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bio-datasets
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re-medical-annotations

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The dataset viewer is not available for this dataset.
Cannot get the config names for the dataset.
Error code:   ConfigNamesError
Exception:    ImportError
Message:      To be able to use bio-datasets/re-medical-annotations, you need to install the following dependency: cassis.
Please install it using 'pip install cassis' for instance.
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 "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/inspect.py", line 347, in get_dataset_config_names
                  dataset_module = dataset_module_factory(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1914, in dataset_module_factory
                  raise e1 from None
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1880, in dataset_module_factory
                  return HubDatasetModuleFactoryWithScript(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 1504, in get_module
                  local_imports = _download_additional_modules(
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/load.py", line 354, in _download_additional_modules
                  raise ImportError(
              ImportError: To be able to use bio-datasets/re-medical-annotations, you need to install the following dependency: cassis.
              Please install it using 'pip install cassis' for instance.

Need help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.

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Dataset Card for re-medical-annotations

Dataset Description

Dataset Summary

HuggingFace Dataset from the Inception Medical Annotations project.

This dataset can be used locally with any archive downloaded from Inception that contains relation annotations.

Loading this dataset requires dkpro-cassis>=0.7.2.

Example: load the dataset from the "RE Temporality POC"

import datasets

ds = datasets.load_dataset(
    "bio-datasets/re-medical-annotations",
    data_dir=<Inception Archive path>,
    labels = ["bound"],
)

Dataset Structure

Data Fields

  • text (str): text of the sentence
  • subj_start (int): start char of the relation subject mention
  • subj_end (int): end char of the relation subject mention, exclusive
  • subj_type (str): NER label of the relation subject
  • obj_start (int): start char of the relation object mention
  • obj_end (int): end char of the relation object mention, exclusive
  • obj_type (str): NER label of the relation object
  • relation (str): the relation label of this instance
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