obophenotype/cell-ontology: 2026-03-26 Release
Zenodo (CERN European Organization for Nuclear Research)
Abstract
Release Notes 2026-03-26 Ontology content summary | Metric | Value | |:------------------------------------------------|--------:| | Number of subclasses of root | 3314 | | Number of annotations on CL terms | 17396 | | Number of synonyms | 7125 | | Number of unique references | 1960 | | Number of unique references in definitions | 2079 | | Number of relationships with CL term as subject | 5109 | | Number of cellxgene classes | 1026 | | Number of HRA classes | 616 | Nodes added to subset: 4 | Term | Subset | ----|----| | osteoblast (CL:0000062) | human_reference_atlas | | chondrocyte (CL:0000138) | human_reference_atlas | | obsolete female germ line stem cell (sensu Vertebrata) (CL:0000090) | human_reference_atlas | | mesenchymal stem cell (CL:0000134) | human_reference_atlas | Classes added: 8 | Term | ----| | tuft cell of parotid gland (CL:0020063) | | serous demilune cell of salivary gland (CL:0020059) | | basal duct cell of salivary gland (CL:0020060) | | ionocyte of salivary gland (CL:0020065) | | junctional epithelial cell (CL:0020062) | | tuft cell of sublingual gland (CL:0020064) | | periductal fibroblast of salivary gland (CL:0020061) | | myoepithelial cell of salivary gland (CL:0020066) | Relationships added: 25 | Subject | Predicate | Object| ----|----|----| | junctional epithelial cell (CL:0020062) | subClassOf (rdfs:subClassOf) | stratified epithelial cell (CL:0000079) | | serous acinar cell of salivary gland (CL:4052065) | subClassOf (rdfs:subClassOf) | serous demilune cell of salivary gland (CL:0020059) | | junctional epithelial cell (CL:0020062) | RO:0002215 | GO:0002227 | | serous demilune cell of salivary gland (CL:0020059) | subClassOf (rdfs:subClassOf) | exocrine cell (CL:0000152) | | junctional epithelial cell (CL:0020062) | BFO:0000050 | UBERON:0001949 | | ionocyte of salivary gland (CL:0020065) | RO:0002215 | GO:0050801 | | tuft cell of sublingual gland (CL:0020064) | subClassOf (rdfs:subClassOf) | tuft cell (CL:0002204) | | myoepithelial cell of salivary gland (CL:0020066) | RO:0002215 | GO:0006939 | | basal duct cell of salivary gland (CL:0020060) | BFO:0000050 | UBERON:0001837 | | myoepithelial cell of salivary gland (CL:0020066) | subClassOf (rdfs:subClassOf) | myoepithelial cell (CL:0000185) | | ionocyte of salivary gland (CL:0020065) | BFO:0000050 | UBERON:0001044 | | myoepithelial cell of salivary gland (CL:0020066) | BFO:0000050 | UBERON:0001044 | | periductal fibroblast of salivary gland (CL:0020061) | subClassOf (rdfs:subClassOf) | fibroblast (CL:0000057) | | periductal fibroblast of salivary gland (CL:0020061) | BFO:0000050 | UBERON:0001044 | | basal duct cell of salivary gland (CL:0020060) | subClassOf (rdfs:subClassOf) | basal cell (CL:0000646) | | tuft cell of parotid gland (CL:0020063) | BFO:0000050 | UBERON:0001831 | | junctional epithelial cell (CL:0020062) | subClassOf (rdfs:subClassOf) | ecto-epithelial cell (CL:0002077) | | junctional epithelial cell (CL:0020062) | subClassOf (rdfs:subClassOf) | epithelial cell of alimentary canal (CL:0002251) | | ionocyte of salivary gland (CL:0020065) | subClassOf (rdfs:subClassOf) | ionocyte (CL:0005006) | | tuft cell of sublingual gland (CL:0020064) | BFO:0000050 | UBERON:0001832 | | serous demilune cell of salivary gland (CL:0020059) | BFO:0000050 | UBERON:0001044 | | serous demilune cell of salivary gland (CL:0020059) | subClassOf (rdfs:subClassOf) | serous secreting cell (CL:0000313) | | serous demilune cell of salivary gland (CL:0020059) | RO:0002215 | GO:0046541 | | tuft cell of sublingual gland (CL:0020064) | subClassOf (rdfs:subClassOf) | epithelial cell of alimentary canal (CL:0002251) | | tuft cell of parotid gland (CL:0020063) | subClassOf (rdfs:subClassOf) | tuft cell (CL:0002204) | Synonyms added: 18 | Term | New Synonym | Predicate | ----|----|----| | serous demilune cell of salivary gland (CL:0020059) | demilune cell of salivary gland | oio:hasRelatedSynonym | | periductal fibroblast of salivary gland (CL:0020061) | immunofibroblast of salivary gland | oio:hasRelatedSynonym | | myoepithelial cell of salivary gland (CL:0020066) | salivary gland myoepithelial cell | oio:hasExactSynonym | | myoepithelial cell of salivary gland (CL:0020066) | salivary myoepithelial cell | oio:hasExactSynonym | | junctional epithelial cell (CL:0020062) | JE cell | oio:hasExactSynonym | | serous demilune cell of salivary gland (CL:0020059) | Crescents of Giannuzzi | oio:hasRelatedSynonym | | tuft cell of sublingual gland (CL:0020064) | sublingual gland tuft cell | oio:hasExactSynonym | | tuft cell of parotid gland (CL:0020063) | brush cell of parotid gland | oio:hasRelatedSynonym | | serous demilune cell of salivary gland (CL:0020059) | serous crescent cell | oio:hasRelatedSynonym | | periductal fibroblast of salivary gland (CL:0020061) | salivary gland fibroblast | oio:hasBroadSynonym | | junctional epithelial cell (CL:0020062) | gingival junctional epithelial cell | oio:hasRelatedSynonym | | serous demilune cell of salivary gland (CL:0020059) | serous demilune cell | oio:hasExactSynonym | | myoepithelial cell of salivary gland (CL:0020066) | basket cell of salivary gland | oio:hasRelatedSynonym | | tuft cell of parotid gland (CL:0020063) | parotid gland tuft cell | oio:hasExactSynonym | | basal duct cell of salivary gland (CL:0020060) | basal ductal cell of salivary gland | oio:hasExactSynonym | | junctional epithelial