[NTR] Add four dentate gyrus cell terms (CL_9900001–CL_9900004) by Copilot · Pull Request #3610 · obophenotype/cell-ontology

Copilot · 2026-04-20T13:47:58Z

Adds four new terms representing the adult hippocampal neurogenesis lineage in the dentate gyrus subgranular zone, as requested in issue #3609.

New terms

ID	Label	Parent	Location
CL:9900001	dentate gyrus neuroblast	CL:0011020 neural progenitor cell	UBERON:0009952 dentate gyrus subgranular zone
CL:9900002	immature dentate gyrus granule neuron	CL:4042028 immature neuron	UBERON:0005381 dentate gyrus granule cell layer
CL:9900003	dentate gyrus type-2a neural progenitor	CL:0011020 neural progenitor cell	UBERON:0009952 dentate gyrus subgranular zone
CL:9900004	dentate gyrus type-2b neural progenitor	CL:0011020 neural progenitor cell	UBERON:0009952 dentate gyrus subgranular zone

Axiom pattern (each term)

AnnotationAssertion(Annotation(oboInOwl:hasDbXref "PMID:...") ... obo:IAO_0000115 obo:CL_990000x "...")
AnnotationAssertion(terms:contributor obo:CL_990000x <https://orcid.org/0000-0002-5507-2103>)
AnnotationAssertion(terms:date obo:CL_990000x "2026-04-20T13:49:06Z"^^xsd:dateTime)
AnnotationAssertion(obo:IAO_0000233 obo:CL_990000x <https://github.com/obophenotype/cell-ontology/issues/3609>)
SubClassOf(obo:CL_990000x obo:CL_<parent>)
SubClassOf(obo:CL_990000x ObjectSomeValuesFrom(obo:RO_0002100 obo:UBERON_<location>))

Other changes

Added Declaration(Class(obo:UBERON_0009952)) — first use of dentate gyrus subgranular zone in this file.
IDs are in the temporary NTR range (CL_99xxxxx) per project convention.
References: PMID:40519263, PMID:37082558, PMID:18385329, PMID:41741649, PMID:23667508, PMID:19482889, PMID:26880934.

Added the following new terms to src/ontology/cl-edit.owl: - CL_9900001: dentate gyrus neuroblast (child of CL_0011020, located in UBERON_0009952) - CL_9900002: immature dentate gyrus granule neuron (child of CL_4042028, located in UBERON_0005381) - CL_9900003: dentate gyrus type-2a neural progenitor (child of CL_0011020, located in UBERON_0009952) - CL_9900004: dentate gyrus type-2b neural progenitor (child of CL_0011020, located in UBERON_0009952) Each term includes: IAO_0000115 definition with PMID xrefs, rdfs:label, terms:contributor (ORCID 0000-0002-5507-2103), terms:creator, terms:date, IAO_0000233 term tracker link, SubClassOf parent, and location axiom. Also added Declaration for UBERON_0009952 (dentate gyrus subgranular zone). Signed-off-by: GitHub Copilot Agent-Logs-Url: https://github.com/obophenotype/cell-ontology/sessions/53d80321-4f18-4743-8785-06f25f27b67c Co-authored-by: RiveraAndrea83 <205639972+RiveraAndrea83@users.noreply.github.com>

RiveraAndrea83 · 2026-04-20T14:16:08Z

#gogoeditdiff

github-actions · 2026-04-20T14:22:44Z

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/2026-04-21/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/2026-04-21/cl-base.owl
Loaded from: file:/__w/cell-ontology/cell-ontology/src/ontology/cl-base-pr.owl/cl-base.owl

Ontology imports

Ontology annotations

GPi Core neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310095`

Removed

GPi Core neuron (Primate) label "GPi Core neuron (Primate)"

Added

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

GPi Shell neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310096`

Removed

GPi Shell neuron (Primate) label "GPi Shell neuron (Primate)"

Added

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

GPin-BF cholinergic-GABAergic neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310083`

