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- Created script to remove redundant is_a and relationship axioms
- Preserves subClassOf axioms when ANY intersection_of clause has cardinality restrictions
- Examples of preserved restrictions: {cardinality="2"}, {minCardinality="1"}, etc.
- Processed 303 terms, removing 336 redundant axioms
- Created backup file before modifications
- Fixes issue #3548
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Co-Authored-By: Claude <noreply@anthropic.com>
@dragon-ai-agent
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#gogoeditdiff |
Contributor
Here's a diff of how these changes impact the classified ontology (on -base file):Ontology comparisonLeft
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Ontology importsOntology annotations1st arch mandibular mesenchyme
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Contributor
Here's a diff of your edit file (unreasoned)Ontology comparisonLeft
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Ontology importsOntology annotations1st arch mandibular mesenchyme
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dosumis
previously approved these changes
Sep 15, 2025
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Looks good to me.
The only thing lost is axiom annotation indicating source. Might be possible to preserve on EC expressions if we really want it.
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Pull Request Overview
This PR enhances the redundant axiom removal script to preserve subClassOf assertions when intersection_of clauses contain cardinality restrictions. The script now detects cardinality, minCardinality, and maxCardinality patterns and preserves ALL subClassOf axioms for terms that have ANY intersection_of clause with such restrictions.
- Updated script logic to detect cardinality restrictions in intersection_of clauses
- Modified preservation logic to keep all subClassOf axioms when cardinality restrictions are present
- Re-ran the script with improved logic, resulting in 336 redundant axioms removed (down from 375)
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| # Create backup | ||
| system("cp '$input_file' '${input_file}${backup_suffix}'"); |
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The system call uses unvalidated user input that could lead to command injection. Use File::Copy's copy() function instead for safer file operations.
| my $intersection_clause = $1; | ||
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| # Check for cardinality restrictions | ||
| if ($intersection_clause =~ /\{.*(?:cardinality|minCardinality|maxCardinality)/) { |
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The regex pattern doesn't require the closing brace, which could match incomplete cardinality restrictions. Consider using \{.*(?:cardinality|minCardinality|maxCardinality).*\} to ensure proper bracketing.
Suggested change
| if ($intersection_clause =~ /\{.*(?:cardinality|minCardinality|maxCardinality)/) { | |
| if ($intersection_clause =~ /\{.*(?:cardinality|minCardinality|maxCardinality).*?\}/) { |
| } | ||
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| # Parse intersection_of clause | ||
| if ($intersection_clause =~ /^([A-Z_]+:\d+)\s*(?:\{.*\})?\s*(?:!\s*.+)?$/) { |
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[nitpick] The regex patterns for parsing intersection_of clauses are duplicated and complex. Consider extracting them into named variables or a helper function to improve readability and maintainability.
| if ($intersection_clause =~ /^([A-Z_]+:\d+)\s*(?:\{.*\})?\s*(?:!\s*.+)?$/) { | ||
| # intersection_of: CLASS | ||
| $intersection_of_classes{$1} = 1; | ||
| } elsif ($intersection_clause =~ /^(\S+)\s+([A-Z_]+:\d+)\s*(?:\{.*\})?\s*(?:!\s*.+)?$/) { |
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[nitpick] The regex patterns for parsing intersection_of clauses are duplicated and complex. Consider extracting them into named variables or a helper function to improve readability and maintainability.
| # | ||
| # Usage: perl remove-redundant-subclass-axioms.pl input.obo > output.obo | ||
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| my $input_file = $ARGV[0] || 'src/ontology/uberon-edit.obo'; |
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Using a hardcoded default file path could lead to unintended file modifications. Consider requiring the input file as a mandatory parameter or validate the default path exists and is writable.
Suggested change
| my $input_file = $ARGV[0] || 'src/ontology/uberon-edit.obo'; | |
| if (!defined $ARGV[0]) { | |
| die "Usage: perl $0 input.obo > output.obo\n"; | |
| } | |
| my $input_file = $ARGV[0]; |
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This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR creator will be allowed to proceed with merging without explicit approval, should they wish to do so. |
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Example of lost axiom annotation with source info: 
But partially compensated for in most cases by and xref on the term: 
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dosumis
approved these changes
Feb 13, 2026
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From a final review, it looks like all changes => compensating inference.
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Summary
Modified the redundant axiom removal script and re-ran it with improved logic to preserve subClassOf assertions when ANY intersection_of clause contains cardinality restrictions.
Key Changes
src/scripts/remove-redundant-subclass-axioms.plto detect cardinality restrictions in intersection_of clausescardinality,minCardinality, andmaxCardinalityrestrictionsExample Preservation
The term
UBERON:0011135(intervertebral cartilage) demonstrates the new behavior:Results
{cardinality="2"}kept their subClassOf axiomsuberon-edit.obo.backup-1757956240Test Plan
Addresses issue #3548
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