NIH RECOVER Release Notes

Adult Observational Cohort Study: Dataset Release Notes

June 2024

Adult Observational Cohort Study: Release Notes

Release file: phs003463.v2.p2

This release contains data collected from the NIH RECOVER Adult Cohort Observational Study between October 29, 2021 and March 15, 2024. These data were obtained from 15,204 adult participants (including a sub-cohort of 2,192 pregnant women) attending 122,029 study visits across 79 geographically dispersed enrolling sites. The dataset also includes a description of 822,310 biospecimens collected during baseline and follow-up visits, plus wearable sensor metadata from 2,602 participants in the Digital Health Program. Overall this release comprises approximately 35 million rows of data and a total of 5,278 data elements. Please refer to the accompanying REDCap Codebook for a Data Dictionary organized as a list of all surveys/forms and their respective data fields. Also, please note that this release does not contain any genomic or metabolomic data.

Data De-identification Protocols

The following steps were undertaken to de-identify the dataset:

• Masking of IDs using a randomly assigned number between 1 and 15,204 (number of unique PARTICIPANT_IDs within the Adult cohort data); NOTE: Participant IDs assigned to the previous data release (202309.1) were maintained in the current release.

• Truncation of ZIP codes to 3 digits.

• Truncation of participant date of birth and deceased date to the year.

• Date shifting of all other dates within the data within a range of 1 year.

• Winsorization of Adult Cohort age at enrollment and date of birth information.

• Removal of free text fields that did not have data entry validation in REDCap.

These steps are described in more detail below.

Participant_ID masking

1. Extract PARTICIPANT_IDs from each table within the Adult cohort (currently Answerdata, Biospecimens, Concepts, Demographics, Visits, and Fitbit) and perform de-duplication to ensure uniqueness.

2. Randomly reorder PARTICIPANT_IDs.

3. Create a sequential list of numbers from 1 to the total number of unique PARTICIPANT_IDs (15204) and join that list to the list of randomly reordered unique PARTICIPANT_IDs, creating the ID lookup table.

   • Note: From the previous release, participant IDs were assigned to 14,662 individuals in a random and not contiguous fashion from integers between 1 – 14702, including an excess of 40 integers left unassigned at random. Of those 14,662 individuals, 7 have withdrawn from the study since the previous release and left their previously assigned integers vacant, for a final tally of 14,655 individuals with randomly assigned integers between 1 – 14702 continuing into the current release.

   • For the current release, 549 new participants were added to the study with randomly assigned integers between 14703 – 15251.

4. Add protocol codes as the prefix for randomly assigned Participant IDs.

   • Adult (RA1), Pediatric (RP2), Autopsy (RD3), Congenital (RG4), Caregiver (RC5)

   • Where R=Recover, A and 1 = Adult, P and 2 = Pediatric, D and 3 = Autopsy, G and 4 = Congenital, C and 5 = Caregiver.

5. Merge the ID lookup table with each of the tables in the Adult cohort by PARTICIPANT_ID to attach the masked IDs.

6. Drop the column of original PARTICIPANT_IDs from the merged tables, leaving just the masked ID to uniquely identify participants.

7. VISIT_ID on the Answerdata and Visits tables also contains PARTICIPANT_ID. Drop that portion of the VISIT_ID within the de-identified data, retaining the rest of the VISIT_ID.

Truncation of ZIP Codes

1. Retain a substring of ZIP codes from the first to the third numbers (removing the fourth and fifth numbers).

Truncation of participant date of birth and deceased date

1. Keep a substring of date of birth and deceased date from the first to the fourth characters, corresponding to the year portion of the date.

2. Top capping age at enrollment at 89.

3. Bottom capping date of birth at 1933 or 1934 (based on enrollment date).

NOTE: To maintain compliance with HIPAA Safe Harbor requirements, participant age at enrollment was top-capped at 89 years old, and participant date of birth was bottom capped at either 1933 or 1934, depending on year of enrollment (2022 or 2023). An additional column containing a flag for whether participants had an age over 89 was added to distinguish them from participants whose age is 89. Data from seven participants were affected by this de-identification protocol.

