PR for adding sdtm->snomed mapping codes #204
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@sadiekelly @ekamau I've uploaded an example mapping file for the VS (vital signs) sdtm file; I'd suggest following this format. Feel free to upload your files to this branch/PR as you create them. |
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Thanks @pipliggins - nice! |
sdtm to snomed mappings
Additional codes added that were used in GECCO mapping for these questions. Pregnancy status loinc code is also used in the International Patient Summary (a core set of elements for data sharing which would be good to comply with where possible).
Additional potential codes added for Estimated Weight
Still plenty of gaps but here's some initial mapping and coding from HO. Some issues here that we will very likely encounter in other domains; - How to make events unique when there are no dates. We used other timing variables in SDTM including VISIT/VISITNUM and CDSTDY (contributor-defined study day), not sure how we can represent something similar as yet - Representation of different timing interval text in EVINTX - Classifying events as 'previous' or from follow up, particularly when we have no dates (previous admissions have no dates at all so will just appear as an admission due to covid-19). Capture of data relating to hospitalisation during follow up also has no dates
Initial thoughts, mapping not completed. IPS = International Patient Summary and forms an ISO standard for data sharing. Pathogen testing is included as a resource in the IPS specification so I think it would be good to ensure we align with this where possible. Commented in the mapping sheet where IPS-aligned terminology is used
LB domain LBTEST variable snomed mappings
LB domain LBSPEC snomed mappings
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File structure should follow that demonstrated in
vital_signs_sdtm.csvfor now.The 'name' column should reflect a single column in the sdtm file being mapped; where possible, use one with CDISC controlled terminology > SDTM modified values > free text from contributors. Some files might only have a few terms that need mapping; if there are files that can be grouped (e.g. pregnancy-related) then put all the terms in a single CSV for brevity (just make sure both files are reflected in the csv name).