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CL_9900000 (intestinal intraepithelial lymphocyte) - new specific subclass
Preserves original intestinal-specific definition
Logical definition: 'mature T cell' and ('located in' some 'intestinal epithelium') and ('capable of' some 'mucosal immune response')
Subclass of CL_0002496
Uses UBERON_0001277 (intestinal epithelium)
This follows standard ontology design: broaden overly-specific parent, create specific child for original narrow scope.
Original prompt
This section details on the original issue you should resolve
<issue_title>Revise intraepithelial lymphocyte and subclasses</issue_title>
<issue_description>The textual and logical definition for this term limits IELs to "intestinal epithelium" only, but IELs are found in multiple epithelial tissues - Gastrointestinal tract, Reproductive tract, oral cavity etc...
Broaden the definition of "intraepithelial lymphocyte"
Add a specific subclass "intestinal intraepithelial lymphocyte"
Improved textual definition
A tissue-resident lymphocyte located within the epithelial layer of mucosal tissues, particularly within the gastrointestinal, respiratory, and reproductive tracts. Characterised by permanent residency, this cell typically expresses CD103 (ntegrin alpha-E), which binds to E-cadherin on epithelial cells, enabling epithelial retention in both mice and humans. Phenotypically, IEL displays an activated, antigen-experienced state characterised by the constitutive expression of cytotoxic molecules (granzyme B, perforin) and innate-like receptors (such as NKG2D), enabling rapid, localised surveillance and immediate response to epithelial stress.
Add these references (DO NOT replace existing ones)
- Updated CL_0002496 (intraepithelial lymphocyte) definition to broaden scope beyond intestinal epithelium
- Changed logical definition to use general 'epithelium' (UBERON_0000483) instead of 'intestinal epithelium' (UBERON_0001277)
- Added new references: PMID:29674648 and WIKIPEDIA:Intraepithelial_lymphocyte
- Added contributor ORCID: https://orcid.org/0009-0000-8480-9277
- Created new term CL_9900000 (intestinal intraepithelial lymphocyte) as specific subclass for intestinal IELs
Co-authored-by: Caroline-99 <[email protected]>
CopilotAI
changed the title
[WIP] Revise definition and subclasses of intraepithelial lymphocytes
Broaden intraepithelial lymphocyte to all epithelial tissues and add intestinal subclass
Jan 5, 2026
intraepithelial lymphocyteIAO_0000115 "A tissue-resident lymphocyte located within the epithelial layer of mucosal tissues, particularly within the gastrointestinal, respiratory, and reproductive tracts. Characterised by permanent residency, this cell typically expresses CD103 (integrin alpha-E), which binds to E-cadherin on epithelial cells, enabling epithelial retention in both mice and humans. Phenotypically, IEL displays an activated, antigen-experienced state characterised by the constitutive expression of cytotoxic molecules (granzyme B, perforin) and innate-like receptors (such as NKG2D), enabling rapid, localised surveillance and immediate response to epithelial stress."
intraepithelial lymphocytedefinition "A tissue-resident lymphocyte located within the epithelial layer of mucosal tissues, particularly within the gastrointestinal, respiratory, and reproductive tracts. Characterised by permanent residency, this cell typically expresses CD103 (integrin alpha-E), which binds to E-cadherin on epithelial cells, enabling epithelial retention in both mice and humans. Phenotypically, IEL displays an activated, antigen-experienced state characterised by the constitutive expression of cytotoxic molecules (granzyme B, perforin) and innate-like receptors (such as NKG2D), enabling rapid, localised surveillance and immediate response to epithelial stress."
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Caroline-99
requested review from
RiveraAndrea83
and removed request for
Caroline-99
CL_0002496 (intraepithelial lymphocyte) was incorrectly restricted to intestinal epithelium only. IELs exist throughout mucosal epithelia - gastrointestinal, respiratory, and reproductive tracts.
Changes
CL_0002496 (intraepithelial lymphocyte) - broadened to general term
'mature T cell' and ('located in' some 'epithelium') and ('capable of' some 'mucosal immune response')CL_9900000 (intestinal intraepithelial lymphocyte) - new specific subclass
'mature T cell' and ('located in' some 'intestinal epithelium') and ('capable of' some 'mucosal immune response')This follows standard ontology design: broaden overly-specific parent, create specific child for original narrow scope.
Original prompt
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