Xavier Fontaine
commited on
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Add first version of the dataset
Browse files- README.md +25 -3
- mednerf_raw.jsonl +100 -0
- mednerf_tokenized.json +2998 -0
README.md
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# MedNERF
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MedNERF is a French medical NER dataset whose aim is to serve as a test set for medical NER models.
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It has been built using a sample of French medical prescriptions annotated with the same guidelines as the [n2c2 dataset](https://academic.oup.com/jamia/article-abstract/27/1/3/5581277?redirectedFrom=fulltext&login=false).
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Entities are annotated with the following labels: `Drug`, `Strength`, `Form`, `Dosage`, `Duration` and `Frequency`.
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It is available in two forms:
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- `mednerf_raw.jsonl`: a JSONlines file containing one JSON object per sample with the sample raw text and its annotations
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- `mednerf_tokenized.json`: a JSON file containing a tokenized version of the dataset with labels in IOB-format corresponding to the tokens of each sample.
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## Licensing Information
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This dataset is distributed under the Creative Commons Attribution Non Commercial Share Alike 4.0 license.
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## Citation information
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```
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@inproceedings{mednerf,
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title = "Multilingual Clinical NER: Translation or Cross-lingual Transfer?",
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author = "Gaschi, Félix and Fontaine, Xavier and Rastin, Parisa and Toussaint, Yannick",
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booktitle = ""Proceedings of the 5th Clinical Natural Language Processing Workshop",
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publisher = "Association for Computational Linguistics",
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year = "2023"
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}
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```
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mednerf_raw.jsonl
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{"id":1,"text":"1 gelule, matin, midi, soir, coucher","label":[[0,1,"Dosage"],[2,8,"Form"],[10,36,"Frequency"]]}
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{"id":2,"text":"1 le matin et le soir pendant 1 mois. CIF MTE Non substituable","label":[[0,1,"Dosage"],[2,21,"Frequency"],[22,36,"Duration"]]}
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{"id":3,"text":"500 mg ou 1g de paracétamol, 1 à 3 fois par jour","label":[[0,6,"Dosage"],[10,12,"Dosage"],[16,27,"Drug"],[29,48,"Frequency"]]}
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{"id":4,"text":"2 comprimés par jour","label":[[0,1,"Dosage"],[2,11,"Form"],[12,20,"Frequency"]]}
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{"id":5,"text":"3 comprimés, pendant 4 jours (1 le Matin, 1 à Midi, 1 le Soir) Voie orale AR 1 fois","label":[[0,1,"Dosage"],[2,11,"Form"],[13,28,"Duration"],[30,31,"Dosage"],[32,40,"Frequency"],[42,43,"Dosage"],[44,50,"Frequency"],[52,53,"Dosage"],[54,61,"Frequency"]]}
