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_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_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}
}