kalyan pamarthy & dharmesh patel, google cloud healthcare · 2020. 12. 1. · kalyan pamarthy...

HL7 FHIR DevDays 2020, Virtual Edition, November 17–20, 2020 | @FirelyTeam | #fhirdevdays | www.devdays.com/november-2020

HL7®, FHIR® and the flame Design mark are the registered trademarks of Health Level Seven International and are used with permission.

Google Cloud FHIR APIs: Data Ingestion, Management, and Analytics

Kalyan Pamarthy & Dharmesh Patel, Google Cloud Healthcare

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About us

Kalyan Pamarthy Product Manager

Google Cloud Healthcare API

Dharmesh PatelSolutions Manager

Google Cloud Healthcare API

● Learn about the Google Cloud Healthcare API & Managed FHIR capabilities

● Preview recently launched features - OSS and Managed APIs

● See Managed FHIR capabilities in action!

Cloud Healthcare API

● Leveraging Synthetic Data to Benchmark a Cloud-Based FHIR APIOnix

Friday, Nov 20th, 2:00 pm-2:45 pm ET

● Let’s Build! Google Cloud FHIR APIs Thursday, Nov 19th, 5:15 pm-6:00 pm CET

● Building FHIR Analytics and AI ApplicationsThursday, Nov 19th, 5:15 pm-5:35 pm CET

● FHIR Analytics using OHDSI Tools on CloudThursday, Nov 19th, 5:40 pm-6:00 pm CET

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1. Google Cloud Healthcare - FHIR APIs

Accelerate your healthcare solution development

Healthcare API

● Primary API surface for healthcare specific data management in the Google Cloud Platform.

● Fully managed, Standards based serverless, REST APIs○ FHIR (DSTU2, STU3 and R4)○ HL7v2○ DICOM

● Value add capabilities (e.g De-Identification, Data Transformation, NLP)● Stores PHI data in compliance with regulations (e.g HIPAA)● Integrated with other Google Cloud applications (e.g BigQuery)● Integrated with Google Cloud components (e.g Cloud PubSub, Cloud Functions)

● Support for Smart on FHIR Apps with Apigee API Management

cloud.google.com/healthcare

Generally Available + new features in Preview

https://cloud.google.com/healthcare

Cloud Healthcare FHIR APIs

Supported FHIR Versions ● DSTU2, STU3 & R4 Support

Import & Export● Import and Export FHIR resources in ndJSON from/to Google Cloud

Storage● Export to BigQuery - Streaming and Batch

Standard FHIR CRUD ● Resource Create/Read/Update/Patch/History/Delete Operations

Advanced FHIR Operations

● FHIR Search● Patient $Everything● Execute Bundle (Batch & Transaction)

Notifications ● Pub/Sub notifications on changes to FHIR server

De-identification ● Standard and custom configurations to de-identify FHIR resources


IG Support & Profiles

● Configure and validate structured definitions ● Configure and validate IGs such as US Core, CARIN and DaVinci profiles

Bulk Data ● $ export (System Level) with _type and _since

Conditional Update/Delete

● Conditionally update and delete FHIR resources that match a search query

Observation Last$n

● Retrieves the N most recent Observation resources for a subject matching search criteria specified as query parameters

New

New

Terminology $translate

● Translates a code from one value set to another using a concept map, or user provided concept maps to translate any code system to another code

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2. Google Cloud Healthcare - Data Transformation


CCD to FHIR ● Transform CCD XML documents to FHIRhttps://github.com/GoogleCloudPlatform/healthcare-data-harmonization/tree/master/mapping_configs/cda_fhir_r4

DICOM to FHIR ● Transform DICOM studies to FHIRhttps://github.com/GoogleCloudPlatform/healthcare-data-harmonization/tree/master/mapping_configs/dicom_fhir_r4

HL7v2 to FHIR ● Transform HL7v2 messages to FHIRhttps://github.com/GoogleCloudPlatform/healthcare-data-harmonization/tree/master/mapping_configs/hl7v2_fhir_r4

New

New

https://github.com/GoogleCloudPlatform/healthcare-data-harmonization

https://github.com/GoogleCloudPlatform/healthcare-data-harmonization/tree/master/mapping_configs/cda_fhir_r4

https://github.com/GoogleCloudPlatform/healthcare-data-harmonization/tree/master/mapping_configs/dicom_fhir_r4

https://github.com/GoogleCloudPlatform/healthcare-data-harmonization/tree/master/mapping_configs/hl7v2_fhir_r4


Transformation library

{ "segmentId": "XAD", "fields": { "1": "55 Fruit Street", "2": "Massachusetts General Hospital", "3": "Boston", "4": "MA", "5": "02114", "6": "USA", "7": "Work", "8": "Other geographic designation", "9": "100" }}

{ "use": "Work", "text": "55 Fruit Street Massachusetts General Hospital Boston MA 02114 USA", "line": [ "55 Fruit Street" ], "city": "Boston", "district": 100, "state": "MA", "zipCode": "02114", "country": "USA", "type": "physical"}

Supports repeated and nested structures,terminology mapping, unit harmonization, clinical entity extraction, user-defined functions

use: XAD.7text: " ", XAD.1, XAD.2, XAD.3, XAD.4,

XAD.5, XAD.6 => _StrJoin

line: XAD.1 => _ListOf

city: XAD.3

district: XAD.9

state: XAD.4

zipCode: XAD.5

country: XAD.6

type: "physical"

Whistle mapping config

Sample maps:- HL7v2 to FHIR for ADT_A01

and ORU_R01 initially- FHIR to OMOP- OMOP to FHIR- CCD to FHIR

FHIR Import API

FHIR Export API

HL7v2 → FHIR API

Cloud Healthcare

Whistle config

Cloud Healthcare

Healthcare API Cloud Data Fusion OSS Dataflow

Cloud Storage

Cloud Healthcare

Whistle config

Cloud Healthcare BigQuery

Whistle config

Fully managed, cloud-native data integration service for building and managing ETL and ELT data pipelines.

