SNOMED FHIR Terminology Server Integration with Bahmni
Objective | Showcase how opensource Bahmni EMR integrates with SNOMED FHIR Terminology server, to leverage advantages of the SNOMED classification system, in areas of recording clinical data, reporting, CDSS, analysis, etc. |
Due date | May 15, 2023 (Phase 1) |
Key outcomes |
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Status | M1-ACTIVE |
This feature will allow customers to start using SNOMED terminology in their health facilities for recording diagnosis/clinical data, and also perform reporting & CDSS use-cases using this recorded data. The full implementation is opensource and SNOMED international is very happy to help support implementations/geographies that wish to adopt SNOMED.
Please contact @Angshuman Sarkar @Vijay Anand Shanmughadass @Gurpreet Luthra @Ketan Goenka @Kai Kewley (SNOMED Team) who can help you understand this integration better if you are interested in exploring SNOMED. Or come to our Slack channel to ask questions directly with the SNOMED team.
As part of Phase2 of this work (May-Dec 2023), the team is focusing on enhancing CDSS use-cases for Drug-Drug interactions, Allergies, Export of Bulk Patient Data as FHIR, Integration with SNOMED Analytics tool, WHO ICD-10 reports, Integration with micro FHIR Terminology server for on-pref/offline hospitals. We look forward for community inputs and contributions.
Bahmni roadmap for Global Standards like FHIR, SNOMED CT, LOINC, DICOM, HL7, etc can be read here: https://bahmni.atlassian.net/wiki/spaces/BAH/pages/3176333313
Objective
Create an open-source reference implementation that displays best practices regarding how EMRs can leverage and benefit from SNOMED CT coding system
SNOMED CT International is interested in incorporating SNOMED-CT codes with Bahmni to create an open-source reference implementation that displays best practices regarding how EMRs can leverage and benefit from SNOMED CT Coding systems. This is especially helpful when governments/countries adopt SNOMED CT, and need to better understand how to enhance and evolve their existing digital systems to realise the benefits of SNOMED CT.
Project Scope (1st Phase)
Record patient diagnosis in Bahmni using SNOMED CT with real time Terminology Search - DIAGNOSIS
Reports in Bahmni displaying the power of SNOMED CT- DIAGNOSIS REPORTS
CDSS alert in Bahmni based on recorded SNOMED diagnosis and drug interaction - CDSS
Support for recording chief complaints H&E forms using SNOMED CT & Support for designing Bahmni - FORM BUILDER
Phase 2 Scope
Generate ICD-10 reports based on SNOMED code mappings - ICD-10 Reporting
Export anonymised, FHIR based, patient data for SNOMED analytics tool - Bulk Export for Analytics Tool
CDSS alert in Bahmni based on drug-drug interaction (possibly with DrugBank) - CDSS
Implementation of micro FHIR terminology server for low resource settings (include Contract Tests) - Micro FHIR
Ability to setup and order procedures using SNOMED CT- PROCEDURES
Sync Procedures with SNOMED TS
Current Landscape of Bahmni-SNOMED Integration
Environments for Dev, QA & Demo
(Go to CLINICAL section. Default creds: superman/Admin123)
Dev Environment - https://dev.snomed.mybahmni.in/
QA Environment - https://qa.snomed.mybahmni.in/
SNOWSTORM(SNOMED Terminology Server) - https://snowstorm.snomed.mybahmni.in/fhir/
SNOLYTICAL Server - https://analytics.snomed.mybahmni.in/
Feature Demo Videos
Recording Diagnosis and Displaying Reports (Video)
CDSS Alert Notification for Drug-Diagnosis Interaction with SNOMED-CT (Video)
COVID-19 Form Designing and Recording Data using SNOMED CT Terms
Procedures Setup in Bahmni using SNOMED CT ValueSet (video)
Generate ICD-10 reports based on SNOMED code mappings (video)
Feedback
Users can try out the demo version of the Bahmni-SNOMED integration and provide the feedback here
Please note that the data will not be shared with any 3rd party. This data will only be used to contact you regarding clarifications on the feedback
Features
Record patient diagnosis in Bahmni using SNOMED CT with real time Terminology Search
Clinicians can search for SNOMED terms for diagnosis or conditions
Upon providing keywords, Bahmni performs real time search in SNOMED CT and displays search results
Clinicians can also provide the SNOMED Code to search for a diagnosis in Bahmni
An advantage of SNOMED is that while searching for diagnosis, the descendants of the searched term are also displayed in search result, leveraging the hierarchical structure of SNOMED clinical terms
Once a term is selected from SNOMED TS, it is mapped and saved into Bahmni Concept Dictionary, and available for use in reports, CDSS, etc.
