Skip to main content

CDISC-ODM

Experimental

CDISC-ODM conversion is still experimental. Please use it with caution.

CDISC stands for Clinical Data Interchange Standards Consortium. ODM stands for Operational Data Model.

RoleInput
Accepted inputODM-XML v1, dictionary, mapping file
Main outputBFF, PXF, OMOP-CDM
NotesODM v2 is not currently supported
CDISC
Image extracted from www.cdisc.org

CDISC is an organization that develops standards for data exchange of clinical research. From their standards, we accept the Operational Data Model (ODM)-XML as input as it is widely used for representing forms for case-reporting in many electronic data capture (EDC) tools.

About ODM-XML

ODM-XML is a vendor-neutral, platform-independent format for exchanging and archiving clinical and translational research data, along with their associated metadata, administrative data, reference data, and audit information.

CDISC-ODM as input​

ODM versions

We're accepting CDISC-ODM v1 (XML). Currently, v2 is in the process of being approved.

We'll need three files:

  1. CDISC-ODM v1 (XML)
  2. REDCap data dictionary (CSV)
  3. Mapping file (YAML or JSON) (see tutorial)
    convert-pheno -icdisc cdisc.xml --redcap-dictionary dictionary.csv --mapping-file mapping.yaml -obff individuals.json

CDISC-ODM follows the same mapping-file path as REDCap. By default, generated BFF records preserve copied source values in info for auditability. Use --no-source-info to omit raw source payloads from the BFF output.

If you also want synthesized Beacon datasets and cohorts, keep -obff and use entity mode:

    convert-pheno -icdisc cdisc.xml --redcap-dictionary dictionary.csv --mapping-file mapping.yaml -obff --entities individuals datasets cohorts --out-dir out/

In this mode, the top-level beacon section of the mapping file can override dataset and cohort metadata.

About other CDISC data exchange standards

We are aware of the Dataset-XML format (an extension of ODM-XML) and the emerging Dataset-JSON specification. While we do not currently support them, we are following their development with interest.