[NTR] Add iron-recycling macrophage (CL:9900001) by Copilot · Pull Request #3614 · obophenotype/cell-ontology

Copilot · 2026-04-24T15:01:59Z

No existing CL term captures a tissue-resident macrophage defined by ferroportin-mediated iron recycling from erythrophagocytosis in a prenatal, cross-organ context. Nearest terms (CL:0000874 splenic red pulp macrophage, CL:0000091 Kupffer cell) are each restricted to a single adult tissue.

New term: `CL:9900001` — iron-recycling macrophage

Parent: tissue-resident macrophage (CL:0000864)
Definition: Inline author citations per editorial convention (Ferreira & Gahl 2017; Suo et al. 2022; Gopee et al. 2024)
Synonyms:
- Related: erythrophagocytic tissue-resident macrophage, SLC40A1-positive tissue-resident macrophage [DOI:10.1126/science.abo0510]
- Narrow: prenatal iron-recycling macrophage [DOI:10.1038/s41586-024-08002-x]

Logical axioms

SubClassOf CL:0000864  (tissue-resident macrophage)
SubClassOf capable_of some GO:1903988  (iron ion export across plasma membrane)
SubClassOf capable_of some GO:0042167  (heme catabolic process)
SubClassOf capable_of_part_of some GO:0035767  (endothelial cell chemotaxis)
SubClassOf capable_of_part_of some GO:0001525  (angiogenesis)
SubClassOf expresses some PR:000015138  (ferroportin / SLC40A1)

ID is in the temporary NTR range (idrange:81: 9900000–9999999).

- Adds NTR iron-recycling macrophage to cl-edit.owl - Definition with inline author citations (Ferreira and Gahl 2017, Suo et al 2022, Gopee et al 2024) - Related synonyms: erythrophagocytic tissue-resident macrophage, SLC40A1-positive tissue-resident macrophage - Narrow synonym: prenatal iron-recycling macrophage - Parent: tissue-resident macrophage (CL:0000864) - Logical axioms: capable_of iron ion export (GO:1903988), heme catabolic process (GO:0042167), capable_of_part_of endothelial cell chemotaxis (GO:0035767) and angiogenesis (GO:0001525), expresses ferroportin (PR:000015138) Signed-off-by: GitHub Copilot Agent-Logs-Url: https://github.com/obophenotype/cell-ontology/sessions/9ca89a14-16d5-4f78-ac2c-8f4f2076f9e8 Co-authored-by: RiveraAndrea83 <205639972+RiveraAndrea83@users.noreply.github.com>

RiveraAndrea83 · 2026-04-24T15:13:22Z

#gogoeditdiff

github-actions · 2026-04-24T15:20:02Z

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/2026-05-15/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/2026-05-15/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

GO_0035767 `http://purl.obolibrary.org/obo/GO_0035767`

Added

Class: GO_0035767

GO_0042167 `http://purl.obolibrary.org/obo/GO_0042167`

Added

Class: GO_0042167

GO_1903988 `http://purl.obolibrary.org/obo/GO_1903988`

Added

Class: GO_1903988

GPe MEIS2-SOX6 GABA arkypallidal neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310093`

Removed

GPe MEIS2-SOX6 GABA arkypallidal neuron (Primate) label "arkypallidal neuron (Primate)"

Added

GPe MEIS2-SOX6 GABA arkypallidal neuron (Primate) label "GPe MEIS2-SOX6 GABA arkypallidal neuron (Primate)"

GPe SOX6-CTXND1 GABA prototypic neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310094`

Removed

GPe SOX6-CTXND1 GABA prototypic neuron (Primate) label "prototypic neuron (Primate)"

Added

GPe SOX6-CTXND1 GABA prototypic neuron (Primate) label "GPe SOX6-CTXND1 GABA prototypic neuron (Primate)"

GPi Core internal globus pallidus core projecting neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310095`

Removed

GPi Core internal globus pallidus core projecting neuron (Primate) label "GPi Core neuron (Primate)"

Added

GPi Core internal globus pallidus core projecting neuron (Primate) label "GPi Core internal globus pallidus core projecting neuron (Primate)"

GPi Shell internal globus pallidus shell projection neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310096`

Removed

GPi Shell internal globus pallidus shell projection neuron (Primate) label "GPi Shell neuron (Primate)"

Added

GPi Shell internal globus pallidus shell projection neuron (Primate) label "GPi Shell internal globus pallidus shell projection neuron (Primate)"

GPin-BF Cholinergic GABA GABA-Chol neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310083`

Removed

GPin-BF Cholinergic GABA GABA-Chol neuron (Primate) label "GPin-BF cholinergic-GABAergic neuron (Primate)"

Added

GPin-BF Cholinergic GABA GABA-Chol neuron (Primate) label "GPin-BF Cholinergic GABA GABA-Chol neuron (Primate)"

IgA plasma cell `http://purl.obolibrary.org/obo/CL_0000987`

Removed

LAMP5-CXCL14 GABA lamp5 GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310084`

Removed

LAMP5-CXCL14 GABA lamp5 GABAergic interneuron (Primate) comment "Based on annotation transfer evidence with MapMyCells, this may not represent a transcriptomicallly distinct cell type, but rather the population of LAMP5 GABAergic neurons located in the striatum. Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
LAMP5-CXCL14 GABA lamp5 GABAergic interneuron (Primate) label "striatal LAMP5 CXCL14 GABAergic interneuron (Primate)"

