README.md

metadata

language:
  - en
license: other
multilinguality: monolingual
pretty_name: BC5CDR
bigbio_language:
  - English
bigbio_license_shortname: PUBLIC_DOMAIN_MARK_1p0
homepage: http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/
bigbio_pubmed: true
bigbio_public: true
bigbio_tasks:
  - NAMED_ENTITY_RECOGNITION
  - NAMED_ENTITY_DISAMBIGUATION
  - RELATION_EXTRACTION
dataset_info:
  - config_name: bc5cdr_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: 2026145
        num_examples: 500
      - name: test
        num_bytes: 2116547
        num_examples: 500
      - name: validation
        num_bytes: 2086230
        num_examples: 500
    download_size: 2180845
    dataset_size: 6228922
  - config_name: bc5cdr_source
    features:
      - name: passages
        list:
          - name: document_id
            dtype: string
          - name: type
            dtype: string
          - name: text
            dtype: string
          - name: entities
            list:
              - name: id
                dtype: string
              - name: offsets
                list:
                  list: int32
              - name: text
                list: string
              - name: type
                dtype: string
              - name: normalized
                list:
                  - name: db_name
                    dtype: string
                  - name: db_id
                    dtype: string
          - name: relations
            list:
              - name: id
                dtype: string
              - name: type
                dtype: string
              - name: arg1_id
                dtype: string
              - name: arg2_id
                dtype: string
    splits:
      - name: train
        num_bytes: 1488733
        num_examples: 500
      - name: test
        num_bytes: 1535335
        num_examples: 500
      - name: validation
        num_bytes: 1492464
        num_examples: 500
    download_size: 1516417
    dataset_size: 4516532
configs:
  - config_name: bc5cdr_bigbio_kb
    data_files:
      - split: train
        path: bc5cdr_bigbio_kb/train-*
      - split: test
        path: bc5cdr_bigbio_kb/test-*
      - split: validation
        path: bc5cdr_bigbio_kb/validation-*
  - config_name: bc5cdr_source
    data_files:
      - split: train
        path: bc5cdr_source/train-*
      - split: test
        path: bc5cdr_source/test-*
      - split: validation
        path: bc5cdr_source/validation-*
    default: true

Dataset Card for BC5CDR

Dataset Description

• Homepage: http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/
• Pubmed: True
• Public: True
• Tasks: NER,NED,RE

The BioCreative V Chemical Disease Relation (CDR) dataset is a large annotated text corpus of human annotations of all chemicals, diseases and their interactions in 1,500 PubMed articles.

Citation Information

@article{DBLP:journals/biodb/LiSJSWLDMWL16,
  author    = {Jiao Li and
               Yueping Sun and
               Robin J. Johnson and
               Daniela Sciaky and
               Chih{-}Hsuan Wei and
               Robert Leaman and
               Allan Peter Davis and
               Carolyn J. Mattingly and
               Thomas C. Wiegers and
               Zhiyong Lu},
  title     = {BioCreative {V} {CDR} task corpus: a resource for chemical disease
               relation extraction},
  journal   = {Database J. Biol. Databases Curation},
  volume    = {2016},
  year      = {2016},
  url       = {https://doi.org/10.1093/database/baw068},
  doi       = {10.1093/database/baw068},
  timestamp = {Thu, 13 Aug 2020 12:41:41 +0200},
  biburl    = {https://dblp.org/rec/journals/biodb/LiSJSWLDMWL16.bib},
  bibsource = {dblp computer science bibliography, https://dblp.org}
}