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@aleixpuigb aleixpuigb released this 13 Feb 14:45
· 18 commits to master since this release
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Release Notes 2025-02-13

Ontology content summary

Metric Value
Number of subclasses of root 2864
Number of annotations on CL terms 13978
Number of synonyms 6088
Number of unique references 2137
Number of unique references in definitions 1642
Number of relationships with CL term as subject 3982
Number of cellxgene classes 804
Number of HRA classes 481
Relationships removed: 19
Subject Predicate Object
kidney afferent arteriole endothelial cell (CL:1001096) subClassOf (rdfs:subClassOf) endothelial cell of artery (CL:1000413)
tanycyte (CL:0002085) subClassOf (rdfs:subClassOf) ependymoglial cell (CL:0000683)
mesothelial cell of appendix (CL:0009029) subClassOf (rdfs:subClassOf) mesothelial cell (CL:0000077)
mesothelial cell of colon (CL:0009025) subClassOf (rdfs:subClassOf) mesothelial cell (CL:0000077)
ganglion mother cell (CL:0000469) subClassOf (rdfs:subClassOf) eukaryotic cell (CL:0000255)
mesothelial cell of small intestine (CL:0009024) subClassOf (rdfs:subClassOf) mesothelial cell (CL:0000077)
obsolete neuronal brush cell (CL:0000555) subClassOf (rdfs:subClassOf) central nervous system neuron (CL:2000029)
basal cell of olfactory epithelium (CL:0002169) subClassOf (rdfs:subClassOf) neural cell (CL:0002319)
beta1-tanycyte (CL:4042019) subClassOf (rdfs:subClassOf) secretory cell (CL:0000151)
tanycyte (CL:0002085) BFO:0000050 UBERON:0004670
enterocyte (CL:0000584) RO:0002202 early enterocyte (CL:4047019)
ganglion mother cell (CL:0000469) subClassOf (rdfs:subClassOf) BFO:0000002
beta1-tanycyte (CL:4042019) subClassOf (rdfs:subClassOf) astrocyte of the forebrain (CL:0012000)
olfactory epithelial supporting cell (CL:0000853) subClassOf (rdfs:subClassOf) basal cell of olfactory epithelium (CL:0002169)
alpha1-tanycyte (CL:4042017) subClassOf (rdfs:subClassOf) astrocyte of the forebrain (CL:0012000)
basal cell of olfactory epithelium (CL:0002169) subClassOf (rdfs:subClassOf) epithelial cell of upper respiratory tract (CL:0002631)
M cell of gut (CL:0000682) subClassOf (rdfs:subClassOf) epithelial cell of alimentary canal (CL:0002251)
basal cell of olfactory epithelium (CL:0002169) BFO:0000050 UBERON:0001997
beta2-tanycyte (CL:4042020) subClassOf (rdfs:subClassOf) astrocyte of the forebrain (CL:0012000)
Classes added: 14
Term
mesothelial cell of intestine (CL:0008041)
biliary tuft cell (CL:4052033)
age-associated B cell (CL:4033094)
stomach smooth muscle inner oblique layer cell (CL:4047037)
type 1 submucosal plexus glia (CL:4047043)
granzyme H-associated CD8 T cell (CL:4052032)
tuft cell of olfactory epithelium (CL:4052037)
tuft cell of nasal cavity respiratory epithelium (CL:4052038)
smooth muscle circular layer cell (CL:4047040)
tuft cell of pancreatic duct (CL:4052035)
diffuse bipolar 4a cell (CL:4033095)
tuft cell of nasal cavity (CL:4052036)
tuft cell of thymus (CL:4052034)
diffuse bipolar 4b cell (CL:4033096)
Relationships added: 61
Subject Predicate Object
tuft cell of pancreatic duct (CL:4052035) subClassOf (rdfs:subClassOf) epithelial cell of exocrine pancreas (CL:1001433)
diffuse bipolar 4b cell (CL:4033096) RO:0002162 NCBITaxon:9606
tuft cell of olfactory epithelium (CL:4052037) RO:0002215 GO:0072091
tuft cell of nasal cavity (CL:4052036) subClassOf (rdfs:subClassOf) brush cell (CL:0002204)
granzyme H-associated CD8 T cell (CL:4052032) subClassOf (rdfs:subClassOf) CD8-positive, alpha-beta memory T cell (CL:0000909)
tuft cell of pancreatic duct (CL:4052035) subClassOf (rdfs:subClassOf) brush cell (CL:0002204)
tuft cell of nasal cavity respiratory epithelium (CL:4052038) subClassOf (rdfs:subClassOf) tuft cell of nasal cavity (CL:4052036)