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{"id":6,"text":"une ampoule sur une petite cuillère suivie d'une boisson à chaque changement de saison fin septembre (automne), fin décembre (hiver), fin mars (printemps) et fin juin (été) QSP 12 mois","label":[[0,3,"Dosage"],[4,11,"Form"],[87,100,"Frequency"],[112,124,"Frequency"],[134,142,"Frequency"],[158,166,"Frequency"],[173,184,"Duration"]]}
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{"id":7,"text":"à garder au réfrigerateur 1 boîte","label":[]}
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{"id":8,"text":"1 dose toutes les 4 heures si douleur ou fièvre, selon besoin, 6 mois.","label":[[0,6,"Dosage"],[7,26,"Frequency"],[63,69,"Duration"]]}
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{"id":9,"text":"A la demande pendant 3 mois","label":[[13,27,"Duration"]]}
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{"id":10,"text":"1 pilule tous les jours à la même heure pendant 21 jours puis pause de 7 jours avant de reprendre une nouvelle plaquette QSP 1 AN","label":[[0,1,"Dosage"],[2,8,"Form"],[9,23,"Frequency"],[40,56,"Duration"],[71,78,"Duration"],[121,129,"Duration"]]}
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{"id":11,"text":"1 cp et demi le matin 6 mois","label":[[0,1,"Dosage"],[2,4,"Form"],[5,12,"Dosage"],[13,21,"Frequency"],[22,28,"Duration"]]}
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{"id":12,"text":"1 sachet 1 à 4 fois par jour selon besoin, en espaçant les prises de 6h.","label":[[0,1,"Dosage"],[2,8,"Form"],[9,28,"Frequency"],[43,71,"Frequency"]]}
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{"id":13,"text":"3 gouttes par jour","label":[[0,1,"Dosage"],[2,9,"Form"],[10,18,"Frequency"]]}
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{"id":14,"text":"1 comprimé le soir, pendant 3 mois.","label":[[0,1,"Dosage"],[2,10,"Form"],[11,18,"Frequency"],[20,34,"Duration"]]}
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{"id":15,"text":"1 matin","label":[[0,1,"Dosage"],[2,7,"Frequency"]]}
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{"id":16,"text":"1 comprimé 1 fois par jour à avaler entier avec de l'eau, pendant 3 mois. A prendre au même moment de la journée.","label":[[0,1,"Dosage"],[2,10,"Form"],[11,26,"Frequency"],[58,72,"Duration"]]}
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{"id":17,"text":"1 comprimé 1 fois par jour à avaler avec un verre d'eau pendant 3 mois.","label":[[0,1,"Dosage"],[2,10,"Form"],[11,26,"Frequency"],[56,70,"Duration"]]}
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{"id":18,"text":"1 comprimé le soir pendant 3 mois.","label":[[0,1,"Dosage"],[2,10,"Form"],[11,18,"Frequency"],[19,33,"Duration"]]}
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{"id":19,"text":"1 comprimé 1 fois par jour à avaler avec un verre d'eau.","label":[[0,1,"Dosage"],[2,10,"Form"],[11,26,"Frequency"]]}
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{"id":20,"text":"1 sachet matin midi et soir si besoin","label":[[0,1,"Dosage"],[2,8,"Form"],[9,27,"Frequency"]]}
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{"id":21,"text":"deux flacons, si besoin","label":[[0,4,"Dosage"],[5,12,"Form"]]}
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{"id":22,"text":"1 (un(e)) Matin, pendant 1 mois, pendant 6 (six) mois.","label":[[0,9,"Dosage"],[10,15,"Frequency"],[17,31,"Duration"],[33,53,"Duration"]]}
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{"id":23,"text":"1 comprimé tous les 2 jours pendant 3 mois.","label":[[0,1,"Dosage"],[2,10,"Form"],[11,27,"Frequency"],[28,42,"Duration"]]}
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{"id":24,"text":"Prendre 2 comprimés par jour, pendant 1 mois","label":[[8,9,"Dosage"],[10,19,"Form"],[20,28,"Frequency"],[30,44,"Duration"]]}
