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EHDEN / ETL-UK-Biobank

ETL UK-Biobank
https://ehden.github.io/ETL-UK-Biobank/
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GP Covid: semantic mapping of local drug codes #239

Closed SofiaMp closed 3 years ago

SofiaMp commented 3 years ago

The covid19_gp_emis_scripts contain mainly dm+d codes. In the scan report there are also some local codes.

Decide to make the semantic mapping for the local emis codes present in the data or ignore them. If keeping them, get a full list of the codes appearing in the data (scan report has only 2 because of the frequency).

spiros commented 3 years ago

Just to confirm, I will generate a frequency count of the local codes and then review them & make a proposal.

MaximMoinat commented 3 years ago

@spiros Did you produce the frequencies?

spiros commented 3 years ago

There are a total of 1.4M prescriptions using local EMIS codes (conversely, there are 79M prescriptions using DM+D)

The following table is a count of the top 20 most frequently prescribed items using EMIS codes - looks like some of them are legit prescriptions while others are more generic things. Some of these are entered I suspect as local EMIS codes because they do not exist in DM+D; for example, "caplet" is not a recognized formulation in DM+D.. others are problematic either way, e.g. Gaviscon.

Ideally, we would map the common ones to DM+D codes but this would require a lot of manual processing.

n coding meaning %
0 100824 FLAQ19556EMIS Fluticasone Propionate Aqueous nasal spray 0.05 % (150 dose spray) 7.17085
1 87224 GAOR29999EMIS Gaviscon Advance Oral suspension 6.20359
2 66106 PACA12515NEMIS Paracetamol Caplets 500 mg 4.70162
3 47508 AMTA10145BRIDL Amlodipine Besilate Tablets 5 mg 3.37889
4 39385 ERST3539 Erythromycin Tablets 250 mg 2.80116
5 35953 GALI1279 Gaviscon Liquid 2.55707
6 30666 DOGE6701NEMIS Doublebase Gel (Pump Dispenser) 2.18104
7 29217 AMTA9080EMIS Amlodipine Besilate Tablets 10 mg 2.07799
8 28283 COCA27287EMIS Co-Codamol 30/500 Caplets 2.01156
9 23567 VEIN3026 Ventolin Inhaler 100 micrograms/puff 1.67614
10 22461 ISSA18818EMIS Ispaghula Husk Sachets (orange) 3.5 g/sachet 1.59748
11 21048 FYSA1270 Fybogel Granules 3.5 grams/sachet 1.49699
12 19860 SAAE6755 Salbutamol Aerosol inhalation 100 micrograms/metered inhalation 1.41249
13 19761 CECR13101NEMIS Cetraben Emollient Cream 1.40545
14 18173 SHCO24024NEMIS Sharpsafe Container 1 litre 1.29251
15 16492 VIEY51060NEMIS Vita-Pos Eye ointment (preservative-free) 1.17295
16 16061 ISSA1527 Ispaghula Husk Sachets 3.5 g/sachet 1.1423
17 13689 LIGE19506NEMIS Liquid Paraffin And Isopropyl Myristate Gel (Pump Dispenser) 15 % + 15 % 0.973596
18 12565 ISEF12644NEMIS Ispaghula Husk Sugar and Gluten Free Effervescent granules (orange) 3.5 grams/sachet 0.893654
19 11135 GLSP1314 Glyceryl Trinitrate Spray 400 micrograms/dose 0.791949

Can I propose we implement a couple, as examples, so we have the functionality in ETL and we can retrospectively add more if there's interest down the line. For example,

PACA12515NEMIS maps to DM+D VMP 322236009 Paracetamol 500mg tablets which is SNOMED-CT 322236009