Reports in Bahmni displaying the power of SNOMED CT
Clinicians can generate diagnosis count reports based on SNOMED terms
Report feature can be accessed under the report module in Bahmni
Clinicians need to select the duration for the report and mode of display
Bahmni displays the patient count report based on gender
Advantage of using SNOMED CT TS
Bahmni leverages the hierarchical structure of Clinical Terms in SNOMED to also identify and report the descendants/children of the selected diagnosis for reporting
CDSS alert in Bahmni based on recorded SNOMED diagnosis and drug interaction
In this feature, the clinicians are notified with an alert when Drug-Diagnosis interaction is contraindicated
The hierarchical classification in SNOMED CT helps to identify all the descendants of a diagnosis and applies the CDSS rules to those as well. Meaning, if a drug is contraindicated to a diagnosis, then the drug will be contraindicated to all its descendants as well
Clinicians can accept the alert and make changes to medication or
Clinicians can choose to dismiss the alert by providing reason for dismissal (only in case of critical alerts)
CDSS Workflow
Features of the Alert Notification implemented in the project
Three different severity (Critical, Warning, Info)
A drug-diagnosis interaction can have multiple alerts
Consists of summary (mandatory) and details (Optional)
Includes link to the source of information (like Wiki, etc.)
Clinician can choose to override critical alerts by providing justification
Support for recording chief complaints H&E forms using SNOMED CT & Support for designing Bahmni
Users can customise set of questions in Bahmni according to their requirements to record patient’s responses
They can customise the questionnaire under the form builder module
SNOMED CT is leveraged to provide the list of responses to a given question
Once saved and published, the form is used by clinicians to record patient responses
Clinicians can also generate a report on the patients’ responses under reports module
Currently, the form names that can be used for creating forms and reporting the same are: "Test Form", "SNOMED H&E Form", "SNOMED Malaria Form", "SNOMED Asthma Form", "SNOMED COVID Form", "SNOMED Accident Intake Form"
Advantage of using SNOMED
Using SNOMED terms helps in standardising the responses from the patient, so that it can be easily exchanged with other EHR systems, hence improving patient healthcare
Ability to setup and order procedures using SNOMED CT
Users can order SNOMED CT procedures from Bahmni which are grouped by body-sites
There are some pre-requisites to upload the procedures in Bahmni
For the pre-requisite, please follow steps mentioned here
User can view the procedures under the orders tab
User can choose the body-site, for which corresponding SNOMED CT procedures is displayed
User can select one or multiple procedures and save it for the patient
Generate ICD-10 reports based on SNOMED code mappings Phase 2
International Classification of Diseases (ICD) is a coding system developed by WHO.
The WHO requires its member countries to report health indicators and statistics to support its global health monitoring and surveillance activities.
Ensures accuracy and comparability of health data, which is essential for global health policy and decision-making.
Map from SNOMED to ICD-10 exists, hence, generating the ICD-10 report is of great value for both healthcare organisations, and the WHO.