tuft cell of thymus (CL:4052034) BFO:0000050 UBERON:0003846
tanycyte (CL:0002085) subClassOf (rdfs:subClassOf) ependymal cell (CL:0000065)
type 1 submucosal plexus glia (CL:4047043) subClassOf (rdfs:subClassOf) enteroglial cell (CL:4040002)
granzyme H-associated CD8 T cell (CL:4052032) RO:0002292 PR:000003490
olfactory epithelial cell (CL:0002167) subClassOf (rdfs:subClassOf) epithelial cell of upper respiratory tract (CL:0002631)
mesothelial cell of small intestine (CL:0009024) subClassOf (rdfs:subClassOf) mesothelial cell of intestine (CL:0008041)
olfactory epithelial cell (CL:0002167) BFO:0000050 UBERON:0001997
surface ectodermal cell (CL:0000114) BFO:0000050 UBERON:0000076
stomach smooth muscle inner oblique layer cell (CL:4047037) subClassOf (rdfs:subClassOf) smooth muscle cell (CL:0000192)
transit amplifying cell of small intestine (CL:0009012) subClassOf (rdfs:subClassOf) epithelial cell of small intestine (CL:0002254)
age-associated B cell (CL:4033094) subClassOf (rdfs:subClassOf) memory B cell (CL:0000787)
tuft cell of thymus (CL:4052034) subClassOf (rdfs:subClassOf) brush cell (CL:0002204)
transit amplifying cell of appendix (CL:0009027) subClassOf (rdfs:subClassOf) epithelial cell of large intestine (CL:0002253)
tuft cell of nasal cavity (CL:4052036) subClassOf (rdfs:subClassOf) epithelial cell of upper respiratory tract (CL:0002631)
tuft cell of nasal cavity respiratory epithelium (CL:4052038) BFO:0000050 UBERON:0005385
follicle associated enterocyte (CL:4052011) BFO:0000050 UBERON:0004693
diffuse bipolar 4a cell (CL:4033095) RO:0002162 NCBITaxon:9606
tuft cell of olfactory epithelium (CL:4052037) subClassOf (rdfs:subClassOf) tuft cell of nasal cavity (CL:4052036)
tuft cell of thymus (CL:4052034) RO:0002215 GO:0002491
diffuse bipolar 4b cell (CL:4033096) subClassOf (rdfs:subClassOf) BFO:0000002
smooth muscle circular layer cell (CL:4047040) subClassOf (rdfs:subClassOf) smooth muscle cell (CL:0000192)
olfactory epithelial cell (CL:0002167) subClassOf (rdfs:subClassOf) neural cell (CL:0002319)
conjunctiva goblet cell (CL:2000084) subClassOf (rdfs:subClassOf) squamous epithelial cell (CL:0000076)
M cell of gut (CL:0000682) BFO:0000050 UBERON:0004693
mesothelial cell of intestine (CL:0008041) subClassOf (rdfs:subClassOf) mesothelial cell (CL:0000077)
trophectodermal cell (CL:1000274) BFO:0000050 UBERON:0004345
transit amplifying cell of gut (CL:4047017) subClassOf (rdfs:subClassOf) intestinal epithelial cell (CL:0002563)
biliary tuft cell (CL:4052033) subClassOf (rdfs:subClassOf) brush cell (CL:0002204)
transit amplifying cell of anorectum (CL:0009056) subClassOf (rdfs:subClassOf) epithelial cell of large intestine (CL:0002253)
basal cell of olfactory epithelium (CL:0002169) BFO:0000050 UBERON:0000482
stomach smooth muscle inner oblique layer cell (CL:4047037) BFO:0000050 UBERON:0008862
diffuse bipolar 4a cell (CL:4033095) subClassOf (rdfs:subClassOf) BFO:0000002
smooth muscle circular layer cell (CL:4047040) BFO:0000050 UBERON:0012368
tuft cell of pancreatic duct (CL:4052035) subClassOf (rdfs:subClassOf) duct epithelial cell (CL:0000068)
diffuse bipolar 4a cell (CL:4033095) subClassOf (rdfs:subClassOf) ON-bipolar cell (CL:0000749)
trophectodermal cell (CL:1000274) RO:0002203 trophoblast cell (CL:0000351)
neural progenitor cell (CL:0011020) subClassOf (rdfs:subClassOf) eukaryotic cell (CL:0000255)
tuft cell of olfactory epithelium (CL:4052037) subClassOf (rdfs:subClassOf) olfactory epithelial cell (CL:0002167)
transit amplifying cell of colon (CL:0009011) subClassOf (rdfs:subClassOf) epithelial cell of large intestine (CL:0002253)
neural progenitor cell (CL:0011020) RO:0002202 neural stem cell (CL:0000047)
type 1 submucosal plexus glia (CL:4047043) BFO:0000050 UBERON:0009566
tuft cell of thymus (CL:4052034) subClassOf (rdfs:subClassOf) medullary thymic epithelial cell (CL:0002365)
