SNOMED FHIR Terminology Server Integration with Bahmni

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)

1. Record patient diagnosis in Bahmni using SNOMED CT with real time Terminology Search - DIAGNOSIS

2. Reports in Bahmni displaying the power of SNOMED CT- DIAGNOSIS REPORTS

3. CDSS alert in Bahmni based on recorded SNOMED diagnosis and drug interaction - CDSS

4. Support for recording chief complaints H&E forms using SNOMED CT & Support for designing Bahmni - FORM BUILDER

Phase 2 Scope

1. Generate ICD-10 reports based on SNOMED code mappings - ICD-10 Reporting

2. Export anonymised, FHIR based, patient data for SNOMED analytics tool - Bulk Export for Analytics Tool

3. CDSS alert in Bahmni based on drug-drug interaction (possibly with DrugBank) - CDSS

4. Implementation of micro FHIR terminology server for low resource settings (include Contract Tests) - Micro FHIR

5. Ability to setup and order procedures using SNOMED CT- PROCEDURES

6. 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

1. Clinicians can search for SNOMED terms for diagnosis or conditions

2. Upon providing keywords, Bahmni performs real time search in SNOMED CT and displays search results

3. Clinicians can also provide the SNOMED Code to search for a diagnosis in Bahmni

4. 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

5. 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

1. Clinicians can generate diagnosis count reports based on SNOMED terms

2. Report feature can be accessed under the report module in Bahmni

3. Clinicians need to select the duration for the report and mode of display

4. 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

1. In this feature, the clinicians are notified with an alert when Drug-Diagnosis interaction is contraindicated

2. 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

3. Clinicians can accept the alert and make changes to medication or

4. 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

1. Three different severity (Critical, Warning, Info)

2. A drug-diagnosis interaction can have multiple alerts

3. Consists of summary (mandatory) and details (Optional)

4. Includes link to the source of information (like Wiki, etc.)

5. 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

1. Users can customise set of questions in Bahmni according to their requirements to record patient’s responses

2. They can customise the questionnaire under the form builder module

3. SNOMED CT is leveraged to provide the list of responses to a given question

4. Once saved and published, the form is used by clinicians to record patient responses

5. Clinicians can also generate a report on the patients’ responses under reports module

6. 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

1. Users can order SNOMED CT procedures from Bahmni which are grouped by body-sites

2. There are some pre-requisites to upload the procedures in Bahmni

3. For the pre-requisite, please follow steps mentioned here

4. User can view the procedures under the orders tab

5. User can choose the body-site, for which corresponding SNOMED CT procedures is displayed

6. User can select one or multiple procedures and save it for the patient

Generate ICD-10 reports based on SNOMED code mappings Phase 2

1. International Classification of Diseases (ICD) is a coding system developed by WHO.

2. The WHO requires its member countries to report health indicators and statistics to support its global health monitoring and surveillance activities.

3. Ensures accuracy and comparability of health data, which is essential for global health policy and decision-making.

4. Map from SNOMED to ICD-10 exists, hence,  generating the ICD-10 report is of great value for both healthcare organisations, and the WHO.

5. 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

All the bulk FHIR resources are exported in NDJSON format

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 research

• Users 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

• Mini Inception Mural Link (SNOMED-Bahmni)

• Jira Board

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

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

1. https://bahmni.atlassian.net/wiki/spaces/BAH/pages/3176333313

2. [Discussion] Bahmni/OpenMRS using SNOMED CT as source (vs CIEL)?