bc5cdr

Tasks:

Token Classification

Sub-tasks:

named-entity-recognition

Languages:

English

Size:

10K<n<100K

License:

Dataset card Files Files and versions

xet

Community

Dataset Viewer

The dataset viewer is not available for this dataset.

Cannot get the config names for the dataset.

Error code:   ConfigNamesError
Exception:    RuntimeError
Message:      Dataset scripts are no longer supported, but found bc5cdr.py
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/dataset/config_names.py", line 66, in compute_config_names_response
                  config_names = get_dataset_config_names(
                                 ^^^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/inspect.py", line 161, in get_dataset_config_names
                  dataset_module = dataset_module_factory(
                                   ^^^^^^^^^^^^^^^^^^^^^^^
                File "/usr/local/lib/python3.12/site-packages/datasets/load.py", line 1207, in dataset_module_factory
                  raise e1 from None
                File "/usr/local/lib/python3.12/site-packages/datasets/load.py", line 1167, in dataset_module_factory
                  raise RuntimeError(f"Dataset scripts are no longer supported, but found {filename}")
              RuntimeError: Dataset scripts are no longer supported, but found bc5cdr.py

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Dataset Card for "tner/bc5cdr"

Dataset Summary

BioCreative V CDR NER dataset formatted in a part of TNER project. The original dataset consists of long documents which cannot be fed on LM because of the length, so we split them into sentences to reduce their size.

Entity Types: Chemical, Disease

Dataset Structure

Data Instances

An example of train looks as follows.

{
    'tags': [2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0],
    'tokens': ['Fasciculations', 'in', 'six', 'areas', 'of', 'the', 'body', 'were', 'scored', 'from', '0', 'to', '3', 'and', 'summated', 'as', 'a', 'total', 'fasciculation', 'score', '.']
}

Label ID

The label2id dictionary can be found at here.

{
    "O": 0,
    "B-Chemical": 1,
    "B-Disease": 2,
    "I-Disease": 3,
    "I-Chemical": 4
}

Data Splits

name	train	validation	test
bc5cdr	5228	5330	5865

Citation Information

@article{wei2016assessing,
  title={Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task},
  author={Wei, Chih-Hsuan and Peng, Yifan and Leaman, Robert and Davis, Allan Peter and Mattingly, Carolyn J and Li, Jiao and Wiegers, Thomas C and Lu, Zhiyong},
  journal={Database},
  volume={2016},
  year={2016},
  publisher={Oxford Academic}
}

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