Add CD14-negative phenotype to human myeloid and plasmacytoid dendritic cells

[Copilot]

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:

1. OMIP-77
2. OMIP-87
3. OMIP-94
4. OMIP-101
5. OMIP-112

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 [Class hierarchy] Add "CD14 lacks" to human dendritic cell terms #3163

---

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[Caroline-99]

#gogoeditdiff

[github-actions]

Here's a diff of how these changes impact the classified ontology (on -base file):

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2025-12-18/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-master.owl/cl-base.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl/cl-base.owl
• Version IRI: http://purl.obolibrary.org/obo/cl/releases/2025-12-18/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

PR_000001182 http://purl.obolibrary.org/obo/PR_000001182

Added

• Class: PR_000001182

myeloid dendritic cell, human http://purl.obolibrary.org/obo/CL_0001057

Removed

• myeloid dendritic cell, human IAO_0000115 "A myeloid dendritic cell with the phenotype HLA-DRA-positive."

  • hasDbXref "PMID:22343568"

  • hasDbXref "GOC:add"

• myeloid dendritic cell, human EquivalentTo myeloid dendritic cell and (RO_0002104 some PR_000002015) and (RO_0002162 some NCBITaxon_9606)

Added

• myeloid dendritic cell, human IAO_0000115 "A myeloid dendritic cell with the phenotype HLA-DRA-positive and CD14-negative."

  • hasDbXref "PMID:37254600"

  • hasDbXref "PMID:40095400"

  • hasDbXref "PMID:22343568"

  • hasDbXref "PMID:34260151"

  • hasDbXref "PMID:36470845"

  • hasDbXref "GOC:add"

  • hasDbXref "PMID:38343094"

• myeloid dendritic cell, human EquivalentTo myeloid dendritic cell and (lacks_plasma_membrane_part some PR_000001182) and (RO_0002104 some PR_000002015) and (RO_0002162 some NCBITaxon_9606)

• myeloid dendritic cell, human SubClassOf lacks_plasma_membrane_part some PR_000001182

plasmacytoid dendritic cell, human http://purl.obolibrary.org/obo/CL_0001058

Removed

• plasmacytoid dendritic cell, human IAO_0000115 "A plasmacytoid dendritic cell with the phenotype HLA-DRA-positive, CD123-positive, and CD11c-negative."

  • hasDbXref "PMID:22343568"

  • hasDbXref "GOC:add"

• plasmacytoid dendritic cell, human EquivalentTo plasmacytoid dendritic cell and (lacks_plasma_membrane_part some PR_000001013) and (RO_0002104 some PR_000001865) and (RO_0002104 some PR_000002015) and (RO_0002162 some NCBITaxon_9606)

Added

• plasmacytoid dendritic cell, human IAO_0000115 "A plasmacytoid dendritic cell with the phenotype HLA-DRA-positive, CD123-positive, CD11c-negative, and CD14-negative."

  • hasDbXref "PMID:37254600"

  • hasDbXref "PMID:40095400"

  • hasDbXref "PMID:22343568"

  • hasDbXref "PMID:34260151"

  • hasDbXref "PMID:36470845"

  • hasDbXref "GOC:add"

  • hasDbXref "PMID:38343094"

• plasmacytoid dendritic cell, human EquivalentTo plasmacytoid dendritic cell and (lacks_plasma_membrane_part some PR_000001013) and (lacks_plasma_membrane_part some PR_000001182) and (RO_0002104 some PR_000001865) and (RO_0002104 some PR_000002015) and (RO_0002162 some NCBITaxon_9606)

• plasmacytoid dendritic cell, human SubClassOf lacks_plasma_membrane_part some PR_000001182

[github-actions]

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

• Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/master/src/ontology/cl-edit.owl

Right

• Ontology IRI: http://purl.obolibrary.org/obo/cl.owl
• Version IRI: None
• Loaded from: file:/__w/cell-ontology/cell-ontology/branch/src/ontology/cl-edit.owl

Ontology imports

Ontology annotations

myeloid dendritic cell, human http://purl.obolibrary.org/obo/CL_0001057

Removed

• myeloid dendritic cell, human definition "A myeloid dendritic cell with the phenotype HLA-DRA-positive."

  • database_cross_reference "GOC:add"

  • database_cross_reference "PMID:22343568"

• myeloid dendritic cell, human EquivalentTo myeloid dendritic cell and (has plasma membrane part some MHC class II histocompatibility antigen alpha chain DRA) and (in taxon some Homo sapiens)

Added

• myeloid dendritic cell, human definition "A myeloid dendritic cell with the phenotype HLA-DRA-positive and CD14-negative."

  • database_cross_reference "PMID:37254600"

  • database_cross_reference "PMID:38343094"

  • database_cross_reference "PMID:36470845"

  • database_cross_reference "GOC:add"

  • database_cross_reference "PMID:34260151"

  • database_cross_reference "PMID:40095400"

  • database_cross_reference "PMID:22343568"

• myeloid dendritic cell, human EquivalentTo myeloid dendritic cell and (lacks_plasma_membrane_part some PR_000001182) and (has plasma membrane part some MHC class II histocompatibility antigen alpha chain DRA) and (in taxon some Homo sapiens)

plasmacytoid dendritic cell, human http://purl.obolibrary.org/obo/CL_0001058

Removed

• plasmacytoid dendritic cell, human definition "A plasmacytoid dendritic cell with the phenotype HLA-DRA-positive, CD123-positive, and CD11c-negative."

  • database_cross_reference "GOC:add"

  • database_cross_reference "PMID:22343568"

• plasmacytoid dendritic cell, human EquivalentTo plasmacytoid dendritic cell and (lacks_plasma_membrane_part some integrin alpha-X) and (has plasma membrane part some interleukin-3 receptor class 2 alpha chain) and (has plasma membrane part some MHC class II histocompatibility antigen alpha chain DRA) and (in taxon some Homo sapiens)

Added

• plasmacytoid dendritic cell, human definition "A plasmacytoid dendritic cell with the phenotype HLA-DRA-positive, CD123-positive, CD11c-negative, and CD14-negative."

  • database_cross_reference "PMID:37254600"

  • database_cross_reference "PMID:38343094"

  • database_cross_reference "PMID:36470845"

  • database_cross_reference "GOC:add"

  • database_cross_reference "PMID:34260151"

  • database_cross_reference "PMID:40095400"

  • database_cross_reference "PMID:22343568"

• plasmacytoid dendritic cell, human EquivalentTo plasmacytoid dendritic cell and (lacks_plasma_membrane_part some integrin alpha-X) and (lacks_plasma_membrane_part some PR_000001182) and (has plasma membrane part some interleukin-3 receptor class 2 alpha chain) and (has plasma membrane part some MHC class II histocompatibility antigen alpha chain DRA) and (in taxon some Homo sapiens)

[Caroline-99]

@copilot you have not used the right PR ID. Please use the ols mcp to find the PR id for this term "CD14 molecule", validate it against the label given, then add it appropriately to the logical definition of the two terms

[Copilot]

@copilot you have not used the right PR ID. Please use the ols mcp to find the PR id for this term "CD14 molecule", validate it against the label given, then add it appropriately to the logical defini...

Fixed in commit 7584464. I used OLS to find the correct PRO ID for "CD14 molecule" (PR_000001889) and updated both CL_0001057 and CL_0001058. The ontology has been validated with robot reasoning successfully.