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Oncology radiology imaging integration into CDM


(Rae Woong Park) #21

@yoon8302 had finished extracting waveform signals from ECG reports in PDF form . The new DB named ECG-ViEW III consists of 1 M of ECG reports and all the clinical information (demographic, condition, drug, selected measurement) in OMOP-CDM format. He will submit a manuscript on it soon. The DB will be opened to any researcher after acceptance of the manuscript. He also made a prototype of CDM extension model to contain the bio-signal waveform data.


(Rae Woong Park) #22

Sorry for this TOO late reply. Extension models for radiology and bio-signals will be different each other. @yoon8302 will try to make a prototype for bio-signal CDM extension model, and he may want to submit it to our community.


(Seng Chan You) #23

Owing to the effort of @SiHyung_No , @mediblue , @NEONKID, the first sample data for radiology extension model is released.
This sample is consists of two tables

  1. Radiology_Occurrence: each row represents one radiologic procedure
  2. Radiology_Image: each row represents one image among the images from single radiologic procedure.

Samples:
Radiology_Ocurrence
Radiology_Image


RadLex and Standardization of ontology for radiology procedures
RadLex and Standardization of ontology for radiology procedures
(Christian Reich) #24

Friends:

As you model this out don’t forget we need to have normalized information as concepts in the concept table. If Dicom has it all, bring it on. If not, pick from SNOMED or so. If nothing helps propose a new controlled vocabulary.


(Seng Chan You) #25

@Christian_Reich

We’re now figuring out which concepts we need to standardize. I’ve already picked RadLex ontology system from LOINC within OMOP concepts for standardized radiology procedure.
Definitely, we need to normalize all this information after completing the pilot model. Thank you for reminding again! :smile:


(Andrew Williams) #26

@SCYou Thanks for leading this work. How do you do so much?

It would provide the basis of a lot of important research if the concepts required for DICOM CT Radiation Dose Structured Reports (RDSRs) were among the concepts you standardized. Here in the US, an estimated 3-5% of incident cancers are attributable to medical radiation and there is ample evidence that CT dosing is frequently too high relative to benchmarks and that there is very high unwarranted variability in CT dosing. Capturing the required data elements for RDSRs would allow the OHDSI community to document and address these important aspects of CT use. Having contributed to some of this research I am interested in being able to continue it with OHDSI partners…

These mature open source toolkits for getting data from DICOM (which uses RadLex) are designed to pull the elements for RDSRs among other useful tasks. PixelMed toolkit: http://www.pixelmed.com/dicomtoolkit.html and GROK: http://dose-grok.sourceforge.net/


(Seng Chan You) #27

Thank you for providing such a precious information, @Andrew

Columns for radiation dosage and the unit exist without details in the pilot radiology extension model above. In order to standardize dosage and the units according to the various modality further, RDSR will be very helpful. Thank you again.


(Daniel Rubin) #28

@SCYou

I am curious to find out the status of this, is there any more recent work on Radiology_CDM? I am interested trying to deploy your current model and code on some test image data at my site, and possibly make extensions to it to fill gaps for our use cases for enabling image dataset discovery for multi-site collaboration in a federated learning setting without sharing data.


(Seng Chan You) #29

Welcome back,@dlrubin It’s really exciting!
We’re now focusing on semantics of R-CDM, and trying to adopt RadLex LOINC as the standardized vocabulary for the radiology process.

It would be great if we work together on the use case for this. :+1:


(Chang Won Jeong) #30

good idea.
Wonkwang University Hospital will be with you.


(Dmytry Dymshyts) #31

We can work this through together and release it on Athena eventually.


(Seng Chan You) #32

@Dymshyts Sure, we have to. Thank you!


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