Date shifting (All other dates)

Date shifting of all other dates was performed as follows:

1. Select ENROLL_DATE as the anchor date for each participant.

2. For participants who do not have an ENROLL_DATE, generate a random anchor date within the year of 2023 (2023/01/01 to 2023/12/31).

3. Shift the anchor date to the first day of the year, i.e., 2023/01/01.

4. Calculate the difference in days from the original to the shifted anchor date.

5. Recalculate all other dates by adding that date difference to those dates.

6. Shift all date values within ANSWER_TEXT_VAL on the Answerdata table according to this protocol.

The following table lists specific variables requiring de-identification, and the de-identification protocol that was applied.

Data Table	Variable	De-identification Protocol
Demographics	PARTICIPANT_ID	ID masking with a random number between 1 and 15251
Demographics	ENROLL_DATE	Date shifting
Demographics	ENROLL_INDEX_DATE	Date shifting
Demographics	CROSSOVER_INDEX_DATE	Date shifting
Demographics	DOB	Truncation to year
Demographics	WITHDRAW_DATE	Date shifting
Demographics	DECEASED_DATE	Truncation to year
Demographics	ENROLL_ZIP_CODE	Truncation to 3 digits
Answerdata	PARTICIPANT_ID	ID masking with a random number between 1 and 15251
Answerdata	VISIT_ID	Removal of PARTICIPANT_ID portion of VISIT_ID
Answerdata	ANSWER_TEXT_VAL	Date shifting
Answerdata	DATA_ENTRY_DATE	Date shifting
Biospecimens	PARTICIPANT_ID	ID masking with a random number between 1 and 15251
Biospecimens	COLLECTION_DATE	Date shifting
Visits	VISIT_ID	Removal of PARTICIPANT_ID portion of VISIT_ID
Visits	PARTICIPANT_ID	ID masking with a random number between 1 and 15251
Visits	VISIT_START_DATE	Date shifting
Fitbit	PARTICIPANT_ID	ID masking with a random number between 1 and 15251
Fitbit	SUMMARY_DATE	Date shifting

The following table provides a brief description of the 6 BDC files in this release.

Filename	Rows	Columns	File Size (MB)	Participants
RECOVERAdult_BDC_202403_answerdata_deid.tsv	24,043,845	14	5,887	15,176
RECOVERAdult_BDC_202403_biospecimens_deid.tsv	822,310	12	77	13,460
RECOVERAdult_BDC_202403_concepts_deid.tsv	173,835	8	106	---
RECOVERAdult_BDC_202403_demographics_deid.tsv	15,204	20	3	15,204
RECOVERAdult_BDC_202403_fitbit_deid.tsv	9,889,039	6	1,030	2,602
RECOVERAdult_BDC_202403_visits_deid.tsv	122,029	7	8	15,185
Total	35,066,262	67	7,112

The following table provides a brief description of the biospecimens included in this release.

Collected Biospecimens	Stored Biospecimens
Stool	Stool
Urine	Urine
Nasal/NP swab	Nasal or NP Cells
Oragene 600 – Saliva	Saliva
Serum Separator Tube (SST) – Whole Blood	Serum
Sodium Citrate – Whole Blood	Plasma
PAXgene RNA – Whole Blood	Whole Blood
Cell Preservation Tube (CPT) – Whole Blood	Peripheral Blood Mononuclear Cells (PBMCs)
EDTA – Whole Blood	Plasma White Blood Cells (WBCs)

The following table lists all 85 REDCap forms in the dataset, and the corresponding number of variables/rows of data associated with each form.

