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@phlobo
phlobo committed Mar 7, 2024
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143 changes: 134 additions & 9 deletions examples/04_Drug_Names_ATC.ipynb
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"\n",
"- Get German ATC 2023 version from: https://www.wido.de/publikationen-produkte/arzneimittel-klassifikation/ \n",
"- Optional: get access to DrugBank (https://go.drugbank.com/releases/latest) for much more aliases (e.g., trade names)\n",
"- `pip install openpyxl`\n",
"- Prepare xMEN KB and indices:\n",
" - `xmen dict examples/conf/atc.yaml --code examples/dicts/atc2023_de.py`\n",
" - `xmen index examples/conf/atc.yaml --all`"
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"predictions = linker.predict_no_context(drug_mentions)"
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"text": [
"Input: Ursodeoxycholsäure, 250 mg - Kapsel\n",
"Confidence: 0.7435341477394104\n",
"CUI: A05AA02, Name: Ursodeoxycholsäure\n",
"Definition: None\n",
"TUI(s): \n",
"Aliases (abbreviated, total: 47): \n",
"\t Litursol, Solutrat, Ursochol, Ag-ursodiol, 3alpha,7beta-Dihydroxy-5beta-cholan-24-oic acid, Urso DS, PMS-ursodiol, Ursodeoxycholic acid, (3alpha,5beta,7beta)-3,7-dihydroxycholan-24-oic acid, Urusa\n",
"------\n",
"Input: Propofol 2%, 20 mg/ml 1000 mg/50 ml Injektionslösung\n",
"Confidence: 0.6950462460517883\n",
"CUI: N01AX10, Name: Propofol\n",
"Definition: None\n",
"TUI(s): \n",
"Aliases (abbreviated, total: 45): \n",
"\t Diprivan, Gobbifol, Hypro, Disoprivan, Propofil, Anesthesia S/I-50, Anesthesia S/I-60, Propofol-II Injection, Propoven, Anepol\n",
"------\n",
"Input: Norepinephrin 20 µg/ml\n",
"Confidence: 0.848741888999939\n",
"CUI: C01CA03, Name: Norepinephrin\n",
"Definition: None\n",
"TUI(s): \n",
"Aliases (abbreviated, total: 27): \n",
"\t (R)-norepinephrine, Norepinephrine Bitartrate In 5% Dextrose Injection, (R)-4-(2-amino-1-hydroxyethyl)-1,2-benzenediol, Norepinephrine Bitartrate Injection USP, Levophed(r) Norepinephrine Bitartrate, Norépinéphrine, Norepinephrine, Levophed, (R)-(−)-norepinephrine, L-noradrenaline\n",
"------\n",
"Input: Amphotericin B, 10 mg - Lutschtablette\n",
"Confidence: 0.6953610181808472\n",
"CUI: J02AA01, Name: Amphotericin B\n",
"Definition: None\n",
"TUI(s): \n",
"Aliases (abbreviated, total: 22): \n",
"\t Amphocin, Amphotericinum B, Liposomal amphotericin B, Amphotericin, Fungizone, Amphotec 50 mg, Amphotec 100 mg, Abelect, Amphotericin B, Amphocil\n",
"------\n",
"Input: Fentanyl (50 µg/ml) i.v.\n",
"Confidence: 0.8534790277481079\n",
"CUI: N02AB03, Name: Fentanyl\n",
"Definition: None\n",
"TUI(s): \n",
"Aliases (abbreviated, total: 70): \n",
"\t Instanyl, Duragesic 12, Fentanyl Buccal, Fentanyl Transdermal, Pecfent, N-(1-phenethylpiperidin-4-yl)-N-phenylpropionamide, Fentora, Lazanda, Mylan-fentanyl Matrix Patch, Abstral\n",
"------\n",
"Input: Vollelektrolyt-Lösung\n",
"Confidence: 0.8366699814796448\n",
"CUI: B05XA, Name: Elektrolytlösungen\n",
"Definition: None\n",
"TUI(s): \n",
"Aliases: (total: 0): \n",
"\t \n",
"------\n",
"Input: Sufentanil 5µg/ml 250 µg/50 ml Injektionslösung\n",
"Confidence: 0.7572200894355774\n",
"CUI: N01AH03, Name: Sufentanil\n",
"Definition: None\n",
"TUI(s): \n",
"Aliases (abbreviated, total: 21): \n",
"\t Sufentanyl, N-(4-(Methoxymethyl)-1-(2-(2-thienyl)ethyl)-4-piperidyl)propionanilide, Sufentanilum, Sufentil, Dsuvia, N-(4-(Methoxymethyl)-1-(2-(2-thienyl)ethyl)-4-piperidinyl)-N-phenylpropanamide, Zalviso, Sufentanil Citrate, Sufenta, Chronogesic\n",
"------\n"
]
}
],
"source": [
"for d, p in zip(drug_mentions, predictions):\n",
" print('Input:', d)\n",
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