Removed

GPin-BF cholinergic-GABAergic neuron (Primate) label "GPin-BF cholinergic-GABAergic neuron (Primate)"

Added

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

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

Removed

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

Removed

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"
Islands of Calleja granule cell (Primate) label "Islands of Calleja granule cell (Primate)"

Added

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"
Islands of Calleja granule cell (Primate) label "OT D1 ICj Islands of Calleja granule cell (Primate)"

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

Removed

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

Added

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

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

Removed

STR 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-GABAergic neuron (Primate) label "STR cholinergic-GABAergic neuron (Primate)"

Added

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

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

Removed

STRd D1 Matrix 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 medium spiny neuron (Primate) label "STRd D1 Matrix medium spiny neuron (Primate)"

Added

STRd D1 Matrix 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 medium spiny neuron (Primate) label "STRd D1 Matrix MSN matrix D1 medium spiny neuron (Primate)"
STRd D1 Matrix medium spiny neuron (Primate) SubClassOf STR D1 MSN direct pathway medium spiny neuron (Primate)

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

Removed

STRd D1/D2-hybrid medium spiny neuron (Primate) label "STRd D1/D2-hybrid medium spiny neuron (Primate)"

Added

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

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

Removed

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

Added

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

STRd D2 Striomat hybrid medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310133`

Removed

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

Added

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

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

Removed

STRd cholinergic-GABAergic neuron (Primate) label "STRd cholinergic-GABAergic neuron (Primate)"

Added

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

STRv D1 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310136`

Removed

STRv D1 medium spiny neuron (Primate) label "STRv D1 medium spiny neuron (Primate)"

Added

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

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

Removed

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

Added

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

STRv D2 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310138`

Removed

STRv D2 medium spiny neuron (Primate) label "STRv D2 medium spiny neuron (Primate)"
STRv D2 medium spiny neuron (Primate) SubClassOf indirect pathway medium spiny neuron

Added

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

UBERON_0009952 `http://purl.obolibrary.org/obo/UBERON_0009952`

Added

Class: UBERON_0009952

arkypallidal neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310093`

Removed

arkypallidal neuron (Primate) label "arkypallidal neuron (Primate)"

Added

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

dentate gyrus neuroblast `http://purl.obolibrary.org/obo/CL_9900001`

Added

Class: dentate gyrus neuroblast
dentate gyrus neuroblast IAO_0000233 3609
dentate gyrus neuroblast contributor 0000-0002-5507-2103
dentate gyrus neuroblast creator "GitHub Copilot"
dentate gyrus neuroblast date "2026-04-20T13:49:06Z"^^dateTime
dentate gyrus neuroblast IAO_0000115 "A forebrain neuroblast located in the subgranular zone (SGZ) of the dentate gyrus, representing the final proliferative stage in the adult hippocampal neurogenesis lineage. This cell expresses doublecortin (DCX), Ki67, and PSA-NCAM while lacking NeuN and calbindin, distinguishing it from upstream nestin-positive type-2 progenitors and downstream postmitotic neurons (Micheli et al., 2025; Stepien, 2021). The transcription factor Tbr2 is co-expressed with DCX at the type-2b to type-3 transition in mice (Hodge et al., 2008). Committed to a glutamatergic fate, this cell bears short tangential processes and migrates a short distance from the SGZ into the inner granule cell layer during differentiation (Stepien, 2021; Hodge et al., 2008)."
- hasDbXref "PMID:37082558"
- hasDbXref "PMID:41741649"
- hasDbXref "PMID:18385329"
- hasDbXref "PMID:40519263"
dentate gyrus neuroblast label "dentate gyrus neuroblast"
dentate gyrus neuroblast SubClassOf neural progenitor cell
dentate gyrus neuroblast SubClassOf dentate gyrus neuron
dentate gyrus neuroblast SubClassOf RO_0002100 some UBERON_0009952

dentate gyrus type-2a neural progenitor `http://purl.obolibrary.org/obo/CL_9900003`