FORM_NAME	Total Variables per Form
acth_and_cortisol_test	70,243
adult_delivery_and_outcome_form	5,749
adult_echo_data	6,173
alcohol_and_tobacco	162,890
alcohol_and_tobacco_followup	381,796
assessment_scores	1,866,843
audiometry_survey	1,188
Biospecimens	485,333
bmri_import	39,678
brain_mri_quality_confirmation	2,703
brain_mri_with_gadolinium	23,510
cardiac_mri	789
cardiac_mri_reading_center	51
cardiopulmonary_exercise_testing	3,283
cardiovagal_innervation_testing	638
change_in_symptoms_since_infection	21,439
chest_ct	47,387
chest_ct_reading_center	185
clinical_labs	92,771
Colonoscopy	90
Comorbidities	1,923,579
comprehensive_audiometry	51,936
covid_treatment	191,414
cpet_reading_center	4
Demographics	115,510
Disability	97,810
drc_data	9,909
echocardiogram_with_strain	73,980
electrocardiogram	91,215
electromyography	112
end_of_participation	5,862
endopat_testing	8,164
Enrollment	160,289
facility_sleep_questionnaire_morning_after	416
facility_sleep_questionnaire_night_before	1,640
facility_sleep_study	2,152
Fibroscan	17,927
formal_neuropsychological_testing	12,294
full_ent_examination	1,253
gastric_emptying_study	115
hepatitis_tests	37,936
home_polysomnography_with_ess_and_isi	22,170
home_sleep_assessment	32,266
hsat_data	85,222
long_covid_treatment_trial	90,359
medication_changes	122,181
Medications	64,630
mhp_data	60,104
Mini	83,729
mini_prequestionnaire	4,447
neonatal_delivery_and_outcome_form	3,754
nerve_conduction_study	157
neuropathy_examination	130,245
new_covid_infection	41,621
nih_toolbox	59,473
oral_glucose_test	36,264
pasc_symptoms	7,714,508
pcl5	21,548
pft_reading_center	6,768
pg13r	1,084
plasma_catecholamine_testing	630
Pregnancy	109,716
pregnancy_followup	86,875
psg_data	6,474
psg_quality_summary_form	2,164
pulmonary_function_tests	85,186
recent_covid_treatment	60,207
rehabilitation_testing	82,645
renal_ultrasound	19,464
research_labs	4,012,350
serum_b12_and_methylmalonic_acid	31,639
six_minute_walk_test	101,931
skin_biopsy	131
sleep_reading_center	25,471
social_determinants_of_health	801,331
social_determinants_of_health_followup	678,872
study_termination	96
tier_12_consent_tracking	113,913
tier_1_office_visit	1,719,894
tilt_table_test	636
upsit_smell_test	184,618
vaccine_status	276,537
vision_testing	64,756
visit_form	978,660
wearable_data	1,910
Withdrawal	953
Total Variables	24,043,845

Data Quality

A detailed list of data quality issues found in this dataset is summarized below.

File	Error Type	N Rows
RECOVERAdult_BDC_202403_demographics_deID	1. Missing enroll_date	39
RECOVERAdult_BDC_202403_demographics_deID	2. Missing DOB	82
RECOVERAdult_BDC_202403_biospecimens_deID	3. Data entry error in collection_date, reported as a future event	7
RECOVERAdult_BDC_202403_visits_deID	4. Data entry error in visit_start_date, reported as a future event	17
RECOVERAdult_BDC_202403_fitbit_deID	5. Data entry error in summary_date, reported as a future event	6
RECOVERAdult_BDC_202403_answerdata_deID	6. Data entry error in data_entry_date, reported as a future event	870
RECOVERAdult_BDC_202403_answerdata_deID	7. Tab characters present in CONCEPT_NAME variable, causing issues when reading file as tab-separated values	53
RECOVERAdult_BDC_202403_concepts	8. Concept codes repeated across multiple entries	4

Information for Authors

The RECOVER Initiative is committed to sharing data with the broader research community in a manner that is both timely and transparent. Because the processing required to make the data useful is complex, the following information is offered to inform responsible use of this dataset:

Protocol Complexity

The RECOVER protocol underlying this dataset is complex. It employs a tiered approach to administer certain tests, evaluations, and data collection procedures to specific subsets of participants. The criteria for triggering these tests and other important information are described in the Adult Cohort Study protocol and design publication; these should be considered when analyzing and interpreting the data.

