search

obophenotype / asct-b_validation

3 stars 0 forks source link

Review Blood v1.1 table #3

Open emquardokus opened 3 years ago

emquardokus commented 3 years ago

Errors WARNING - Unrecognised cell content '' WARNING - Different labels found for CL:0000938. Uberongraph: CD16-negative, CD56-bright natural killer cell, human ; ASCT+b table: CD16-negative, CD56-bright natural killer cell

Table s slabel user_slabel o olabel user_olabel
1 CL:0000990 conventional dendritic cell dendritic cell type 2 (DC2) CL:0001056 dendritic cell, human dendritic cell (DC)
2 CL:0000840 immature conventional dendritic cell transitional Dendritic Cell (tDC) CL:0001056 dendritic cell, human dendritic cell (DC)
3 CL:0000938 CD16-negative, CD56-bright natural killer cell, human CD56 bright Natural killer CL:0000814 mature NK T cell NK lymphocytes
4 CL:0000824 mature natural killer cell mature Natural killer CL:0000814 mature NK T cell NK lymphocytes
emquardokus commented 3 years ago

Errors mostly from blank spreadsheet cells for label/ID --> WARNING - Unrecognised cell content ''

Corrected mismatched label: WARNING - Different labels found for CL:0000938. Uberongraph: CD16-negative, CD56-bright natural killer cell, human ; ASCT+b table: CD16-negative, CD56-bright natural killer cell

ASCT+B table log issues Seems like there is an issue in CL with human lineage vs generic immune cell lineages. Dendritic cells and Nature killer cell types have both generic and human versions, we are dealing with human representations, but then relationships are not present that should be.

Partially Resolved issue 1 CL:0000990 | conventional dendritic cell | dendritic cell type 2 (DC2) | CL:0001056 | dendritic cell, human | dendritic cell (DC) Consulted Azimuth Reference Map and Authors manuscript regarding identity, lineage of DC2 cell type; parent would be myeloid dendritic cell, but given human specificity, seems like there is a relationship missing in ontology.

Revised cell type CL to dendritic cell type 2 (DC2) CD1c-positive myeloid dendritic cell CL:0002399

Parent likely should be myeloid dendritic cell, human CL:0001057; however, if human version is selected, no subclasses exist for CD1c-positive myeloid dendritic cell | CL:0002399

Issues 3 and 4 seem like a problem from author in that NK T cell are a subset of T cells. Melsen, Janine E, Gertjan Lugthart, Arjan C Lankester, and Marco W Schilham. 2016. “Human Circulating and Tissue-Resident CD56(Bright) Natural Killer Cell Populations.” Frontiers in Immunology 7 (June): 262–262. https://doi.org/10.3389/fimmu.2016.00262.

"In humans, two conventional NK cell subsets have been phenotypically defined based on CD56 and CD16 (FCRγIII) surface expression: CD56brightCD16−/+ and CD56dimCD16+. " "Based on this cytokine secretion profile, NK cells are classified into group 1 of the large family of innate lymphoid cells (ILCs). Developmentally, NK
cells are not related to the other (non-cytotoxic) ILCs"

NK lymphocytes mature NK T cell CL:0000814 CD56 bright Natural killer CD16-negative, CD56-bright natural killer cell, human CL:0000938

NK lymphocytes | mature NK T cell | CL:0000814 | mature Natural killer | mature natural killer cell | CL:0000824