biliary tuft cell (CL:4052033) RO:0002215 GO:0050728
olfactory epithelial supporting cell (CL:0000853) subClassOf (rdfs:subClassOf) olfactory epithelial cell (CL:0002167)
M cell of gut (CL:0000682) subClassOf (rdfs:subClassOf) intestinal epithelial cell (CL:0002563)
neural progenitor cell (CL:0011020) subClassOf (rdfs:subClassOf) BFO:0000002
mesothelial cell of appendix (CL:0009029) subClassOf (rdfs:subClassOf) mesothelial cell of intestine (CL:0008041)
tuft cell of nasal cavity (CL:4052036) BFO:0000050 UBERON:0005384
mesothelial cell of colon (CL:0009025) subClassOf (rdfs:subClassOf) mesothelial cell of intestine (CL:0008041)
mesothelial cell of intestine (CL:0008041) BFO:0000050 UBERON:0001243
tuft cell of pancreatic duct (CL:4052035) BFO:0000050 UBERON:0009970
beta1-tanycyte (CL:4042019) subClassOf (rdfs:subClassOf) secretory epithelial cell (CL:1100001)
conjunctiva goblet cell (CL:2000084) BFO:0000050 UBERON:0006763
diffuse bipolar 4b cell (CL:4033096) subClassOf (rdfs:subClassOf) ON-bipolar cell (CL:0000749)
Synonyms added: 24
Term New Synonym Predicate
tuft cell of olfactory epithelium (CL:4052037) TRPM5+ microvillous tuft cell oio:hasRelatedSynonym
conjunctiva goblet cell (CL:2000084) CGC oio:hasRelatedSynonym
tuft cell of nasal cavity respiratory epithelium (CL:4052038) nasal respiratory solitary chemosensory cell oio:hasRelatedSynonym
tuft cell of olfactory epithelium (CL:4052037) tuft-microvillous cell oio:hasRelatedSynonym
granzyme H-associated CD8 T cell (CL:4052032) GZMH+ CD8+ T cell oio:hasRelatedSynonym
diffuse bipolar 4b cell (CL:4033096) DB4b oio:hasRelatedSynonym
tuft cell of thymus (CL:4052034) thymic tuft cell oio:hasExactSynonym
stomach smooth muscle inner oblique layer cell (CL:4047037) stomach smooth muscle oblique layer cell oio:hasExactSynonym
tuft cell of olfactory epithelium (CL:4052037) olfactory tuft cell oio:hasExactSynonym
tuft cell of nasal cavity respiratory epithelium (CL:4052038) Gɑ-gustducin high respiratory tuft cell oio:hasRelatedSynonym
type 1 submucosal plexus glia (CL:4047043) type I SMP oio:hasRelatedSynonym
biliary tuft cell (CL:4052033) gallbladder/extrahepatic bile duct tuft cell oio:hasExactSynonym
tuft cell of nasal cavity (CL:4052036) nasal tuft cell oio:hasExactSynonym
tuft cell of olfactory epithelium (CL:4052037) TRPM5+ microvillous cell oio:hasRelatedSynonym
tuft cell of pancreatic duct (CL:4052035) pancreatic brush cell oio:hasExactSynonym
unipolar brush cell (CL:4023161) neuronal brush cell oio:hasExactSynonym
tuft cell of nasal cavity respiratory epithelium (CL:4052038) tuft-solitary chemosensory cell oio:hasRelatedSynonym
tuft cell of nasal cavity (CL:4052036) nasal brush cell oio:hasExactSynonym
tuft cell of pancreatic duct (CL:4052035) pancreatic tuft cell oio:hasExactSynonym
tuft cell of large intestine (CL:0002203) brush cell of epithelium proper of large intestine oio:hasExactSynonym
granzyme H-associated CD8 T cell (CL:4052032) granzyme H+ CD8 T cell oio:hasExactSynonym
age-associated B cell (CL:4033094) ABC oio:hasRelatedSynonym
diffuse bipolar 4a cell (CL:4033095) DB4a oio:hasRelatedSynonym
tuft cell of olfactory epithelium (CL:4052037) TPRM5+ tuft-MVC oio:hasRelatedSynonym
Text definitions added: 16
Term New Text Definition
biliary tuft cell (CL:4052033) A tuft cell that is part of the extrahepatic biliary tree, including the gallbladder and extrahepatic bile ducts. It shares a core genetic program with intestinal tuft cells but has unique tissue-specific genes. Biliary tuft cell functions as a bile acid-sensitive regulator, suppressing inflammation and modulating microbiome-dependent neutrophil infiltration in biliary tissues. Unlike its intestinal counterparts, this cell decreases in number postnatally as bile acid production matures, with its abundance negatively regulated by bile acids.
