Cantemist corpus: gold standard of oncology clinical cases annotated with CIE-O 3 terminology

Intro:

Cantemist shared task dataset (divided in train, dev1, dev2 and test). In addition, we include here the Cantemist background set.

It contains the train, development and test sets of the three subtasks: cantemist-ner, cantemist-norm and cantemist-coding with Gold Standard annotations.

In addition, it contains the documents of the background set, without annotations.

Please cite if you use this dataset:

Miranda-Escalada, A., Farré, E., & Krallinger, M. (2020). Named entity recognition, concept normalization and clinical coding: Overview of the cantemist track for cancer text mining in spanish, corpus, guidelines, methods and results. In Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings.

@inproceedings{miranda2020named,
  title={Named entity recognition, concept normalization and clinical coding: Overview of the cantemist track for cancer text mining in spanish, corpus, guidelines, methods and results},
  author={Miranda-Escalada, A and Farr{\'e}, E and Krallinger, M},
  booktitle={Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings},
  year={2020}
}

Format:

For subtasks cantemist-norm and cantemist-ner, annotations are distributed in Brat format. See Brat webpage for more information

For subtask cantemist-coding, codes are grouped in a TSV file with the following columns (this follows the format used in CodiEsp shared task): 

filename    code

Shared task goal:

In the three subtasks, the goal will be to predict the annotations (either the ANN files or the TSV with the codes) given only the plain text files. 

Resources:

• Web
• Citation: Miranda-Escalada, A., Farré, E., & Krallinger, M. (2020). Named entity recognition, concept normalization and clinical coding: Overview of the cantemist track for cancer text mining in spanish, corpus, guidelines, methods and results. In Proceedings of the Iberian Languages Evaluation Forum (IberLEF 2020), CEUR Workshop Proceedings.
• Silver Standard corpus
• Annotation guidelines
• YouTube presentations
• Participant codes

For further information, please visit https://temu.bsc.es/cantemist/ or email us at encargo-pln-life@bsc.es