Author Acknowledgements

RECOVER investigators request that publications based on the information in this dataset include the following acknowledgement:

The authors of this publication wish to acknowledge that the data utilized in this study were obtained from RECOVER Adult Cohort dataset version phs003463.v2.p2, supported by 1OT2HL156812-01, OT2HL161847-01, and 1OT2HL161841-01 awards from the NIH. This research was conducted independently of RECOVER, and the authors did not collaborate with RECOVER investigators, patient community or caregiver representatives during the course of this study.

April 2024

Adult Observational Cohort Study: Dataset Release Notes

Release file: phs003463.v1.p1

This release contains subsets of data collected from the NIH RECOVER Adult Cohort Observational Study between October 29, 2021 and September 15, 2023. These data were obtained from 14,662 participants attending 92,355 study visits across 79 geographically dispersed enrolling sites. The dataset also includes an inventory of 611,882 biospecimens collected at various timepoints, wearable sensor data from the digital health program for 195 participants, and a total of 3,175 data elements. Please refer to the RECOVER Data Dictionary/REDCap Codebook for this release for a list of all surveys/forms and their respective data fields.

Data De-identification Protocols

The following steps were undertaken to de-identify the dataset:

• Masking of IDs using a randomly assigned number between 1 and 14702 (number of unique PARTICIPANT_IDs within the Adult cohort data)

• Truncation of ZIP codes to 3 digits

• Truncation of participant date of birth and deceased date to the year

• Date shifting of all other dates within the data within a range of 1 year

• Winsorization of Adult Cohort age at enrollment and date of birth information

• Removal of free text fields that did not have data entry validation in REDCap

These steps are discussed in more detail below.

Participant_ID masking

1. Extract PARTICIPANT_IDs from each table within the Adult cohort (currently Answerdata, Biospecimens, Concepts, Demographics, Visits, and Fitbit) and perform deduplication to ensure uniqueness.

2. Randomly reorder PARTICIPANT_IDs.

3. Create a sequential list of numbers from 1 to the total number of unique PARTICIPANT_IDs (14702) and join that list to the list of randomly reordered unique PARTICIPANT_IDs, creating the ID lookup table.

4. Merge the ID lookup table with each of the tables in the Adult cohort by PARTICIPANT_ID to attach the masked IDs.

5. Drop the column of original PARTICIPANT_IDs from the merged tables, leaving just the masked ID to uniquely identify participants.

6. VISIT_ID on the Answerdata and Visits tables also contains PARTICIPANT_ID. Drop that portion of the VISIT_ID within the de-identified data, retaining the rest of the VISIT_ID.

Truncation of ZIP Codes

1. Retain a substring of ZIP codes from the first to the third numbers (removing the fourth and fifth numbers).

Truncation of participant date of birth and deceased date

1. Keep a substring of date of birth and deceased date from the first to the fourth characters, corresponding to the year portion of the date.

Date shifting (All other dates)

1. Select ENROLL_DATE as the anchor date for each participant.

2. For participants who do not have an ENROLL_DATE, generate random anchor date within the year of 2023 (2023/01/01 to 2023/12/31).

3. Shift the anchor date to the first day of the year, i.e., 2023/01/01.

4. Calculate the difference in days from the original to the shifted anchor date.

5. Recalculate all other dates by adding that date difference to those dates.

6. All date values within ANSWER_TEXT_VAL on the Answerdata table were shifted according to this protocol. The concepts that correspond to date values within the Answerdata table are provided in the file “RECOVERAdult_i2b2_concepts_BDC_dateshift.xlsx”.

Winsorization of participant ages

To maintain compliance with HIPAA Safe Harbor requirements, participant age at enrollment was top-capped at 89 years old, and participant date of birth was bottom capped at either 1933 or 1934, depending on year of enrollment (2022 or 2023). An additional column containing a flag for whether participants had an age over 89 was added to distinguish them from participants whose age is 89. Data from seven participants were affected by this de-identification protocol.

