Add CL term for nerve-associated tissue-resident macrophage (CL:9900001)

[Copilot]

This PR adds a missing Cell Ontology term for a conserved nerve-adjacent tissue-resident macrophage subset, including the requested nomenclature, literature-backed definition, and core biological constraints. It models the dermis context while preserving the cross-tissue niche-based identity described in the request.

• New ontology class

  • Added obo:CL_9900001 with label: nerve-associated tissue-resident macrophage
  • Added issue tracker annotation (IAO:0000233) and term metadata (terms:creator, terms:date)

• Definition + evidence annotations

  • Added a definition capturing:
    • nerve-adjacent tissue residency
    • MHCII-high / LYVE1-low / CCR2-negative phenotype
    • mouse and human cross-tissue context
  • Added supporting PMID xrefs corresponding to the cited key publications

• Synonym model

  • Added exact synonyms:
    • MHC class II-high macrophage
    • MHCIIhi macrophage
    • MHCII+ macrophage
  • Added related synonym:
    • nerve- and airway-associated macrophage
  • Synonyms include source references as provided

• Logical placement and axioms

  • Parent: SubClassOf(obo:CL_9900001 obo:CL_0000864) (tissue-resident macrophage)
  • Location: part_of some UBERON:0002067 (dermis)
  • Functional axioms:
    • capable_of some GO:0002495 (MHC class II antigen processing/presentation)
    • capable_of_part_of some GO:0001525 (angiogenesis)

# Class: obo:CL_9900001 (nerve-associated tissue-resident macrophage)
SubClassOf(obo:CL_9900001 obo:CL_0000864)
SubClassOf(obo:CL_9900001 ObjectSomeValuesFrom(obo:BFO_0000050 obo:UBERON_0002067))
SubClassOf(obo:CL_9900001 ObjectSomeValuesFrom(obo:RO_0002215 obo:GO_0002495))
SubClassOf(obo:CL_9900001 ObjectSomeValuesFrom(obo:RO_0002216 obo:GO_0001525))

[RiveraAndrea83]

#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/2026-06-16/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/2026-06-16/cl-base.owl
• Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

GO_0001525 http://purl.obolibrary.org/obo/GO_0001525

Added

• Class: GO_0001525

nerve-associated tissue-resident macrophage http://purl.obolibrary.org/obo/CL_9900001

Added

• Class: nerve-associated tissue-resident macrophage

• nerve-associated tissue-resident macrophage IAO_0000233 3612

• nerve-associated tissue-resident macrophage creator "GitHub Copilot"

• nerve-associated tissue-resident macrophage date "2026-06-11T09:17:56Z"^^dateTime

• nerve-associated tissue-resident macrophage hasExactSynonym "MHCII+ macrophage"

  • hasDbXref "DOI:10.1038/s41586-024-08002-x"

• nerve-associated tissue-resident macrophage hasExactSynonym "MHCIIhi macrophage"

  • hasDbXref "DOI:10.1126/science.aau0964"

• nerve-associated tissue-resident macrophage hasExactSynonym "MHC class II-high macrophage"

  • hasDbXref "DOI:10.1126/science.abf7777"

• nerve-associated tissue-resident macrophage hasRelatedSynonym "nerve- and airway-associated macrophage"

  • hasDbXref "DOI:10.1126/sciimmunol.aax8756"

• nerve-associated tissue-resident macrophage IAO_0000115 "A tissue-resident macrophage that preferentially occupies nerve-adjacent niches across multiple tissues. In mouse skin, this cell ensheathes peripheral nerves and its depletion impairs axon regrowth after injury. It is characterized by high MHC class II and low LYVE1 expression with CCR2 negativity, and in mice shows a Lyve1lo MHCIIhi CX3CR1hi profile. In humans, a corresponding population expresses HLA-DPA1, HLA-DRA, and CLEC7A and is found across fetal organs and prenatal skin."

  • hasDbXref "PMID:31462493"

  • hasDbXref "PMID:35390060"

  • hasDbXref "PMID:30523129"

  • hasDbXref "PMID:31348891"

  • hasDbXref "PMID:33958446"

  • hasDbXref "PMID:38735380"

• nerve-associated tissue-resident macrophage label "nerve-associated tissue-resident macrophage"

• nerve-associated tissue-resident macrophage SubClassOf tissue-resident macrophage

• nerve-associated tissue-resident macrophage SubClassOf BFO_0000050 some UBERON_0002067

• nerve-associated tissue-resident macrophage SubClassOf RO_0002215 some GO_0002495

• nerve-associated tissue-resident macrophage SubClassOf RO_0002216 some GO_0001525

[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

nerve-associated tissue-resident macrophage http://purl.obolibrary.org/obo/CL_9900001

Added

• Class: nerve-associated tissue-resident macrophage

• nerve-associated tissue-resident macrophage term tracker item 3612

• nerve-associated tissue-resident macrophage creator "GitHub Copilot"

• nerve-associated tissue-resident macrophage date "2026-06-11T09:17:56Z"^^dateTime

• nerve-associated tissue-resident macrophage has exact synonym "MHCII+ macrophage"

  • database_cross_reference "DOI:10.1038/s41586-024-08002-x"

• nerve-associated tissue-resident macrophage has exact synonym "MHCIIhi macrophage"

  • database_cross_reference "DOI:10.1126/science.aau0964"

• nerve-associated tissue-resident macrophage has exact synonym "MHC class II-high macrophage"

  • database_cross_reference "DOI:10.1126/science.abf7777"

• nerve-associated tissue-resident macrophage has_related_synonym "nerve- and airway-associated macrophage"

  • database_cross_reference "DOI:10.1126/sciimmunol.aax8756"

• nerve-associated tissue-resident macrophage definition "A tissue-resident macrophage that preferentially occupies nerve-adjacent niches across multiple tissues. In mouse skin, this cell ensheathes peripheral nerves and its depletion impairs axon regrowth after injury. It is characterized by high MHC class II and low LYVE1 expression with CCR2 negativity, and in mice shows a Lyve1lo MHCIIhi CX3CR1hi profile. In humans, a corresponding population expresses HLA-DPA1, HLA-DRA, and CLEC7A and is found across fetal organs and prenatal skin."

  • database_cross_reference "PMID:30523129"

  • database_cross_reference "PMID:35390060"

  • database_cross_reference "PMID:38735380"

  • database_cross_reference "PMID:31462493"

  • database_cross_reference "PMID:33958446"

  • database_cross_reference "PMID:31348891"

• nerve-associated tissue-resident macrophage label "nerve-associated tissue-resident macrophage"

• nerve-associated tissue-resident macrophage SubClassOf tissue-resident macrophage

• nerve-associated tissue-resident macrophage SubClassOf part of some dermis

• nerve-associated tissue-resident macrophage SubClassOf capable of some antigen processing and presentation of peptide antigen via MHC class II

• nerve-associated tissue-resident macrophage SubClassOf capable of part of some angiogenesis

[github-actions]

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so.