changes and commit: git commit -am 'Add new feature'
4. Push to the branch: git push origin feature-branch
5. Open a pull request

License

This project is licensed under the MIT License. See the LICENSE file for more details.

Acknowledgements

• Library
• Tutorial
• Stack Overflow for answering my questions

Contact

• Email: [e-mail]
• Website: https://nursingdatascience.emory.edu