Multi-head CRF classifier for biomedical multi-class Named Entity Recognition on Spanish clinical notes

This contains the merged dataset as described in the work "Multi-head CRF classifier for biomedical multi-class Named Entity Recognition on Spanish clinical notes".

This dataset consists of 4 seperate datasets:

MedProcNer

DisTEMIST

PharmaCoNER

SympTEMIST

The dataset contains two tasks:

Task 1: This task is related to multi-class Named Entity Recognition. This dataset contains 5 possible classes: SYMPTOM, PROCEDURE, DISEASE, CHEMICAL and PROTEIN.

Task 2: This task is related to Named Entity Linking, where each code corresponds to a code within the SNOMED-CT corpus. The exact corpus used can be obtained here. Further for the MedProcNER, SympTEMIST and DisTEMIST datasets, a gazetteer is provided in the original datasets. 

For more information on the construction of the dataset, aswell as dataloaders, we refer you to our GitHub repository.Further this also contains the embeddings from the SapBERT model.

Please, cite:

@article{jonker2024a, title = {Multi-head {{CRF}} classifier for biomedical multi-class named entity recognition on {{Spanish}} clinical notes}, author = {Jonker, Richard A. A. and Almeida, Tiago and Antunes, Rui and Almeida, Jo{\~a}o R. and Matos, S{\'e}rgio}, year = {2024}, journal = {Database}, publisher = {Oxford University Press} }

Jonker, R. A. A., Almeida, T., Antunes, R., Almeida, J. R., & Matos, S. (2024). Multi-head CRF classifier for biomedical multi-class named entity recognition on Spanish clinical notes. (Submitted.) 

License

This work is licensed under a Creative Commons Attribution 4.0 International License.