| # PIE Dataset Card for "CoMAGC" | |
| This is a [PyTorch-IE](https://github.com/ChristophAlt/pytorch-ie) wrapper for the | |
| [CoMAGC Huggingface dataset loading script](https://huggingface.co/datasets/DFKI-SLT/CoMAGC). | |
| ## 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](https://github.com/ArneBinder/pie-modules/blob/main/src/pie_modules/annotations.py) and | |
| [here](https://github.com/ChristophAlt/pytorch-ie/blob/main/src/pytorch_ie/annotations.py) 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](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-323/tables/3)), | |
| 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](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-14-323/tables/7)). | |
| See [here](https://github.com/ArneBinder/pie-modules/blob/main/src/pie_modules/documents.py) and | |
| [here](https://github.com/ChristophAlt/pytorch-ie/blob/main/src/pytorch_ie/documents.py) for the document type | |
| definitions. | |