hubmapconsortium/ccf-asct-reporter

Support cell type lineage with biomarkers per level of cell type

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Current implementation of ASCT+B reporter supports multiple cell type levels CT/1—> CT/2—> CT/3 ; however, all biomarkers are applied only to the terminal CT/3 cell type.

If we want to represent a more meaningful cell type lineage representation, we want to be able to do the following and capture each cell type level with it's distinctive biomarkers as follows:

CT/1 with its biomarkers—> CT/2 with its biomarkers + CT/1 biomarkers —> CT/3 with its biomarkers + CT/1 +CT/2 biomarkers.

Real example:
CT/1 is epithelial cell BGene/1, BGene/2, BGene/3 biomarkers identify the broad category of epithelial cells
CT/2 is a type of epithelial cell called epithelial cell of tracheobronchial tree
CT/3 is the most specific epithelial cell type annotation called ciliated columnar cell of tracheobronchial tree