README.md

metadata

language:
  - es
license: cc-by-4.0
multilinguality: monolingual
pretty_name: CANTEMIST
bigbio_language:
  - Spanish
bigbio_license_shortname: CC_BY_4p0
homepage: https://temu.bsc.es/cantemist/?p=4338
bigbio_pubmed: false
bigbio_public: true
bigbio_tasks:
  - NAMED_ENTITY_RECOGNITION
  - NAMED_ENTITY_DISAMBIGUATION
  - TEXT_CLASSIFICATION
dataset_info:
  config_name: cantemist_source
  features:
    - name: id
      dtype: string
    - name: document_id
      dtype: string
    - name: text
      dtype: string
    - name: labels
      list: string
    - name: text_bound_annotations
      list:
        - name: offsets
          sequence:
            list: int32
        - name: text
          sequence: string
        - name: type
          dtype: string
        - name: id
          dtype: string
    - name: events
      list:
        - name: trigger
          dtype: string
        - name: id
          dtype: string
        - name: type
          dtype: string
        - name: arguments
          sequence:
            - name: role
              dtype: string
            - name: ref_id
              dtype: string
    - name: relations
      list:
        - name: id
          dtype: string
        - name: head
          struct:
            - name: ref_id
              dtype: string
            - name: role
              dtype: string
        - name: tail
          struct:
            - name: ref_id
              dtype: string
            - name: role
              dtype: string
        - name: type
          dtype: string
    - name: equivalences
      list:
        - name: id
          dtype: string
        - name: ref_ids
          sequence: string
    - name: attributes
      list:
        - name: id
          dtype: string
        - name: type
          dtype: string
        - name: ref_id
          dtype: string
        - name: value
          dtype: string
    - name: normalizations
      list:
        - name: id
          dtype: string
        - name: type
          dtype: string
        - name: ref_id
          dtype: string
        - name: resource_name
          dtype: string
        - name: cuid
          dtype: string
        - name: text
          dtype: string
    - name: notes
      list:
        - name: id
          dtype: string
        - name: type
          dtype: string
        - name: ref_id
          dtype: string
        - name: text
          dtype: string
  splits:
    - name: train
      num_bytes: 3451245
      num_examples: 501
    - name: test
      num_bytes: 1892436
      num_examples: 300
    - name: validation
      num_bytes: 3126466
      num_examples: 500
  download_size: 3927340
  dataset_size: 8470147
configs:
  - config_name: cantemist_source
    data_files:
      - split: train
        path: cantemist_source/train-*
      - split: test
        path: cantemist_source/test-*
      - split: validation
        path: cantemist_source/validation-*
    default: true

Dataset Card for CANTEMIST

Dataset Description

• Homepage: https://temu.bsc.es/cantemist/?p=4338
• Pubmed: False
• Public: True
• Tasks: NER,NED,TXTCLASS

Collection of 1301 oncological clinical case reports written in Spanish, with tumor morphology mentions manually annotated and mapped by clinical experts to a controlled terminology. Every tumor morphology mention is linked to an eCIE-O code (the Spanish equivalent of ICD-O).

The original dataset is distributed in Brat format, and was randomly sampled into 3 subsets. The training, development and test sets contain 501, 500 and 300 documents each, respectively.

This dataset was designed for the CANcer TExt Mining Shared Task, sponsored by Plan-TL. The task is divided in 3 subtasks: CANTEMIST-NER, CANTEMIST_NORM and CANTEMIST-CODING.

CANTEMIST-NER track: requires finding automatically tumor morphology mentions. All tumor morphology mentions are defined by their corresponding character offsets in UTF-8 plain text medical documents.

CANTEMIST-NORM track: clinical concept normalization or named entity normalization task that requires to return all tumor morphology entity mentions together with their corresponding eCIE-O-3.1 codes i.e. finding and normalizing tumor morphology mentions.

CANTEMIST-CODING track: requires returning for each of document a ranked list of its corresponding ICD-O-3 codes. This it is essentially a sort of indexing or multi-label classification task or oncology clinical coding.

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

Citation Information

@article{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, Antonio and Farr{'e}, Eul{\`a}lia and Krallinger, Martin},
  journal={IberLEF@ SEPLN},
  pages={303--323},
  year={2020}
}