MIT-LCP
Updates concept mappings for MIMIC-IV and NW datasets.
This pull request updates the existing concept mappings for the chartevents and procedureevents tables, and adds new mapping files for clinical concepts from the labevents and prescriptions tables in MIMIC-IV v2.0, as well as from the Northwestern ICU (NWICU) database.
These mappings align local concept identifiers (itemid, ndc) with standard clinical vocabularies, including LOINC, RxNorm, SNOMED, and OMOP, to support interoperability across ICU datasets.
All mapping files are formatted according to the Simple Standard for Sharing Ontology Mappings (SSSOM) specification @sssom.
@danamouk , thanks for this contribution.
Does this mix Northwestern and MIMIC terms in these concept mappings? If so, would it be possible to separate them, keeping only the MIMIC terms under mimic-code and putting the Northwestern terms in a separate repo?
thanks @briangow for the suggestion, this is an iteration on the previous concept maps in the repository which already contains both mimic and nw under mimic-code/mimic-iv/concepts/concept_map as discussed with @tompollard , this is just an extension with additional updates for chartevents/procedureevents along with the other mappings for labevents and prescriptions. For reference, the subject-id distinguishes the source either as mimic or nw to comply with sssom format. These mappings will be useful to harmonize mimic and nw datasets.
@danamouk I have mixed feelings about mixing northwestern and mimic concepts in a single file. I wonder whether it is cleaner to separate them?
Sounds good, we can go ahead and separate mimic and nw to keep things clean, currently the mappings reside in the following directory mimic-code/mimic-iv/concepts/concept_map, which would seems like the right place for MIMIC mappings, @tompollard is there a specific directory in the mimic-code repo you’d suggest for adding the NWICU concept maps, possibly mimic-code/nwicu/concepts/concept_map ?
@tompollard, MIMIC mappings are now under mimic-code/mimic-iv/concepts/concept_map, and NWICU concept maps are in mimic-code/nw/concepts/concept_map to keep things consistent.