umls_preprocess.txt

Start from MRCONSO to extract concept list
#This command filters out inactive, nonpreferred concepts and only keeps relevant columns
awk -F '|' '$3=="P" && $5=="PF" && $7=="Y" && $12=="SNOMEDCT_US" && $13=="PT" && $17=="N" {OFS="\t"; print$1,$15}' MRCONSO.RRF > active_concepts.txt

#This command filters out inactive relations and only keeps relevant columns
awk -F '|' '$11=="SNOMEDCT_US" && $15=="N" {OFS="\t"; print$1,$4,$5,$8}' MRREL.RRF > active_relations.txt

#This command keeps only relevant columsn from MRSTY
awk -F '|' '{OFS="\t"; print$1,$2,$4}' MRSTY.RRF > semantic_types.txt

Then we use the notebook umls_utils.ipynb to subset the concepts by semantic types/groups using MRSTY and SemGroups.txt, and subset MRREL using those concepts