Added

LAMP5-CXCL14 GABA lamp5 GABAergic interneuron (Primate) comment "Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
LAMP5-CXCL14 GABA lamp5 GABAergic interneuron (Primate) label "LAMP5-CXCL14 GABA lamp5 GABAergic interneuron (Primate)"

LAMP5-LHX6 GABA Lamp5 Lhx6 neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310085`

Removed

LAMP5-LHX6 GABA Lamp5 Lhx6 neuron (Primate) comment "Based on annotation transfer evidence with MapMyCells, this may not represent a transcriptomicallly distinct cell type, but rather the population of LAMP5 LHX6 GABAergic neurons located in the striatum. Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
LAMP5-LHX6 GABA Lamp5 Lhx6 neuron (Primate) label "striatal LAMP5 LHX6 GABAergic interneuron (Primate)"

Added

LAMP5-LHX6 GABA Lamp5 Lhx6 neuron (Primate) comment "Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
LAMP5-LHX6 GABA Lamp5 Lhx6 neuron (Primate) label "LAMP5-LHX6 GABA Lamp5 Lhx6 neuron (Primate)"

OB Dopa-GABA OB-Dopa-GABA (Primate) `http://purl.obolibrary.org/obo/CL_4310147`

Removed

OB Dopa-GABA OB-Dopa-GABA (Primate) label "OB Dopa-GABA neuron (Primate)"

Added

OB Dopa-GABA OB-Dopa-GABA (Primate) label "OB Dopa-GABA OB-Dopa-GABA (Primate)"

OT D1 ICj Islands of Calleja granule cell (Primate) `http://purl.obolibrary.org/obo/CL_4310104`

Removed

OT D1 ICj Islands of Calleja granule cell (Primate) comment "Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
- hasDbXref "https://doi.org/10.1016/j.cub.2021.10.015"
OT D1 ICj Islands of Calleja granule cell (Primate) label "Islands of Calleja granule cell (Primate)"

Added

OT D1 ICj Islands of Calleja granule cell (Primate) comment "Rationale for assigning this type to reference data: Mapping to the general type VIP GABAergic neuron is supported by MapMyCells heirarchical annotation transfer mapping to 060 OT D3 Folh1 Gaba in the whole mouse brain taxonomy v1. Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
- hasDbXref "https://doi.org/10.1016/j.cub.2021.10.015"
OT D1 ICj Islands of Calleja granule cell (Primate) label "OT D1 ICj Islands of Calleja granule cell (Primate)"

PR_000015138 `http://purl.obolibrary.org/obo/PR_000015138`

Added

Class: PR_000015138

SN EBF2 GABA GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310110`

Added

SN EBF2 GABA GABAergic interneuron (Primate) SubClassOf SN PAX7 GABA GABAergic neuron (Primate)

SN PAX7 GABA GABAergic neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310056`

Added

Class: SN PAX7 GABA GABAergic neuron (Primate)
SN PAX7 GABA GABAergic neuron (Primate) IAO_0000028 "SN PAX7 GABA (Primate)"
SN PAX7 GABA GABAergic neuron (Primate) hasExactSynonym "SN PAX7 GABA"
SN PAX7 GABA GABAergic neuron (Primate) IAO_0000115 "A GABAergic neuron of the Primates brain. Reference transcriptomic data for this type can be found in the dataset/taxonomy - HMBA Basal Ganglia Consensus Taxonomy in cell set Subclass:SN PAX7 GABA."
- hasDbXref "https://alleninstitute.github.io/HMBA_BasalGanglia_Consensus_Taxonomy/"
SN PAX7 GABA GABAergic neuron (Primate) seeAlso "https://purl.brain-bican.org/taxonomy/CCN20230722/CS20250428_NEIGH_0002.h5ad"
- label "h5ad data file for CS20250428_NEIGH_0002"
- comment "Warning large data file!"
SN PAX7 GABA GABAergic neuron (Primate) seeAlso "https://knowledge.brain-map.org/abcatlas#AQQBTlhKOU5aQVFBNU1FSFFOT1dKUQACVEdCUTJGRVYyN04wQ1BMS1ZBWgADBQFFM0hHQllIUkM5OEdBNkZXOUY2AAIAAAEzWEJPRkJSMzAyRVlDMFVRRDUxAAIAAAFTUTZXSk8wR05VSkdGVThMSFZWAAIBU04gUEFYNyBHQUJBAAABSEsxNE8xQVNBTlBZSE9ORkxMUQACAAABNkVXQlNFSjRZRlZHS0kyQVBCTAACAAAEAQAChMpFmYR%2BVoYDhQxy%2FoU8XEUEV01QOE5NSjVEOFhPMUFPSTFMOQAFg2xvMYI24kGDwAnEgzgCUgAFAAYBAQJTUTZXSk8wR05VSkdGVThMSFZWAAN%2BAAAABAAACElBNlk2U043UVpTSUVKMEZaMFUACVBPWjJIQ1BCVDYwRFNESjhVQTcACgALATc0MTZCNVhKRFNZMEhERjkzUk8AAkNSRUhSQ0syWVhSV0pLMkowQUwAAwEEAQACIzAwMDAwMAADyAEABQEBAiMwMDAwMDAAA8gBAAAAAVZNNEU2SjlEUFlZRDdFMEJITkIAAktHWkxBV0lQQ1I0Vzk4RjVMRDYAAwUBRTNIR0JZSFJDOThHQTZGVzlGNgACAAABM1hCT0ZCUjMwMkVZQzBVUUQ1MQACAAABU1E2V0pPMEdOVUpHRlU4TEhWVgACAVNOIFBBWDcgR0FCQQAAAUhLMTRPMUFTQU5QWUhPTkZMTFEAAgAAATZFV0JTRUo0WUZWR0tJMkFQQkwAAgAABAEAAoX%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%2Bp7yQAFAAYBAQJTUTZXSk8wR05VSkdGVThMSFZWAAN%2BAAAABAAACEZUTEFVT1Y2U0xCMDcxU1ZOVTkACVBPWjJIQ1BCVDYwRFNESjhVQTcACgALAW5vbmUAAm5vbmUAAwEEAQACIzAwMDAwMAADyAEABQEBAiMwMDAwMDAAA8gBAAAAAggA"
- label "Reference data on Allen Brain Cell Atlas"
SN PAX7 GABA GABAergic neuron (Primate) comment "Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
SN PAX7 GABA GABAergic neuron (Primate) label "SN PAX7 GABA GABAergic neuron (Primate)"
SN PAX7 GABA GABAergic neuron (Primate) SubClassOf GABAergic neuron

