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pie
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drugprot

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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 pie/drugprot, you need to install the following dependencies: pytorch_ie, pie_datasets.
Please install them using 'pip install pytorch_ie pie_datasets' 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 pie/drugprot, you need to install the following dependencies: pytorch_ie, pie_datasets.
              Please install them using 'pip install pytorch_ie pie_datasets' for instance.

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PIE Dataset Card for "DrugProt"

This is a PyTorch-IE wrapper for the DrugProt Huggingface dataset loading script.

Data Schema

There are two versions of the dataset supported, drugprot_source and drugprot_bigbio_kb.

DrugprotDocument for drugprot_source

defines following fields:

  • text (str)
  • id (str, optional)
  • metadata (dictionary, optional)
  • title (str, optional)
  • abstract (str, optional)

and the following annotation layers:

  • entities (annotation type: LabeledSpan, target: text)
  • relations (annotation type: BinaryRelation, target: entities)

DrugprotBigbioDocument for drugprot_bigbio_kb

defines following fields:

  • text (str)
  • id (str, optional)
  • metadata (dictionary, optional)

and the following annotation layers:

  • passages (annotation type: LabeledSpan, target: text)
  • entities (annotation type: LabeledSpan, target: text)
  • relations (annotation type: BinaryRelation, target: entities)

See here for the annotation type definitions.

Document Converters

The dataset provides predefined document converters for the following target document types:

  • pie_modules.documents.TextDocumentWithLabeledSpansAndBinaryRelations for DrugprotDocument
  • pie_modules.documents.TextDocumentWithLabeledSpansBinaryRelationsAndLabeledPartitions for DrugprotBigbioDocument

See here for the document type definitions.

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