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A Logical Model of Homology for Comparative Biology
Paula M Mabee1, James P Balhoff2, Wasila M Dahdul1
1Department of Biology, University of South Dakota, 414 East Clark Street, Vermillion, SD 57069, USA.
Systematic Biology
|October 10, 2019
Summary
The Ancestral Value Axioms (AVA) model effectively represents anatomical homology for computational analysis, outperforming the Reciprocal Existential Axioms (REA) model. This advances comparative anatomy and evolutionary studies.
Area of Science:
- Evolutionary biology
- Comparative anatomy
- Bioinformatics
Background:
- Computational methods can accelerate discoveries in evolutionary anatomy.
- Homology, including historical and serial homology, is crucial for comparing anatomical structures across organisms.
- Existing knowledge bases lack robust computational reasoning for homology.
Purpose of the Study:
- To evaluate logical models for representing historical and serial homology computationally.
- To facilitate computational reasoning across different studies and organisms.
- To link anatomical modifications with responsible genes.
Main Methods:
- Assembled homology assertions and taxon phenotypes from the Phenoscape Knowledgebase.
- Utilized seven competency questions to evaluate two logical models: AVA and REA.
- Assessed reasoning capabilities for skeletal elements of vertebrate fins and limbs.
Main Results:
- The AVA model successfully returned all expected results, including superclasses and subclasses.
- The REA model met expectations for five out of seven queries.
- Identified limitations in OWL reasoning for complete homology queries.
Conclusions:
- The AVA model provides a more comprehensive approach to homology reasoning.
- This work establishes a foundation for integrating homology reasoning into ontology-based tools.
- Enables advancements in synthetic supermatrix construction and candidate gene discovery.
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