obophenotype
Add 25 epithelium terms for mucosal structures
UBERON had ~120 mucosa terms but only ~60 corresponding epithelium terms with proper part_of relationships, breaking the navigation path: mucosa → epithelium → cell types.
Changes
Added 25 new epithelium terms (UBERON:9900000-9900024) following the standard pattern:
[Term]
id: UBERON:9900000
name: epithelium of cecum mucosa
def: "An epithelium that is part of a cecum mucosa." [UBERON:automated]
intersection_of: UBERON:0000483 ! epithelium
intersection_of: part_of UBERON:0000314 ! cecum mucosa
relationship: part_of UBERON:0000314 ! cecum mucosa
is_a: UBERON:0003350 ! epithelium of mucosa
Coverage Added
GI tract (16 terms): cecum, colorectum, ascending/transverse/descending/sigmoid colon, stomach, small intestine, anal canal, rectum, esophagogastric junction, lower esophagus, alveolar
Respiratory (5 terms): trachea, bronchi, olfactory/respiratory segments of nasal mucosa, larynx
Urogenital (4 terms): urinary bladder, ureter, cervix, vagina, reproductive system
Terms Already Covered
- mouth mucosa → oral epithelium (UBERON:0002424)
- stomach glandular region mucosa → stomach glandular epithelium (UBERON:0006924)
- mucosa of large intestine → epithelium of large intestine (UBERON:0001278)
All terms validated with robot convert.
Original prompt
This section details on the original issue you should resolve
<issue_title>populate mucosal epithelium terms</issue_title> <issue_description>Aim: Users querying for parts a specific mucosa should find the epithelium term and from there the cell types that are part of that epithelium
We have 120 mucosa terms:
But only 60 'epithelium of muscosa' terms
To fix:
- Generate lists of terms
- modify to isolate general anatomical component & align/diff.
- --> list of terms to add
- Remaining terms, review manually. </issue_description>
<agent_instructions>use the OLS MCP to find terms to edit/add</agent_instructions>
Comments on the Issue (you are @copilot in this section)
@dosumis Formal def:
Strategy for query with UberGraph:
- Find all mucosa --> what they are part_of
- Find all epithelia that are part_of these structures --> check if they are subClassOf "epithelium of mucosa"
FOr those that are not - we should be adding part relationship to the relevant mucosa term
Potential difficulty - UberGraph + reasoning will give too many results. Also do we want to add for all grouping terms?</comment_new>
- Fixes obophenotype/uberon#3449
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