obophenotype/cell-ontology: 2025-11-04 Release

Zenodo (CERN European Organization for Nuclear Research)

Abstract

Release Notes 2025-11-04 Ontology content summary | Metric | Value | |:------------------------------------------------|--------:| | Number of subclasses of root | 3164 | | Number of annotations on CL terms | 16360 | | Number of synonyms | 6816 | | Number of unique references | 1960 | | Number of unique references in definitions | 1945 | | Number of relationships with CL term as subject | 4696 | | Number of cellxgene classes | 955 | | Number of HRA classes | 516 | Text definitions changed: 9 | Term | Old Text Definition | New Text Definition | ----|----|----| | Lugaro cell (Mmus) (CL:4301575) | A Purkinje layer interneuron of the Mus musculus brain. It is distinguished from other cells in the brain by selective expression of Pthlh (Mmus), Tfap2b (Mmus), Rspo2 (Mmus). Reference transcriptomic data for this type can be found in the dataset/taxonomy - Yao et al. (2023), Whole Mouse Brain in cell set Supertype:1145 CB PLI Gly-Gaba_2. | A Lugaro cell of the Mus musculus brain. It is distinguished from other cells in the brain by selective expression of Pthlh (Mmus), Tfap2b (Mmus), Rspo2 (Mmus). Reference transcriptomic data for this type can be found in the dataset/taxonomy - Yao et al. (2023), Whole Mouse Brain in cell set Supertype:1145 CB PLI Gly-Gaba_2. | | pvalb GABAergic interneuron (CL:4023018) | A transcriptomically distinct GABAergic interneuron with a soma located in a cerebral cortex and it expresses Parvalbumin. | A transcriptomically distinct GABAergic interneuron with a soma located in the pallium. These neurons express Parvalbumin. | | otic fibrocyte (CL:0002665) | A mesenchymal cell of the cochlea that has specialized structural and molecular adaptions. | A mesenchymal cell within the inner ear, specifically localised to supportive connective tissues such as the spiral ligament and spiral limbus. This cell has specialised structural and molecular adaptations, and it contributes to the homeostasis of the cochlear environment by participating in ionic regulation crucial for auditory function. | | D1-NUDAP medium spiny neuron (CL:4030054) | A DRD1-expressing medium spiny neuron that is part of dense, RXFP1-positive cell islands throughout the nucleus accumbens, putamen, and near the adjacent septal nuclei. | A DRD1-expressing medium spiny neuron that is part of dense, RXFP1-positive cell islands throughout the nucleus accumbens, putamen, and near the adjacent septal nuclei. | | fibrocyte of adventitia of ureter (CL:1000308) | A fibrocyte that is part of the adventitia of ureter. | A stromal cell that is part of the outer adventitial layer of the ureter. This cell type is marked by expression of periostin (POSTN) in mice, and it is derived from Foxd1+ mesenchymal progenitors around embryonic day 12.5. The adventitial fibrocyte initiates differentiation earlier than smooth muscle cells and becomes terminally differentiated by E16.5-18.5 in mice, exhibiting low proliferative capacity in adulthood. | | pvalb chandelier GABAergic interneuron (Homo sapiens) (CL:4072046) | A transcriptomically definined chandelierl pvalb GABAergic interneuron in humans. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Chandelier. | A transcriptomically definined GABAergic interneuron of the human pallium. These cells correspond to the classically defined pvalb chandelier neuron type. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Chandelier. | | cerebellar inhibitory GABAergic interneuron (CL:4023057) | Any GABAergic interneuron that has its soma located in some cerebellar cortex. | A GABAergic interneuron whose soma is located in the cerebellar cortex. | | internal globus pallidus core projecting neuron (CL:0020003) | A projection neuron that has its soma located in the internal segment of the globus pallidus (GPi) of primates, in the central "core" region. It expresses parvalbumin, is primarily GABAergic, and projects to motor thalamic nuclei including the ventral anterior, ventrolateral, and ventromedial nuclei. This neuron corresponds to the sensorimotor output population of the