1 of 105

CS342/MED253 Building for Digital Health

Lecture 8A (02/22): Data Collection with HealthKit

Vishnu Ravi

Surabhi Mundada

Varun Shenoy

Oliver Aalami

Winter 2022

https://cs342.stanford.edu

cardinalkit.slack.com

Welcome!

2 of 105

What’s new in Digital Health?

Medicare Advantage? Why the growth?

Zero to no premium for patients!

Narrow network

Administered by commercial insurance company

Primary care gatekeeper

CMS pays ~1000/mo to

Insurance company makes ~1,600

Per patient profit (2x employer

3 of 105

Overview for today

- Announcements

- Revisiting HealthKit. How can we use it?

- Quick overview on sensor data

- Data processing tips

https://cs342.stanford.edu

cardinalkit.slack.com

Don’t forget to record lecture 🎬

4 of 105

In-Person Today!! Yay!!

Tuesday 05:30p-07:00p

CCSR Rm 4107

Thursday 05:20p-07:00p

CCSR Rm 4205

5 of 105

Assignment #2 (Jan 27th)

Set up a CardinalKit App with a

Firebase Backend.

Assignment #1: Getting Started (Jan 18th)

Install Xcode & join our GitHub

ResearchKit

Firebase

Assignment #4: Beta App code review (Feb 22nd)

Assignment #3: Midterm Presentation (Feb 10th)

Alpha App demo

Assignment #5: Final Presentation (Mar 10th)

MVP App code review + demo

Due 2/24!

6 of 105

Assignment 4 (Beta Release)

Look at link in syllabus!

Add new feature
Add visualization for study progress
Define a secure set of rules for Firebase
Contact card

Due 2/24/22 (Thursday)

7 of 105

8 of 105

HealthKit is a store of health and fitness data.

pedometer, accelerometer; gyro; etc

Sensors

Hardware

e.g. sleep tracking

Apps

CardinalKit

any iOS app

iPhone AND Apple Watch

9 of 105

HealthKit is a store of health and fitness data.

CardinalKit

any iOS app

Google

Cloud Healthcare API

10 of 105

11 of 105

21st Century Cures Act

Final Rule (March 2020)

Rules to prevent INFORMATION BLOCKING
FHIR standard based APIs for patients to receive health information by 2021
All data elements need to be exposed via API by 2021!
Huge opportunity for third party developers
Patients become stewards of their own health records!

12 of 105

accessing data in HealthKit

use one of three available methods

Direct Access
Queries
Long-Running Queries

13 of 105

https://cs342.stanford.edu

HealthKit Sample

Small playground that you can use to try out different HealthKit queries.

Available via

https://github.com/cs342/HealthKit-Sample

14 of 105

accessing data in HealthKit

use one of three available methods

Direct Access

used for profile information that is rarely updated.

15 of 105

accessing data in HealthKit

use one of three available methods

Direct Access
Queries

everything else with entries over time is queried — from step count, to health records. Returns a snapshot.

16 of 105

accessing data in HealthKit

use one of three available methods

Direct Access
Queries
Long-Running Queries

similar to a query, but with the option to receive a callback when more similar data becomes available.

17 of 105

Getting Authorization from HealthKit

18 of 105

Getting Authorization from HealthKit

19 of 105

HealthKit Data Types

20 of 105

HealthKit Data Types

21 of 105

Getting Authorization from HealthKit

22 of 105

Getting Authorization from HealthKit

23 of 105

HealthKit is a store of health and fitness data.

pedometer, accelerometer, gyro, etc

Sensors

Ext. Wearables

e.g. sleep tracking

Apps

CardinalKit

any iOS app

24 of 105

Getting Authorization from HealthKit

25 of 105

Getting Authorization from HealthKit

26 of 105

Getting Authorization from HealthKit

27 of 105

28 of 105

accessing data in HealthKit

use one of three available methods

Direct Access
Queries
Long-Running Queries

29 of 105

accessing data in HealthKit

use one of three available methods

Direct Access
Queries
Long-Running Queries

30 of 105

accessing data from HK

(1) direct access

31 of 105

accessing data from HK

(1) direct access

32 of 105

accessing data from HK

(1) direct access

33 of 105

accessing data from HK

(1) direct access

34 of 105

accessing data in HealthKit

use one of three available methods

Direct Access
Queries
Long-Running Queries

35 of 105

accessing data from HK

(2) using queries

Sample Query

General-purpose. You will be using these most!

Anchored Query

Only return new/modified elements.

Statistics Query

Quickly find the sum, min, max, or avg of a data set.

Activity Query

Move, exercise, and stand data. Three rings.

Document Query

Useful to find health records!

https://developer.apple.com/documentation/healthkit/hkunit

42 of 105

accessing data from HK

(2) using queries

Anchored Query

Only return new/modified elements.

Statistics Query

Quickly find the sum, min, max, or avg of a data set.

Activity Query

Move, exercise, and stand data. Three rings.

Document Query

Useful to find health records!

More Information

https://developer.apple.com/documentation/healthkit/reading_data_from_healthkit

43 of 105

accessing data from HK

using anchor queries

44 of 105

accessing data from HK

using anchor queries

45 of 105

accessing data from HK

using anchor queries

46 of 105

accessing data from HK

(2) using queries

Statistics Query

Quickly find the sum, min, max, or avg of a data set.