stomach smooth muscle inner oblique layer cell (CL:4047037) A smooth muscle cell found in the innermost layer of the muscularis externa of the stomach wall. This cell forms a unique layer of smooth muscle fibers oriented obliquely to the stomach's longitudinal axis. It is responsible for aiding in the mixing and churning of gastric contents, contributing to mechanical digestion within the stomach.
tuft cell of pancreatic duct (CL:4052035) A tuft cell that is part of the epithelium of pancreatic duct. Present in humans and rats, this cell is absent in the murine pancreas under normal conditions but emerges during acinar-to-ductal metaplasia triggered by injury, inflammation, or oncogenic mutations. It modulates the immune response and protects against pancreatic ductal adenocarcinoma progression by producing suppressive eicosanoids, such as prostaglandin D2. A tuft cell in the pancreatic duct highly expresses the transcription factor POU2F3, which is essential for its development and presence.
tuft cell of nasal cavity respiratory epithelium (CL:4052038) A tuft cell that is part of the nasal cavity respiratory epithelium. Acting as a chemosensor, it detects bitter taste ligands and bacterial signals via taste receptors, maintaining epithelial-microbial homeostasis by stimulating antimicrobial peptide secretion from adjacent epithelial cells. This cell is a major source of IL-25, promoting type 2 immune responses and potentially contributing to chronic rhinosinusitis (O'Leary et al., 2019).
mesothelial cell of intestine (CL:0008041) A mesothelial cell that is part of the intestinal serosa.
surface ectodermal cell (CL:0000114) An ectodermal cell that is part of the external ectoderm, forming the outermost layer of the developing embryo. It is characterized by its polarized nature, with distinct apical and basal surfaces (Ferrante Jr., Reinke, & Stanley, 1995). Surface ectodermal cell gives rise to the epidermis, hair follicles, nails, sensory organs, and specialized structures like the apical ectodermal ridge crucial for limb development (Skoufa et al., 2024).
diffuse bipolar 4a cell (CL:4033095) An ON bipolar cell that has high expression of DIRC3, KCNJ3, LINC01915, PTPRK compared with other bipolar cells.
type 1 submucosal plexus glia (CL:4047043) An enteric glial cell that is associated with neuron cell bodies within submucosal ganglia of the gastrointestinal tract. This cell is located in the submucosa, a layer of connective tissue beneath the intestinal mucosa. This cell plays a role in modulating secretomotor neuron activity and contributes to the regulation of digestive fluid secretion and absorption.
trophectodermal cell (CL:1000274) An extraembryonic cell that is part of the trophectoderm, representing the first lineage to differentiate in the embryo. This cell is crucial for implantation into the uterine wall and differentiates into trophoblast cells, which contribute to placenta formation and facilitate maternal-fetal nutrient and signal exchange.
diffuse bipolar 4b cell (CL:4033096) An ON bipolar cell that has high expression of NOS1AP compared with other bipolar cells.
granzyme H-associated CD8 T cell (CL:4052032) A CD8 T cell characterized by high expression of Granzyme H (GZMH). This cell exhibits a restricted TCR repertoire and elevated expression of cytotoxic, exhaustion, and type I interferon-stimulated gene signatures compared to controls.
tuft cell of nasal cavity (CL:4052036) A tuft cell that is part of the nasal cavity epithelium, located in both the respiratory and olfactory epithelia of the nose. This cell plays key roles in chemosensation, lipid mediator production, immune responses, and epithelial homeostasis.