GPi, as demonstrated in human tissue and cross-species comparative studies (Wallace et al., 2017) and by classic tracing in primates (Parent & De Bellefeuille, 1982; Parent et al., 2001). | A projection neuron that has its soma located in the internal segment of the globus pallidus (GPi) of primates, in the central "core" region. It expresses parvalbumin, is primarily GABAergic, and projects to motor thalamic nuclei including the ventral anterior, ventrolateral, and ventromedial nuclei. In the rodent homolog (entopeduncular nucleus), the core subregion is characterized by concentrated parvalbumin-positive neurons targeting the ventral anterior-ventral lateral thalamic nucleus and receives inputs from the dorsolateral striatum innervated by sensorimotor cortices (Miyamoto & Fukuda, 2022). This neuron corresponds to the sensorimotor output population of the GPi, as demonstrated in human tissue and cross-species comparative studies (Wallace et al., 2017) and by classic tracing in primates (Parent & De Bellefeuille, 1982; Parent et al., 2001). | | pvalb chandelier GABAergic interneuron (CL:4023036) | A transcriptomically distinct pvalb GABAergic interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. | A transcriptomically distinct pvalb GABAergic interneuron located in the pallium. It is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. These cells are fast-spiking. | Classes added: 6 | Term | ----| | dorso-striatal cholinergic-GABAergic neuron (CL:0020007) | | prototypic neuron (CL:0020009) | | OB-Dopa-GABA (CL:0020006) | | spiral ligament fibrocyte (CL:0020005) | | striatal cholinergic-GABAergic neuron (CL:0020008) | | arkypallidal neuron (CL:0020010) | Relationships added: 40 | Subject | Predicate | Object| ----|----|----| | mesangial cell (CL:0000650) | subClassOf (rdfs:subClassOf) | kidney cortical cell (CL:0002681) | | arkypallidal neuron (CL:0020010) | subClassOf (rdfs:subClassOf) | GABAergic neuron (CL:0000617) | | kidney interstitial fibrocyte (CL:1000693) | subClassOf (rdfs:subClassOf) | stromal cell (CL:0000499) | | dorso-striatal cholinergic-GABAergic neuron (CL:0020007) | subClassOf (rdfs:subClassOf) | GABA-Chol neuron (CL:0008061) | | Lugaro cell (Mmus) (CL:4301575) | subClassOf (rdfs:subClassOf) | Lugaro cell (CL:0011006) | | pvalb GABAergic interneuron (CL:4023018) | subClassOf (rdfs:subClassOf) | neuron of the forebrain (CL:0012001) | | OB-Dopa-GABA (CL:0020006) | subClassOf (rdfs:subClassOf) | dopaminergic neuron (CL:0000700) | | dorso-striatal cholinergic-GABAergic neuron (CL:0020007) | subClassOf (rdfs:subClassOf) | GABAergic interneuron (CL:0011005) | | mesangial cell (CL:0000650) | BFO:0000050 | UBERON:0002319 | | arkypallidal neuron (CL:0020010) | subClassOf (rdfs:subClassOf) | neuron of the forebrain (CL:0012001) | | spiral ligament fibrocyte (CL:0020005) | subClassOf (rdfs:subClassOf) | otic fibrocyte (CL:0002665) | | otic fibrocyte (CL:0002665) | BFO:0000050 | UBERON:0001846 | | arkypallidal neuron (CL:0020010) | RO:0002100 | UBERON:0002476 | | pvalb GABAergic interneuron (CL:4023018) | subClassOf (rdfs:subClassOf) | medial ganglionic eminence derived interneuron (CL:4023063) | | fibrocyte of adventitia of ureter (CL:1000308) | subClassOf (rdfs:subClassOf) | stromal cell (CL:0000499) | | dorso-striatal cholinergic-GABAergic neuron (CL:0020007) | subClassOf (rdfs:subClassOf) | striatum neuron (CL:0002613) | | pvalb chandelier GABAergic interneuron (CL:4023036) | RO:0002292 | PR:000013502 | | striatal cholinergic-GABAergic neuron (CL:0020008) | subClassOf (rdfs:subClassOf) | GABA-Chol neuron (CL:0008061) | | prototypic neuron (CL:0020009) | subClassOf (rdfs:subClassOf) | BFO:0000002 | | prototypic neuron (CL:0020009) | RO:0002292 | PR:000011241 | | fibrocyte of adventitia of ureter (CL:1000308) | RO:0002292 | PR:000013031 | | prototypic neuron (CL:0020009) | RO:0002202 | UBERON:0004024 | | kidney interstitial fibrocyte (CL:1000693) | RO:0002202 | circulating fibrocyte (CL:0000135) | | OB-Dopa-GABA (CL:0020006) | subClassOf (rdfs:subClassOf) | striatum neuron (CL:0002613) | | pvalb chandelier GABAergic interneur

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