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{"id":25,"text":"1 comprimé 1 fois par jour pendant 3 mois.","label":[[0,1,"Dosage"],[2,10,"Form"],[11,26,"Frequency"],[27,41,"Duration"]]}
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{"id":26,"text":"Prendre 1 sachet par jour, Traitement pour 3 mois.","label":[[8,9,"Dosage"],[10,16,"Form"],[17,25,"Frequency"],[38,49,"Duration"]]}
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{"id":27,"text":"1 application de 2.5 g 3 fois par jour pendant 1 mois.","label":[[0,22,"Dosage"],[23,38,"Frequency"],[39,53,"Duration"]]}
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{"id":28,"text":"1 comprimé le soir pendant 1 mois.","label":[[0,1,"Dosage"],[2,10,"Form"],[11,18,"Frequency"],[19,33,"Duration"]]}
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{"id":29,"text":"2 CP /J 1-0-1 QSP 3 MOIS","label":[[0,1,"Dosage"],[2,4,"Form"],[5,7,"Frequency"],[14,24,"Duration"]]}
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{"id":30,"text":"Prendre 1 comprimé le matin et le soir, pendant 1 mois, 1 boite","label":[[8,9,"Dosage"],[10,18,"Form"],[19,38,"Frequency"],[40,54,"Duration"]]}
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{"id":31,"text":"Faire 2 inhalations le matin et le soir, pendant 1 mois.","label":[[6,19,"Dosage"],[20,39,"Frequency"],[41,55,"Duration"]]}
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{"id":32,"text":"1 comprimé, 3 fois par jour, pendant 30 jours","label":[[0,1,"Dosage"],[2,10,"Form"],[12,27,"Frequency"],[29,45,"Duration"]]}
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{"id":33,"text":"loratadine 10 1 /jour","label":[[0,10,"Drug"],[11,13,"Strength"],[14,15,"Dosage"],[16,21,"Frequency"]]}
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{"id":34,"text":"trulicity 3 mg 1 injection par semaine apres un repas léger chaque mardi","label":[[0,9,"Drug"],[10,14,"Strength"],[15,26,"Dosage"],[27,72,"Frequency"]]}
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{"id":35,"text":"1 gélule, 1 fois par jour, pendant 28 jours","label":[[0,1,"Dosage"],[2,8,"Form"],[10,25,"Frequency"],[27,43,"Duration"]]}
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{"id":36,"text":"prendre 1 comprimé le soir, pendant 3 mois.","label":[[8,9,"Dosage"],[10,18,"Form"],[19,26,"Frequency"],[28,42,"Duration"]]}
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{"id":37,"text":"prendre 1 comprimé le soir, pendant 6 mois.","label":[[8,9,"Dosage"],[10,18,"Form"],[19,26,"Frequency"],[28,42,"Duration"]]}
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{"id":38,"text":"kardegic 75 mg 1 sachet par jour","label":[[0,8,"Drug"],[9,14,"Strength"],[15,16,"Dosage"],[17,23,"Form"],[24,32,"Frequency"]]}
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{"id":39,"text":"irbesartan 150 mg 1 comprimé matin","label":[[0,10,"Drug"],[11,17,"Strength"],[18,19,"Dosage"],[20,28,"Form"],[29,34,"Frequency"]]}
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{"id":40,"text":"un comprimé (voie orale) le matin et soir pendant 1 mois modification de posologie","label":[[0,2,"Dosage"],[3,11,"Form"],[25,41,"Frequency"],[42,56,"Duration"]]}
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{"id":41,"text":"1 comprimé 1 fois par jour.","label":[[0,1,"Dosage"],[2,10,"Form"],[11,26,"Frequency"]]}
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{"id":42,"text":"1 gélule de préférence le matin pendant 6 semaines.","label":[[0,1,"Dosage"],[2,8,"Form"],[23,31,"Frequency"],[32,50,"Duration"]]}
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{"id":43,"text":"prendre 1 sachet par jour, au cours du repas, pendant 1 mois","label":[[8,9,"Dosage"],[10,16,"Form"],[17,44,"Frequency"],[46,60,"Duration"]]}
