Release Notes 2026-06-08

Ontology content summary

| Metric | Value | |:------------------------------------------------|--------:| | Number of subclasses of root | 3325 | | Number of annotations on CL terms | 17098 | | Number of synonyms | 7161 | | Number of unique references | 1960 | | Number of unique references in definitions | 2120 | | Number of relationships with CL term as subject | 5141 | | Number of cellxgene classes | 1026 | | Number of HRA classes | 655 |

<details> <summary>Nodes added to subset: 198</summary>

| Term | Subset | ----|----| | cervical dorsal root ganglion TRPV1 neuron (CL:4079008) | human_reference_atlas | | T follicular regulatory cell (CL:0009113) | added_by_HRA | | mucus secreting cell of trachea gland (CL:4033020) | added_by_HRA | | ON parasol ganglion cell (CL:4033052) | added_by_HRA | | endothelial cell of arteriole of lymph node (CL:4033001) | added_by_HRA | | kidney loop of Henle long descending thin limb outer medulla epithelial cell (CL:4030013) | added_by_HRA | | lumbar dorsal root ganglion Piezo2 neuron (CL:4079016) | human_reference_atlas | | lung resident memory CD8-positive, CD103-positive, alpha-beta T cell (CL:4033040) | added_by_HRA | | T cell zone reticular cell (CL:0009105) | added_by_HRA | | kidney connecting tubule alpha-intercalated cell (CL:4030020) | added_by_HRA | | cervical dorsal root ganglion peripherin neuron (CL:4079004) | human_reference_atlas | | goblet cell of epithelium of lobar bronchus (CL:4033009) | added_by_HRA | | invaginating midget bipolar cell (CL:4033034) | added_by_HRA | | luminal hormone-sensing cell of mammary gland (CL:4033058) | added_by_HRA | | cycling myeloid cell (CL:4033081) | added_by_HRA | | sacral dorsal root ganglion Nav1.9 neuron (CL:4079023) | human_reference_atlas | | cuboidal granulosa cell (CL:4033084) | added_by_HRA | | thymic fibroblast type 2 (CL:0009079) | added_by_HRA | | CD8aa(II) thymocyte (CL:0009069) | added_by_HRA | | thoracic dorsal root ganglion Nav1.7 neuron (CL:4079031) | human_reference_atlas | | diffuse bipolar 5 cell (CL:4033085) | added_by_HRA | | lung resident memory CD8-positive, alpha-beta T cell (CL:4033039) | added_by_HRA | | metallothionein-positive alveolar macrophage (CL:4033042) | added_by_HRA | | bronchiolar smooth muscle cell (CL:4033017) | added_by_HRA | | preplasmablast (CL:4033065) | added_by_HRA | | kidney connecting tubule principal cell (CL:4030018) | added_by_HRA | | myoepithelial cell of bronchus submucosal gland (CL:4033003) | added_by_HRA | | thoracic dorsal root ganglion CGRP neuron (CL:4079029) | human_reference_atlas | | medium field retinal amacrine cell (CL:0004252) | added_by_HRA | | cycling basal cell (CL:4033082) | added_by_HRA | | cycling macrophage (CL:4033076) | added_by_HRA | | serous secreting cell of bronchus submucosal gland (CL:4033005) | added_by_HRA | | diffuse bipolar 4 cell (CL:4033031) | added_by_HRA | | lumbar dorsal root ganglion endothelin-1 neuron (CL:4079012) | human_reference_atlas | | lung resident memory CD4-positive, alpha-beta T cell (CL:4033038) | added_by_HRA | | lung migratory dendritic cell (CL:4033045) | added_by_HRA | | cycling mononuclear phagocyte (CL:4033078) | added_by_HRA | | squamous granulosa cell (CL:4033083) | added_by_HRA | | diffuse bipolar 6 cell (CL:4033032) | added_by_HRA | | centroblast (CL:0009112) | added_by_HRA | | diffuse bipolar 2 cell (CL:4033028) | added_by_HRA | | cycling stromal cell (CL:4047001) | added_by_HRA | | renal medullary fibroblast (CL:4030022) | added_by_HRA | | airway submucosal gland collecting duct epithelial cell (CL:4033023) | added_by_HRA | | parasol ganglion cell of retina (CL:4023189) | added_by_HRA | | myo-medullary thymic epithelial cell (CL:0009075) | added_by_HRA | | lumbar dorsal root ganglion TRPV1 neuron (CL:4079019) | human_reference_atlas | | cycling plasma cell (CL:4047003) | added_by_HRA | | placental resident macrophage (CL:4033087) | added_by_HRA | | thymic fibroblast type 1 (CL:0009078) | added_by_HRA | | cervical dorsal root ganglion CGRP neuron (CL:4079000) | human_reference_atlas | | flat midget bipolar cell (CL:4033033) | added_by_HRA | | lymph node fibroblastic reticular cell (CL:0009102) | added_by_HRA | | B cell zone reticular cell (CL:0009104) | added_by_HRA | | corticomedullary thymic epithelial cell (CL:0009070) | added_by_HRA | | lung perichondrial fibroblast (CL:4033026) | added_by_HRA | | cycling natural killer cell (CL:4033071) | added_by_HRA | | thoracic dorsal root ganglion peripherin neuron (CL:4079033) | human_reference_atlas | | mural granulosa cell (CL:4033067) | added_by_HRA | | respiratory tract suprabasal cell (CL:4033048) | added_by_HRA | | cycling CD8-positive, alpha-beta T cell (CL:4033074) | added_by_HRA | | perichondrial fibroblast (CL:4033025) | added_by_HRA | | vein endothelial cell of respiratory system (CL:4033008) | added_by_HRA | | neural cell (CL:0002319) | human_reference_atlas | | kidney collecting duct alpha-intercalated cell (CL:4030015) | added_by_HRA | | giant bipolar cell (CL:4033035) | added_by_HRA | | lumbar dorsal root ganglion substance P neuron (CL:4079018) | human_reference_atlas | | lymphatic endothelial cell of trabecula (CL:0009109) | added_by_HRA | | subcapsular thymic epithelial cell (CL:0009077) | added_by_HRA | | lumbar dorsal root ganglion Nav1.7 neuron (CL:4079013) | human_reference_atlas | | midget ganglion cell of retina (CL:4023188) | added_by_HRA | | glycinergic-GABAergic amacrine cell (CL:4033091) | added_by_HRA | | lymphatic endothelial cell of medulla ceiling (CL:0009110) | added_by_HRA | | committed double negative thymocyte (Homo sapiens) (CL:0009082) | added_by_HRA | | kidney connecting tubule intercalated cell (CL:4030019) | added_by_HRA | | monocytoid B cell (CL:0009114) | added_by_HRA | | deuterosomal cell (CL:4033044) | added_by_HRA | | medullary reticular cell (CL:0009106) | added_by_HRA | | luminal adaptive secretory precursor cell of mammary gland (CL:4033057) | added_by_HRA | | early luteal cell (CL:4052046) | added_by_HRA | | myelinating glial cell (CL:4023154) | human_reference_atlas | | diffuse bipolar 1 cell (CL:4033027) | added_by_HRA | | inner wall Schlemm's canal endothelial cell (CL:4033098) | added_by_HRA | | epithelial cell of late distal convoluted tubule (CL:4030017) | added_by_HRA | | lactocyte (CL:0002325) | added_by_HRA | | specified double negative thymocyte (Homo sapiens) (CL:0009081) | added_by_HRA | | lumbar dorsal root ganglion Nav1.9 neuron (CL:4079014) | human_reference_atlas | | cervical dorsal root ganglion Nav1.9 neuron (CL:4079003) | human_reference_atlas | | endothelial cell of central vein of liver (CL:4033061) | added_by_HRA | | cycling alveolar macrophage (CL:4033077) | added_by_HRA | | uterine resident macrophage (CL:4033064) | added_by_HRA | | lumbar dorsal root ganglion peripherin neuron (CL:4079015) | human_reference_atlas | | mucus secreting cell of tracheobronchial tree submucosal gland (CL:4033037) | added_by_HRA | | secondary crest myofibroblast (CL:4033016) | added_by_HRA | | kidney loop of Henle long descending thin limb inner medulla epithelial cell (CL:4030014) | added_by_HRA | | airway submucosal gland duct multiciliated cell (CL:4033055) | added_by_HRA | | starburst amacrine cell (CL:0004232) | added_by_HRA | | lactocyte type 2 (CL:4033060) | added_by_HRA | | cycling type EC enteroendocrine cell (CL:4047004) | added_by_HRA | | airway submucosal gland duct basal cell (CL:4033024) | added_by_HRA | | lumbar dorsal root ganglion RET neuron (CL:4079017) | human_reference_atlas | | thoracic dorsal root ganglion TRPV1 neuron (CL:4079037) | human_reference_atlas | | cycling glial cell (CL:4047002) | added_by_HRA | | mucus secreting cell of bronchus submucosal gland (CL:4033022) | added_by_HRA | | sacral dorsal root ganglion peripherin neuron (CL:4079024) | human_reference_atlas | | cycling gamma-delta T cell (CL:4033072) | added_by_HRA | | atretic granulosa cell (CL:4033090) | added_by_HRA | | medullary thymic epithelial cell type 4 (CL:0009074) | added_by_HRA | | perivascular cell (CL:4033054) | added_by_HRA | | thoracic dorsal root ganglion RET neuron (CL:4079035) | human_reference_atlas | | lung megakaryocyte (CL:4033018) | added_by_HRA | | late luteal cell (CL:4052047) | added_by_HRA | | sacral dorsal root ganglion substance P neuron (CL:4079027) | human_reference_atlas | | ON midget ganglion cell (CL:4033046) | added_by_HRA | | centrocyte (CL:0009111) | added_by_HRA | | cycling endothelial cell of lymphatic vessel (CL:4033079) | added_by_HRA | | rearranging double negative thymocyte (Homo sapiens) (CL:0009083) | added_by_HRA | | cycling dendritic cell (CL:4033070) | added_by_HRA | | smooth muscle cell of large intestine smooth muscle circular layer (CL:4033011) | added_by_HRA | | OFFx cell (CL:4033036) | added_by_HRA | | diffuse bipolar 4b cell (CL:4033096) | added_by_HRA | | glycinergic amacrine cell (CL:4030028) | added_by_HRA | | lumbar dorsal root ganglion CGRP neuron (CL:4079011) | human_reference_atlas | | lung interstitial macrophage (CL:4033043) | added_by_HRA | | cycling B cell (CL:4033068) | added_by_HRA | | CD57-positive enterocyte (CL:4033092) | added_by_HRA | | medullary thymic epithelial cell type 3 (CL:0009073) | added_by_HRA | | prehypertrophic chondrocyte (CL:0020022) | human_reference_atlas | | pre-granulosa cell (CL:4033066) | added_by_HRA | | diffuse bipolar 3b cell (CL:4033030) | added_by_HRA | | epithelial cell of early distal convoluted tubule (CL:4030016) | added_by_HRA | | sacral dorsal root ganglion TRPV1 