Activity Query

Move, exercise, and stand data. Three rings.

Document Query

Useful to find health records!

55 of 105

accessing data from HK

(2) using queries

Document Query

Useful to find health records!

accessing data from HK

health records 🏥

https://github.com/CardinalKit/CardinalKit/blob/30a8066ba43276f0f685c2be9b595419bec478cf/CardinalKit-Example/CardinalKit/Library/HealthKit/CKHealthRecordsManager.swift#L48

62 of 105

accessing data in HealthKit

use one of three available methods

Direct Access
Queries
Long-Running Queries

63 of 105

accessing data from HK

(3) long queries

Observer Query

Notifies when samples change

Anchored Query

Only return new/modified elements.

Statistics Collection Query

Multiple statistic queries over time

Activity Query

Move, exercise, and stand data. Three rings.

accessing data from HK

(3) long queries

Anchored Query

Only return new/modified elements.

Statistics Collection Query

Multiple statistic queries over time

Activity Query

Move, exercise, and stand data. Three rings.

More Information

https://developer.apple.com/documentation/healthkit/reading_data_from_healthkit

70 of 105

accessing data from HK

(3) long queries

Anchored Query

Only return new/modified elements.

Statistics Collection Query

Multiple statistic queries over time

Activity Query

Move, exercise, and stand data. Three rings.

More Information

https://developer.apple.com/documentation/healthkit/reading_data_from_healthkit

71 of 105

accessing data from HK

using anchor queries

72 of 105

accessing data from HK

(3) long queries

Statistics Collection Query

Multiple statistic queries over time

Activity Query

Move, exercise, and stand data. Three rings.

More Information

https://developer.apple.com/documentation/healthkit/reading_data_from_healthkit

73 of 105

accessing data from HK

(3) long queries

Statistics Collection Query

Multiple statistic queries over time

74 of 105

accessing data from HK

(3) long queries

Activity Query

Move, exercise, and stand data. Three rings.

75 of 105

accessing data in HealthKit

use one of three available methods

Direct Access
Queries
Long-Running Queries

76 of 105

HealthKit is a store of health and fitness data.

pedometer, accelerometer; gyro; etc

Sensors

Hardware

e.g. sleep tracking

Apps

CardinalKit

any iOS app

iPhone AND Apple Watch

77 of 105

pedometer, accelerometer; gyro; etc

Sensors

iPhone AND Apple Watch

78 of 105

See MotionController.swift file in CardinalKit

Sensors & CoreMotion examples

79 of 105

80 of 105

81 of 105

https://developer.apple.com/documentation/coremotion/cmmotionmanager

82 of 105

Compress resulting files (into .zip):

https://github.com/marmelroy/Zip

Convert data in-memory to data on-disk:

https://github.com/silverfoxlabs/csv-export-swift

https://github.com/vigneshuvi/SwiftCSVExport

Send the .zip to the cloud!

(or can send to the iPhone if on Apple Watch)

Data Processing Tips

83 of 105

Data Processing Tips

In both iOS + Watch, use a WCSession to send information from/to.

On the watch, design around limited storage and limited connectivity.

84 of 105

https://developer.apple.com/documentation/watchconnectivity/using_watch_connectivity_to_communicate_between_your_apple_watch_app_and_iphone_app

85 of 105

https://cs342.stanford.edu

BigQuery

86 of 105

https://cs342.stanford.edu

Using BigQuery

https://cloud.google.com/bigquery/docs/loading-data-cloud-storage-csv

87 of 105

https://cs342.stanford.edu

Using BigQuery

Activate the Firestore -> BigQuery Extension https://firebase.google.com/products/extensions/firestore-bigquery-export

88 of 105

https://firebase.google.com/products/extensions/firestore-bigquery-export

89 of 105

https://cs342.stanford.edu

Using BigQuery

Activate the Firestore -> BigQuery Extension https://firebase.google.com/products/extensions/firestore-bigquery-export
Create a schema, follow the steps here to initialize it: https://github.com/firebase/extensions/blob/master/firestore-bigquery-export/guides/GENERATE_SCHEMA_VIEWS.md

90 of 105

https://cs342.stanford.edu

Using BigQuery

Activate the Firestore -> BigQuery Extension https://firebase.google.com/products/extensions/firestore-bigquery-export
Create a schema, follow the steps here to initialize it: https://github.com/firebase/extensions/blob/master/firestore-bigquery-export/guides/GENERATE_SCHEMA_VIEWS.md
Use the gcloud console and run this command to use your schema:

91 of 105

https://cs342.stanford.edu

Using BigQuery

Activate the Firestore -> BigQuery Extension https://firebase.google.com/products/extensions/firestore-bigquery-export
Create a schema, follow the steps here to initialize it: https://github.com/firebase/extensions/blob/master/firestore-bigquery-export/guides/GENERATE_SCHEMA_VIEWS.md
Use the gcloud console and run this command to use your schema: [link]
Query away!

92 of 105

Data Studio

Unlock the power of your data with interactive dashboards

https://support.google.com/datastudio/answer/10043514?hl=en

https://cloud.google.com/bigquery/docs/visualize-data-studio

https://datastudio.google.com/overview

93 of 105

94 of 105

95 of 105

If we have time…

Let’s explore some examples of other ResearchKit applications!

https://cs342.stanford.edu

cs342-aut1920.slack.com

Don’t forget to record lecture 🎬