hubmapconsortium/ccf-asct-reporter

feature request: support for OMAP extension for cell types and biomarker sets

Opened this issue · 0 comments

**Feature needed: capturing specific cell types with their biomarker sets in an OMAP

Organ mapping antibody panels have antibodies that recognize protein targets.
A subset of these protein targets when they light up a cell in an image, tell you what kind of cell it is.
** OMAP Extension proposed:**
Add cell type space parenthesis CL ID parenthesis. Example: Epithelial cell (CL:0000066)
Complexity of nomenclature:*
Needs to be able to recognize longer cell type names with many spaces between words and sometimes hyphens and commas Example: CD4-positive, alpha-beta cytotoxic T cell (CL:0000934)

For the individual rows of targets, each column representing a cell type would have one of 3 choices: POS for positive, NEG for negative, NA for not applicable for determining the cell type listed in the column header. The reason for these choices is because some cells, especially immune cells, the marker presence or absence can be critical for determining the cell type. We use letters rather than symbols so we do not have problems with spreadsheet programs interpreting + or - as math symbols.