neuron (CL:4079028) | human_reference_atlas | | cycling neuroblast (sensu Vertebrata) (CL:4047005) | added_by_HRA | | diffuse bipolar 4a cell (CL:4033095) | added_by_HRA | | cervical dorsal root ganglion Nav1.7 neuron (CL:4079002) | human_reference_atlas | | lymph node lymphatic vessel endothelial cell (CL:0009115) | added_by_HRA | | cycling pulmonary alveolar type 2 cell (CL:4033080) | added_by_HRA | | onychocyte (CL:4033056) | added_by_HRA | | thoracic dorsal root ganglion Piezo2 neuron (CL:4079034) | human_reference_atlas | | sacral dorsal root ganglion endothelin-1 neuron (CL:4079021) | human_reference_atlas | | lymph node marginal reticular cell (CL:0009103) | added_by_HRA | | basal-myoepithelial cell of mammary gland (CL:0002324) | added_by_HRA | | small bistratified retinal ganglion cell (CL:4033053) | added_by_HRA | | endovascular extravillous trophoblast cell (CL:4033063) | added_by_HRA | | medullary thymic epithelial cell type 1 (CL:0009071) | added_by_HRA | | GABAergic amacrine cell (CL:4030027) | added_by_HRA | | sacral dorsal root ganglion CGRP neuron (CL:4079020) | human_reference_atlas | | cervical dorsal root ganglion substance P neuron (CL:4079007) | human_reference_atlas | | neuroendocrine cell of epithelium of crypt of Lieberkuhn (CL:4033002) | added_by_HRA | | sacral dorsal root ganglion RET neuron (CL:4079026) | human_reference_atlas | | peg cell (CL:4033014) | added_by_HRA | | lymphatic endothelial cell of subcapsular sinus ceiling (CL:0009107) | added_by_HRA | | atretic follicular cell of ovary (CL:4033089) | added_by_HRA | | medullary thymic epithelial cell type 2 (CL:0009072) | added_by_HRA | | cycling T cell (CL:4033069) | added_by_HRA | | epithelial cell of proximal tubule segment 3 (CL:4030011) | added_by_HRA | | diffuse bipolar 3a cell (CL:4033029) | added_by_HRA | | kidney loop of Henle short descending thin limb epithelial cell (CL:4030012) | added_by_HRA | | ON-blue cone bipolar cell (CL:4033019) | added_by_HRA | | cycling monocyte (CL:4033073) | added_by_HRA | | thoracic dorsal root ganglion substance P neuron (CL:4079036) | human_reference_atlas | | interstitial extravillous trophoblast cell (CL:4033062) | added_by_HRA | | endothelial cell of venule of lymph node (CL:4033000) | added_by_HRA | | CCL3-positive alveolar macrophage (CL:4033041) | added_by_HRA | | lipid-associated macrophage (CL:4033086) | added_by_HRA | | age-associated B cell (CL:4033094) | added_by_HRA | | endothelial cell of efferent lymphatic vessel (CL:4033006) | added_by_HRA | | epithelial cell of proximal tubule segment 2 (CL:4030010) | added_by_HRA | | neuro-medullary thymic epithelial cell (CL:0009076) | added_by_HRA | | CD8aa(I) thymocyte (CL:0009068) | added_by_HRA | | cervical dorsal root ganglion RET neuron (CL:4079006) | human_reference_atlas | | effector chondrocyte (CL:0020023) | human_reference_atlas | | sacral dorsal root ganglion Nav1.7 neuron (CL:4079022) | human_reference_atlas | | retinal astrocyte (CL:4033015) | added_by_HRA | | myoepithelial cell of trachea gland (CL:4033021) | added_by_HRA | | cervical dorsal root ganglion Piezo2 neuron (CL:4079005) | human_reference_atlas | | lymphatic endothelial cell of subcapsular sinus floor (CL:0009108) | added_by_HRA | | cycling CD4-positive, alpha-beta T cell (CL:4033075) | added_by_HRA | | brush cell of epithelium of lobar bronchus (CL:4033007) | added_by_HRA | | kidney connecting tubule beta-intercalated cell (CL:4030021) | added_by_HRA | | epithelial cell of proximal tubule segment 1 (CL:4030009) | added_by_HRA | | smooth muscle cell of taenia coli (CL:4033004) | added_by_HRA | | outer wall Schlemm's canal endothelial cell (CL:4033099) | added_by_HRA | | neuroendocrine cell of epithelium of lobar bronchus (CL:4033010) | added_by_HRA | | limbal epithelial stem cell of cornea (CL:4033093) | added_by_HRA | | thoracic dorsal root ganglion endothelin-1 neuron (CL:4079030) | human_reference_atlas | | OFF parasol ganglion cell (CL:4033051) | added_by_HRA | | OFF midget ganglion cell (CL:4033047) | added_by_HRA | | catecholaminergic neuron (CL:4033050) | added_by_HRA | | Schlemm's canal endothelial cell (CL:4033097) | added_by_HRA | | decidual resident macrophage (CL:4033088) | added_by_HRA | | thoracic dorsal root ganglion Nav1.9 neuron (CL:4079032) | human_reference_atlas | | smooth muscle cell of large intestine smooth muscle longitudinal layer (CL:4033012) | added_by_HRA | | sacral dorsal root ganglion Piezo2 neuron (CL:4079025) | human_reference_atlas | | non-myelinating Schwann cell (CL:0002376) | human_reference_atlas | | lactocyte type 1 (CL:4033059) | added_by_HRA | | taste receptor cell of tongue (CL:4033049) | added_by_HRA | | cervical dorsal root ganglion endothelin-1 neuron (CL:4079001) | human_reference_atlas |