With a graphical interface and a broad open source library of preconfigured connectors and transformations, Cloud Data Fusion shie s an organization’s focus away from code and integration to insights and action.

Reference Cloud Dataflow (Apache Beam) pipeline to converting streaming HL7v2 messages to FHIR resources



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3. Google Cloud Healthcare - FHIR De-identification

Proprietary + Confidential


Raw FHIR data

Analytics

Secure sharing

AI/ML training and prediction

DelDRedacted FHIR data

Evaluation and validation


Original (FHIR) record De-identified FHIR record


Leverage the Google Cloud Healthcare

API serverless capabilities to receive

ADT, ORU, ORM & MDM messages,

transform to FHIR and project into

BigQuery for analytics at scale (circa

2M messages per day):-

HL7 > FHIR > BigQuery > Looker

All components running in Google

Cloud, with multiple (5) feeds from HL7

interface engines. Processing 1000

messages per minute through the data

pipeline.

Project deployed (from start to finish) in 3 weeks

COVID monitoring dashboards available for C-Suite

Drill down : Health System > Hospital > Unit > Patient

Data latency circa 2-3 minutes


1

2 replace sensitive data with a fixed character, ex. “John” > “****”

3 replace input with a category label, ex. “John” > “[NAME]”

4 shie by a random number of days, with the option to maintain chronological order between dates belonging to the same patient or population

5 replace input with a hashed value generated using a (customer-defined) encryption key

Demo time!

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Ingest, Manage and Analyze Healthcare Data using FHIR

A.Configure

FHIR Server in Google

Cloud

B. Ingest HL7v2 Data in

FHIR Store

C.De-identify FHIR Store

D.Export Data to GCS &

BigQuery

E.Analyze

Data using BigQuery & Looker

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Configure FHIR API in Google Cloud

2 Import

Impl. Guide

3 Enable

Impl. Guide

1Create FHIR

Store

4 Ingest FHIR

Data

5Browse

FHIR Data

A.Configure


Cloud


FHIR Store



BigQuery

E.Analyze


curl -X GET \

-H "Authorization: Bearer $(gcloud auth print-access-token)" \

"https://healthcare.googleapis.com/v1alpha2/projects/ha-portal/locations/us-central1/datasets/default-dataset/fhirStores/default-fhir-store"

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Ingest HL7v2 data in FHIR Store

1. https://github.com/GoogleCloudPlatform/mllp2. https://github.com/GoogleCloudPlatform/healthcare-data-harmonization-dataflow3. https://github.com/GoogleCloudPlatform/healthcare-data-harmonization/tree/master/mapping_configs/hl7v2_fhir_r4

A.Configure


Cloud


FHIR Store



BigQuery

E.Analyze


MLLP Adapter1 HL7v2 Store

Cloud Pub/Sub

Cloud Dataflow2

FHIR Store

HL7v2 HL7v2 HL7v2 FHIR

Simulated EHR

https://github.com/GoogleCloudPlatform/healthcare-data-harmonization/tree/master/mapping_configs/hl7v2_fhir_r4

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De-identify FHIR Store

A.Configure FHIR API in

Google Cloud


FHIR Store



BigQuery

E.Analyze


FHIR Store(FHIR Data with PII/PHI)

FHIR Store(De-identified FHIR Data)

De-identify

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Export Data to Cloud Storage & BigQuery


Google Cloud


FHIR Store



BigQuery

E.Analyze


FHIR Store

:export

$export

BigQuery

Cloud Storage

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Analyze Data using Looker


Google Cloud


FHIR Store


D.Stream Data to

BigQuery

E.Analyze


BigQuery Looker

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Let’s Build! on Thursday

1. Submit a request for the Google Cloud Sandbox environment (QwikLab) at bit.ly/google-cloud-fhir

2. You will receive instructions to access the Google Cloud Sandbox Environment (QwikLab)

3. During the Let’s Build, we will walk through setting up a Cloud FHIR server and using FHIR APIs with synthetic data

4. Follow along and ask questions!

Let’s Build: Google Cloud FHIR APIs Thursday, Nov 19th, 5:15pm - 6pm CET

http://bit.ly/google-cloud-fhir

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Email us or find us on Zulip to chat about FHIR@Google

Kalyan Pamarthy Product Manager

Google Cloud Healthcare [email protected]

Dharmesh PatelSolutions Manager

Google Cloud Healthcare [email protected]

mailto:[email protected]

mailto:[email protected]

kalyan pamarthy & dharmesh patel, google cloud healthcare · 2020. 12. 1. · kalyan pamarthy...

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