OMAP extension for cell types and biomarker sets

[bherr2]

DO Processor side of: hubmapconsortium/ccf-asct-reporter#821

**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.

[bherr2]

CC @emquardokus

[bherr2]

@emquardokus how can we move this issue forward in 2025?

[emquardokus]

@emquardokus how can we move this issue forward in 2025?

@bherr2 ive been working with all the OMAP authors and have 2 preliminary ones filled. In that exercise we explored potentially better or automated ways to get the information from microscopy data directly. These discussions are on-going and we as a microscopy community are trying to work out best method to get there.
In the mean time we do have 2 we could work with.
Some additional issues came up in discussion for this so ARWG (affinity reagents working group) is working these issues through.
I believe we could deliver this for June 2025.