</details>

<details> <summary>Nodes renamed: 26</summary>

| ID | Old Label | New Label | ----|----|----| | CL:4310121 | striatal SST-LYPD6-RSPO2 GABAergic interneuron (Primate) | STR LYPD6-RSPO2 GABA GABAergic interneuron (Primate) | | CL:4310084 | striatal LAMP5 CXCL14 GABAergic interneuron (Primate) | LAMP5-CXCL14 GABA lamp5 GABAergic interneuron (Primate) | | CL:4310096 | GPi Shell neuron (Primate) | GPi Shell internal globus pallidus shell projection neuron (Primate) | | CL:4310137 | STRv D1-NUDAP medium spiny neuron (Primate) | STRv D1 NUDAP MSN D1-NUDAP medium spiny neuron (Primate) | | CL:4310135 | STR cholinergic-GABAergic neuron (Primate) | STR Cholinergic GABA striatal cholinergic-GABAergic neuron (Primate) | | CL:4310134 | striosomal D2 medium spiny neuron (Primate) | STRd D2 Striosome MSN striosomal D2 medium spiny neuron (Primate) | | CL:4310120 | striatal pthlh-expressing interneuron (Primate) | STR FS PTHLH-PVALB GABA striatal pthlh-expressing interneuron (Primate) | | CL:4310129 | STRd D1 Matrix medium spiny neuron (Primate) | STRd D1 Matrix MSN matrix D1 medium spiny neuron (Primate) | | CL:4310128 | STRd cholinergic-GABAergic neuron (Primate) | STRd Cholinergic GABA dorso-striatal cholinergic-GABAergic neuron (Primate) | | CL:4310138 | STRv D2 medium spiny neuron (Primate) | STRv D2 MSN nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron (Primate) | | CL:4310093 | arkypallidal neuron (Primate) | GPe MEIS2-SOX6 GABA arkypallidal neuron (Primate) | | CL:4310122 | striatal SST-ADARB2 GABAergic interneuron (Primate) | STR SST-ADARB2 GABA sst GABAergic interneuron (Primate) | | CL:4310124 | striatal SST-RSPO2 GABAergic interneuron (Primate) | STR SST-RSPO2 GABA sst GABAergic interneuron (Primate) | | CL:4310094 | prototypic neuron (Primate) | GPe SOX6-CTXND1 GABA prototypic neuron (Primate) | | CL:4310133 | STRd D2 Striomat hybrid medium spiny neuron (Primate) | STRd D2 StrioMat Hybrid MSN indirect pathway medium spiny neuron (Primate) | | CL:4310136 | STRv D1 medium spiny neuron (Primate) | STRv D1 MSN nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron (Primate) | | CL:4310123 | striatal SST-CHODL GABAergic interneuron (Primate) | STR SST-CHODL GABA sst chodl GABAergic interneuron (Primate) | | CL:4310127 | striatal VIP GABAergic interneuron (Primate) | VIP GABA VIP GABAergic interneuron (Primate) | | CL:4310104 | Islands of Calleja granule cell (Primate) | OT D1 ICj Islands of Calleja granule cell (Primate) | | CL:4310132 | STRd D2 Matrix medium spiny neuron (Primate) | STRd D2 Matrix MSN matrix D2 medium spiny neuron (Primate) | | CL:4310095 | GPi Core neuron (Primate) | GPi Core internal globus pallidus core projecting neuron (Primate) | | CL:4310083 | GPin-BF cholinergic-GABAergic neuron (Primate) | GPin-BF Cholinergic GABA GABA-Chol neuron (Primate) | | CL:4310147 | OB Dopa-GABA neuron (Primate) | OB Dopa-GABA OB-Dopa-GABA (Primate) | | CL:4310131 | STRd D1/D2-hybrid medium spiny neuron (Primate) | STR D1D2 Hybrid MSN D1/D2-hybrid medium spiny neuron (Primate) | | CL:4310130 | striosomal D1 medium spiny neuron (Primate) | STRd D1 Striosome MSN striosomal D1 medium spiny neuron (Primate) | | CL:4310085 | striatal LAMP5 LHX6 GABAergic interneuron (Primate) | LAMP5-LHX6 GABA Lamp5 Lhx6 neuron (Primate) |

</details>

<details> <summary>Text definitions changed: 5</summary>

| Term | Old Text Definition | New Text Definition | ----|----|----| | somatic muscle myoblast (CL:0008018) | A myoblast that is commited to developing into a somatic muscle. | A myoblast that is committed to developing into a somatic muscle. | | glioblast (CL:0000030) | A non-terminally differentiated cell that develops form the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes. | A non-terminally differentiated cell that develops from the neuroectoderm. Glioblast has the potential to differentiate into various types of glial cells, including astrocytes and oligodendrocytes. | | myoblast (CL:0000056) | A cell that is commited to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair. | A cell that is committed to differentiating into a muscle cell. Embryonic myoblasts develop from the mesoderm. They undergo proliferation, migrate to their various sites, and then differentiate into the appropriate form of myocytes. Myoblasts also occur as transient populations of cells in muscles undergoing repair. | | obsolete immortal cell line cell (CL:0000002) | OBSOLETE: A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of a immortal cell line. | OBSOLETE: A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite growth/propagation in vitro as part of an immortal cell line. | | early embryonic cell (metazoa) (CL:0000007) | A cell found in the embryo before the formation of all the gem layers is complete. | A cell found in the embryo before the formation of all the germ layers is complete. |