Added

Class: dentate gyrus type-2a neural progenitor
dentate gyrus type-2a neural progenitor IAO_0000233 3609
dentate gyrus type-2a neural progenitor contributor 0000-0002-5507-2103
dentate gyrus type-2a neural progenitor creator "GitHub Copilot"
dentate gyrus type-2a neural progenitor date "2026-04-20T13:49:06Z"^^dateTime
dentate gyrus type-2a neural progenitor IAO_0000115 "A proliferating intermediate progenitor cell of the subgranular zone of the dentate gyrus, representing the first amplifying stage in the adult hippocampal neurogenesis lineage. This cell expresses nestin and Sox2 and is negative for doublecortin (DCX), distinguishing it from the downstream type-2b stage and from the quiescent type-1 radial glia-like stem cell from which it derives (Micheli et al., 2025; Stepien, 2021). It does not yet express neuroblast markers and retains progenitor morphology. Evidence is primarily from mouse and rat studies; systematic species equivalence in primates has not been established (Micheli et al., 2025)."
- hasDbXref "PMID:37082558"
- hasDbXref "PMID:40519263"
dentate gyrus type-2a neural progenitor label "dentate gyrus type-2a neural progenitor"
dentate gyrus type-2a neural progenitor SubClassOf neural progenitor cell
dentate gyrus type-2a neural progenitor SubClassOf dentate gyrus neuron
dentate gyrus type-2a neural progenitor SubClassOf RO_0002100 some UBERON_0009952

dentate gyrus type-2b neural progenitor `http://purl.obolibrary.org/obo/CL_9900004`

Added

Class: dentate gyrus type-2b neural progenitor
dentate gyrus type-2b neural progenitor IAO_0000233 3609
dentate gyrus type-2b neural progenitor contributor 0000-0002-5507-2103
dentate gyrus type-2b neural progenitor creator "GitHub Copilot"
dentate gyrus type-2b neural progenitor date "2026-04-20T13:49:06Z"^^dateTime
dentate gyrus type-2b neural progenitor IAO_0000115 "A transiently amplifying progenitor of the subgranular zone of the dentate gyrus, intermediate between the nestin-positive/DCX-negative type-2a progenitor and the nestin-negative/DCX-positive type-3 neuroblast. This cell co-expresses nestin and doublecortin (DCX) at low levels and displays short tangential processes typical of type-2 morphology (Micheli et al., 2025; Hodge et al., 2008). The transcription factor Tbr2 marks cells at this stage in mice, with the majority of Tbr2-positive cells co-labelling with DCX (Hodge et al., 2008). Progression through this stage is governed by a transcription factor cascade (Pax6 - Ngn2 - Tbr2 - NeuroD - Tbr1) (Hodge et al., 2008)."
- hasDbXref "PMID:18385329"
- hasDbXref "PMID:40519263"
dentate gyrus type-2b neural progenitor label "dentate gyrus type-2b neural progenitor"
dentate gyrus type-2b neural progenitor SubClassOf neural progenitor cell
dentate gyrus type-2b neural progenitor SubClassOf dentate gyrus neuron
dentate gyrus type-2b neural progenitor SubClassOf RO_0002100 some UBERON_0009952

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

Added

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

Removed

immature NK T cell `http://purl.obolibrary.org/obo/CL_0000914`

Added

immature dentate gyrus granule neuron `http://purl.obolibrary.org/obo/CL_9900002`