SN SEMA5A GABA GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310114`

Added

SN SEMA5A GABA GABAergic interneuron (Primate) SubClassOf SN PAX7 GABA GABAergic neuron (Primate)

STR Cholinergic GABA striatal cholinergic-GABAergic neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310135`

Removed

STR Cholinergic GABA striatal cholinergic-GABAergic neuron (Primate) comment "Despite the name, this type is not a parent type to STRd cholinergic-GABAergic neuron (Primate), but is instead a transcriptomically distinct sibling. Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
STR Cholinergic GABA striatal cholinergic-GABAergic neuron (Primate) label "STR cholinergic-GABAergic neuron (Primate)"

Added

STR Cholinergic GABA striatal cholinergic-GABAergic neuron (Primate) comment "Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
STR Cholinergic GABA striatal cholinergic-GABAergic neuron (Primate) label "STR Cholinergic GABA striatal cholinergic-GABAergic neuron (Primate)"

STR D1 MSN direct pathway medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310058`

Added

Class: STR D1 MSN direct pathway medium spiny neuron (Primate)
STR D1 MSN direct pathway medium spiny neuron (Primate) IAO_0000028 "STR D1 MSN (Primate)"
STR D1 MSN direct pathway medium spiny neuron (Primate) hasExactSynonym "STR D1 MSN"
STR D1 MSN direct pathway medium spiny neuron (Primate) IAO_0000115 "A direct pathway medium spiny neuron of the Primates brain. Reference transcriptomic data for this type can be found in the dataset/taxonomy - HMBA Basal Ganglia Consensus Taxonomy in cell set Subclass:STR D1 MSN."
- hasDbXref "https://alleninstitute.github.io/HMBA_BasalGanglia_Consensus_Taxonomy/"
STR D1 MSN direct pathway medium spiny neuron (Primate) seeAlso "https://purl.brain-bican.org/taxonomy/CCN20230722/CS20250428_NEIGH_0002.h5ad"
- label "h5ad data file for CS20250428_NEIGH_0002"
- comment "Warning large data file!"
STR D1 MSN direct pathway medium spiny neuron (Primate) seeAlso "https://knowledge.brain-map.org/abcatlas#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%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%3D%3D"
- label "Reference data on Allen Brain Cell Atlas"
STR D1 MSN direct pathway medium spiny neuron (Primate) comment "Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
STR D1 MSN direct pathway medium spiny neuron (Primate) label "STR D1 MSN direct pathway medium spiny neuron (Primate)"
STR D1 MSN direct pathway medium spiny neuron (Primate) SubClassOf direct pathway medium spiny neuron

STR D1D2 Hybrid MSN D1/D2-hybrid medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310131`

Removed

STR D1D2 Hybrid MSN D1/D2-hybrid medium spiny neuron (Primate) label "STRd D1/D2-hybrid medium spiny neuron (Primate)"

Added

STR D1D2 Hybrid MSN D1/D2-hybrid medium spiny neuron (Primate) label "STR D1D2 Hybrid MSN D1/D2-hybrid medium spiny neuron (Primate)"

STR D2 MSN indirect pathway medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310059`

Added

Class: STR D2 MSN indirect pathway medium spiny neuron (Primate)
STR D2 MSN indirect pathway medium spiny neuron (Primate) IAO_0000028 "STR D2 MSN (Primate)"
STR D2 MSN indirect pathway medium spiny neuron (Primate) hasExactSynonym "STR D2 MSN"
STR D2 MSN indirect pathway medium spiny neuron (Primate) IAO_0000115 "A indirect pathway medium spiny neuron of the Primates brain. Reference transcriptomic data for this type can be found in the dataset/taxonomy - HMBA Basal Ganglia Consensus Taxonomy in cell set Subclass:STR D2 MSN."
- hasDbXref "https://alleninstitute.github.io/HMBA_BasalGanglia_Consensus_Taxonomy/"
STR D2 MSN indirect pathway medium spiny neuron (Primate) seeAlso "https://purl.brain-bican.org/taxonomy/CCN20230722/CS20250428_NEIGH_0002.h5ad"
- label "h5ad data file for CS20250428_NEIGH_0002"
- comment "Warning large data file!"
STR D2 MSN indirect pathway medium spiny neuron (Primate) seeAlso "https://knowledge.brain-map.org/abcatlas#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%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%3D%3D"
- label "Reference data on Allen Brain Cell Atlas"
STR D2 MSN indirect pathway medium spiny neuron (Primate) comment "Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
STR D2 MSN indirect pathway medium spiny neuron (Primate) label "STR D2 MSN indirect pathway medium spiny neuron (Primate)"
STR D2 MSN indirect pathway medium spiny neuron (Primate) SubClassOf indirect pathway medium spiny neuron