</details>

<details> <summary>Classes added: 11</summary>

| Term | ----| | entorhinal cortex layer II stellate cell (CL:0020067) | | Oriens-Lacunosum Moleculare neuron (CL:0020074) | | SN PAX7 GABA GABAergic neuron (Primate) (CL:4310056) | | parvalbumin-positive basket cell (CL:0020071) | | hilar mossy cell (CL:0020069) | | STR D2 MSN indirect pathway medium spiny neuron (Primate) (CL:4310059) | | CA2 pyramidal cell (CL:0020070) | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | | STR D1 MSN direct pathway medium spiny neuron (Primate) (CL:4310058) | | CA3 pyramidal cell (CL:0020068) | | CA1 pyramidal cell (CL:0020072) |

</details>

<details> <summary>Synonyms added: 25</summary>

| Term | New Synonym | Predicate | ----|----|----| | entorhinal cortex layer II stellate cell (CL:0020067) | reelin-positive entorhinal cortex layer II neuron | oio:hasRelatedSynonym | | CA3 pyramidal cell (CL:0020068) | pyramidal cell of CA3 | oio:hasExactSynonym | | hilar mossy cell (CL:0020069) | mossy cell | oio:hasExactSynonym | | Oriens-Lacunosum Moleculare neuron (CL:0020074) | OLM | oio:hasRelatedSynonym | | CA3 pyramidal cell (CL:0020068) | CA3 pyramidal neuron | oio:hasExactSynonym | | parvalbumin-positive basket cell (CL:0020071) | PV basket cell | oio:hasExactSynonym | | Oriens-Lacunosum Moleculare neuron (CL:0020074) | OLM neuron | oio:hasExactSynonym | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | PeN kisspeptin neuron | oio:hasRelatedSynonym | | parvalbumin-positive basket cell (CL:0020071) | Parvalbumin (PV) positive basket cell | oio:hasExactSynonym | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | AVPV Kiss1 neuron | oio:hasExactSynonym | | hilar mossy cell (CL:0020069) | dentate hilar mossy cell | oio:hasExactSynonym | | entorhinal cortex layer II stellate cell (CL:0020067) | layer II stellate cell of medial entorhinal cortex | oio:hasExactSynonym | | CA2 pyramidal cell (CL:0020070) | pyramidal cell of CA2 | oio:hasExactSynonym | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | PeN Kiss1 neuron | oio:hasRelatedSynonym | | STR D2 MSN indirect pathway medium spiny neuron (Primate) (CL:4310059) | STR D2 MSN | oio:hasExactSynonym | | CA1 pyramidal cell (CL:0020072) | pyramidal cell of CA1 | oio:hasExactSynonym | | entorhinal cortex layer II stellate cell (CL:0020067) | entorhinal stellate cell | oio:hasExactSynonym | | STR D1 MSN direct pathway medium spiny neuron (Primate) (CL:4310058) | STR D1 MSN | oio:hasExactSynonym | | CA1 pyramidal cell (CL:0020072) | CA1 pyramidal neuron | oio:hasExactSynonym | | CA2 pyramidal cell (CL:0020070) | CA2 pyramidal neuron | oio:hasExactSynonym | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | AVPV kisspeptin neuron | oio:hasRelatedSynonym | | entorhinal cortex layer II stellate cell (CL:0020067) | MEC layer II stellate cell | oio:hasExactSynonym | | entorhinal cortex layer II stellate cell (CL:0020067) | EC LII stellate cell | oio:hasExactSynonym | | SN PAX7 GABA GABAergic neuron (Primate) (CL:4310056) | SN PAX7 GABA | oio:hasExactSynonym | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | anteroventral periventricular nucleus kisspeptin neuron | oio:hasExactSynonym |

