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Add 'cantemist_bigbio_text' config data files
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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_bigbio_kb
    features:
      - name: id
        dtype: string
      - name: document_id
        dtype: string
      - name: passages
        list:
          - name: id
            dtype: string
          - name: type
            dtype: string
          - name: text
            sequence: string
          - name: offsets
            sequence:
              list: int32
      - name: entities
        list:
          - name: id
            dtype: string
          - name: type
            dtype: string
          - name: text
            sequence: string
          - name: offsets
            sequence:
              list: int32
          - name: normalized
            list:
              - name: db_name
                dtype: string
              - name: db_id
                dtype: string
      - name: events
        list:
          - name: id
            dtype: string
          - name: type
            dtype: string
          - name: trigger
            struct:
              - name: text
                sequence: string
              - name: offsets
                sequence:
                  list: int32
          - name: arguments
            list:
              - name: role
                dtype: string
              - name: ref_id
                dtype: string
      - name: coreferences
        list:
          - name: id
            dtype: string
          - name: entity_ids
            sequence: string
      - name: relations
        list:
          - name: id
            dtype: string
          - name: type
            dtype: string
          - name: arg1_id
            dtype: string
          - name: arg2_id
            dtype: string
          - name: normalized
            list:
              - name: db_name
                dtype: string
              - name: db_id
                dtype: string
    splits:
      - name: train
        num_bytes: 3431289
        num_examples: 501
      - name: test
        num_bytes: 1883309
        num_examples: 300
      - name: validation
        num_bytes: 3111616
        num_examples: 500
    download_size: 4000409
    dataset_size: 8426214
  - config_name: cantemist_bigbio_text
    features:
      - name: id
        dtype: string
      - name: document_id
        dtype: string
      - name: text
        dtype: string
      - name: labels
        list: string
    splits:
      - name: train
        num_bytes: 2704288
        num_examples: 501
      - name: test
        num_bytes: 1468362
        num_examples: 300
      - name: validation
        num_bytes: 2425597
        num_examples: 500
    download_size: 3605238
    dataset_size: 6598247
  - 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_bigbio_kb
    data_files:
      - split: train
        path: cantemist_bigbio_kb/train-*
      - split: test
        path: cantemist_bigbio_kb/test-*
      - split: validation
        path: cantemist_bigbio_kb/validation-*
  - config_name: cantemist_bigbio_text
    data_files:
      - split: train
        path: cantemist_bigbio_text/train-*
      - split: test
        path: cantemist_bigbio_text/test-*
      - split: validation
        path: cantemist_bigbio_text/validation-*
  - 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

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 [email protected]

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}
}