201901 FHIR Storage and Analytics

Community:

• Zulip Analytics stream

Previous tracks:

• 2018-05

Track Name

FHIR Storage & Analytics ([1])

FHIR foundation project

Track Overview

With this track we want to put together people, which are interested in implementation and usage of FHIR persistence layer, implementing FHIR servers on top and analysing FHIR data.

We hope this group can produce useful feedback for FHIR community and potentially propose new aspects for standard - like SQL on FHIR or FHIRPath for databases.

Another goal is to collect solutions and best practices to store and query FHIR data, using popular databases.

Please fill out: TODO [TODO Track Registration Spreadsheet]

Justification

Initial set of questions to be answered or discussed

• How to store FHIR data and do analytics?
• What is database schema design?
• SQL (as common query language) on FHIR
• FHIR data representation for storage
• FHIRPath subset for databases
• Initial Import and sync of data
• Integration with Bulk API

Proposed Track Lead

Nikolai Ryzhikov

Participants

• Patrik Sundberg (Google)
• Kenny Blanchette (Athena Health)
• Nikolai Ryzhikov & Mike Lapshin (Health Samurai)
• Shantha Andrews
• ADD YOURSELF!

Roles

• Database Provider: provides access to database with FHIR data
• Database User: design queries

Discussions

SQL on FHIR

Initial notes for creating a standard representation of FHIR that is directly usable in scalable SQL-based systems.

Original document by Ryan Brush - https://docs.google.com/document/d/1IPyI-4GYlF400vmZvrtjDYL6jauHdjeLfjGJMo6yWtA/edit#heading=h.ch8y6lqurlaj

Github repo - https://github.com/rbrush/sql-on-fhir/blob/master/sql-on-fhir.md

FHIR data representation in database

JSON and other JSON like formats like yaml, edn, avro, protobuf are very popular in avantе-garde of programmers, some modern databases now could understad JSON as first-class data-structures, that’s why we think, good design for it is strictly required for FHIR adoption.

Original github - https://github.com/fhir-fuel/fhir-fuel.github.io/issues

FHIRPath subset for databases

It worth to discuss subset of FHIRPath, which is implementable in databases

Issue to discuss - https://github.com/fhir-fuel/fhir-fuel.github.io/issues/10

Scenarios

Scenario: Bulk Loader

Implement and demonstrate bulk loader script for your specific database.

• Provide Bulk Loader for your specific database to easily and efficiently load data from FHIR server thro Bulk API into db.
• Loader for Mitre Synthea (https://github.com/synthetichealth/synthea) - where source is file system as synthea generate.
• Loader for FHIR examples - zipped dir of resources and bundles in json

Test-Drive fist implementations

• Bunsen Project (https://github.com/cerner/bunsen)
• BiqQuery and Health API (https://github.com/google/fhir/tree/master/examples/bigquery)
• fhirbase PostgreSQL (https://www.health-samurai.io/fhirbase)

Discussion at https://github.com/fhir-fuel/fhir-storage-and-analytics-track/issues/6