obophenotype
Add CD14-negative phenotype to human myeloid and plasmacytoid dendritic cells
Standard flow cytometry gating strategies consistently define human myeloid and plasmacytoid dendritic cells as CD14-negative to distinguish them from monocytes. This PR adds the CD14-negative phenotype to CL_0001057 and CL_0001058 per OMIP references provided.
Changes
CL_0001057 (myeloid dendritic cell, human):
- Added logical axiom:
lacks_plasma_membrane_part PR_000001889(CD14) - Updated definition: "HLA-DRA-positive and CD14-negative"
- Added references: PMID:34260151, 36470845, 37254600, 38343094, 40095400
CL_0001058 (plasmacytoid dendritic cell, human):
- Added logical axiom:
lacks_plasma_membrane_part PR_000001889(CD14) - Updated definition: "HLA-DRA-positive, CD123-positive, CD11c-negative, and CD14-negative"
- Added references: PMID:34260151, 36470845, 37254600, 38343094, 40095400
Scope
Per @Caroline-99's comment, CL_0001056 (general dendritic cell, human) is intentionally unchanged as tissue-specific DC subsets may express CD14.
Note
The correct PRO ID for "CD14 molecule" (PR_000001889) was verified using the Ontology Lookup Service (OLS).
Original prompt
This section details on the original issue you should resolve
<issue_title>[Class hierarchy] Add "CD14 lacks" to human dendritic cell terms</issue_title> <issue_description>CL term CL_0001057 — myeloid dendritic cell, human CL_0001058 — plasmacytoid dendritic cell, human
Suggested revision of class hierarchy Add: lacks expression of CD14 Although there were previous attempts to annotate DCs with CD14-negative expression (Issue #123, #125, #127), these were unfortunately closed without resolution.
textual def please add in the textual def that this cell is CD14-negative.
References Add these references but do not replace exisiting references
Relevant OMIP references demonstrating standard gating strategy:
These human dendritic cell populations are consistently defined as CD14-negative in flow cytometry gating strategies. Although some tissue-specific DC subsets (e.g., dermal DCs) may express CD14, the general population of human DCs is gated as CD14⁻ to distinguish them from monocytes.
Thank you for your consideration. </issue_description>
Comments on the Issue (you are @copilot in this section)
@Caroline-99 @addiehl could you please check this out ? I agree with adding lack CD14 expression to "[CL_0001057](http://purl.obolibrary.org/obo/CL_0001057) — myeloid dendritic cell, human and [CL_0001058](http://purl.obolibrary.org/obo/CL_0001058) — plasmacytoid dendritic cell, human". However, I am not sure about adding it to the general human term [CL_0001056](http://purl.obolibrary.org/obo/CL_0001056) — dendritic cell, human as there are some human dendritic cells that do express CD14 (PMID: [23621371](https://pubmed.ncbi.nlm.nih.gov/23621371/), [PMID: 34279540](https://pmc.ncbi.nlm.nih.gov/articles/PMC8292131/). Thank you
- Fixes obophenotype/cell-ontology#3163
✨ Let Copilot coding agent set things up for you — coding agent works faster and does higher quality work when set up for your repo.