tuft cell of olfactory epithelium (CL:4052037) A tuft cell that is part of the olfactory epithelium, characterized by a globular body and the expression of neurogranin (Nrgn) in mice. This cell plays a crucial role in allergen recognition and regulating olfactory stem cell proliferation via TRPM5-dependent ATP sensing and cysteinyl leukotriene production. Unlike nasal respiratory tuft cells, it has low to absent expression of taste receptors, including the G protein Gα gustducin, and rarely contacts olfactory sensory neurons directly.
age-associated B cell (CL:4033094) A transcriptionally distinct memory B cell whose presence increases with age, during infections, and in autoimmune diseases. In humans and mice, this cell type can be identified by the expression of T-bet, CD11c, CD11b, and the lack of CD21. An age-associated B cell responds to TLR stimuli, may produce autoantibodies, and participates in antiviral responses and pathogen clearance.
tuft cell of thymus (CL:4052034) A tuft cell that is part of the medullary epithelium of the thymus, characterized by lateral microvilli and specific markers, including L1CAM in both mice (Zhang et al., 2022) and humans (Sun et al., 2023), as well as MHC II in mice (Kotas et al., 2023). This cell is pivotal in immune functions such as antigen presentation, central tolerance, and type 2 immunity. A tuft cell in the thymus exhibits characteristics of both a medullary thymic epithelial cell (mTEC) and a peripheral tuft cell. Its development is governed by transcription factors such as POU2F3.
smooth muscle circular layer cell (CL:4047040) A smooth muscle cell that is found in the inner muscular layer of hollow organs. It is characterized by its spiral/helical arrangement around organ lumens. This cell is crucial for peristaltic movements in organs.
Text definitions changed: 5
Term Old Text Definition New Text Definition
femoral osteoblast (CL:2000057) Any osteoblast that is part of a femur. Any osteoblast that is part of a femur.
conjunctiva goblet cell (CL:2000084) Any goblet cell that is part of a conjunctiva. A goblet cell that is part of the conjunctival epithelium, characterized by apical accumulation of mucin granules (containing MUC5AC in humans; Muc5ac/Muc5b in mice). These gel-forming mucins support tear film stability, ocular lubrication, and pathogen defence. The conjunctival goblet cell forms tight junctions with neighbouring epithelial cells via species-specific claudins (claudin-10 in humans, claudin-2 in mice) and regulates immune homeostasis by facilitating soluble antigen transport to dendritic cells through goblet cell-associated antigen passages (GAPs) (Barbosa et al., 2017). The transcription factor SPDEF is essential for its differentiation.
neural progenitor cell (CL:0011020) An undifferentiated cell that originates from a neural stem cell and has the capacity to generate multiple types of lineage-restricted progenitors but not to self-renew. An undifferentiated cell derived from a neural stem cell, with a limited capacity to self-renew (Dibajnia and Morshead, 2013) and the ability to generate multiple types of lineage-restricted progenitors, contributing to the formation of neurons, astrocytes, and oligodendrocytes.
tuft cell of large intestine (CL:0002203) Brush cell found in the epithelial layer of the colon. A tuft cell that is part of the epithelium of large intestine.
intestinal tuft cell (CL:0019032) Any brush cell that is part of the intestinal epithelium. A tuft cell that is part of the intestinal epithelium, characterized by a distinctive apical tuft and lateral cytospinules connecting to neighbouring cells. This cell senses luminal stimuli via taste receptors and succinate signalling, initiating type 2 immune responses through the secretion of interleukin-25 while modulating epithelial regeneration through prostaglandin synthesis. It expresses key molecular markers such as doublecortin-like kinase 1 (DCLK1) in mice (Hendel et al., 2022), and KIT proto-oncogene in humans (Huang et al., 2024). Developed from intestinal crypt stem cells, this cell requires transcription factor POU2F3 for its development.
Nodes renamed: 3
ID Old Label New Label
CL:0002203 brush cell of epithelium proper of large intestine tuft cell of large intestine
CL:2000057 femural osteoblast femoral osteoblast
CL:0000555 neuronal brush cell obsolete neuronal brush cell
Nodes obsoleted with replacement: 1
Term Replacement
obsolete neuronal brush cell (CL:0000555) unipolar brush cell (CL:4023161)
Synonyms removed: 1
Term Removed Synonym
tuft cell of large intestine (CL:0002203) tuft cell of large intestine

What's Changed

Full Changelog: v2025-01-08...v2025-02-13