dictionary: A data dictionary describing dbGaP metadata variables

In waldronlab/HMP16SData: 16S rRNA Sequencing Data from the Human Microbiome Project

A data dictionary describing dbGaP metadata variables

Description

A data dictionary containing descriptions of the metadata variables attached using the attach_dbGaP method, as translated from dbGaP XLM data dictionary files.

Usage

dictionary

Format

A data.frame with 789 rows and 8 variables:

VARIABLE

The name of the variable as it appears in SummarizedExperiment colData

DESCRIPTION

A description of the variable

TYPE

The type of variable, as specified by dbGaP

UNITS

The units of the variable (e.g. days)

MINIMUM

The smallest possible value of the variable

MAXIMUM

The largest possible value of the variable

CODED_VALUES

The encoding of coded categorical variables, if needed

COMMENT

Any comments from dbGaP, most pertain to gated fields

Source

The following dbGaP XLM data dictionary files were used to construct the data dictionary.

Data dictionary for data table pht001185.v4.p1: https://tinyurl.com/y7rgelao. No description provided by dbGaP.

Data dictionary for data table pht001193.v3.p1: https://tinyurl.com/y7at85tv. The data table contains subject data with sample information for the Global Trace Screen (GTV). Variables include the specimen type (based on 18 specimens from 6 body sites), nucleic extraction method, and sample administrative information. The Global Trace dataset will be updated when additional visits or subjects have been added.

Data dictionary for data table pht002157.v1.p1: https://tinyurl.com/y7af3arf. The Targeted Physical Forms (DTP), Medical History Screening Forms (DHX), and the Visit Documentation Forms (DVD) have been combined into a single data table. The DTP variables include measurements collected for blood pressure, pulse, body weight, height, and BMI. Variables also include physical assessment of areas/systems and the specific details of the abnormalities. Areas/Systems consist of general appearance, HEENT, cardiovascular, pulmonary, abdomen, neurological, musculoskeletal, and extremities. The DHX variables include data that indicate whether the subject noted medical problems in various areas/systems and the indications and specifications of medical problems. Areas/Systems consist of HEENT, cardiovascular, pulmonary, GI, hepatobiliary, renal, neurologic, blood lymphatic, endocrine/metabolic, musculoskeletal, genital/reproductive, dermatologic, allergies, cancer, immunodeficiency, drug or alcohol dependence, and autoimmune disease. Data were also collected for relevant medical or surgical history, medical abnormality with ongoing treatment and presence of acute disease. The DVD variables include education level, insurance status, occupation status, tobacco usage, and visit-specific information. This visit-specific information pertains to subject's oral temperature, pregnancy test results, education level, insurance status, occupation, and if blood and GI specimens were collected. DTP, DHX and DVD data will be collected at each visit though not every variable was collected.

Data dictionary for data table pht001187.v3.p1: https://tinyurl.com/ych4wywl. The data table contains data that were collected from the Concomitant Medications Form (DCM). Variables include medication number and code, indication, if the medication is ongoing, and the duration of the medication.

Data dictionary for data table pht001184.v3.p1: https://tinyurl.com/y9hwfn9e. The data table contains the subject and consent group information.

Data dictionary for data table pht002158.v1.p1: https://tinyurl.com/y7jtghxv. The Demographics Form (DEM) and the Eligibility Checklist (ENR) have been combined into a single data table. The DEM variables include sociodemographic measurements such as gender, ethnicity, race, and place of birth, while the ENR variables include the enrollment/first sampling time of subjects (n=1 variable) and administrative variables (n=4 variables). Both the Medical History and Targeted Physical exams must be completed prior to the completion of the Exclusion Criteria found in the ENR form. Data derived from the Medical History (DHX) and Targeted Physical (DTP) exams can be found in EMMES_HMP_DTP_DHX_DVD dataset.

Data dictionary for data table pht002156.v1.p1: https://tinyurl.com/y7znjmak. The data table contains data that were collected from the Suppplemental Questions Form (DSU) upon the completion of HMP study enrollment. Variables include additional health history such as dietary habits, breastfeeding, birthing history, delivery method, and if the subject failed any initial screenings prior to enrollment.

See Also

attach_dbGaP

Examples

head(dictionary)

waldronlab/HMP16SData documentation built on Oct. 26, 2023, 5:42 a.m.