Added

Class: immature dentate gyrus granule neuron
immature dentate gyrus granule neuron IAO_0000233 3609
immature dentate gyrus granule neuron contributor 0000-0002-5507-2103
immature dentate gyrus granule neuron creator "GitHub Copilot"
immature dentate gyrus granule neuron date "2026-04-20T13:49:06Z"^^dateTime
immature dentate gyrus granule neuron IAO_0000115 "A postmitotic glutamatergic neuron located in the inner granule cell layer of the dentate gyrus, arising from adult hippocampal neurogenesis and representing a transitional maturational stage between the DCX-positive neuroblast and the terminally differentiated granule neuron. This cell co-expresses DCX, NeuN, and PSA-NCAM, and is negative for calbindin (Micheli et al., 2025). Calretinin is transiently expressed during this stage in mice (Merz et al., 2013). In rodents, Tis21 expression persists postmitotically at this stage, unlike in the fetal brain (Attardo et al., 2009). The cell extends dendrites toward the molecular layer and projects axons through the hilus toward CA3 as synaptic integration proceeds (Regalado-Santiago et al., 2016)."
- hasDbXref "PMID:19482889"
- hasDbXref "PMID:23667508"
- hasDbXref "PMID:26880934"
- hasDbXref "PMID:40519263"
immature dentate gyrus granule neuron label "immature dentate gyrus granule neuron"
immature dentate gyrus granule neuron SubClassOf dentate gyrus neuron
immature dentate gyrus granule neuron SubClassOf immature neuron
immature dentate gyrus granule neuron SubClassOf RO_0002100 some UBERON_0005381

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

prototypic neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310094`

Removed

prototypic neuron (Primate) label "prototypic neuron (Primate)"

Added

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

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

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

Removed

striatal LAMP5 CXCL14 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."
striatal LAMP5 CXCL14 GABAergic interneuron (Primate) label "striatal LAMP5 CXCL14 GABAergic interneuron (Primate)"

Added

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

striatal LAMP5 LHX6 GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310085`

Removed

striatal LAMP5 LHX6 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 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."
striatal LAMP5 LHX6 GABAergic interneuron (Primate) label "striatal LAMP5 LHX6 GABAergic interneuron (Primate)"

Added

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

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

Removed

striatal SST-ADARB2 GABAergic interneuron (Primate) label "striatal SST-ADARB2 GABAergic interneuron (Primate)"

Added

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

striatal SST-CHODL GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310123`

Removed

striatal 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"
striatal SST-CHODL GABAergic interneuron (Primate) label "striatal SST-CHODL GABAergic interneuron (Primate)"

Added

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

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

Removed

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

Added

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

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

Removed

striatal SST-RSPO2 GABAergic interneuron (Primate) label "striatal SST-RSPO2 GABAergic interneuron (Primate)"

Added

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

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

Removed

striatal 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"
striatal VIP GABAergic interneuron (Primate) label "striatal VIP GABAergic interneuron (Primate)"

Added

striatal 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"
striatal VIP GABAergic interneuron (Primate) label "VIP GABA VIP GABAergic interneuron (Primate)"

striatal pthlh-expressing interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310120`

Removed

striatal pthlh-expressing interneuron (Primate) label "striatal pthlh-expressing interneuron (Primate)"

Added

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

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

Removed

striosomal D1 medium spiny neuron (Primate) label "striosomal D1 medium spiny neuron (Primate)"

Added

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

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

Removed

striosomal D2 medium spiny neuron (Primate) label "striosomal D2 medium spiny neuron (Primate)"

Added

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

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

Removed

github-actions · 2026-04-20T14:22:46Z

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

dentate gyrus neuroblast `http://purl.obolibrary.org/obo/CL_9900001`

Added

Class: dentate gyrus neuroblast
dentate gyrus neuroblast term tracker item 3609
dentate gyrus neuroblast contributor 0000-0002-5507-2103
dentate gyrus neuroblast creator "GitHub Copilot"
dentate gyrus neuroblast date "2026-04-20T13:49:06Z"^^dateTime
dentate gyrus neuroblast definition "A forebrain neuroblast located in the subgranular zone (SGZ) of the dentate gyrus, representing the final proliferative stage in the adult hippocampal neurogenesis lineage. This cell expresses doublecortin (DCX), Ki67, and PSA-NCAM while lacking NeuN and calbindin, distinguishing it from upstream nestin-positive type-2 progenitors and downstream postmitotic neurons (Micheli et al., 2025; Stepien, 2021). The transcription factor Tbr2 is co-expressed with DCX at the type-2b to type-3 transition in mice (Hodge et al., 2008). Committed to a glutamatergic fate, this cell bears short tangential processes and migrates a short distance from the SGZ into the inner granule cell layer during differentiation (Stepien, 2021; Hodge et al., 2008)."
- has cross-reference "PMID:18385329"
- has cross-reference "PMID:41741649"
- has cross-reference "PMID:37082558"
- has cross-reference "PMID:40519263"
dentate gyrus neuroblast label "dentate gyrus neuroblast"
dentate gyrus neuroblast SubClassOf neural progenitor cell
dentate gyrus neuroblast SubClassOf has soma location some dentate gyrus subgranular zone

