README.md

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.