Please see these slides for screenshots of this SNOMED CT to ICD10 Mapping Reporting feature: https://docs.google.com/presentation/d/1q-qCwNxsZd18j-4DaFctb1zJKNnLar97g9H802rye4M/edit?usp=sharing
ICD-10 Workflow
Export anonymised, FHIR based, patient data for SNOMED analytical tool phase 2
Below diagram depicts the implementation of bulk FHIR export in Bahmni-SNOMED engagement
Benefits of bulk FHIR export and SNOMED Analytics Tool
SNOMED Analytics Tool
Integration with the SNOMED Analytics tool enables Bahmni adopters to leverage the
SNOMED CT ontology for analytics and researchUsers can make meaning based selections across patient to generate practical insights
Bulk FHIR Export
Anonymised clinical data can be exported for import into the SNOMED Analytics Tool or to support other research tooling
A full patient data export has also been provided that enables patient data to be transferred between EHRs that are FHIR compliant
Anonymisation has been enabled by default. All exports are protected by privileges
Project Leads
@Vijay Anand Shanmughadass - Tech Lead
@Ketan Goenka - Business Analyst
@Kai Kewley - SNOMED
@Angshuman Sarkar, @Akhil Malhotra , @Gurpreet Luthra - Bahmni Core team support
Slack Communication Channel
Slack Channel: snomed-integration-dev
Reference materials
Release Artefacts
List of Release Artefacts can be found here
Note: In order to try out the features of SNOMED integration with Bahmni in your local environment, please visit our deployment guide here
Code Repos
List of code repos enhanced for SNOMED CT support
Repository Name | URL | Change introduced | |
---|---|---|---|
1 | openmrs-module-snomed | Module that offers FHIR compatible integration with SNOMED terminology server | |
2 | bahmni-core | Plugin extensions for integration with SNOMED terminology services | |
3 | bahmni-reports | Enhance generic and gender-based diagnosis count report to support SNOMED descendant diagnosis | |
4 | snomed-default-config | To manage terminology services configuration | |
5 | snomed-clinic-config | To manage terminology services configuration for clinics in india | |
6 | implementer-interface | Enhance form designer to accommodate new form field for FHIR based SNOMED value set selection | |
7 | form-controls | Enhance coded concept controls to support answers from FHIR based SNOMED value sets | |
8 | openmrs-module-cdss | Module that offers FHIR compatible integration with CDSS server | |
9 | snomed-fhir-cds-service | Forked from https://github.com/IHTSDO/snomed-fhir-cds-service. Offers alerting mechanism for drug-diagnosis contraindications. | |
10 | openmrs-module-bahmniapps | Enhancements to Diagnosis and Medications tab to leverage integration with terminology services and CDSS | |
11 | snomed-bahmni-docker | Docker based deployment for Bahmni SNOMED integration | |
12 | openmrs-distro-bahmni | Encapsulates CDSS and Terminology Services integration features along with other bahmni modules | |
13 | snomed-utilities | Utilities to create SNOMED entities stay here. i.e. Creation of Custom ValueSets |
Architecture Notes (MoM)
https://docs.google.com/document/d/1yzHWbXBZ2yjHT7jBBiji-R8NJ-VXZWTVnGU9_5uJ8iI
Bahmni SNOMED Engagement Blog
https://medium.com/bahmni-blog/bridging-the-gap-in-healthcare-bahmni-snomed-integration-project-f0e8d45e9907
On this page:
- 1 Objective
- 2 Project Scope (1st Phase)
- 3 Phase 2 Scope
- 4 Current Landscape of Bahmni-SNOMED Integration
- 5 Environments for Dev, QA & Demo
- 6 Feature Demo Videos
- 6.1 Recording Diagnosis and Displaying Reports (Video)
- 6.2 CDSS Alert Notification for Drug-Diagnosis Interaction with SNOMED-CT (Video)
- 6.3 COVID-19 Form Designing and Recording Data using SNOMED CT Terms
- 6.4 Procedures Setup in Bahmni using SNOMED CT ValueSet (video)
- 6.5 Generate ICD-10 reports based on SNOMED code mappings (video)
- 7 Feedback
- 8 Features
- 8.1 Record patient diagnosis in Bahmni using SNOMED CT with real time Terminology Search
- 8.2 Reports in Bahmni displaying the power of SNOMED CT
- 8.3 CDSS alert in Bahmni based on recorded SNOMED diagnosis and drug interaction
- 8.4 Support for recording chief complaints H&E forms using SNOMED CT & Support for designing Bahmni
- 8.5 Ability to setup and order procedures using SNOMED CT
- 8.6 Generate ICD-10 reports based on SNOMED code mappings Phase 2
- 8.7 Export anonymised, FHIR based, patient data for SNOMED analytical tool phase 2
- 9 Project Leads
- 10 Slack Communication Channel
- 11 Reference materials
- 12 Release Artefacts
- 13 Code Repos
- 14 Architecture Notes (MoM)
- 15 Bahmni SNOMED Engagement Blog
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