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pie
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comagc

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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/comagc, 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/comagc, 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 "CoMAGC"

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

Data Schema

The document type for this dataset is ComagcDocument which defines the following data fields:

  • pmid (str): unique sentence identifier
  • sentence (str)
  • cancer_type (str)
  • cge (str): change in gene expression
  • ccs (str): change in cell state
  • pt (str, optional): proposition type
  • ige (str, optional): initial gene expression level

and the following annotation layers:

  • gene (annotation type: NamedSpan, target: sentence)
  • cancer (annotation type: NamedSpan, target: sentence)
  • expression_change_keyword1 (annotation type: SpanWithNameAndType, target: sentence)
  • expression_change_keyword2 (annotation type: SpanWithNameAndType, target: sentence)

NamedSpan is a custom annotation type that extends typical Span with the following data fields:

  • name (str): entity string between span start and end

SpanWithNameAndType is a custom annotation type that extends typical Span with the following data fields:

  • name (str): entity string between span start and end
  • type (str): entity type classifying the expression

See here and here for the annotation type definitions.

Document Converters

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

  • pie_modules.documents.TextDocumentWithLabeledSpansAndBinaryRelations:

    • labeled_spans: There are always two labeled spans in each sentence. The first one refers to the gene, while the second one refers to the cancer. Therefore, the label is either "GENE" or "CANCER".
    • binary_relations: There is always one binary relation in each sentence. This relation is always established between the gene as head and the cancer as tail. The specific label is the related gene-class. It is obtained from inference rules (cf here), that are based on the values of the columns CGE, CCS, IGE and PT. In case no gene-class can be inferred, no binary relation is added to the document. In total to 303 of the 821 examples, there is no rule is applicable (cf here).

See here and here for the document type definitions.

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