</details>

<details> <summary>Text definitions added: 11</summary>

| Term | New Text Definition | ----|----| | hilar mossy cell (CL:0020069) | A dentate gyrus neuron with soma in the polymorphic layer (Scharfman & Myers, 2012), capable of glutamate secretion as a neurotransmitter (Scharfman & Bernstein, 2015). Distinguished by a large multipolar soma, thorny excrescences on proximal dendrites, and commissural/associational axon projections terminating in the inner molecular layer of the dentate gyrus (Scharfman & Myers, 2012). In rodents, serves as a major excitatory neuron of the dentate hilus providing feedback excitation to granule cells (Sun et al., 2017). | | entorhinal cortex layer II stellate cell (CL:0020067) | A glutamatergic principal neuron with its soma located in layer II of the entorhinal cortex, distinguished by stellate morphology, lack of calbindin expression, and expression of reelin in rodents. This cell type is a major source of perforant pathway projections from entorhinal cortex layer II to the dentate gyrus of the hippocampal formation. It displays electrophysiological properties including a prominent hyperpolarisation-activated inward current, voltage sag, and theta-frequency membrane resonance. | | CA1 pyramidal cell (CL:0020072) | A hippocampal pyramidal neuron with soma located in the pyramidal layer of hippocampal area CA1 (Cembrowski et al., 2016; Müller & Remy, 2017), forming the dominant excitatory projection population of the CA1 subfield. As the primary output cell of Ammon's horn, it projects via the subiculum to entorhinal cortex and is capable of glutamate secretion as a neurotransmitter (Dale et al., 2015). In mouse, it is distinguished from CA2 and CA3 pyramidal neurons by soma position within the CA1 stratum pyramidale and by expression of wolframin (Wfs1), an endoplasmic reticulum-resident membrane protein enriched in deep-sublayer CA1 cells (Cembrowski et al., 2016). | | CA2 pyramidal cell (CL:0020070) | A hippocampal pyramidal neuron with soma located in the pyramidal layer of hippocampal area CA2 (Cembrowski et al., 2016; Sanchez-Aguilera et al., 2021). Distinguished from CA1 and CA3 pyramidal neurons by expression of Pcp4, Rgs14, and Amigo2 in rodents (San Antonio et al., 2014; Caruana et al., 2012), and by absence of the CA1 marker wolframin (Wfs1) (Evans et al., 2018). Receives strong LTP-competent input from entorhinal cortex at distal dendrites, while Schaffer collateral inputs to proximal dendrites are resistant to canonical LTP in wild-type animals (Chevaleyre & Siegelbaum, 2010). Required for social memory in mice (Hitti & Siegelbaum, 2014). | | STR D2 MSN indirect pathway medium spiny neuron (Primate) (CL:4310059) | 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. | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | A hypothalamic kisspeptin neuron with its soma located in the anteroventral periventricular nucleus (AVPV) and the posterior part of the periventricular hypothalamic nucleus in the rostral hypothalamus (Stephens et al., 2017; Nejad et al., 2017). It mediates estrogen positive feedback by driving gonadotropin-releasing hormone (GnRH) and luteinizing hormone (LH) secretion and is required for the preovulatory LH surge (Adachi et al., 2007; Nejad et al., 2017). In mice, it co-expresses kisspeptin (Kiss1) and tyrosine hydroxylase (TH), indicating a dopaminergic component within an otherwise primarily GABAergic phenotype (Kauffman et al., 2007; Stephens et al., 2017, 2024). It also expresses estrogen receptor alpha (Esr1), enabling direct regulation by estradiol (Frazao et al., 2013; Wartenberg et al., 2021). It belongs to a sexually dimorphic population, with higher cell numbers observed in females than in males in rodents (Stephens et al., 2017; Nejad et al., 2017). | | Oriens-Lacunosum Moleculare neuron (CL:0020074) | A GABAergic interneuron of the hippocampal CA1 region whose horizontally oriented soma is located in the stratum oriens at the stratum oriens–alveus border, with spiny dendrites confined to stratum oriens; the axon ascends vertically to arborize exclusively in stratum lacunosum-moleculare, innervating the apical tufts of pyramidal neurons. Electrophysiologically, these cells display regular-to-adapting spiking with a prominent hyperpolarization-activated cation current (Ih) and theta-frequency resonance. In rodents, canonical markers include somatostatin (Sst) and metabotropic glutamate receptor 1 (Grm1/mGluR1); the alpha-2 nicotinic acetylcholine receptor subunit (Chrna2) is a highly specific marker in mouse. | | SN PAX7 GABA GABAergic neuron (Primate) (CL:4310056) | 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. | | CA3 pyramidal cell (CL:0020068) | A hippocampal pyramidal neuron with soma located in the pyramidal layer of hippocampal area CA3 (Cembrowski et al., 2016; Wheeler et al., 2015). Capable of glutamate secretion as a neurotransmitter (Dale et al., 2015) and distinguished from CA1 and CA2 pyramidal neurons by thorny excrescences on the proximal apical dendrites — postsynaptic specializations that receive excitatory mossy fiber input from dentate gyrus granule cells (Munster-Wandowski et al., 2013). Harbours a dense recurrent Schaffer collateral network; individual neurons can act as hub neurons capable of triggering hippocampal network bursts (Marissal et al., 2012). | | STR D1 MSN direct pathway medium spiny neuron (Primate) (CL:4310058) | 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. | | parvalbumin-positive basket cell (CL:0020071) | A basket cell of the hippocampal formation that expresses the calcium-binding protein parvalbumin (Pvalb) in rodents (Rivera et al., 2014; Que et al., 2021; Contreras et al., 2019). Somata are located in the pyramidal layers of CA1 and CA3 and the granule cell layer of the dentate gyrus. Axon collaterals are confined to the pyramidal layer, forming dense perisomatic inhibitory synapses on the somata of principal neurons; a single cell contacts more than 1500 pyramidal neurons (Sik et al., 1995). This cell is a fast-spiking GABAergic interneuron and is distinguished from CCK basket cells by absence of cannabinoid receptor 1 (Cnr1) expression (Whissell et al., 2015). |