dentate gyrus subgranular zone `http://purl.obolibrary.org/obo/UBERON_0009952`

Added

Class: dentate gyrus subgranular zone

dentate gyrus type-2a neural progenitor `http://purl.obolibrary.org/obo/CL_9900003`

Added

Class: dentate gyrus type-2a neural progenitor
dentate gyrus type-2a neural progenitor term tracker item 3609
dentate gyrus type-2a neural progenitor contributor 0000-0002-5507-2103
dentate gyrus type-2a neural progenitor creator "GitHub Copilot"
dentate gyrus type-2a neural progenitor date "2026-04-20T13:49:06Z"^^dateTime
dentate gyrus type-2a neural progenitor definition "A proliferating intermediate progenitor cell of the subgranular zone of the dentate gyrus, representing the first amplifying stage in the adult hippocampal neurogenesis lineage. This cell expresses nestin and Sox2 and is negative for doublecortin (DCX), distinguishing it from the downstream type-2b stage and from the quiescent type-1 radial glia-like stem cell from which it derives (Micheli et al., 2025; Stepien, 2021). It does not yet express neuroblast markers and retains progenitor morphology. Evidence is primarily from mouse and rat studies; systematic species equivalence in primates has not been established (Micheli et al., 2025)."
- has cross-reference "PMID:37082558"
- has cross-reference "PMID:40519263"
dentate gyrus type-2a neural progenitor label "dentate gyrus type-2a neural progenitor"
dentate gyrus type-2a neural progenitor SubClassOf neural progenitor cell
dentate gyrus type-2a neural progenitor SubClassOf has soma location some dentate gyrus subgranular zone

dentate gyrus type-2b neural progenitor `http://purl.obolibrary.org/obo/CL_9900004`

Added

Class: dentate gyrus type-2b neural progenitor
dentate gyrus type-2b neural progenitor term tracker item 3609
dentate gyrus type-2b neural progenitor contributor 0000-0002-5507-2103
dentate gyrus type-2b neural progenitor creator "GitHub Copilot"
dentate gyrus type-2b neural progenitor date "2026-04-20T13:49:06Z"^^dateTime
dentate gyrus type-2b neural progenitor definition "A transiently amplifying progenitor of the subgranular zone of the dentate gyrus, intermediate between the nestin-positive/DCX-negative type-2a progenitor and the nestin-negative/DCX-positive type-3 neuroblast. This cell co-expresses nestin and doublecortin (DCX) at low levels and displays short tangential processes typical of type-2 morphology (Micheli et al., 2025; Hodge et al., 2008). The transcription factor Tbr2 marks cells at this stage in mice, with the majority of Tbr2-positive cells co-labelling with DCX (Hodge et al., 2008). Progression through this stage is governed by a transcription factor cascade (Pax6 - Ngn2 - Tbr2 - NeuroD - Tbr1) (Hodge et al., 2008)."
- has cross-reference "PMID:18385329"
- has cross-reference "PMID:40519263"
dentate gyrus type-2b neural progenitor label "dentate gyrus type-2b neural progenitor"
dentate gyrus type-2b neural progenitor SubClassOf neural progenitor cell
dentate gyrus type-2b neural progenitor SubClassOf has soma location some dentate gyrus subgranular zone

immature dentate gyrus granule neuron `http://purl.obolibrary.org/obo/CL_9900002`

