Kalyan Pamarthy & Dharmesh Patel, Google Cloud Healthcare · 2020. 12. 1. · Kalyan Pamarthy &...
Transcript of 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
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
Cloud Healthcare FHIR APIs
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
Cloud Healthcare FHIR APIs
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
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
https://github.com/GoogleCloudPlatform/healthcare-data-harmonization
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3. Google Cloud Healthcare - FHIR De-identification
Proprietary + Confidential
Proprietary + Confidential
Raw FHIR data
Analytics
Secure sharing
AI/ML training and prediction
DelDRedacted FHIR data
Evaluation and validation
Proprietary + Confidential
Proprietary + Confidential
Original (FHIR) record De-identified FHIR record
Proprietary + Confidential
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
Proprietary + Confidential
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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
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
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
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
MLLP Adapter1 HL7v2 Store
Cloud Pub/Sub
Cloud Dataflow2
FHIR Store
HL7v2 HL7v2 HL7v2 FHIR
Simulated EHR
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De-identify FHIR Store
A.Configure FHIR API 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
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
A.Configure FHIR API 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
FHIR Store
:export
$export
BigQuery
Cloud Storage
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Analyze Data using Looker
A.Configure FHIR API in
Google Cloud
B. Ingest HL7v2 Data in
FHIR Store
C.De-identify FHIR Store
D.Stream Data to
BigQuery
E.Analyze
Data using BigQuery & Looker
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
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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]