diff --git a/CHANGES_SUMMARY.md b/CHANGES_SUMMARY.md new file mode 100644 index 000000000..d7e355f00 --- /dev/null +++ b/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 ! +``` + +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 diff --git a/src/ontology/uberon-edit.obo b/src/ontology/uberon-edit.obo index 0239d1945..c0c28fcb3 100644 --- a/src/ontology/uberon-edit.obo +++ b/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 diff --git a/terms/additional_mucosal_epithelia.obo b/terms/additional_mucosal_epithelia.obo new file mode 100644 index 000000000..9a254b9e2 --- /dev/null +++ b/terms/additional_mucosal_epithelia.obo @@ -0,0 +1,134 @@ +format-version: 1.2 + +[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 + diff --git a/terms/new_mucosal_epithelia.obo b/terms/new_mucosal_epithelia.obo new file mode 100644 index 000000000..107958df6 --- /dev/null +++ b/terms/new_mucosal_epithelia.obo @@ -0,0 +1,145 @@ +format-version: 1.2 + +[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 + diff --git a/tools/obo-scripts b/tools/obo-scripts new file mode 160000 index 000000000..cb38971ce --- /dev/null +++ b/tools/obo-scripts @@ -0,0 +1 @@ +Subproject commit cb38971ce39654bc9e4e96efcd22e950c3561f5d diff --git a/tools/robot b/tools/robot new file mode 100755 index 000000000..5408a0516 --- /dev/null +++ b/tools/robot @@ -0,0 +1,35 @@ +#!/bin/sh + +## Check for Cygwin, use grep for a case-insensitive search +IS_CYGWIN="FALSE" +if uname | grep -iq cygwin; then + IS_CYGWIN="TRUE" +fi + +# Variable to hold path to this script +# Start by assuming it was the path invoked. +ROBOT_SCRIPT="$0" + +# Handle resolving symlinks to this script. +# Using ls instead of readlink, because bsd and gnu flavors +# have different behavior. +while [ -h "$ROBOT_SCRIPT" ] ; do + ls=`ls -ld "$ROBOT_SCRIPT"` + # Drop everything prior to -> + link=`expr "$ls" : '.*-> \(.*\)$'` + if expr "$link" : '/.*' > /dev/null; then + ROBOT_SCRIPT="$link" + else + ROBOT_SCRIPT=`dirname "$ROBOT_SCRIPT"`/"$link" + fi +done + +# Directory that contains the this script +DIR=$(dirname "$ROBOT_SCRIPT") + +if [ $IS_CYGWIN = "TRUE" ] +then + exec java $ROBOT_JAVA_ARGS -jar "$(cygpath -w $DIR/robot.jar)" "$@" +else + exec java $ROBOT_JAVA_ARGS -jar "$DIR/robot.jar" "$@" +fi diff --git a/tools/robot.jar b/tools/robot.jar new file mode 100644 index 000000000..5906df171 Binary files /dev/null and b/tools/robot.jar differ