The National Health and Nutrition Examination Survey (NHANES) provides data and have considerable potential to study the health and environmental exposure of the non-institutionalized US population. However, as NHANES data are plagued with multiple inconsistencies, processing these data is required before deriving new insights through large-scale analyses. Thus, we developed a set of curated and unified datasets by merging 614 separate files and harmonizing unrestricted data across NHANES III (1988-1994) and Continuous (1999-2018), totaling 135,310 participants and 5,078 variables. The variables conveydemographics (281 variables),dietary consumption (324 variables),physiological functions (1,040 variables),occupation (61 variables),questionnaires (1444 variables, e.g., physical activity, medical conditions, diabetes, reproductive health, blood pressure and cholesterol, early childhood),medications (29 variables),mortality information linked from the National Death Index (15 variables),survey weights (857 variables),environmental exposure biomarker measurements (598 variables), andchemical comments indicating which measurements are below or above the lower limit of detection (505 variables).csv Data Record: The curated NHANES datasets and the data dictionaries includes 23 .csv files and 1 excel file.The curated NHANES datasets involves 20 .csv formatted files, two for each module with one as the uncleaned version and the other as the cleaned version. The modules are labeled as the following: 1) mortality, 2) dietary, 3) demographics, 4) response, 5) medications, 6) questionnaire, 7) chemicals, 8) occupation, 9) weights, and 10) comments."dictionary_nhanes.csv" is a dictionary that lists the variable name, description, module, category, units, CAS Number, comment use, chemical family, chemical family shortened, number of measurements, and cycles available for all 5,078 variables in NHANES."dictionary_harmonized_categories.csv" contains the harmonized categories for the categorical variables.“dictionary_drug_codes.csv” contains the dictionary for descriptors on the drugs codes.“nhanes_inconsistencies_documentation.xlsx” is an excel file that contains the cleaning documentation, which records all the inconsistencies for all affected variables to help curate each of the NHANES modules.R Data Record: For researchers who want to conduct their analysis in the R programming language, only cleaned NHANES modules and the data dictionaries can be downloaded as a .zip file which include an .RData file and an .R file.“w - nhanes_1988_2018.RData” contains all the aforementioned datasets as R data objects. We make available all R scripts on customized functions that were written to curate the data.“m - nhanes_1988_2018.R” shows how we used the customized functions (i.e. our pipeline) to curate the original NHANES data.Example starter codes: The set of starter code to help users conduct exposome analysis consists of four R markdown files (.Rmd). We recommend going through the tutorials in order.“example_0 - merge_datasets_together.Rmd” demonstrates how to merge the curated NHANES datasets together.“example_1 - account_for_nhanes_design.Rmd” demonstrates how to conduct a linear regression model, a survey-weighted regression model, a Cox proportional hazard model, and a survey-weighted Cox proportional hazard model.“example_2 - calculate_summary_statistics.Rmd” demonstrates how to calculate summary statistics for one variable and multiple variables with and without accounting for the NHANES sampling design.“example_3 - run_multiple_regressions.Rmd” demonstrates how run multiple regression models with and without adjusting for the sampling design.

The National Health and Nutrition Examination Survey (NHANES) is designed to assess the health and nutritional status of adults and children in the United States. The survey is unique in that it combines interviews with standardized physical examinations and laboratory tests.
NHANES was conducted on a periodic basis from 1971 to 1994. In 1999 NHANES became continuous. Every year, approximately 5,000 people of all ages are interviewed in their homes and complete the health examination conducted in a mobile examination center.
The NHANES interview includes demographic, socioeconomic, dietary, and health-related questions. The examination component consists of medical, dental, and physiological measurements, as well as the collection of biospecimens, such as blood and urine for laboratory testing.

This set of restricted data contains indirect identifying and/or sensitive information collected in continuous NHANES since 1999. Please refer to the links below for additional data available from NHANES:

• NHANES Public Use Data at: https://wwwn.cdc.gov/nchs/nhanes/Default.aspx
• NHANES Genetic Restricted Data at: https://data.cdc.gov/dataset/National-Health-and-Nutrition-Examination-Survey-N/hdx4-e4uu
• NHANES Restricted Data: Prior to 1999 at: https://data.cdc.gov/dataset/National-Health-and-Nutrition-Examination-Survey-N/ic32-yq9m
• NHANES National Youth Fitness Survey (NNYFS) Restricted Data at: https://data.cdc.gov/dataset/3-NHANES-National-Youth-Fitness-Survey-NNYFS-Restr/5u84-m4rs

The National Health and Nutrition Examination Survey (NHANES) provides data and have considerable potential to study the health and environmental exposure of the non-institutionalized US population. However, as NHANES data are plagued with multiple inconsistencies, processing these data is required before deriving new insights through large-scale analyses. Thus, we developed a set of curated and unified datasets by merging 614 separate files and harmonizing unrestricted data across NHANES III (1988-1994) and Continuous (1999-2018), totaling 135,310 participants and 5,078 variables. The variables convey 1. demographics (281 variables), 2. dietary consumption (324 variables), 3. physiological functions (1,040 variables), 4. occupation (61 variables), 5. questionnaires (1444 variables, e.g., physical activity, medical conditions, diabetes, reproductive health, blood pressure and cholesterol, early childhood), 6. medications (29 variables), 7. mortality information linked from the National Death Index (15 variables), 8. survey weights (857 variables), 9. environmental exposure biomarker measurements (598 variables), and 10. chemical comments indicating which measurements are below or above the lower limit of detection (505 variables).