STR FS PTHLH-PVALB GABA striatal pthlh-expressing interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310120`

Removed

STR FS PTHLH-PVALB GABA striatal pthlh-expressing interneuron (Primate) label "striatal pthlh-expressing interneuron (Primate)"

Added

STR FS PTHLH-PVALB GABA striatal pthlh-expressing interneuron (Primate) label "STR FS PTHLH-PVALB GABA striatal pthlh-expressing interneuron (Primate)"

STR LYPD6-RSPO2 GABA GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310121`

Removed

STR LYPD6-RSPO2 GABA GABAergic interneuron (Primate) label "striatal SST-LYPD6-RSPO2 GABAergic interneuron (Primate)"

Added

STR LYPD6-RSPO2 GABA GABAergic interneuron (Primate) label "STR LYPD6-RSPO2 GABA GABAergic interneuron (Primate)"

STR SST-ADARB2 GABA sst GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310122`

Removed

STR SST-ADARB2 GABA sst GABAergic interneuron (Primate) label "striatal SST-ADARB2 GABAergic interneuron (Primate)"

Added

STR SST-ADARB2 GABA sst GABAergic interneuron (Primate) label "STR SST-ADARB2 GABA sst GABAergic interneuron (Primate)"

STR SST-CHODL GABA sst chodl GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310123`

Removed

STR SST-CHODL GABA sst chodl GABAergic interneuron (Primate) comment "Based on annotation transfer evidence with MapMyCells, this may not represent a transcriptomicallly distinct cell type, but rather the population of SST CHODL GABAergic neurons located in the striatum. Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
- hasDbXref "https://doi.org/10.1038/s41586-020-2874-8"
STR SST-CHODL GABA sst chodl GABAergic interneuron (Primate) label "striatal SST-CHODL GABAergic interneuron (Primate)"

Added

STR SST-CHODL GABA sst chodl GABAergic interneuron (Primate) comment "Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
- hasDbXref "https://doi.org/10.1038/s41586-020-2874-8"
STR SST-CHODL GABA sst chodl GABAergic interneuron (Primate) label "STR SST-CHODL GABA sst chodl GABAergic interneuron (Primate)"

STR SST-RSPO2 GABA sst GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310124`

Removed

STR SST-RSPO2 GABA sst GABAergic interneuron (Primate) label "striatal SST-RSPO2 GABAergic interneuron (Primate)"

Added

STR SST-RSPO2 GABA sst GABAergic interneuron (Primate) label "STR SST-RSPO2 GABA sst GABAergic interneuron (Primate)"

STRd Cholinergic GABA dorso-striatal cholinergic-GABAergic neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310128`

Removed

STRd Cholinergic GABA dorso-striatal cholinergic-GABAergic neuron (Primate) label "STRd cholinergic-GABAergic neuron (Primate)"

Added

STRd Cholinergic GABA dorso-striatal cholinergic-GABAergic neuron (Primate) label "STRd Cholinergic GABA dorso-striatal cholinergic-GABAergic neuron (Primate)"

STRd D1 Matrix MSN matrix D1 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310129`

Removed

STRd D1 Matrix MSN matrix D1 medium spiny neuron (Primate) comment "Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
- hasDbXref "https://doi.org/10.1016/j.cub.2021.10.015"
STRd D1 Matrix MSN matrix D1 medium spiny neuron (Primate) label "STRd D1 Matrix medium spiny neuron (Primate)"

Added

STRd D1 Matrix MSN matrix D1 medium spiny neuron (Primate) comment "Rationale for assigning this type to reference data: Mapping to the general type VIP GABAergic neuron is supported by MapMyCells heirarchical annotation transfer mapping to 0267 STR D1 Gaba_3 in the whole mouse brain taxonomy v1. Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
- hasDbXref "https://doi.org/10.1016/j.cub.2021.10.015"
STRd D1 Matrix MSN matrix D1 medium spiny neuron (Primate) label "STRd D1 Matrix MSN matrix D1 medium spiny neuron (Primate)"
STRd D1 Matrix MSN matrix D1 medium spiny neuron (Primate) SubClassOf STR D1 MSN direct pathway medium spiny neuron (Primate)

STRd D1 Striosome MSN striosomal D1 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310130`

Removed

STRd D1 Striosome MSN striosomal D1 medium spiny neuron (Primate) label "striosomal D1 medium spiny neuron (Primate)"

Added

STRd D1 Striosome MSN striosomal D1 medium spiny neuron (Primate) label "STRd D1 Striosome MSN striosomal D1 medium spiny neuron (Primate)"
STRd D1 Striosome MSN striosomal D1 medium spiny neuron (Primate) SubClassOf STR D1 MSN direct pathway medium spiny neuron (Primate)

STRd D2 Matrix MSN matrix D2 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310132`

Removed

STRd D2 Matrix MSN matrix D2 medium spiny neuron (Primate) label "STRd D2 Matrix medium spiny neuron (Primate)"

Added

STRd D2 Matrix MSN matrix D2 medium spiny neuron (Primate) label "STRd D2 Matrix MSN matrix D2 medium spiny neuron (Primate)"
STRd D2 Matrix MSN matrix D2 medium spiny neuron (Primate) SubClassOf STR D2 MSN indirect pathway medium spiny neuron (Primate)

STRd D2 StrioMat Hybrid MSN indirect pathway medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310133`

