Introduction to All of Us Survey Collection and Data Transformation Methods

Introduction

Within the All of Us Research Program, participant provided information (PPI) is collected via surveys and is meant as a way to augment data collected from other sources such as the electronic health record (EHR). Surveys are developed and deployed following a methodical process which includes prioritization of scientific domains, content creation based on sourcing of items from well-established studies and the literature, pilot evaluation and refinement, and scheduled deployment. Surveys are deployed on the secure online All of Us Participant Portal. Baseline surveys include questions on sociodemographics, health, and lifestyle. Additional surveys on other domains of interest are regularly developed and deployed. You can view survey questions and learn more about their sources by browsing the All of Us Research Hub Survey Explorer.

 

Methods

Beginning at program establishment in May 2017, all participants - whether enrolled through their participating health care providers (HPOs) or not (direct volunteers) - responded to surveys via the All of Us Participant Portal supported by the program’s Participant Technology Support Center (Vibrent Health). Beginning in December 2019, a new version of the Participant Portal, supported by the program’s Participant Center (Scripps University with CareEvolution), was introduced as a pilot approach to enrolling a limited number of direct volunteer participants. 

 

Survey questions and answers are transformed into structural survey metadata and stored and transmitted from the online Participant Portals to the All of Us Data and Research Center’s Raw Data Repository via an artifact referred to as a “survey codebook.” Survey codebooks are created using REDCap data dictionary format and contain not only survey content, but also assigned variables (e.g., codes), branching logic, and field validation rules. Besides serving as the codebook from survey data collection and transmission, resulting REDCap data dictionary artifacts are also made available through the REDCap Consortium’s Shared Library for reuse in other studies. Codebook variables (e.g., source codes) are deposited into the OMOP Common Data Model’s observation table and stored as an AoU specific “PPI” vocabulary. This vocabulary is both browsable and downloadable via Athena, the online OMOP repository.  Survey response data are extracted from the All of Us program’s Raw Data Repository (RDR) and transmitted to the Curated Data Repository (CDR) for the purpose of research-grade dataset creation. Extracted response data are mapped according to the codebook source codes, as well OMOP concept codes and IDs. All survey-specific OMOP concepts are assessed for Registered and Controlled Tier privacy methodology application and resulting decisions are logged and implemented within the corresponding CDRs.

 

Definitions of Survey Relevant Variable Names in OMOP CDM v 5.2.1. 

Variable Name

Definition 

observation _id

A unique identifier for each observation.

person_id

A foreign key identifier to the Person about whom the observation was recorded. The demographic details

of that Person are stored in the PERSON table.

observation_concept_id

A foreign key to the standard observation concept identifier in the Standardized Vocabularies.

observation_date

The date of the observation.

observation_datetime

The date and time of the observation.

observation_type_concept_id

A foreign key to the predefined concept identifier in the

Standardized Vocabularies reflecting the type of the observation.

value_as_number

Survey numeric answers.

value_as_string

Survey free text answers: suppressed by privacy rules. 

value_as_concept_id

OMOP standard concept ID for survey answer, note the code “PMI_SKIP (903096) is applied when a participant was presented with an item and chose not to specify an answer. 

qualifier_concept_id

A foreign key to a Standard Concept ID for a qualifier (e.g., severity of drug-drug interaction alert).

unit_concept_id

A foreign key to a Standard Concept ID of measurement units in the Standardized Vocabularies.

provider_id

A foreign key to the provider in the PROVIDER table who was responsible for making the observation.

visit_occurrence_id

A foreign key to the visit in the VISIT_OCCURRENCE table during which the observation was recorded.

observation_source_value

All of Us question code.

observation_source_concept_id

OMOP concept ID for survey question.

unit_source_value

The source code for the unit as it appears in the source data. This code is mapped to a standard unit concept in the Standardized Vocabularies and the original code is stored here for reference.

qualifier_source_value

The source value associated with a qualifier to characterize the observation.



Inclusion Criteria

With the exception of defined CDR “cut-off” dates and CDR privacy methodology, there are no exclusion factors for the survey response data. In terms of inclusion criteria, participants who met eligibility criteria for the surveys are included in the dataset. 

 

Survey Names, Eligibility Criteria, and Release Date Ranges

Survey 

Sample

Release Date Range

The Basics

Baseline survey, available to all after primary consent completed.

Fielding in process

Lifestyle

Baseline survey, available to all after primary consent & the Basics completed.

Fielding in process

Overall Health

Baseline survey, available to all after primary consent & the Basics completed.

Fielding in process

Personal Medical History (PMH)

Follow up survey, available to all after baseline surveys completed.

Fielding complete. Replaced by combined Personal & Family Health History survey intended for release in future CDR.

Family Health History (FHH)

Follow up survey, available to all after baseline surveys completed.

Fielding complete.Replaced by combined Personal & Family Health History survey intended for release in future CDR. 

Healthcare Access & Utilization (HCAU)

Follow up survey, available to all after baseline surveys completed.

Fielding in process. 

COVID-19 Participant Experience (COPE) - May 2020 version

Available to all after primary consent & the Basics completed for specified timeframe only.

Fielding complete, released May 7, 2020 through May 30, 2020.

COVID-19 Participant Experience (COPE) - June 2020 version

Available to all after primary consent & the Basics completed for specified timeframe only.

Fielding complete, released June 2, 2020 through June 26, 2020. 

COVID-19 Participant Experience (COPE) - July 2020 version

Available to all after primary consent & the Basics completed for specified timeframe only.

Fielding complete, released July 7, 2020 through September 25, 2020. 

COVID-19 Participant Experience (COPE) - November 2020 version

Available to all after primary consent & the Basics completed for specified timeframe only.

Fielding complete, released October 27, 2020 through December 3, 2020. 

COVID-19 Participant Experience (COPE) - December 2020 version

Available to all after primary consent & the Basics completed for specified timeframe only.

Fielding complete, released December 8, 2020 through January 4, 2021. 

COVID-19 Participant Experience (COPE) - February 2021 version

Available to all after primary consent & the Basics completed for specified timeframe only.

Fielding complete, released February 8, 2021 through March 5, 2021. 

Summer 2021 Minute Survey on COVID-19 Vaccines

Available to all after primary consent & the Basics completed for specified timeframe only. Also dependent on February 2021 COPE & Summer 2021 Minute survey response - see COVID-19-related Survey Series Details and Resources for more details.  

Released June 10, 2021 through August 19, 2021.

Fall 2021 Minute Survey on COVID-19 Vaccines

Available to all after primary consent & the Basics completed for specified timeframe only. Also dependent on February 2021 COPE & Summer 2021 Minute survey response - see COVID-19-related Survey Series Details and Resources for more details. 

Released August 19, 2021 through October 28, 2021.

Winter 2021 Minute Survey on COVID-19 Vaccines

Available to all after primary consent & the Basics completed for specified timeframe only. Also dependent on February 2021 COPE & Summer 2021 Minute survey response - see COVID-19-related Survey Series Details and Resources for more details. 

Released October 28, 2021 through January 20, 2022.

Social Determinants of Health

Available to all after primary consent & the baseline surveys are complete

Fielding in process. 



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