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{"id":44,"text":"prendre 1 comprimé le matin et le soir, au cours du repas, pendant 1 mois","label":[[8,9,"Dosage"],[10,18,"Form"],[19,57,"Frequency"],[59,73,"Duration"]]}
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{"id":45,"text":"paracetamol adulte 1 gramme, 4 fois /j si douleur ou fièvre","label":[[0,11,"Drug"],[19,27,"Strength"],[29,38,"Frequency"]]}
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{"id":46,"text":"1 gélule le soir pendant 6 mois.","label":[[0,1,"Dosage"],[2,8,"Form"],[9,16,"Frequency"],[17,31,"Duration"]]}
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{"id":47,"text":"1 gélule de préférence le matin à jeun, pendant 6 mois.","label":[[0,1,"Dosage"],[2,8,"Form"],[23,31,"Frequency"],[40,54,"Duration"]]}
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{"id":48,"text":"1 (un(e)) comprimé matin, 1 (un(e)) comprimé soir, pendant 3 (trois) mois, 6 (six) boite(s)","label":[[0,9,"Dosage"],[10,18,"Form"],[19,24,"Frequency"],[26,35,"Dosage"],[36,44,"Form"],[45,49,"Frequency"],[51,73,"Duration"]]}
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{"id":49,"text":"hydrochlorothiazide 25 mg cp (esidrex 25 mg cp séc) à prendre par voie orale","label":[[0,19,"Drug"],[20,25,"Strength"],[26,28,"Form"],[30,37,"Drug"],[38,43,"Strength"],[44,50,"Form"]]}
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{"id":50,"text":"dose à augmenter de 2 ui tous les 3 jours, si la glycémie au réveil reste > 150mg/dl","label":[[20,24,"Dosage"],[25,41,"Frequency"]]}
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{"id":51,"text":"dosette 2 fois par jour","label":[[0,7,"Form"],[8,23,"Frequency"]]}
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{"id":52,"text":"en fréquence nébulisations de ventoline jusqu'à 6 fois par jour","label":[[30,39,"Drug"],[39,63,"Frequency"]]}
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{"id":53,"text":"DOLIPRANE 1G COMP. B/08","label":[[0,9,"Drug"],[10,12,"Strength"],[13,17,"Form"]]}
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{"id":54,"text":"CHONDROSULF 1200MG GEL SACH SIS30","label":[[0,11,"Drug"],[12,18,"Strength"],[19,22,"Form"]]}
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{"id":55,"text":"Furosémide 40 mg un le matin","label":[[0,10,"Drug"],[11,16,"Strength"],[17,19,"Dosage"],[20,28,"Frequency"]]}
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{"id":56,"text":"SITAGLIPTINE (phosphate) 100 mg cp,","label":[[0,12,"Drug"],[14,23,"Drug"],[25,31,"Strength"],[32,34,"Form"]]}
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{"id":57,"text":"LANTUS 100/ML SOLOSTAR STYLO 3 MLS","label":[[0,6,"Drug"],[7,13,"Strength"],[14,22,"Drug"],[23,28,"Form"],[29,34,"Dosage"]]}
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{"id":58,"text":"LYNPARZA 150 MG","label":[[0,8,"Drug"],[9,15,"Strength"]]}
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{"id":59,"text":"OMEPRAZOLE 20 mg, gélule","label":[[0,10,"Drug"],[11,16,"Strength"],[18,24,"Form"]]}
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{"id":60,"text":"XELEVIA 100 mg Cpr pell Plq/30,","label":[[0,7,"Drug"],[8,14,"Strength"],[15,23,"Form"]]}
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{"id":61,"text":"VALSARTAN/HYD 160/12,5MG RANB CP90 (Valsartan hydrochlorothiazide 160 mg/12,5 mg)","label":[[0,13,"Drug"],[14,24,"Strength"],[36,65,"Drug"],[66,80,"Strength"]]}
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{"id":62,"text":"APRANAX 550MG CPR SECABLE 16 (Naproxėne sodique 550 mg comprimé)","label":[[0,7,"Drug"],[8,13,"Strength"],[14,25,"Form"],[30,48,"Drug"],[48,54,"Strength"],[55,63,"Form"]]}