The following table details the variables that were de-identified, and the de-identification protocol that was applied.

Data Table	Variable	De-Identification Protocol
Demographics	PARTICIPANT_ID	ID masking with a random number between 1 and 14702
Demographics	ENROLL_DATE	Date shifting
Demographics	ENROLL_INDEX_DATE	Date shifting
Demographics	CROSSOVER_INDEX_DATE	Date shifting
Demographics	DOB	Truncation to year; bottom capping at 1933 or 1934
Demographics	AGE_AT_ENROLLMENT	Top capping at 89
Demographics	WITHDRAW_DATE	Date shifting
Demographics	DECEASED_DATE	Truncation to year
Demographics	ENROLL_ZIP_CODE	Truncation to 3 digits
Answerdata	PARTICIPANT_ID	ID masking with a random number between 1 and 14702
Answerdata	VISIT_ID	Removal of PARTICIPANT_ID portion of VISIT_ID
Answerdata	ANSWER_TEXT_VAL	Date shifting
Answerdata	DATA_ENTRY_DATE	Date shifting
Biospecimens	PARTICIPANT_ID	ID masking with a random number between 1 and 14702
Biospecimens	COLLECTION_DATE	Date shifting
Visits	VISIT_ID	Removal of PARTICIPANT_ID portion of VISIT_ID
Visits	PARTICIPANT_ID	ID masking with a random number between 1 and 14702
Visits	VISIT_START_DATE	Date shifting
Fitbit	PARTICIPANT_ID	ID masking with a random number between 1 and 14702
Fitbit	SUMMARY_DATE	Date shifting

Included Data

The forms in this release are inclusive of baseline (first) enrollment visits and all subsequent follow-up visits through September 15, 2023. Collectively they represent 8.9 million rows of data (54% of the REDCap data) and were selected as they have a limited number of outstanding data queries (outside of missingness). When combined with the wearable sensor data and biospecimen inventory data, the release includes 10.1 million rows of data.

FORM_NAME	n
alcohol_and_tobacco	156,454
alcohol_and_tobacco_followup	251,039
assessment_scores	1,281,009
covid_treatment	183,355
demographics	110,778
disability	93,956
end_of_participation	3,771
enrollment	154,305
long_covid_treatment_trial	38,801
new_covid_infection	26,366
pasc_symptoms	5,081,366
pregnancy	103,109
pregnancy_followup	54,437
recent_covid_treatment	41,019
social_determinants_of_health	769,434
social_determinants_of_health_followup	445,687
study_termination	96
tier_12_consent_tracking	97,222
visit_form	749
withdrawal	961

Important Information for Authors

The RECOVER Initiative is committed to sharing data with the broader research community in a manner that is both timely and transparent. Because the processing required to make the data useful is complex, the following information is offered to inform responsible use of this dataset:

Data Completeness

This is a partial dataset that includes information on adult cohort participants for whom data were collected on or before September 15, 2023. Additionally, some variables with a high degree of missingness or requiring further quality control have been removed. Future releases will restore these redactions.

Protocol Complexity

The RECOVER protocol underlying this dataset is complex. It employs a tiered approach to administer certain tests, evaluations, and data collection procedures to specific subsets of participants. The criteria for triggering these tests and other important information are described in the Adult Cohort Study protocol and design publication; these should be considered when analyzing and interpreting the data.

Author Acknowledgements

RECOVER investigators request that publications based on the information in this dataset include the following acknowledgement:

The authors of this publication wish to acknowledge that the data utilized in this study were obtained from RECOVER Adult Cohort dataset version phs003463.v1.p1, supported by 1OT2HL156812-01, OT2HL161847-01, and 1OT2HL161841-01 awards from the NIH. This research was conducted independently of RECOVER, and the authors did not collaborate with RECOVER investigators, patient community or caregiver representatives during the course of this study.