Removed

STRd D2 StrioMat Hybrid MSN indirect pathway medium spiny neuron (Primate) label "STRd D2 Striomat hybrid medium spiny neuron (Primate)"
STRd D2 StrioMat Hybrid MSN indirect pathway medium spiny neuron (Primate) SubClassOf indirect pathway medium spiny neuron

Added

STRd D2 StrioMat Hybrid MSN indirect pathway medium spiny neuron (Primate) label "STRd D2 StrioMat Hybrid MSN indirect pathway medium spiny neuron (Primate)"
STRd D2 StrioMat Hybrid MSN indirect pathway medium spiny neuron (Primate) SubClassOf STR D2 MSN indirect pathway medium spiny neuron (Primate)

STRd D2 Striosome MSN striosomal D2 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310134`

Removed

STRd D2 Striosome MSN striosomal D2 medium spiny neuron (Primate) label "striosomal D2 medium spiny neuron (Primate)"

Added

STRd D2 Striosome MSN striosomal D2 medium spiny neuron (Primate) label "STRd D2 Striosome MSN striosomal D2 medium spiny neuron (Primate)"
STRd D2 Striosome MSN striosomal D2 medium spiny neuron (Primate) SubClassOf STR D2 MSN indirect pathway medium spiny neuron (Primate)

STRv D1 MSN nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310136`

Removed

STRv D1 MSN nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron (Primate) label "STRv D1 medium spiny neuron (Primate)"

Added

STRv D1 MSN nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron (Primate) label "STRv D1 MSN nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron (Primate)"
STRv D1 MSN nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron (Primate) SubClassOf STR D1 MSN direct pathway medium spiny neuron (Primate)

STRv D1 NUDAP MSN D1-NUDAP medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310137`

Removed

STRv D1 NUDAP MSN D1-NUDAP medium spiny neuron (Primate) label "STRv D1-NUDAP medium spiny neuron (Primate)"

Added

STRv D1 NUDAP MSN D1-NUDAP medium spiny neuron (Primate) label "STRv D1 NUDAP MSN D1-NUDAP medium spiny neuron (Primate)"

STRv D2 MSN nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310138`

Removed

STRv D2 MSN nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron (Primate) label "STRv D2 medium spiny neuron (Primate)"
STRv D2 MSN nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron (Primate) SubClassOf indirect pathway medium spiny neuron

Added

STRv D2 MSN nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron (Primate) label "STRv D2 MSN nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron (Primate)"
STRv D2 MSN nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron (Primate) SubClassOf STR D2 MSN indirect pathway medium spiny neuron (Primate)

VIP GABA VIP GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310127`

Removed

VIP GABA VIP GABAergic interneuron (Primate) comment "Based on annotation transfer evidence with MapMyCells, this may not represent a transcriptomicallly distinct cell type, but rather the population of VIP GABAergic neurons located in the striatum. Rationale for assigning this type to reference data: Mapping to the general type VIP GABAergic neuron is supported by MapMyCells heirarchical annotation transfer mapping to 046 Vip Gaba in the whole mouse brain taxonomy v1. Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
- hasDbXref "https://doi.org/10.1038/s41586-020-2874-8"
VIP GABA VIP GABAergic interneuron (Primate) label "striatal VIP GABAergic interneuron (Primate)"

Added

VIP GABA VIP GABAergic interneuron (Primate) comment "Rationale for assigning this type to reference data: Mapping to the general type VIP GABAergic neuron is supported by MapMyCells heirarchical annotation transfer mapping to 046 Vip Gaba in the whole mouse brain taxonomy v1. Location is inferred from registration of MerFish Data. Registration may be inaccurate, giving misleading location to adjacent anatomical regions."
- hasDbXref "https://doi.org/10.1038/s41586-020-2874-8"
VIP GABA VIP GABAergic interneuron (Primate) label "VIP GABA VIP GABAergic interneuron (Primate)"

effector chondrocyte `http://purl.obolibrary.org/obo/CL_0020023`

Added

helper T cell `http://purl.obolibrary.org/obo/CL_0000912`

Removed

iron-recycling macrophage `http://purl.obolibrary.org/obo/CL_9900001`

Added

Class: iron-recycling macrophage
iron-recycling macrophage IAO_0000233 3613
iron-recycling macrophage creator "GitHub Copilot"
iron-recycling macrophage date "2026-04-24T15:02:51Z"^^dateTime
iron-recycling macrophage hasNarrowSynonym "prenatal iron-recycling macrophage"
- hasDbXref "DOI:10.1038/s41586-024-08002-x"
iron-recycling macrophage IAO_0000115 "A tissue-resident macrophage specialised in the phagocytosis of senescent erythrocytes and the recycling of iron from degraded haemoglobin, with iron export mediated by ferroportin (SLC40A1) (Ferreira and Gahl, 2017). Identified across multiple prenatal human organs during fetal development, with highest enrichment in later gestation when immune effector gene programmes are progressively upregulated (Suo et al., 2022). In prenatal skin (7-17 post-conception weeks), this macrophage subset co-localises with endothelial cells in neurovascular microenvironments and specifically promotes endothelial cell chemotaxis and angiogenesis (Gopee et al., 2024). The closest postnatal counterparts are splenic red pulp macrophages and Kupffer cells."
- hasDbXref "DOI:10.1126/science.abo0510"
- hasDbXref "DOI:10.1038/s41586-024-08002-x"
- hasDbXref "DOI:10.3233/TRD-170015"
iron-recycling macrophage hasRelatedSynonym "SLC40A1-positive tissue-resident macrophage"
- hasDbXref "DOI:10.1126/science.abo0510"
iron-recycling macrophage hasRelatedSynonym "erythrophagocytic tissue-resident macrophage"
- hasDbXref "DOI:10.1126/science.abo0510"
iron-recycling macrophage label "iron-recycling macrophage"
iron-recycling macrophage SubClassOf tissue-resident macrophage
iron-recycling macrophage SubClassOf RO_0002215 some GO_0042167
iron-recycling macrophage SubClassOf RO_0002215 some GO_1903988
iron-recycling macrophage SubClassOf RO_0002216 some GO_0001525
iron-recycling macrophage SubClassOf RO_0002216 some GO_0035767
iron-recycling macrophage SubClassOf RO_0002292 some PR_000015138