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{"id":63,"text":"(DCI) BETAMETHASONE (dipropionate) 0,05 % crème","label":[[6,19,"Drug"],[21,33,"Drug"],[35,41,"Strength"],[42,47,"Form"]]}
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{"id":64,"text":"KARDEGIC 75 MG PDR SOL BUV EN SACHET (Acétylsalicylique acide 75 mg Prévention)","label":[[0,8,"Drug"],[9,14,"Strength"],[15,36,"Form"],[38,61,"Drug"],[62,67,"Strength"]]}
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{"id":65,"text":"DOLIPRANETABS 1000 MG CPR PELL PLQ/8 (Paracétamol 1.000 mg comprimé)","label":[[0,13,"Drug"],[14,21,"Strength"],[22,30,"Form"],[38,49,"Drug"],[50,58,"Strength"],[59,67,"Form"]]}
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{"id":66,"text":"OMEPRAZOLE 20 MG GÉL (OMEPRAZOLE ALMUS 20 MG GÉL GASTRO RÉS FL/14)","label":[[0,10,"Drug"],[11,16,"Strength"],[17,20,"Form"],[22,38,"Drug"],[39,44,"Strength"],[45,59,"Form"]]}
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{"id":67,"text":"Ventoline (deux flacons, si besoin)","label":[[0,9,"Drug"],[11,23,"Dosage"]]}
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{"id":68,"text":"IRBESARTAN APROVEL 300 MG 1 CP MATIN","label":[[0,18,"Drug"],[19,25,"Strength"],[26,27,"Dosage"],[28,30,"Form"],[31,36,"Frequency"]]}
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{"id":69,"text":"MICONAZOLE 2% ; voie buccale; gel bucc","label":[[0,10,"Drug"],[11,13,"Strength"],[30,38,"Form"]]}
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{"id":70,"text":"CIRCADIN 2MG CPR LP 30 (Méiatonine 2 mg comprimé LP),","label":[[0,8,"Drug"],[9,12,"Strength"],[13,19,"Form"],[24,34,"Drug"],[35,39,"Strength"],[40,51,"Form"]]}
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{"id":71,"text":"RAMIPRIL 1.25 mg 1 cp le matin","label":[[0,8,"Drug"],[9,16,"Strength"],[17,18,"Dosage"],[19,21,"Form"],[22,30,"Frequency"]]}
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{"id":72,"text":"PARACETAMOL 1G 3 CP /J SI BESOIN","label":[[0,11,"Drug"],[12,14,"Strength"],[15,16,"Dosage"],[17,19,"Form"],[20,22,"Frequency"]]}
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{"id":73,"text":"PARACÉTAMOL 1 G; voie orale; cp","label":[[0,11,"Drug"],[12,15,"Strength"],[29,31,"Form"]]}
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{"id":74,"text":"UVEDOSE 100 000 UI 1 AMP / 2 MOIS","label":[[0,7,"Drug"],[8,18,"Strength"],[19,20,"Dosage"],[21,24,"Form"],[25,33,"Frequency"]]}
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{"id":75,"text":"BILASKA 20MG CPR 30 (Bilastine)","label":[[0,7,"Drug"],[8,12,"Drug"],[13,16,"Form"],[21,30,"Drug"]]}
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{"id":76,"text":"GAVISCON 4 SACHETS /J","label":[[0,8,"Drug"],[9,10,"Dosage"],[11,18,"Form"],[19,21,"Frequency"]]}
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{"id":77,"text":"UVEDOSE 50 000 U/2ML AMP BUV","label":[[0,7,"Drug"],[8,20,"Strength"],[21,28,"Form"]]}
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{"id":78,"text":"RAMIPRIL 5 mg cp,","label":[[0,8,"Drug"],[9,13,"Strength"],[14,16,"Form"]]}
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{"id":79,"text":"NAPROXENE SEL DE NA 550 MG CP (APRANAX 550 MG CPR PELL SÉC B/16) (16 comprimés, comprimé pelliculé)","label":[[0,19,"Drug"],[20,26,"Strength"],[27,29,"Form"],[31,38,"Drug"],[39,45,"Strength"],[46,58,"Form"],[69,78,"Form"],[80,98,"Form"]]}
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{"id":80,"text":"ESOMEPRAZOLE 40MG ZENTIVA GEL 28 (Esoméprazole 40 mg gélule)","label":[[0,12,"Drug"],[13,17,"Strength"],[26,29,"Form"],[34,46,"Drug"],[47,52,"Strength"],[53,59,"Form"]]}
