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stratum corneum of esophageal epithelium #3424

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definition and refs

@JABelfiore JABelfiore added HCA Human Cell Atlas GutCellAtlas labels Nov 14, 2024
@JABelfiore JABelfiore self-assigned this Nov 14, 2024
@JABelfiore JABelfiore linked an issue Nov 14, 2024 that may be closed by this pull request
@cmungall
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Hi, thanks for your contributions! I don't see any changes in this PR? In earlier commits it looked like PMID xrefs at the term level which we should disallow

[Term]
id: UBERON:8700003
name: stratum corneum of esophageal epithelium
def: "The outermost layer of the stratified squamous epithelium lining the esophagus, composed of several layers of flattened, anucleated keratinocytes called corneocytes. It forms the primary protective barrier against mechanical, chemical, and microbial insults, while regulating permeability and contributing to tissue integrity. This layer is characterized by corneocytes embedded in a lipid-rich extracellular matrix, providing mechanical reinforcement and maintaining essential barrier functions of the esophageal lining." [doi:10.1038/gimo15, PMID:21126700, PMID:26019440]
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I could not find anything in the provided references describing the stratum corneum of esophageal epithelium as containing anucleated keratinocytes (corneocytes). I believe corneocytes are more commonly associated with the keratinized cells of the skin. The esophagus typically has a non-keratinized or partially keratinized stratified squamous epithelium, where the outermost cells retain their nuclei and do not form corneocytes as seen in the skin

[Term]
id: UBERON:8700003
name: stratum corneum of esophageal epithelium
def: "The outermost layer of the stratified squamous epithelium lining the esophagus, composed of several layers of flattened, anucleated keratinocytes called corneocytes. It forms the primary protective barrier against mechanical, chemical, and microbial insults, while regulating permeability and contributing to tissue integrity. This layer is characterized by corneocytes embedded in a lipid-rich extracellular matrix, providing mechanical reinforcement and maintaining essential barrier functions of the esophageal lining." [doi:10.1038/gimo15, PMID:21126700, PMID:26019440]
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I would also suggest removing the details about anucleated if there is no supporting evidence specific to the esophagus as I found that the state of the nucleus is not consistent across species. For example, cells in the human esophageal stratum corneum (and other mammals) seem to retain their nuclei, whereas in mice they do not (https://doi.org/10.1152/ajpgi.00088.2015, https://en.wikipedia.org/wiki/Stratified_squamous_epithelium).

[Term]
id: UBERON:8700003
name: stratum corneum of esophageal epithelium
def: "The outermost layer of the stratified squamous epithelium lining the esophagus, composed of several layers of flattened, anucleated keratinocytes called corneocytes. It forms the primary protective barrier against mechanical, chemical, and microbial insults, while regulating permeability and contributing to tissue integrity. This layer is characterized by corneocytes embedded in a lipid-rich extracellular matrix, providing mechanical reinforcement and maintaining essential barrier functions of the esophageal lining." [doi:10.1038/gimo15, PMID:21126700, PMID:26019440]
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I would suggest editing the definition a little bit ie.

The outermost layer of the stratified squamous epithelium lining the esophagus, composed of several layers of flattened epithelial cells that are partially or non-keratinized. This layer provides a protective barrier against mechanical and chemical insults, contributing to tissue integrity and regulating permeability through its apical cell membranes and intercellular junctional complexes.

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This PR violates some taxon constraints. Here is what the reasoner has to say:

pyloric dilator nerve (sensu Cancer borealis) SubClassOf Nothing

superior esophageal nerve (sensu Cancer borealis) SubClassOf Nothing

inferior esophageal nerve (sensu Cancer borealis) SubClassOf Nothing

esophageal ganglion (sensu Cancer borealis) SubClassOf Nothing

esophageal nerve (sensu Cancer borealis) SubClassOf Nothing

commissural ganglion (sensu Cancer borealis) SubClassOf Nothing

stomatogastric nerve (sensu Cancer borealis) SubClassOf Nothing

median ventricular nerve (sensu Cancer borealis) SubClassOf Nothing

dorsal gastric nerve (sensu Cancer borealis) SubClassOf Nothing

gastropyloric nerve (sensu Cancer borealis) SubClassOf Nothing

junction of superior esophageal nerve and stomatogastric nerve (sensu Cancer borealis) SubClassOf Nothing

stomatogastric ganglion SubClassOf Nothing

lateral ventricular nerve (sensu Cancer borealis) SubClassOf Nothing

lateral gastric nerve (sensu Cancer borealis) SubClassOf Nothing

pyloric nerve (sensu Cancer borealis) SubClassOf Nothing

Axiom Impact

Axioms used 15 times

Axioms used 1 times

Ontologies used:

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stratum corneum of esophageal epithelium
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