Add 25 epithelium terms for mucosal structures

CHANGES_SUMMARY.md

@@ -0,0 +1,76 @@
+# Mucosal Epithelium Terms - Changes Summary
+
+## Overview
+This change addresses the issue where many mucosa terms in UBERON lacked corresponding epithelium terms with proper `part_of` relationships, making it difficult for users to navigate from mucosa → epithelium → cell types.
+
+## Problem
+- UBERON had ~120 mucosa terms
+- Only ~60 had corresponding "epithelium of mucosa" terms
+- Users querying for parts of a specific mucosa could not easily find the epithelium term
+- From epithelium, users should be able to find cell types that are part of that epithelium
+
+## Solution
+Added 25 new epithelium terms with proper logical definitions following the pattern:
+```
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of <MUCOSA_ID> ! <mucosa name>
+```
+
+All new terms are subclasses of UBERON:0003350 (epithelium of mucosa).
+
+## New Terms Created
+
+### Terms for General Mucosa Locations (13 terms)
+- UBERON:9900000 - epithelium of cecum mucosa
+- UBERON:9900001 - epithelium of tracheal mucosa
+- UBERON:9900002 - epithelium of bronchial mucosa
+- UBERON:9900003 - epithelium of olfactory segment of nasal mucosa
+- UBERON:9900004 - epithelium of cervical mucosa
+- UBERON:9900005 - epithelium of gland of nasal mucosa
+- UBERON:9900006 - epithelium of colorectal mucosa
+- UBERON:9900007 - epithelium of respiratory segment of nasal mucosa
+- UBERON:9900008 - epithelium of reproductive system mucosa
+- UBERON:9900009 - epithelium of viscerocranial mucosa
+- UBERON:9900010 - epithelium of lower esophagus mucosa
+- UBERON:9900011 - epithelium of esophagogastric junction mucosa
+- UBERON:9900012 - epithelium of alveolar mucosa
+
+### Terms for Specific Anatomical Regions (12 terms)
+- UBERON:9900013 - epithelium of mucosa of stomach
+- UBERON:9900014 - epithelium of mucosa of small intestine
+- UBERON:9900015 - epithelium of mucosa of urinary bladder
+- UBERON:9900016 - epithelium of mucosa of larynx
+- UBERON:9900017 - epithelium of mucosa of anal canal
+- UBERON:9900018 - epithelium of mucosa of rectum
+- UBERON:9900019 - epithelium of mucosa of ureter
+- UBERON:9900020 - epithelium of mucosa of vagina
+- UBERON:9900021 - epithelium of mucosa of ascending colon
+- UBERON:9900022 - epithelium of mucosa of transverse colon
+- UBERON:9900023 - epithelium of mucosa of descending colon
+- UBERON:9900024 - epithelium of mucosa of sigmoid colon
+
+## Terms Already Properly Covered
+The following mucosa terms already had epithelium terms with correct part_of relationships:
+- 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)
+- mucosa of appendix → epithelium of appendix
+
+## Validation
+- All terms validated using `robot convert` with no syntax errors
+- All terms follow the standard UBERON pattern for logical definitions
+- All terms include proper metadata (dcterms:date, created_by)
+
+## Files Modified
+- `src/ontology/uberon-edit.obo` - Main ontology file with 25 new terms
+- `terms/new_mucosal_epithelia.obo` - First batch of 13 new terms
+- `terms/additional_mucosal_epithelia.obo` - Second batch of 12 new terms
+
+## Testing Recommendations
+1. Run reasoner to verify inferred relationships
+2. Test queries for parts of specific mucosae to confirm epithelium terms are found
+3. Verify that cell types can be reached from epithelium terms
+
+## Future Work
+- Consider adding similar terms for other specialized mucosa subclasses if needed
+- Review with ontology maintainers for any additional mucosa terms that may need coverage

src/ontology/uberon-edit.obo

@@ -225660,6 +225660,283 @@ is_a: UBERON:0006914 ! squamous epithelium
 relationship: has_part CL:4030023 ! respiratory tract hillock cell
 relationship: part_of UBERON:0007196 ! tracheobronchial tree
 