Added

Class: immature dentate gyrus granule neuron
immature dentate gyrus granule neuron term tracker item 3609
immature dentate gyrus granule neuron contributor 0000-0002-5507-2103
immature dentate gyrus granule neuron creator "GitHub Copilot"
immature dentate gyrus granule neuron date "2026-04-20T13:49:06Z"^^dateTime
immature dentate gyrus granule neuron definition "A postmitotic glutamatergic neuron located in the inner granule cell layer of the dentate gyrus, arising from adult hippocampal neurogenesis and representing a transitional maturational stage between the DCX-positive neuroblast and the terminally differentiated granule neuron. This cell co-expresses DCX, NeuN, and PSA-NCAM, and is negative for calbindin (Micheli et al., 2025). Calretinin is transiently expressed during this stage in mice (Merz et al., 2013). In rodents, Tis21 expression persists postmitotically at this stage, unlike in the fetal brain (Attardo et al., 2009). The cell extends dendrites toward the molecular layer and projects axons through the hilus toward CA3 as synaptic integration proceeds (Regalado-Santiago et al., 2016)."
- has cross-reference "PMID:23667508"
- has cross-reference "PMID:26880934"
- has cross-reference "PMID:19482889"
- has cross-reference "PMID:40519263"
immature dentate gyrus granule neuron label "immature dentate gyrus granule neuron"
immature dentate gyrus granule neuron SubClassOf immature neuron
immature dentate gyrus granule neuron SubClassOf has soma location some dentate gyrus granule cell layer

Added UBERON term for dentate gyrus subgranunar zone

github-actions · 2026-04-21T08:43:35Z

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 · 2026-04-21T09:48:55Z

#gogoeditdiff

dosumis · 2026-04-21T18:30:29Z

Terms look good. Consider linking some stage terms - or we could add that to a subsequent ticket. Import + updated BG making a bit of a mess of inferred file. @ubyndr wondering if we can decouple component update here? Maybe not as we are using workflow used in release build. One option that might work would be to switch gogoeditdiff to just use -simple file (no imports).

ubyndr · 2026-04-22T12:17:09Z

@ubyndr wondering if we can decouple component update here? Maybe not as we are using workflow used in release build. One option that might work would be to switch gogoeditdiff to just use -simple file (no imports).

The unreasoned one, which uses the cl-edit.owl comparison, is tailored for this purpose, isn't it?

dosumis

Review species specificity. For general classes make sure that species applicabiltiy mouse/rodent markers is clearly flagged in def. For type 2a/b if this is mouse specific, then add taxon restriction and flag in name.

dosumis · 2026-05-14T14:07:40Z

#gogoeditdiff /clara

github-actions · 2026-05-14T14:09:09Z

Your branch is 13 commit/s behind, please update your branch.

Initial plan

9a080d9

Copilot AI assigned Copilot and RiveraAndrea83 Apr 20, 2026

Copilot AI linked an issue Apr 20, 2026 that may be closed by this pull request

[NTR] Add Dentate gyrus cell terms #3609

Open

Copilot started work on behalf of RiveraAndrea83 April 20, 2026 13:48 View session

Copilot AI changed the title ~~[WIP] Add Dentate gyrus neuroblast term to ontology~~ [NTR] Add four dentate gyrus cell terms (CL_9900001–CL_9900004) Apr 20, 2026

Copilot stopped work on behalf of RiveraAndrea83 due to an error April 20, 2026 14:07
The "Post Install uv" custom setup step from your .github/workflows/copilot-setup-steps.yml file failed.

Copilot AI requested a review from RiveraAndrea83 April 20, 2026 14:07

RiveraAndrea83 requested a review from dosumis April 20, 2026 15:38

RiveraAndrea83 added this to CL_wtgc_ticket_tracker Apr 20, 2026

github-project-automation Bot moved this to In Progress in CL_wtgc_ticket_tracker Apr 20, 2026

refreshed imports

90b8c95

Added UBERON term for dentate gyrus subgranunar zone

fixed HRA_subset error

5225642

RiveraAndrea83 marked this pull request as ready for review April 21, 2026 09:48

github-actions Bot mentioned this pull request Apr 21, 2026

cell-ontology report for 2026-04-21 ai4curation/agent-watcher#25

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

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

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Merge branch 'master' into copilot/add-dentate-gyrus-neuroblast-term

