README.md

---
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}
}

```