+[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
+property_value: dcterms:date "2025-11-03T17:50:27Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900001
+name: epithelium of tracheal mucosa
+def: "An epithelium that is part of a tracheal mucosa." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0000379 ! tracheal mucosa
+relationship: part_of UBERON:0000379 ! tracheal mucosa
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:50:27Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900002
+name: epithelium of bronchial mucosa
+def: "An epithelium that is part of a bronchial mucosa." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0000410 ! bronchial mucosa
+relationship: part_of UBERON:0000410 ! bronchial mucosa
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:50:27Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900003
+name: epithelium of olfactory segment of nasal mucosa
+def: "An epithelium that is part of a olfactory segment of nasal mucosa." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0005386 ! olfactory segment of nasal mucosa
+relationship: part_of UBERON:0005386 ! olfactory segment of nasal mucosa
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:50:27Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900004
+name: epithelium of cervical mucosa
+def: "An epithelium that is part of a cervical mucosa." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0012248 ! cervical mucosa
+relationship: part_of UBERON:0012248 ! cervical mucosa
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:50:27Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900005
+name: epithelium of gland of nasal mucosa
+def: "An epithelium that is part of a gland of nasal mucosa." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0012278 ! gland of nasal mucosa
+relationship: part_of UBERON:0012278 ! gland of nasal mucosa
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:50:27Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900006
+name: epithelium of colorectal mucosa
+def: "An epithelium that is part of a colorectal mucosa." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0013067 ! colorectal mucosa
+relationship: part_of UBERON:0013067 ! colorectal mucosa
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:50:27Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900007
+name: epithelium of respiratory segment of nasal mucosa
+def: "An epithelium that is part of a respiratory segment of nasal mucosa." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0015786 ! respiratory segment of nasal mucosa
+relationship: part_of UBERON:0015786 ! respiratory segment of nasal mucosa
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:50:27Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900008
+name: epithelium of reproductive system mucosa
+def: "An epithelium that is part of a reproductive system mucosa." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0019042 ! reproductive system mucosa
+relationship: part_of UBERON:0019042 ! reproductive system mucosa
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:50:27Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900009
+name: epithelium of viscerocranial mucosa
+def: "An epithelium that is part of a viscerocranial mucosa." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0034885 ! viscerocranial mucosa
+relationship: part_of UBERON:0034885 ! viscerocranial mucosa
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:50:27Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900010
+name: epithelium of lower esophagus mucosa
+def: "An epithelium that is part of a lower esophagus mucosa." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0035834 ! lower esophagus mucosa
+relationship: part_of UBERON:0035834 ! lower esophagus mucosa
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:50:27Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900011
+name: epithelium of esophagogastric junction mucosa
+def: "An epithelium that is part of a esophagogastric junction mucosa." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0035838 ! esophagogastric junction mucosa
+relationship: part_of UBERON:0035838 ! esophagogastric junction mucosa
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:50:27Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900012
+name: epithelium of alveolar mucosa
+def: "An epithelium that is part of a alveolar mucosa." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0035967 ! alveolar mucosa
+relationship: part_of UBERON:0035967 ! alveolar mucosa
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:50:27Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+
+[Term]
+id: UBERON:9900013
+name: epithelium of mucosa of stomach
+def: "An epithelium that is part of a mucosa of stomach." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0001199 ! mucosa of stomach
+relationship: part_of UBERON:0001199 ! mucosa of stomach
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:54:53Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900014
+name: epithelium of mucosa of small intestine
+def: "An epithelium that is part of a mucosa of small intestine." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0001204 ! mucosa of small intestine
+relationship: part_of UBERON:0001204 ! mucosa of small intestine
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:54:53Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900015
+name: epithelium of mucosa of urinary bladder
+def: "An epithelium that is part of a mucosa of urinary bladder." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0001259 ! mucosa of urinary bladder
+relationship: part_of UBERON:0001259 ! mucosa of urinary bladder
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:54:53Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900016
+name: epithelium of mucosa of larynx
+def: "An epithelium that is part of a mucosa of larynx." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0001824 ! mucosa of larynx
+relationship: part_of UBERON:0001824 ! mucosa of larynx
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:54:53Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900017
+name: epithelium of mucosa of anal canal
+def: "An epithelium that is part of a mucosa of anal canal." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0003342 ! mucosa of anal canal
+relationship: part_of UBERON:0003342 ! mucosa of anal canal
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:54:53Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900018
+name: epithelium of mucosa of rectum
+def: "An epithelium that is part of a mucosa of rectum." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0003346 ! mucosa of rectum
+relationship: part_of UBERON:0003346 ! mucosa of rectum
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:54:53Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900019
+name: epithelium of mucosa of ureter
+def: "An epithelium that is part of a mucosa of ureter." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0004980 ! mucosa of ureter
+relationship: part_of UBERON:0004980 ! mucosa of ureter
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:54:53Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900020
+name: epithelium of mucosa of vagina
+def: "An epithelium that is part of a mucosa of vagina." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0004983 ! mucosa of vagina
+relationship: part_of UBERON:0004983 ! mucosa of vagina
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:54:53Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900021
+name: epithelium of mucosa of ascending colon
+def: "An epithelium that is part of a mucosa of ascending colon." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0004990 ! mucosa of ascending colon
+relationship: part_of UBERON:0004990 ! mucosa of ascending colon
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:54:53Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900022
+name: epithelium of mucosa of transverse colon
+def: "An epithelium that is part of a mucosa of transverse colon." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0004991 ! mucosa of transverse colon
+relationship: part_of UBERON:0004991 ! mucosa of transverse colon
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:54:53Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900023
+name: epithelium of mucosa of descending colon
+def: "An epithelium that is part of a mucosa of descending colon." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0004992 ! mucosa of descending colon
+relationship: part_of UBERON:0004992 ! mucosa of descending colon
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:54:53Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+[Term]
+id: UBERON:9900024
+name: epithelium of mucosa of sigmoid colon
+def: "An epithelium that is part of a mucosa of sigmoid colon." [UBERON:automated]
+intersection_of: UBERON:0000483 ! epithelium
+intersection_of: part_of UBERON:0004993 ! mucosa of sigmoid colon
+relationship: part_of UBERON:0004993 ! mucosa of sigmoid colon
+is_a: UBERON:0003350 ! epithelium of mucosa
+property_value: dcterms:date "2025-11-03T17:54:53Z" xsd:dateTime
+created_by: dragon-ai-agent
+
+
 [Typedef]
 id: aboral_to
 name: aboral to