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dosumis requested changes Apr 30, 2026

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RiveraAndrea83 added 3 commits May 1, 2026 10:45

fixed definitions and removet item tracker

0b4e7d6

Merge branch 'master' into copilot/add-dentate-gyrus-neuroblast-term

83dedae

Merge branch 'master' into copilot/add-dentate-gyrus-neuroblast-term

f1e6f0d

github-actions Bot mentioned this pull request May 12, 2026

cell-ontology report for 2026-05-12 ai4curation/agent-watcher#43

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RiveraAndrea83 added 2 commits May 18, 2026 09:24

Merge branch 'master' into copilot/add-dentate-gyrus-neuroblast-term

3a5e1d1

refreshed imports, added expression of DCX and updated definition

aa08c54

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

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

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

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

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Copilot AI commented Apr 20, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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New terms

Axiom pattern (each term)

Other changes

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RiveraAndrea83 commented Apr 20, 2026

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Ontology comparison

Left

Right

Ontology imports

Ontology annotations

GPi Core neuron (Primate) http://purl.obolibrary.org/obo/CL_4310095

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GPi Shell neuron (Primate) http://purl.obolibrary.org/obo/CL_4310096

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GPin-BF cholinergic-GABAergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310083

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

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

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

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

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

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

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

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

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

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

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STRd D1/D2-hybrid medium spiny neuron (Primate) http://purl.obolibrary.org/obo/CL_4310131

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

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STRd D2 Striomat hybrid medium spiny neuron (Primate) http://purl.obolibrary.org/obo/CL_4310133

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STRd cholinergic-GABAergic neuron (Primate) http://purl.obolibrary.org/obo/CL_4310128

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STRv D1 medium spiny neuron (Primate) http://purl.obolibrary.org/obo/CL_4310136

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

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STRv D2 medium spiny neuron (Primate) http://purl.obolibrary.org/obo/CL_4310138

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UBERON_0009952 http://purl.obolibrary.org/obo/UBERON_0009952

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arkypallidal neuron (Primate) http://purl.obolibrary.org/obo/CL_4310093

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dentate gyrus neuroblast http://purl.obolibrary.org/obo/CL_9900001

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dentate gyrus type-2a neural progenitor http://purl.obolibrary.org/obo/CL_9900003

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dentate gyrus type-2b neural progenitor http://purl.obolibrary.org/obo/CL_9900004

Copilot AI commented Apr 20, 2026 •

edited

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github-actions Bot commented Apr 20, 2026 •

edited

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GPi Core neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310095`

GPi Shell neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310096`

GPin-BF cholinergic-GABAergic neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310083`

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

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

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

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

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

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

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

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

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

STRd D2 Striomat hybrid medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310133`

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

STRv D1 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310136`

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

STRv D2 medium spiny neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310138`

UBERON_0009952 `http://purl.obolibrary.org/obo/UBERON_0009952`

arkypallidal neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310093`

dentate gyrus neuroblast `http://purl.obolibrary.org/obo/CL_9900001`

dentate gyrus type-2a neural progenitor `http://purl.obolibrary.org/obo/CL_9900003`

dentate gyrus type-2b neural progenitor `http://purl.obolibrary.org/obo/CL_9900004`

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

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

immature NK T cell `http://purl.obolibrary.org/obo/CL_0000914`

immature dentate gyrus granule neuron `http://purl.obolibrary.org/obo/CL_9900002`

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`

prototypic neuron (Primate) `http://purl.obolibrary.org/obo/CL_4310094`

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`

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

striatal LAMP5 LHX6 GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310085`

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

striatal SST-CHODL GABAergic interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310123`

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

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

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

striatal pthlh-expressing interneuron (Primate) `http://purl.obolibrary.org/obo/CL_4310120`

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

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

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

github-actions Bot commented Apr 20, 2026 •

edited

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