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OHDSI / Radiology-CDM

Pilot model and converter for integration of radiology data into OMOP-CDM
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Listing required vocabularies for radiology-CDM #9

Open chandryou opened 5 years ago

chandryou commented 5 years ago

We need to list potential vocabulary candidates for radiology-CDM from RSNA-LOINC playbook and RadLex. We need to figure out where to store and how to organize these candidate codes.

hihipch commented 5 years ago

We want to modify the names of the columns and their corresponding values in the R-CDM table. And the names are from RadLex, which will be integrated later into OMOP.

  1. Radiology_Occurance table

    • In the Person_position_concept column : The value named 'HFS'(Head First Supine) will be modified into 'RID10421'(you can search the name 'supine position' in RadLex).
    • Person_orientation_concept column : This column will be deleted.
    • Radiology_modality_concept_ID : The value named 'CT' will be modified as 'RID10321'(you can search 'Computed tomography' in RadLex), 'MR' will be modified as 'RID10312'
    • Radiology_protocol_concept_ID : The value named 'Precontrast' will be modified as 'RID28768'('Imaging without iv contrast' in RadLex), and 'Postcontrast' will be 'RID28771'(Imaging without than with IV contrast)
    • Anatomic_site_concept_id : Values are all assigned as 4119359, which means brain. But we will modify this value into 'RID6434'(brain in Radlex)

  2. Radiology_Image table

    • Radiology_protocol_concept_id : The value named 'Precontrast' will be modified as 'RID28768'('Imaging without iv contrast' in RadLex), and 'Postcontrast' will be 'RID28769'(Imaging with IV contrast)

    • Since 'postcontrast' of the Radiology_Occurance table was including Pre & Post contrast brain CT image, we modified this column as Imaging without than with IV contrast('RID28771'). However 'postcontast' in Radiology_Image table only includes the postcontast brain CT image.

  3. We will include 'Body_region_concept_id' column in Radiology_Occurance table, which means the 'CT shooting range'. For instance, if we want to see the liver CT image, we should search for the 'abdominal' CT, which will be classified in 'Body_region_concept_id', and then target specifically to the liver, which will be classified in 'Anatomic_site_concept_id'.

NEONKID commented 5 years ago

@hihipch Thank you for your investigation. The reference ID should be kept in the form of an Integer, which will be modified again to the standard OMOP.

Body_region_concept_id information seems to be useful in non-Brain CT such as Chest CT. I will take this information seriously.

Can you find the link to where you obtained this information?

hihipch commented 5 years ago

@NEONKID Thank you for your considerations. The reference ID was searched in the 'http://www.radlex.org/'. I made the column name 'Body_region_concept_id', and I hope there will be more discussion on the name. Thank you sir.

NEONKID commented 5 years ago

@hihipch I have incorporated changes to this issue. However, in some sample images, we found Modality called OT. The contents can be seen below.

https://travis-ci.com/OHDSI/Radiology-CDM/jobs/189202929

We need to make sure that Modality OT is a Radiology Modality that is formally present.

hihipch commented 5 years ago

@NEONKID In the Radiology_Occurance table, there is a Radiology_modality_concept column. And the DICOM images which are not classifined anywhere in the column can have a value of 'OT', which means 'other modality in DICOM image'. Therefore we have to assign the RadLex ID for 'OT', and it is 'RID49585'. Thank you.