I wanted to add a small update here, since it might be useful to people not in the Medical Imaging WG searching online. I also thought it would be good to link in this previous post from user @Jgallo, even though it is from 2021.
I’m still looking into how I want to represent findings from the radiology report. I’ve noted the recommendation to use Radlex codes, although these are not yet in Athena, so I’m not yet ready to create custom vocabulary tables for our implementation (though that will have to come at some point if we want to represent DICOM tags).
It sounds like we shouldn’t use the condition_occurrence table for radiological findings, particularly negative findings (which do need to be represented, as they are a positive fact). I’m assuming that there can’t be an exception to the rule that the observation table cannot include concepts from the condition domain (which would be the easiest way to pair a condition with an assertion or negation). So, I thought we might use the Morph Abnormality class in observation_class_id, in conjunction with image_feature.anatomic_site_concept_id.
Examples:
| Report phrase | Anatomic site | Observation |
|---|---|---|
| “pleural effusion” | Both lungs (4250192) | Effusion (4215818) |
| “congestive cardiac failure” | Heart structure (4217142) | Congestive hypertrophy (4298307) |
This approach feels a bit hacky, because we have the exact concepts usually appearing in the radiology report text as conditions, and not all combinations to represent them in terms of morphological abnormalities might be available.
There are also codes like 4236310 “Computed tomography of brain abnormal”, which are clearly radiological findings, but are in the condition domain.
A final thing that isn’t clear is the relationship between an image_occurrence and either the study or series in DICOM. In the paper, it says it can be either. Radiology reports often combine information from multiple series in a study (e.g. in MRI with multiple sequences, or CT pre- and post-contrast). In this case we would want to link the findings to the study level. Is it possible to do this? E.g. one could have one image_occurrence entry for the study, and then additional entries for each series, with image_series_UID blank for the study. Or has it been settled in the WG since the paper came out to only use series?
Thanks @kyulee.jeon and others for help, and I hope this might be useful to other forum users.