cell (CL:0020062) | DAT cell | oio:hasNarrowSynonym | | tuft cell of sublingual gland (CL:0020064) | brush cell of sublingual gland | oio:hasRelatedSynonym | | junctional epithelial cell (CL:0020062) | cell of junctional epithelium | oio:hasExactSynonym | Text definitions added: 8 | Term | New Text Definition | ----|----| | tuft cell of parotid gland (CL:0020063) | A tuft cell that is part of the epithelium of the parotid gland, localized to the striated ducts and never observed in acini. This cell is characterized by expression of POU2F3 and is expected to possess chemosensory function consistent with tuft cells in other tissues. Immunohistochemical analysis of normal human parotid gland tissue detected POU2F3-positive cells as a very rare population within the ductal compartment, positioned on the luminal side (Hoki et al., 2024). | | tuft cell of sublingual gland (CL:0020064) | A tuft cell that is part of the epithelium of the sublingual gland, localized to the ductal compartment. This cell is characterized by expression of POU2F3, consistent with tuft cell identity. Immunohistochemical analysis detected POU2F3-positive cells in normal human sublingual gland tissue (Hoki et al., 2024). | | ionocyte of salivary gland (CL:0020065) | An ionocyte that is part of a salivary gland, localized to the ductal compartment on the luminal side. This specialized epithelial cell is characterized by expression of FOXI1 and is involved in regulating and maintaining osmotic pressure within the glandular environment (Dong et al., 2024). In normal human salivary glands, FOXI1-positive cells constitute less than 5% of ductal epithelial cells and are found exclusively in ducts, never in acini, across all major gland types including parotid, submandibular, sublingual, and minor salivary glands (Hoki et al., 2024). Like ionocytes in other tissues, this cell is expected to express high levels of CFTR and possess abundant mitochondria and ion transporters. | | myoepithelial cell of salivary gland (CL:0020066) | A myoepithelial cell that is part of a salivary gland, positioned between the basal lamina and the secretory or ductal epithelial cells surrounding acini and intercalated ducts. This cell adopts a stellate morphology with four to eight cellular processes around acini and an elongated form parallel to the ductal axis around intercalated ducts (Amano et al., 2012). It expresses alpha-smooth muscle actin (ACTA2/alpha-SMA) as a primary marker, along with p63 and aquaporin 1 (AQP1), and contracts rhythmically in response to neural stimulation to facilitate saliva expulsion from secretory acini into the ductal system (Amano et al., 2012). This cell also produces FGF7, which activates FGFR2b-dependent transcriptional programs essential for seromucous acinar cell differentiation (Aure et al., 2023). In mice, myoepithelial cells express SOX2 and possess regenerative capacity, contributing to acinar cell restoration during tissue repair after severe injury. | | junctional epithelial cell (CL:0020062) | An epithelial cell that is part of the junctional epithelium of the gingiva, forming a collar-like band around the cervix of the tooth. This cell attaches to the tooth surface via hemidesmosomes and an internal basal lamina rich in laminin-332 and ODAM (Gavriiloglou et al., 2024). The junctional epithelium is a stratified squamous non-keratinized epithelium ranging from 15-30 cell layers coronally to 1-3 cell layers apically. This cell expresses cytokeratin 19 (CK19) as a specific marker, along with ODAM and FDC-SP, and participates in innate immune defense by producing IL-8, IL-1alpha, and MMP-7, facilitating the transmigration of polymorphonuclear leukocytes through the epithelium (Gavriiloglou et al., 2024). This cell has a high turnover rate, with complete renewal occurring every 4
Authors 28
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Lawrence Berkeley National Laboratory
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Lawrence Berkeley National Laboratory
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European Bioinformatics Institute · European Molecular Biology Laboratory · European Molecular Biology Laboratory
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EBI-EMBL
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Critical Path Institute
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www.virtualflybrain.org
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semanticly.ai
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German BioImaging – Gesellschaft für Mikroskopie und Bildanalyse
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German BioImaging e.V
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University at Buffalo, State University of New York
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University at Buffalo
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German BioImaging – Gesellschaft für Mikroskopie und Bildanalyse
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German BioImaging GMB-eV
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ARC Semantics
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Oregon Health & Science University
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Oregon Health and Science University
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Charles Tapley Hoyt Aachen
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RWTH Aachen University
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