README.md

metadata

language:
  - en
bigbio_language:
  - English
license: other
multilinguality: monolingual
bigbio_license_shortname: PUBLIC_DOMAIN_MARK_1p0
pretty_name: ChemProt
homepage: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vi/track-5/
bigbio_pubmed: true
bigbio_public: true
bigbio_tasks:
  - RELATION_EXTRACTION
  - NAMED_ENTITY_RECOGNITION
dataset_info:
  - config_name: chemprot_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: sample
        num_bytes: 174378
        num_examples: 50
      - name: train
        num_bytes: 3509825
        num_examples: 1020
      - name: test
        num_bytes: 2838045
        num_examples: 800
      - name: validation
        num_bytes: 2098255
        num_examples: 612
    download_size: 3644874
    dataset_size: 8620503
  - config_name: chemprot_full_source
    features:
      - name: pmid
        dtype: string
      - name: text
        dtype: string
      - name: entities
        sequence:
          - name: id
            dtype: string
          - name: type
            dtype: string
          - name: text
            dtype: string
          - name: offsets
            sequence: int64
      - name: relations
        sequence:
          - name: type
            dtype: string
          - name: arg1
            dtype: string
          - name: arg2
            dtype: string
    splits:
      - name: sample
        num_bytes: 159878
        num_examples: 50
      - name: train
        num_bytes: 3161241
        num_examples: 1020
      - name: test
        num_bytes: 2550891
        num_examples: 800
      - name: validation
        num_bytes: 1902042
        num_examples: 612
    download_size: 2938603
    dataset_size: 7774052
  - config_name: chemprot_shared_task_eval_source
    features:
      - name: pmid
        dtype: string
      - name: text
        dtype: string
      - name: entities
        sequence:
          - name: id
            dtype: string
          - name: type
            dtype: string
          - name: text
            dtype: string
          - name: offsets
            sequence: int64
      - name: relations
        sequence:
          - name: type
            dtype: string
          - name: arg1
            dtype: string
          - name: arg2
            dtype: string
    splits:
      - name: sample
        num_bytes: 157609
        num_examples: 50
      - name: train
        num_bytes: 3109953
        num_examples: 1020
      - name: test
        num_bytes: 2499388
        num_examples: 800
      - name: validation
        num_bytes: 1876378
        num_examples: 612
    download_size: 2924370
    dataset_size: 7643328
configs:
  - config_name: chemprot_bigbio_kb
    data_files:
      - split: sample
        path: chemprot_bigbio_kb/sample-*
      - split: train
        path: chemprot_bigbio_kb/train-*
      - split: test
        path: chemprot_bigbio_kb/test-*
      - split: validation
        path: chemprot_bigbio_kb/validation-*
  - config_name: chemprot_full_source
    data_files:
      - split: sample
        path: chemprot_full_source/sample-*
      - split: train
        path: chemprot_full_source/train-*
      - split: test
        path: chemprot_full_source/test-*
      - split: validation
        path: chemprot_full_source/validation-*
    default: true
  - config_name: chemprot_shared_task_eval_source
    data_files:
      - split: sample
        path: chemprot_shared_task_eval_source/sample-*
      - split: train
        path: chemprot_shared_task_eval_source/train-*
      - split: test
        path: chemprot_shared_task_eval_source/test-*
      - split: validation
        path: chemprot_shared_task_eval_source/validation-*

Dataset Card for ChemProt

Dataset Description

• Homepage: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vi/track-5/
• Pubmed: True
• Public: True
• Tasks: RE,NER

The BioCreative VI Chemical-Protein interaction dataset identifies entities of chemicals and proteins and their likely relation to one other. Compounds are generally agonists (activators) or antagonists (inhibitors) of proteins.

Citation Information

@article{DBLP:journals/biodb/LiSJSWLDMWL16,
  author    = {Krallinger, M., Rabal, O., Lourenço, A.},
  title     = {Overview of the BioCreative VI chemical-protein interaction Track},
  journal   = {Proceedings of the BioCreative VI Workshop,},
  volume    = {141-146},
  year      = {2017},
  url       = {https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vi/track-5/},
  doi       = {},
  biburl    = {},
  bibsource = {}
}