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I used SCIO to load 3 CDX 1.4 XML SBOMs and the loads did not include any dependency. There was no related processing error from the pipeline. I have not reproduced this for JSON format but I expect the same issue.
This was data for a container image so the dependency data is likely secondary, but for SBOM processing in general we need to capture what is in the input SBOM for general use and for inclusion in an output SBOM.
There is a similar issue for loading SPDX SBOMs where the data is stored as Elements with Relationship Types. Fixing this for CDX where the dependency data structure is simpler and more clear should be the priority.
The SCIO version is 34.2.0