CSV
Experimental feature
CSV conversion to BFF and PXF data exchange formats is still in the development phase. Use it with caution.
CSV with clinical data as input¶
Note
The purpose of this conversion method is to provide a user-friendly solution for those lacking the knowledge or resources to perform an ad hoc transformation of their raw clinical data into one of our output formats. We understand that handling clinical data can be a formidable task, and our goal is to accurately convert essential fields necessary for cross-study comparisons. Initially, Convert-Pheno was not designed for ingesting raw CSV files. However, we leveraged the functions we developed for converting REDCap projects, which also come in CSV format.
If you use our tool and identify areas for improvement, please contact us or create a GitHub issue. Thank you.
When using the convert-pheno command-line interface, simply ensure the correct syntax is provided.
CSV Separator Notice
Please note that the default separator for CSV files is ;. If your file uses a different character (e.g., , or :), please specify it using the --sep option.
convert-pheno -icsv clinical_data.csv --mapping-file clinical_data_mapping.yaml -obff individuals.json --sep ,
Please refer to the Convert-Pheno tutorial for more information.
How do I convert other Beacon v2 Models entities?
We recommend using the maintaned version of the original Beacon v2 Reference Implementation tools (beacon2-ri-tools).
See examples:
While it is technically possible to perform a transformation via the Convert-Pheno API, we don't think this is how most people will transform CSV files (due to the need of the mapping file). Therefore, we recommend using the command-line version.
| 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 |