DisTEMIST corpus: detection and normalization of disease mentions in spanish clinical cases

DisTEMIST corpus - training set

Introduction

The DisTEMIST corpus is a collection of 1000 clinical cases with disease annotations linked with Snomed-CT concepts. All documents are released in the context of the BioASQ DisTEMIST track for CLEF 2022. For more information about the track and its schedule, please visit the website.

File structure:

The DisTEMIST corpus has been randomly divided into a training set, containing 750 clinical cases, and a test set, consisting of 250 additional cases. Participants must train their systems using the train set and submit predictions for the test set, on which they will be evaluated.  The file structure of the corpus is as follows:

• train_set:
  • text_files: Folder with plain text files of the clinical cases  
  • subtrack1_entities: It contains annotations in a tab-separated file (TSV) with the following columns:
    • filename: document name
    • mark: identifier mention id
    • label: mentions type (ENFERMEDAD)
    • off0: starting position of the mention in the document
    • off1: ending position of the mention in the document
    • span:  text span
  • subtrack2_linking: It will be released on 15 April. It will contain the disease mentions normalized to Snomed-CT concepts.

• test_set: The 250 clinical cases that will be used to evaluate the systems will be published in accordance with the schedule of the task.

Resources 

• Web
• Evaluation Library
• DISTEMIST gazetteer
• DISTEMIST guidelines
• More resources soon