myelinating glial cell `http://purl.obolibrary.org/obo/CL_4023154`

Added

myoepithelial cell `http://purl.obolibrary.org/obo/CL_0000185`

Removed

neural cell `http://purl.obolibrary.org/obo/CL_0002319`

Added

non-myelinating Schwann cell `http://purl.obolibrary.org/obo/CL_0002376`

Added

prehypertrophic chondrocyte `http://purl.obolibrary.org/obo/CL_0020022`

Added

seromucous acinar cell of salivary gland `http://purl.obolibrary.org/obo/CL_4052067`

Removed

serous acinar cell of salivary gland `http://purl.obolibrary.org/obo/CL_4052065`

Removed

tuft cell `http://purl.obolibrary.org/obo/CL_0002204`

Removed

github-actions · 2026-04-24T15:20:05Z

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

iron-recycling macrophage `http://purl.obolibrary.org/obo/CL_9900001`

Added

Class: iron-recycling macrophage
iron-recycling macrophage term tracker item 3613
iron-recycling macrophage creator "GitHub Copilot"
iron-recycling macrophage date "2026-04-24T15:02:51Z"^^dateTime
iron-recycling macrophage has narrow synonym "prenatal iron-recycling macrophage"
- database_cross_reference "DOI:10.1038/s41586-024-08002-x"
iron-recycling macrophage definition "A tissue-resident macrophage specialised in the phagocytosis of senescent erythrocytes and the recycling of iron from degraded haemoglobin, with iron export mediated by ferroportin (SLC40A1) (Ferreira and Gahl, 2017). Identified across multiple prenatal human organs during fetal development, with highest enrichment in later gestation when immune effector gene programmes are progressively upregulated (Suo et al., 2022). In prenatal skin (7-17 post-conception weeks), this macrophage subset co-localises with endothelial cells in neurovascular microenvironments and specifically promotes endothelial cell chemotaxis and angiogenesis (Gopee et al., 2024). The closest postnatal counterparts are splenic red pulp macrophages and Kupffer cells."
- database_cross_reference "DOI:10.1038/s41586-024-08002-x"
- database_cross_reference "DOI:10.1126/science.abo0510"
- database_cross_reference "DOI:10.3233/TRD-170015"
iron-recycling macrophage has_related_synonym "SLC40A1-positive tissue-resident macrophage"
- database_cross_reference "DOI:10.1126/science.abo0510"
iron-recycling macrophage has_related_synonym "erythrophagocytic tissue-resident macrophage"
- database_cross_reference "DOI:10.1126/science.abo0510"
iron-recycling macrophage label "iron-recycling macrophage"
iron-recycling macrophage SubClassOf tissue-resident macrophage
iron-recycling macrophage SubClassOf capable of some heme catabolic process
iron-recycling macrophage SubClassOf capable of some iron ion export across plasma membrane
iron-recycling macrophage SubClassOf capable of part of some angiogenesis
iron-recycling macrophage SubClassOf capable of part of some endothelial cell chemotaxis
iron-recycling macrophage SubClassOf expresses some ferroportin

refreshed imports

github-actions · 2026-04-27T10:10:35Z

http://purl.obolibrary.org/obo/CL_0002042 in taxon http://purl.obolibrary.org/obo/NCBITaxon_9606 SubClassOf Nothing

http://purl.obolibrary.org/obo/CL_0002042 in taxon http://purl.obolibrary.org/obo/NCBITaxon_9606 SubClassOf immature NK T cell stage IV, mouse
- immature NK T cell stage IV, mouse EquivalentTo immature NK T cell and (lacks_plasma_membrane_part some KLRB1-like protein) and (has plasma membrane part some CD44 molecule) and (in taxon some Mus musculus) and (has high plasma membrane amount some integrin alpha-2) and (has low plasma membrane amount some signal transducer CD24)
  - Mus musculus SubClassOf Mus
    - Mus SubClassOf Mus
      - Mus SubClassOf Murinae
        
        Murinae SubClassOf Muridae
        
        Muridae SubClassOf Muroidea
        
        Muroidea SubClassOf Myomorpha
        
        Myomorpha SubClassOf Rodentia
        
        Rodentia SubClassOf Glires
http://purl.obolibrary.org/obo/CL_0002042 in taxon http://purl.obolibrary.org/obo/NCBITaxon_9606 SubClassOf in taxon some Homo sapiens
- Homo sapiens SubClassOf Homo
  - Homo SubClassOf Homininae
    - Homininae SubClassOf Hominidae
      - Hominidae SubClassOf Hominoidea
        
        Hominoidea SubClassOf Catarrhini
        
        Catarrhini SubClassOf Simiiformes
        
        Simiiformes SubClassOf Haplorrhini
        
        Haplorrhini SubClassOf Primates
in taxon some Glires DisjointWith in taxon some Primates