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{"id":81,"text":"(DCI) AMLODIPINE (bésilate) 10 mg VALSARTAN 160 mg cp (AMLODIPINE/VALSARTAN)","label":[[6,16,"Drug"],[18,26,"Drug"],[28,33,"Strength"],[34,43,"Drug"],[44,50,"Strength"],[51,53,"Form"],[55,75,"Drug"]]}
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{"id":82,"text":"PARACETAMOL 1G 3 CP /J SI BESOIN","label":[[0,11,"Drug"],[12,14,"Strength"],[15,16,"Dosage"],[17,19,"Form"],[20,22,"Frequency"]]}
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{"id":83,"text":"ACIDE ACETYLSALICYLIQUE 100 mg cp gastrorésis,","label":[[0,23,"Drug"],[24,30,"Strength"],[31,45,"Form"]]}
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{"id":84,"text":"ELIQUIS 5 MG CPR PELL PLQ/60 (Apixaban 5 mg comprimé)","label":[[0,7,"Drug"],[8,12,"Strength"],[13,21,"Form"],[30,38,"Drug"],[39,43,"Strength"],[44,52,"Form"]]}
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{"id":85,"text":"DICLOFENAC GEL 3 APPL /J SI BESOIN","label":[[0,10,"Drug"],[11,14,"Form"],[15,21,"Dosage"],[22,24,"Frequency"]]}
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{"id":86,"text":"ACIDE ACETYLSALICYLIQUE (sel de lysine) 75 mg pdre p sol buv sach (KARDEGIC)","label":[[0,23,"Drug"],[25,38,"Drug"],[40,45,"Strength"],[46,65,"Form"],[67,75,"Drug"]]}
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{"id":87,"text":"1 amp buvable","label":[[0,1,"Dosage"],[1,12,"Form"]]}
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{"id":88,"text":"1 sachet par voie orale le midi, pendant 3 mois","label":[[0,1,"Dosage"],[2,8,"Form"],[24,31,"Frequency"],[33,47,"Duration"]]}
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{"id":89,"text":"2 sachets le matin, à midi et le soir, pendant 1 mois","label":[[0,1,"Dosage"],[2,9,"Form"],[10,37,"Frequency"],[39,53,"Duration"]]}
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{"id":90,"text":"Ramipril 2,5 mg comprimé","label":[[0,8,"Drug"],[9,15,"Strength"],[16,24,"Form"]]}
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{"id":91,"text":"1 application 2 fois par jour pendant 6 jours","label":[[0,13,"Dosage"],[14,29,"Frequency"],[30,45,"Duration"]]}
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92 |
+
{"id":92,"text":"fortimel 1 par jour","label":[[0,8,"Drug"],[9,10,"Dosage"],[11,19,"Frequency"]]}
|
93 |
+
{"id":93,"text":"1 comprimé le matin à jeun pendant 6 mois.","label":[[0,1,"Dosage"],[2,10,"Form"],[11,19,"Frequency"],[27,41,"Duration"]]}
|
94 |
+
{"id":94,"text":"1 sachet par jour pendant 6 mois.","label":[[0,1,"Dosage"],[2,8,"Form"],[9,17,"Frequency"],[18,32,"Duration"]]}
|
95 |
+
{"id":95,"text":"2 comprimés (voie orale) 2 fois par jour pendant 1 mois","label":[[0,1,"Dosage"],[2,11,"Form"],[25,40,"Frequency"],[41,55,"Duration"]]}
|
96 |
+
{"id":96,"text":"TRAMADOL/PARACETAMOL 37,5mg/325mg","label":[[0,20,"Drug"],[21,33,"Strength"]]}
|
97 |
+
{"id":97,"text":"1 comprimé par jour à avaler entier avec un demi-verre d'eau, pendant 3 mois.","label":[[0,1,"Dosage"],[2,10,"Form"],[11,19,"Frequency"],[62,76,"Duration"]]}
|
98 |
+
{"id":98,"text":"0,5 comprimé matin, 1 comprimé soir pendant 30 jour(s)","label":[[0,3,"Dosage"],[4,12,"Form"],[13,18,"Frequency"],[20,21,"Dosage"],[22,30,"Form"],[31,35,"Frequency"],[36,54,"Duration"]]}
|
99 |
+
{"id":99,"text":"FORXIGA 10 mg 1 cp le matin","label":[[0,7,"Drug"],[8,13,"Strength"],[14,15,"Dosage"],[16,18,"Form"],[19,27,"Frequency"]]}
|
100 |
+
{"id":100,"text":"AMLODIPINE 5 mg; cpr 1 comprimé matin 1 comprimé soir","label":[[0,10,"Drug"],[11,15,"Strength"],[17,20,"Form"],[21,22,"Dosage"],[23,31,"Form"],[32,37,"Frequency"],[38,39,"Dosage"],[40,48,"Form"],[49,53,"Frequency"]]}
|
mednerf_tokenized.json
ADDED
@@ -0,0 +1,2998 @@
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