</details>

<details> <summary>Relationships added: 52</summary>

| Subject | Predicate | Object| ----|----|----| | SN PAX7 GABA GABAergic neuron (Primate) (CL:4310056) | subClassOf (rdfs:subClassOf) | GABAergic neuron (CL:0000617) | | parvalbumin-positive basket cell (CL:0020071) | subClassOf (rdfs:subClassOf) | cerebral cortex GABAergic interneuron (CL:0010011) | | entorhinal cortex layer II stellate cell (CL:0020067) | subClassOf (rdfs:subClassOf) | glutamatergic neuron (CL:0000679) | | SN SEMA5A GABA GABAergic interneuron (Primate) (CL:4310114) | subClassOf (rdfs:subClassOf) | SN PAX7 GABA GABAergic neuron (Primate) (CL:4310056) | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | RO:0002100 | UBERON:0002690 | | Oriens-Lacunosum Moleculare neuron (CL:0020074) | subClassOf (rdfs:subClassOf) | hippocampal interneuron (CL:1001569) | | parvalbumin-positive basket cell (CL:0020071) | RO:0002292 | PR:000013502 | | CA1 pyramidal cell (CL:0020072) | RO:0002100 | UBERON:0014548 | | CA2 pyramidal cell (CL:0020070) | subClassOf (rdfs:subClassOf) | hippocampal pyramidal neuron (CL:1001571) | | hilar mossy cell (CL:0020069) | subClassOf (rdfs:subClassOf) | glutamatergic neuron (CL:0000679) | | cuboidal granulosa cell (CL:4033084) | subClassOf (rdfs:subClassOf) | cuboidal epithelial cell (CL:0020029) | | CA2 pyramidal cell (CL:0020070) | subClassOf (rdfs:subClassOf) | glutamatergic neuron (CL:0000679) | | STR D2 MSN indirect pathway medium spiny neuron (Primate) (CL:4310059) | subClassOf (rdfs:subClassOf) | indirect pathway medium spiny neuron (CL:4023029) | | Oriens-Lacunosum Moleculare neuron (CL:0020074) | subClassOf (rdfs:subClassOf) | cerebral cortex GABAergic interneuron (CL:0010011) | | interna theca cell (CL:4052012) | subClassOf (rdfs:subClassOf) | secretory epithelial cell (CL:1100001) | | entorhinal cortex layer II stellate cell (CL:0020067) | subClassOf (rdfs:subClassOf) | cerebral cortex neuron (CL:0010012) | | CA1 pyramidal cell (CL:0020072) | subClassOf (rdfs:subClassOf) | hippocampal pyramidal neuron (CL:1001571) | | STRd D2 StrioMat Hybrid MSN indirect pathway medium spiny neuron (Primate) (CL:4310133) | subClassOf (rdfs:subClassOf) | STR D2 MSN indirect pathway medium spiny neuron (Primate) (CL:4310059) | | STRd D1 Matrix MSN matrix D1 medium spiny neuron (Primate) (CL:4310129) | subClassOf (rdfs:subClassOf) | STR D1 MSN direct pathway medium spiny neuron (Primate) (CL:4310058) | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | RO:0002292 | PR:Q6Y4S4 | | entorhinal cortex layer II stellate cell (CL:0020067) | RO:0002292 | PR:000013879 | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | subClassOf (rdfs:subClassOf) | hypothalamus kisspeptin neuron (CL:4023123) | | entorhinal cortex layer II stellate cell (CL:0020067) | RO:0002100 | UBERON:0022337 | | STRv D1 MSN nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron (Primate) (CL:4310136) | subClassOf (rdfs:subClassOf) | STR D1 MSN direct pathway medium spiny neuron (Primate) (CL:4310058) | | hilar mossy cell (CL:0020069) | RO:0002100 | UBERON:0002928 | | SN EBF2 GABA GABAergic interneuron (Primate) (CL:4310110) | subClassOf (rdfs:subClassOf) | SN PAX7 GABA GABAergic neuron (Primate) (CL:4310056) | | STRd D2 Matrix MSN matrix D2 medium spiny neuron (Primate) (CL:4310132) | subClassOf (rdfs:subClassOf) | STR D2 MSN indirect pathway medium spiny neuron (Primate) (CL:4310059) | | hilar mossy cell (CL:0020069) | subClassOf (rdfs:subClassOf) | dentate gyrus neuron (CL:4023062) | | entorhinal cortex layer II stellate cell (CL:0020067) | subClassOf (rdfs:subClassOf) | stellate neuron (CL:0000122) | | STRd D1 Striosome MSN striosomal D1 medium spiny neuron (Primate) (CL:4310130) | subClassOf (rdfs:subClassOf) | STR D1 MSN direct pathway medium spiny neuron (Primate) (CL:4310058) | | CA3 pyramidal cell (CL:0020068) | subClassOf (rdfs:subClassOf) | glutamatergic neuron (CL:0000679) | | STRd D2 Striosome MSN striosomal D2 medium spiny neuron (Primate) (CL:4310134) | subClassOf (rdfs:subClassOf) | STR D2 MSN indirect pathway medium spiny neuron (Primate) (CL:4310059) | | mucosal-associated invariant T cell, human (CL:0020002) | RO:0015015 | PR:Q12918 | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | RO:0002292 | PR:P19785 | | parvalbumin-positive basket cell (CL:0020071) | subClassOf (rdfs:subClassOf) | hippocampal interneuron (CL:1001569) | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | subClassOf (rdfs:subClassOf) | GABAergic neuron (CL:0000617) | | granulosa cell (CL:0000501) | subClassOf (rdfs:subClassOf) | secretory epithelial cell (CL:1100001) | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | RO:0002100 | UBERON:0002708 | | CA3 pyramidal cell (CL:0020068) | RO:0002100 | UBERON:0014550 | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | subClassOf (rdfs:subClassOf) | dopaminergic neuron (CL:0000700) | | entorhinal cortex layer II stellate cell (CL:0020067) | subClassOf (rdfs:subClassOf) | BFO:0000002 | | Oriens-Lacunosum Moleculare neuron (CL:0020074) | RO:0002100 | UBERON:0014552 | | CA2 pyramidal cell (CL:0020070) | RO:0002100 | UBERON:0014549 | | AVPV/PeN kisspeptin neuron, mouse (CL:0020073) | RO:0002292 | PR:P24529 | | follicular cell of ovary (CL:0002174) | subClassOf (rdfs:subClassOf) | epithelial cell (CL:0000066) | | parvalbumin-positive basket cell (CL:0020071) | subClassOf (rdfs:subClassOf) | basket cell (CL:0000118) | | STRv D2 MSN nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron (Primate) (CL:4310138) | subClassOf (rdfs:subClassOf) | STR D2 MSN indirect pathway medium spiny neuron (Primate) (CL:4310059) | | CA3 pyramidal cell (CL:0020068) | subClassOf (rdfs:subClassOf) | hippocampal pyramidal neuron (CL:1001571) | | CA1 pyramidal cell (CL:0020072) | subClassOf (rdfs:subClassOf) | glutamatergic neuron (CL:0000679) | | squamous granulosa cell (CL:4033083) | subClassOf (rdfs:subClassOf) | squamous epithelial cell (CL:0000076) | | STR D1 MSN direct pathway medium spiny neuron (Primate) (CL:4310058) | subClassOf (rdfs:subClassOf) | direct pathway medium spiny neuron (CL:4023026) | | mucosal-associated invariant T cell, human (CL:0020002) | subClassOf (rdfs:subClassOf) | mature NK T cell (CL:0000814) |