Axiom Impact

Axioms used 1 times

immature NK T cell stage IV, mouse EquivalentTo immature NK T cell and (lacks_plasma_membrane_part some KLRB1-like protein) and (has plasma membrane part some CD44 molecule) and (in taxon some Mus musculus) and (has high plasma membrane amount some integrin alpha-2) and (has low plasma membrane amount some signal transducer CD24) [cl.owl]
Muridae SubClassOf Muroidea [cl.owl]
Mus SubClassOf Murinae [cl.owl]
Mus musculus SubClassOf Mus [cl.owl]
Myomorpha SubClassOf Rodentia [cl.owl]
Homininae SubClassOf Hominidae [cl.owl]
Simiiformes SubClassOf Haplorrhini [cl.owl]
Hominoidea SubClassOf Catarrhini [cl.owl]
Muroidea SubClassOf Myomorpha [cl.owl]
Haplorrhini SubClassOf Primates [cl.owl]
Murinae SubClassOf Muridae [cl.owl]
Mus SubClassOf Mus [cl.owl]
Catarrhini SubClassOf Simiiformes [cl.owl]
Hominidae SubClassOf Hominoidea [cl.owl]
Homo SubClassOf Homininae [cl.owl]
Homo sapiens SubClassOf Homo [cl.owl]
Rodentia SubClassOf Glires [cl.owl]
http://purl.obolibrary.org/obo/CL_0002042 in taxon http://purl.obolibrary.org/obo/NCBITaxon_9606 SubClassOf immature NK T cell stage IV, mouse [cl.owl]
http://purl.obolibrary.org/obo/CL_0002042 in taxon http://purl.obolibrary.org/obo/NCBITaxon_9606 SubClassOf in taxon some Homo sapiens [cl.owl]
in taxon some Glires DisjointWith in taxon some Primates [cl.owl]

Ontologies used:

cl.owl (http://purl.obolibrary.org/obo/cl.owl)

RiveraAndrea83 · 2026-04-27T11:05:22Z

#gogoeditdiff

RiveraAndrea83 · 2026-04-27T13:14:34Z

#gogoeditdiff

dosumis

Double check evidence on angiogenesis role. if LoF evidence then happy for it to be retained. If only GO enrichment then I think remove.

RiveraAndrea83 · 2026-05-15T14:18:07Z

#gogoeditdiff /clara

Initial plan

ffd4687

Copilot AI assigned Copilot and RiveraAndrea83 Apr 24, 2026

Copilot started work on behalf of RiveraAndrea83 April 24, 2026 15:02 View session

Copilot AI linked an issue Apr 24, 2026 that may be closed by this pull request

[NTR] iron-recycling macrophage #3613

Open

Copilot AI changed the title ~~[WIP] Add iron-recycling macrophage definition and synonyms~~ [NTR] Add iron-recycling macrophage (CL:9900001) Apr 24, 2026

RiveraAndrea83 requested review from RiveraAndrea83 and dosumis April 24, 2026 15:13

Copilot stopped work on behalf of RiveraAndrea83 due to an error April 24, 2026 15:17
An unexpected error occurred. For more details, see the detailed logs in GitHub Actions.

RiveraAndrea83 marked this pull request as ready for review April 27, 2026 08:27

added PRO:ID and GO:TERM

b32698b

refreshed imports

fixed conflict with immature NK cell IV mouse

a919547

github-actions Bot mentioned this pull request Apr 28, 2026

cell-ontology report for 2026-04-28 ai4curation/agent-watcher#32

Open

dosumis previously approved these changes Apr 30, 2026

View reviewed changes

refreshed imports

89f5396

RiveraAndrea83 dismissed dosumis’s stale review via 89f5396 May 15, 2026 14:16

RiveraAndrea83 added 2 commits May 15, 2026 15:18

Merge branch 'master' into copilot/add-iron-recycling-macrophage

052df64

refreshed imports

d6f12b6

github-actions Bot mentioned this pull request May 19, 2026

cell-ontology report for 2026-05-19 ai4curation/agent-watcher#50

Open

github-actions Bot mentioned this pull request May 26, 2026

cell-ontology report for 2026-05-26 ai4curation/agent-watcher#56

Open

Conversation

Copilot AI commented Apr 24, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

New term: CL:9900001 — iron-recycling macrophage

Logical axioms

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RiveraAndrea83 commented Apr 24, 2026

Uh oh!

github-actions Bot commented Apr 24, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Ontology comparison

Left

Right

Ontology imports

Ontology annotations

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

Added

GO_0035767 http://purl.obolibrary.org/obo/GO_0035767

Added

GO_0042167 http://purl.obolibrary.org/obo/GO_0042167

Added

GO_1903988 http://purl.obolibrary.org/obo/GO_1903988

Added

GPe MEIS2-SOX6 GABA arkypallidal neuron (Primate) http://purl.obolibrary.org/obo/CL_4310093

Removed

Added

GPe SOX6-CTXND1 GABA prototypic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310094

Removed

Added

GPi Core internal globus pallidus core projecting neuron (Primate) http://purl.obolibrary.org/obo/CL_4310095

Removed

Added

GPi Shell internal globus pallidus shell projection neuron (Primate) http://purl.obolibrary.org/obo/CL_4310096

Removed

Added

GPin-BF Cholinergic GABA GABA-Chol neuron (Primate) http://purl.obolibrary.org/obo/CL_4310083

Removed

Added

IgA plasma cell http://purl.obolibrary.org/obo/CL_0000987

Removed

LAMP5-CXCL14 GABA lamp5 GABAergic interneuron (Primate) http://purl.obolibrary.org/obo/CL_4310084

