Dataset for training and evaluating Named Entity Recognition systems on medical texts in Swedish.
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1177_annotated_sentences.txt
LT_annotated_60.txt
README.md
Wiki_annotated_60.txt

README.md

Dataset for training and evaluating Named Entity Recognition systems on medical texts in Swedish.

Data comes from Swedish Wikipedia, Läkartidningen, and 1177.se.

Authors

Chalmers University of Techbology

Citing this work

If you are using this work, please cite the following:

@inproceedings{almgrenpavlovmogren2016bioner, title="Named Entity Recognition in Swedish Medical Journals with Deep Bidirectional Character-Based LSTMs", author="Simon Almgren, Sean Pavlov, Olof Mogren", booktitle="Proceedings of the Fifth Workshop on Building and Evaluating Resources for Biomedical Text Mining (BioTxtM 2016)", pages="1", year="2016"
}

License

This work is shared under the Attribution-ShareAlike 4.0 International license. See http://creativecommons.org/licenses/by-sa/4.0/ for details.

Swedish Wikipedia

Pages were downloaded and then automatically annotated by finding words in a dictionary and extracting 60 character long context windows randomly positioned around the main word.

* Infektionssjukdom
* Cancer
* Patogen
* Sjukdomar i blodet och blodbildande organ
* Endokrina sjukdomar
* Autoimmunitet
* Reumatism
* Medicinsk diagnostik
* Förkylning
* Depression
* Sjukdomar i nervsystemet
* Hjärntumör
* Allergi
* Astma
* Smitta
* Stress
* Människans anatomi
* Kroppsdel
* Muskel
* Anatomi
* Anatomisk variation
* Nervsystemet
* Skelett
* Perifera nervsystemet
* Ansikte
* Magsäck
* Ryggrad
* Tarm
* Hormon
* Läkemedel
* Antibiotikum
* Medicinalväxt
* Kirurgi
* Selektiva serontinåterupptagshämmare
* Ibuprofen
* Enzym
* Aminosyror
* Vitamin
* Näringsämne
* Fettvävnad
* Vaccination
* Farmakokinetik
* Insulin
* Pencillin

Läkartidningen

Pages were downloaded and then automatically annotated by finding words in a dictionary and extracting 60 character long context windows randomly positioned around the main word.

1177.se

Pages were downloaded in May 2016 and manually annotated. The file contains one sentence per line, and the lines were shuffled.

Articles included:

* Demens - Alzheimers sjukdom
* Bedövning och smärtlindring vid tandvård
* Receptfria läkemedel vid tillfällig smärta
* Så åldras kroppen
* Läkemedel vid pollenallergi
* Vaccinationsprogram för barn
* Stroke – slaganfall
* Behöver jag testa mig för zikaviruset?
* Denguefeber
* KOL – kroniskt obstruktiv lungsjukdom
* Knöl i bröstet
* Läkemedel som tas upp genom huden
* Drick sundare
* Myggbett och knottbett
* Ibumetin

Data format

Tags are as follows:

  • Prenthesis, (): Disorder and Finding
  • Brackets, []: Pharmaceutical Drug
  • Curly brackets, {}: Body Structure