</details>

<details> <summary>Relationships removed: 6</summary>

| Subject| Predicate| Object| ----|----|----| | STRv D2 MSN nucleus accumbens shell and olfactory tubercle D2 medium spiny neuron (Primate) (CL:4310138) | subClassOf (rdfs:subClassOf) | indirect pathway medium spiny neuron (CL:4023029) | | mucosal-associated invariant T cell, human (CL:0020002) | lacks_plasma_membrane_part (CL:4030046) | PR:Q12918 | | follicular cell of ovary (CL:0002174) | subClassOf (rdfs:subClassOf) | eukaryotic cell (CL:0000255) | | cuboidal granulosa cell (CL:4033084) | RO:0000053 | PATO:0001872 | | STRd D2 StrioMat Hybrid MSN indirect pathway medium spiny neuron (Primate) (CL:4310133) | subClassOf (rdfs:subClassOf) | indirect pathway medium spiny neuron (CL:4023029) | | squamous granulosa cell (CL:4033083) | RO:0000053 | PATO:0002254 |

</details>

<details> <summary>Nodes removed from subset: 2</summary>

| Term | Subset | ----|----| | myoepithelial cell (CL:0000185) | human_reference_atlas | | tuft cell (CL:0002204) | human_reference_atlas |

</details>

CL Links to External Ontologies

<summary>UBERON → CL (count: 1285)</summary> <summary>GO → CL (count: 1701)</summary> <summary>HPO → CL (count: 145)</summary> <summary>MONDO → CL (count: 185)</summary>

Click here for a complete current summary release report

What's Changed

• Update AI agent workflow for mentions and responses by @dosumis in https://github.com/obophenotype/cell-ontology/pull/3618
• Use PAT_FOR_PR for dragon-ai execution workflow by @cmungall in https://github.com/obophenotype/cell-ontology/pull/3621
• Update citations in cite.md by @lubianat in https://github.com/obophenotype/cell-ontology/pull/3615
• Revise Cell Ontology citation in README by @dosumis in https://github.com/obophenotype/cell-ontology/pull/3627
• Fix typos in definitions by @anitacaron in https://github.com/obophenotype/cell-ontology/pull/3617
• ci: add PR-triggered CLARA review workflow by @ubyndr in https://github.com/obophenotype/cell-ontology/pull/3629
• Replace use of obsoleted NCBITaxon:6657. by @gouttegd in https://github.com/obophenotype/cell-ontology/pull/3633
• ci: wire routed CLARA review workflow by @ubyndr in https://github.com/obophenotype/cell-ontology/pull/3638
• clara-mcp-runtime-fix by @ubyndr in https://github.com/obophenotype/cell-ontology/pull/3640
• ci: allow CLARA report comments without git writes by @ubyndr in https://github.com/obophenotype/cell-ontology/pull/3641
• Add NTR: entorhinal cortex layer II stellate cell (CL_9900001) by @Copilot in https://github.com/obophenotype/cell-ontology/pull/3631
• Add new CL term for CA3 pyramidal cell with requested definitional and logical axioms by @Copilot in https://github.com/obophenotype/cell-ontology/pull/3654
• Add new CL term for hilar mossy cell with requested definition and axiomatization by @Copilot in https://github.com/obophenotype/cell-ontology/pull/3649
• Add new CL term for CA2 pyramidal cell with CA2-specific anatomical and functional axioms by @Copilot in https://github.com/obophenotype/cell-ontology/pull/3652
• Add CL_9900000: parvalbumin-positive basket cell (hippocampal PV basket interneuron) by @Copilot in https://github.com/obophenotype/cell-ontology/pull/3645
• assert superclass for 'follicular cell of ovary' by @nicolevasilevsky in https://github.com/obophenotype/cell-ontology/pull/3656
• Add CA1 pyramidal cell NTR (CL:9900001) by @Copilot in https://github.com/obophenotype/cell-ontology/pull/3647
• Align CL_0020002 CD161 axiom with stated high expression by @Copilot in https://github.com/obophenotype/cell-ontology/pull/3655
• Add CL:9900001 AVPV/PeN kisspeptin neuron by @Copilot in https://github.com/obophenotype/cell-ontology/pull/3624
• [NTR] Add Oriens-Lacunosum Moleculare neuron (CL_9900001) by @Copilot in https://github.com/obophenotype/cell-ontology/pull/3603
• Add cl:added_by_HRA annotations to 157 CL terms by @zhengj2007 in https://github.com/obophenotype/cell-ontology/pull/3628
• refreshed imports 2026-06-08 by @RiveraAndrea83 in https://github.com/obophenotype/cell-ontology/pull/3658
• new release 2026-06-08 by @RiveraAndrea83 in https://github.com/obophenotype/cell-ontology/pull/3659

New Contributors

• @zhengj2007 made their first contribution in https://github.com/obophenotype/cell-ontology/pull/3628

Full Changelog: https://github.com/obophenotype/cell-ontology/compare/v2026-03-26...v2026-06-08