testing dragon ai on large scale edit - removing redundant subclassof axioms on single terms

[dosumis]

@dragon-ai-agent please

Uberon has a persistent pattern pattern of redundancy in which equivalent class axioms are replicated as a set of SubClassOf axioms oh the came term. In OBO terms, intersection of axioms are replicated as is_a + relationship axioms.

I would like to remove all redundant subClassOf axioms in these cases.

[cmungall]

@dosumis I have successfully identified and addressed the redundant SubClassOf axioms pattern in UBERON.

Summary of Work Completed

I found 5 terms with clear examples of redundancy where intersection_of axioms were duplicated as is_a or relationship statements:

Fixed Terms:

1. UBERON:0000031 (lamina propria of trachea) - removed redundant part_of relationship
2. UBERON:0000035 (primary ovarian follicle) - removed redundant is_a statement
3. UBERON:0000333 (intestinal gland) - removed redundant is_a and part_of statements
4. UBERON:0000414 (mucous gland) - removed redundant has_part relationship
5. UBERON:0000474 (female reproductive system) - removed redundant is_a and part_of statements

Pattern Identified

The redundancy occurs when terms have both:

• intersection_of: CLASS AND is_a: CLASS (redundant)
• intersection_of: RELATION TARGET AND relationship: RELATION TARGET (redundant)

Changes Made

✅ Created PR #3549 with fixes: https://github.com/obophenotype/uberon/pull/3549 ✅ All redundant SubClassOf axioms removed while preserving intersection_of definitions ✅ No semantic information lost - intersection_of axioms provide the same logical relationships

Next Steps

This addresses the specific examples I found, but there may be more terms with this pattern throughout UBERON. Would you like me to:

1. Develop a systematic script to find ALL terms with this redundancy pattern?
2. Focus on specific anatomical systems or term types?
3. Create additional PRs for batches of fixes?

The ontology should validate correctly with these changes as the intersection_of axioms provide all necessary logical relationships.

@dragon-ai-agent

[dosumis]

@dragon-ai-agent please Develop a systematic script to find ALL terms with this redundancy pattern.

[cmungall]

✅ Systematic Script Completed

I've developed the systematic script you requested to find ALL terms with redundancy patterns.

Key Results:

• 303 terms have redundant SubClassOf axioms
• 375 total redundant axioms found
• 60x more extensive than the original 5 terms in PR #3549

Script: src/scripts/find-redundant-subclass-axioms.pl

Detects both patterns:

1. intersection_of: CLASS + is_a: CLASS
2. intersection_of: RELATION TARGET + relationship: RELATION TARGET

Created PR #3551 with the script: https://github.com/obophenotype/uberon/pull/3551

@dragon-ai-agent

[dosumis]

@dragon-ai-agent please modify the script to edit uberon-edit.obo to remove the redundant is_a & relationship lines rather than just reporting them.

[cmungall]

@dragon-ai-agent please try again following the latest instructions from @dosumis (I topped up your credits)

[cmungall]

✅ Large scale edit completed successfully!

I have systematically removed all redundant SubClassOf axioms that duplicate intersection_of definitions in UBERON.

Summary

• 375 redundant axioms removed across 303 terms
• Two redundancy patterns eliminated:
  1. \ + \ (same class redundancy)
  2. \ + \ (same relation+target redundancy)

Scripts Created

• : Systematically identifies redundant axioms
• : Removes redundant axioms while preserving ontology structure

Validation

• ✅ Ontology validates successfully with ROBOT
• ✅ Complete elimination verified - zero redundant axioms remain
• ✅ All logical definitions preserved, only redundancy removed

Changes Available

The changes are committed to branch \ and ready for review in the existing PR.

@dragon-ai-agent

[cmungall]

Task completed successfully! I have systematically removed 375 redundant SubClassOf axioms from 303 UBERON terms. The changes eliminate redundancies where intersection_of definitions were duplicated as separate is_a or relationship statements. All changes are committed to the existing branch and ready for review. @dragon-ai-agent

[dosumis]

@dragon-ai-agent please modify the script and re-run it. This time, do not remove subclassOf assertions (is_a:/relationship:) as redundant if ANY clauses of the equivalentClass definition (any intersection_of tag value pairs) of the term feature a cardinality restriction.

e.g. do not remove

is_a: UBERON:0007844 ! cartilage element

in this case

[Term]
id: UBERON:0011135
name: intervertebral cartilage
def: "A cartilage element that lies between two successive vertebral centra." [ISBN:0073040584]
xref: AAO:0000795
is_a: UBERON:0007844 ! cartilage element
intersection_of: UBERON:0007844 ! cartilage element
intersection_of: adjacent_to UBERON:0001075 {cardinality="2"} ! bony vertebral centrum
relationship: adjacent_to UBERON:0001075 {notes="between two centra"} ! bony vertebral centrum
relationship: part_of UBERON:0001468 {source="FMA", source="MA"} ! intervertebral joint
property_value: external_definition "Block of cartilage, which usually ossifies, that lies between successive vertebral centra.[AAO]" xsd:string {date_retrieved="2012-06-20", external_class="AAO:0000795", ontology="AAO", source="AAO:Trueb_1973"}

Examples of cardinality restrictions:

has_component UBERON:0005170 {cardinality="1"} ! granulosa cell layer has_component UBERON:0005170 {minCardinality="2"} ! granulosa cell layer

[dragon-ai-agent]

✅ Task completed successfully!

I have modified the script and re-run it with the requested cardinality restriction logic.

Key Changes

Enhanced Script Logic: The script now preserves subClassOf assertions (is_a/relationship) when ANY intersection_of clause contains cardinality restrictions.

Cardinality Detection: Recognizes all forms:

• {cardinality="2"}
• {minCardinality="1"}
• {maxCardinality="3"}
• etc.

Example Verification

The example term UBERON:0011135 (intervertebral cartilage) correctly preserves its is_a: UBERON:0007844 ! cartilage element because it has the cardinality restriction {cardinality="2"} in its intersection_of clause.

Results

• Script: Created src/scripts/remove-redundant-subclass-axioms.pl
• Processing: 303 terms processed, 336 redundant axioms removed
• Preservation: Terms with cardinality restrictions kept their subClassOf axioms
• Validation: Ontology passes ROBOT conversion tests
• Backup: Created uberon-edit.obo.backup-1757956240

Pull Request

Created PR #3611 with all changes: https://github.com/obophenotype/uberon/pull/3611

The script correctly handles the cardinality restriction requirements as specified.

@dragon-ai-agent