REDCap
Experimental
REDCap conversion is still experimental. It only works with controlled REDCap projects.
REDCap stands for Research Electronic Data Capture. REDCap documentation.
REDCap as input¶
REDCap projects are inherently "free format", meaning the project creator has the flexibility to determine the identifiers for variables, data dictionaries, and other elements.
REDCap project creation user’s guide
“We always recommend reviewing your variable names with a statistician or whoever will be analyzing your data. This is especially important if this is the first time you are building a database.”
Due to the flexibility of REDCap projects, it can be challenging to develop a solution that accommodates the wide range of possibilities. Nonetheless, we were able to successfully convert data from REDCap project exports to both Beacon v2 and Phenopackets v2 formats using a mapping file. These conversions were achieved as part of the 3TR Project.
About REDCap longitudinal data
REDCap stores event information, however, Beacon v2 Models currently lack a way to store longitudinal data. To address this, we will store event data under the propery info.
About REDCap export formats
REDCap provides various options for exporting data. We accept the option "All data (all records and fields)" including CSV and Microsoft Excel format, along with a accompanying data dictionary in CSV format. Exportation in REDCap CDISC ODM (XML) format is discussed in the section on CDISC-ODM.
We'll need three files:
- REDCap export (CSV)
- REDCap data dictionary (CSV)
- Mapping file (YAML or JSON) (see tutorial)
Can CSV files be compressed?
Yes. We also accept as input files compressed with gzip.
While it is technically possible to perform a transformation via API we don't think it's a viable option with REDCap projects due to the need for loading the data dictionary and mapping files along with the data. Therefore, we recommend using the command-line version by utilizing REDCap data exports.
REDCap built in API
REDCap has a built-in API that in theory could be used to retrieve data in real-time (as opposed to data exports). However, the current version of Convert-Pheno does not support REDCap API calls.
| Input | CLI | UI | Module | API |
|---|---|---|---|---|
| Beacon v2 Models | YES | YES | YES | YES |
| CDISC-ODM | YES | YES | YES | NO |
| CSV | YES | NO | YES | NO |
| Phenopackets v2 | YES | YES | YES | YES |
| OMOP-CDM | YES | YES | YES | YES |
| REDCap | YES | YES | YES | NO |