CDISC-ODM
Category: eCRF and EDC exchange standard
The CDISC Operational Data Model (ODM)
is a vendor-neutral XML standard for exchanging clinical study data and its
metadata between data-capture and research systems. Convert-Pheno reads
participant ClinicalData from Snapshot documents using ODM 1.3.1, 1.3.2,
or the supported ODM 2.0 ClinicalData profile.
Choose The Input Profile
The metadata source depends on where the ODM file came from:
| ODM input | Mapping declaration | REDCap dictionary | Metadata used |
|---|---|---|---|
| REDCap ODM export | source.profile: redcap | Required | External REDCap data dictionary |
| Standard or OpenClinica ODM | source.profile: cdisc-odm | Not used | Embedded MetaDataVersion, ItemDef, and CodeList |
REDCap ODM can therefore reuse the same mapping and dictionary as the corresponding REDCap CSV export. Standard and OpenClinica ODM use their embedded item definitions and code lists instead.
Run The Conversion
Standard or OpenClinica ODM with embedded metadata:
convert-pheno -icdisc-odm study.xml \
--mapping-file odm-mapping.yaml \
-obff individuals.json
REDCap-origin ODM:
convert-pheno -icdisc-odm redcap-export.xml \
--redcap-dictionary redcap-dictionary.csv \
--mapping-file redcap-mapping.yaml \
-obff individuals.json
PXF and OMOP-CDM output use the same input and mapping. See the CDISC-ODM recipes and Mapping Files.
Repeated Records
Convert-Pheno preserves the study event, form, item group, and repeat context needed to distinguish repeated clinical records. ODM 1.x and 2.0 use different XML structures, but both are normalized before the project mapping is applied.
Repeated BFF collections such as diseases, measures, and treatments receive one result per matching item-group occurrence. Conflicting repeated values for a scalar target stop the conversion instead of being combined silently.
Source Data
With the default --source-info, generic ODM output stores structured source
context under info.CDISC_ODM, including study, subject, event, form or nested
group path, repeat keys, and original values. REDCap ODM retains its established
info.REDCap_columns representation.
Use --no-source-info to omit these source copies. Mapped BFF properties and
project metadata are retained.
Dataset-XML and Dataset-JSON use separate SDTM dataset routes. They do not use this operational ODM mapping workflow; Dataset-XML requires accompanying Define-XML metadata.
The namespace and declared ODM version must agree. Transactional ODM and full ODM 2 study-design, workflow, audit, and attachment processing are outside this route. Standard and OpenClinica profiles are regression-tested but have less independent export coverage than the REDCap ODM profile.