This repository contains files used to curate the metadata associated with BioLINCC studies for search in BioData Catalyst Powered by PIC-SURE. The final output of this process is a JSON file containing information about the study, forms, and variables. The table below describes the general format of these JSON files.
| Level | Info | Name in JSON | Info in JSON |
|---|---|---|---|
| Study-level | Study abbreviation | study | Abbreviation of the study |
| Study name | study_name | Full name of the study | |
| Study phs number | study_phs_number | PHS number of the study | |
| Study description or link | study_url | For BioLINCC, this will be a link to the main dbGaP page of the study | |
| Study metadata | study_metadata | Any additional information to include at the study level | |
| Form group level | Form group-level name | form_group | Name of the following level of JSON |
| Group name of forms | form_group_name | Name of the form group | |
| Form group description | form_group_description | Description association with the form group | |
| Form group metadata | form_group_metadata | Any additional information to include at the form group level | |
| Form-level | Form-level name | form | Name of the following level of JSON |
| Form name | form_name | Name/number of the form | |
| Form description | form_description | Description of the form | |
| Data file name | data_file_name | Name of the file corresponding to the data in SAS or otherwise (from MEMNAME column) | |
| Form/file metadata | form_metadata | Any additional information to include at the form level | |
| Variable group. | Variable group-level name | variable_group | Name of the following level of JSON |
| Variable group name | variable_group_name | Name of the variable group | |
| Variable group description | variable_group_description | Description of the variable group | |
| Variable group metadata | variable_group_metadata | Any additional information to include at the variable group level | |
| Variable-level | Variable level name | variable | Name of the following level of JSON |
| Variable id | variable_id | Encoded name of the variable found in the data | |
| Variable name | variable_name | Decoded name of the variable. If multiple decoded names found, select one. (For example: in REDCORAL, if SAS decoded name is present, use SAS decoded name, else use datadictionary name) | |
| Type of variable | variable_type | Categorical, continuous, or unknown. Transformed from SAS output | |
| Variable-level metadata | Variable level metadata name | variable_metadata | Name of following level of JSON |
| Data dictionary label | variable_label_from_data_dictionary | Decoded name of the variable found in data dictionary or other documentation | |
| Data file label | variable_label_from_data_file | Decoded name of the variable found in the SAS files | |
| Variable description | variable_description | Description about the variable |
For example, the JSON file could look like this:
[{
"study":"STUDY ONE",
"study_name":"Full Name of Study One (STUDY ONE)",
"phs_number":"phs000000",
"study_description":"link_to_dbGaP_study_one",
"study_metadata":[{
"some..":"information…"
}],
"form_group":[{
"form_group_name":"Group one of forms",
"form_group_description":"Description about group one of forms from STUDY ONE",
"form_group_metadata":[{
"some..":"information.."
}],
"form":[{
"form_name":"Form 1",
"form_description":"Description of Form 1 from group one of forms of STUDY ONE",
"data_file_name":"name_of_corresponding_data_file",
"form_metadata":[{
"some..":"information.."
}],
"variable_group":[{
"variable_group_name":"Variable group 1",
"variable_group_description":"Description of variable group 1 from Form 1 of form group one",
"variable_group_metadata":[{
"some":"information"
}],
"variable":[{
"variable_id":"variable_one",
"variable_name":"Variable One",
"var_type":"categorical/continuous",
"variable_metadata":[{
"variable_label_from_data_dictionary":"Variable number One",
"variable_label_from_data_file":"Variable One",
"variable_description":"Description of variable one",
"some":"information"
}]
}]
}]
}]
}]
}]