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clinical-biomarkers / biomarker-partnership

CFDE Biomarker Partnership
https://hivelab.biochemistry.gwu.edu/biomarker-partnership
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Loinc code mapping #23

Closed seankim658 closed 10 months ago

seankim658 commented 10 months ago

Realized that the current mapping code for loinc numbers doesn't work 100% of the time. For genes with multiple entries in the loinc.csv file, we only want the loinc code corresponding with the "gene targeted mutation analysis". For example, in the below snippet we only want the loinc code corresponding to the first row when mapping on the gene ATP7B. 

21626-7,ATP7B gene targeted mutation analysis,Bld/Tiss
21627-5,ATP7B gene.c.2010_2016del,Bld/Tiss
21628-3,ATP7B gene.c.2337delC,Bld/Tiss
21629-1,ATP7B gene.c.2487insT,Bld/Tiss
21630-9,ATP7B gene.c.1711G>C,Bld/Tiss
21631-7,ATP7B gene.p.Gly1267Arg,Bld/Tiss
21632-5,ATP7B gene.p.His1070Gln,Bld/Tiss
21633-3,ATP7B gene.p.His714Gln,Bld/Tiss
seankim658 commented 10 months ago

Initial idea is to drop rows that are not labeled as gene targeted mutation analysis to reduce mapping space.