Removed

Added

LAMP5-LHX6 GABA Lamp5 Lhx6 neuron (Primate) http://purl.obolibrary.org/obo/CL_4310085

Removed

Added

OB Dopa-GABA OB-Dopa-GABA (Primate) http://purl.obolibrary.org/obo/CL_4310147

Removed

Added

OT D1 ICj Islands of Calleja granule cell (Primate) http://purl.obolibrary.org/obo/CL_4310104

Removed

Added

PR_000015138 http://purl.obolibrary.org/obo/PR_000015138

Added

SN EBF2 GABA GABAergic interneuron (Primate) http://purl.obolibrary.org/obo/CL_4310110

Added

SN PAX7 GABA GABAergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310056

Added

SN SEMA5A GABA GABAergic interneuron (Primate) http://purl.obolibrary.org/obo/CL_4310114

Added

STR Cholinergic GABA striatal cholinergic-GABAergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310135

Removed

Added

STR D1 MSN direct pathway medium spiny neuron (Primate) http://purl.obolibrary.org/obo/CL_4310058

Added

STR D1D2 Hybrid MSN D1/D2-hybrid medium spiny neuron (Primate) http://purl.obolibrary.org/obo/CL_4310131

Removed

Added

STR D2 MSN indirect pathway medium spiny neuron (Primate) http://purl.obolibrary.org/obo/CL_4310059

Added

STR FS PTHLH-PVALB GABA striatal pthlh-expressing interneuron (Primate) http://purl.obolibrary.org/obo/CL_4310120

Removed

Added

STR LYPD6-RSPO2 GABA GABAergic interneuron (Primate) http://purl.obolibrary.org/obo/CL_4310121

Removed

Added

STR SST-ADARB2 GABA sst GABAergic interneuron (Primate) http://purl.obolibrary.org/obo/CL_4310122

Removed

Added

STR SST-CHODL GABA sst chodl GABAergic interneuron (Primate) http://purl.obolibrary.org/obo/CL_4310123

Copilot AI commented Apr 24, 2026 •

edited

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New term: `CL:9900001` — iron-recycling macrophage

github-actions Bot commented Apr 24, 2026 •

edited

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

GO_0035767 `http://purl.obolibrary.org/obo/GO_0035767`

GO_0042167 `http://purl.obolibrary.org/obo/GO_0042167`

GO_1903988 `http://purl.obolibrary.org/obo/GO_1903988`

GPe MEIS2-SOX6 GABA arkypallidal neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310093`

GPe SOX6-CTXND1 GABA prototypic neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310094`

GPi Core internal globus pallidus core projecting neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310095`

GPi Shell internal globus pallidus shell projection neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310096`

GPin-BF Cholinergic GABA GABA-Chol neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310083`

IgA plasma cell `http://purl.obolibrary.org/obo/CL_0000987`

LAMP5-CXCL14 GABA lamp5 GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310084`

LAMP5-LHX6 GABA Lamp5 Lhx6 neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310085`

OB Dopa-GABA OB-Dopa-GABA (Primate) `http://purl.obolibrary.org/obo/CL_4310147`

OT D1 ICj Islands of Calleja granule cell (Primate) `http://purl.obolibrary.org/obo/CL_4310104`

PR_000015138 `http://purl.obolibrary.org/obo/PR_000015138`

SN EBF2 GABA GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310110`

SN PAX7 GABA GABAergic neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310056`

SN SEMA5A GABA GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310114`

STR Cholinergic GABA striatal cholinergic-GABAergic neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310135`

STR D1 MSN direct pathway medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310058`

STR D1D2 Hybrid MSN D1/D2-hybrid medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310131`

STR D2 MSN indirect pathway medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310059`

STR FS PTHLH-PVALB GABA striatal pthlh-expressing interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310120`

STR LYPD6-RSPO2 GABA GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310121`

STR SST-ADARB2 GABA sst GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310122`

STR SST-CHODL GABA sst chodl GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310123`

STR SST-RSPO2 GABA sst GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310124`

STRd Cholinergic GABA dorso-striatal cholinergic-GABAergic neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310128`

STRd D1 Matrix MSN matrix D1 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310129`

STRd D1 Striosome MSN striosomal D1 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310130`

STRd D2 Matrix MSN matrix D2 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310132`

STRd D2 StrioMat Hybrid MSN indirect pathway medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310133`

STRd D2 Striosome MSN striosomal D2 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310134`

STRv D1 MSN nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310136`

STRv D1 NUDAP MSN D1-NUDAP medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310137`

STRv D2 MSN nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310138`

VIP GABA VIP GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310127`

effector chondrocyte `http://purl.obolibrary.org/obo/CL_0020023`

helper T cell `http://purl.obolibrary.org/obo/CL_0000912`

iron-recycling macrophage `http://purl.obolibrary.org/obo/CL_9900001`

myelinating glial cell `http://purl.obolibrary.org/obo/CL_4023154`

myoepithelial cell `http://purl.obolibrary.org/obo/CL_0000185`

neural cell `http://purl.obolibrary.org/obo/CL_0002319`

non-myelinating Schwann cell `http://purl.obolibrary.org/obo/CL_0002376`

prehypertrophic chondrocyte `http://purl.obolibrary.org/obo/CL_0020022`

seromucous acinar cell of salivary gland `http://purl.obolibrary.org/obo/CL_4052067`

serous acinar cell of salivary gland `http://purl.obolibrary.org/obo/CL_4052065`

tuft cell `http://purl.obolibrary.org/obo/CL_0002204`

github-actions Bot commented Apr 24, 2026 •

edited

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