csv Data Record: The curated NHANES datasets and the data dictionaries includes 23 .csv files and 1 excel file. - The curated NHANES datasets involves 20 .csv formatted files, two for each module with one as the uncleaned version and the other as the cleaned version. The modules are labeled as the following: 1) mortality, 2) dietary, 3) demographics, 4) response, 5) medications, 6) questionnaire, 7) chemicals, 8) occupation, 9) weights, and 10) comments. - "dictionary_nhanes.csv" is a dictionary that lists the variable name, description, module, category, units, CAS Number, comment use, chemical family, chemical family shortened, number of measurements, and cycles available for all 5,078 variables in NHANES. - "dictionary_harmonized_categories.csv" contains the harmonized categories for the categorical variables. - “dictionary_drug_codes.csv” contains the dictionary for descriptors on the drugs codes. - “nhanes_inconsistencies_documentation.xlsx” is an excel file that contains the cleaning documentation, which records all the inconsistencies for all affected variables to help curate each of the NHANES modules.

R Data Record: For researchers who want to conduct their analysis in the R programming language, only cleaned NHANES modules and the data dictionaries can be downloaded as a .zip file which include an .RData file and an .R file. - “w - nhanes_1988_2018.RData” contains all the aforementioned datasets as R data objects. We make available all R scripts on customized functions that were written to curate the data. - “m - nhanes_1988_2018.R” shows how we used the customized functions (i.e. our pipeline) to curate the original NHANES data.

Example starter codes: The set of starter code to help users conduct exposome analysis consists of four R markdown files (.Rmd). We recommend going through the tutorials in order. - “example_0 - merge_datasets_together.Rmd” demonstrates how to merge the curated NHANES datasets together. - “example_1 - account_for_nhanes_design.Rmd” demonstrates how to conduct a linear regression model, a survey-weighted regression model, a Cox proportional hazard model, and a survey-weighted Cox proportional hazard model. - “example_2 - calculate_summary_statistics.Rmd” demonstrates how to calculate summary statistics for one variable and multiple variables with and without accounting for the NHANES sampling design. - “example_3 - run_multiple_regressions.Rmd” demonstrates how run multiple regression models with and without adjusting for the sampling design.

The National Health and Nutrition Examination Survey (NHANES) is a population survey implemented by the Centers for Disease Control and Prevention (CDC) to monitor the health of the United States whose data is publicly available in hundreds of files. This Data Descriptor describes a single unified and universally accessible data file, merging across 255 separate files and stitching data across 4 surveys, encompassing 41,474 individuals and 1,191 variables. The variables consist of phenotype and environmental exposure information on each individual, specifically (1) demographic information, physical exam results (e.g., height, body mass index), laboratory results (e.g., cholesterol, glucose, and environmental exposures), and (4) questionnaire items. Second, the data descriptor describes a dictionary to enable analysts find variables by category and human-readable description. The datasets are available on DataDryad and a hands-on analytics tutorial is available on GitHub. Through a new big data platform, BD2K Patient Centered Information Commons (http://pic-sure.org), we provide a new way to browse the dataset via a web browser (https://nhanes.hms.harvard.edu) and provide application programming interface for programmatic access.

This dataset was created to be the base of the data.world SQL tutorial exercises. Data was genererated using Synthea, a synthetic patient generator that models the medical history of synthetic patients. Their mission is to output high-quality synthetic, realistic but not real, patient data and associated health records covering every aspect of healthcare. The resulting data is free from cost, privacy, and security restrictions, enabling research with Health IT data that is otherwise legally or practically unavailable. De-identified real data still presents a challenge in the medical field because there are peopel who excel at re-identification of these data. For that reason the average medical center, etc. will not share their patient data. Most governmental data is at the hospital level. NHANES data is an exception.

You can read Synthea's first academic paper here.

Original Data

Acknowlegement

Foto von Rubaitul Azad auf Unsplash

This database was developed with support from the Office of Dietary Supplements, National Institutes of Health for flavonoid intake studies. The database is a useful tool for flavonoid intake and health outcome studies for any population globally. It contains data for 29 individual flavonoid compounds in six subclasses of flavonoids for every food in a subset of 2,926 food items which provide the basis for the Food and Nutrient Database for Dietary Studies (FNDDS 4.1). Proanthocyanidins data are not included at the present time. For flavonoid intake data for the U.S. population based on NHANES 2007-08, please refer to the Food Surveys Research Group website. Resources in this dataset:Resource Title: READ ME - USDA’s Expanded Flavonoid Database for the Assessment of Dietary Intakes Documentation and User Guide. File Name: FDB-EXP.pdfResource Description: Information regarding documentation, development of the database, limitations, format, and references.Resource Software Recommended: Adobe Acrobat Reader,url: http://www.adobe.com/prodindex/acrobat/readstep.html Resource Title: Data Dictionary. File Name: FDB_EXP_DD.pdfResource Title: FDB-EXP_R01-1.accdb. File Name: FDB-EXP_R01-1.accdb_.zipResource Description: This file contains USDA's Expanded Flavonoid Database for the Assessment of Dietary Intakes imported into a MS Access database version 2007 or later. The file structure is the same as that of the USDA National Nutrient Database for Standard Reference.