A Logical Model of Homology for Comparative Biology.

Christopher J Mungall,Todd J Vision,James P Balhoff,Paula M Mabee,Hilmar Lapp,Wasila M Dahdul,Stephen Smith

doi:10.1093/sysbio/syz067

Abstract

There is a growing body of research on the evolution of anatomy in a wide variety of organisms. Discoveries in this field could be greatly accelerated by computational methods and resources that enable these findings to be compared across different studies and different organisms and linked with the genes responsible for anatomical modifications. Homology is a key concept in comparative anatomy; two important types are historical homology (the similarity of organisms due to common ancestry) and serial homology (the similarity of repeated structures within an organism). We explored how to most effectively represent historical and serial homology across anatomical structures to facilitate computational reasoning. We assembled a collection of homology assertions from the literature with a set of taxon phenotypes for the skeletal elements of vertebrate fins and limbs from the Phenoscape Knowledgebase. Using seven competency questions, we evaluated the reasoning ramifications of two logical models: the Reciprocal Existential Axioms (REA) homology model and the Ancestral Value Axioms (AVA) homology model. The AVA model returned all user-expected results in addition to the search term and any of its subclasses. The AVA model also returns any superclass of the query term in which a homology relationship has been asserted. The REA model returned the user-expected results for five out of seven queries. We identify some challenges of implementing complete homology queries due to limitations of OWL reasoning. This work lays the foundation for homology reasoning to be incorporated into other ontology-based tools, such as those that enable synthetic supermatrix construction and candidate gene discovery. [Homology; ontology; anatomy; morphology; evolution; knowledgebase; phenoscape.]

Highlights

Distinguishing homology, i.e., similarity due to inheritance from a common ancestor, from similarities that arise independently, is the foundation of the comparative approach that is applied across many different fields of biology
In total 46 homology assertions were collected for the paired fins and limbs, including ten statements pertaining to serial homology
Incorporating homology relationships into anatomy ontologies lays the groundwork for this knowledge to be used in other ontology-based tools and reasoning applications, including candidate gene discovery and phenotypic matrix assembly

Summary

Introduction

Distinguishing homology, i.e., similarity due to inheritance from a common ancestor, from similarities that arise independently, is the foundation of the comparative approach that is applied across many different fields of biology. Comparative genomics, for instance, has led to the identification of homologous patterns of gene activity and regulation that have been conserved over hundreds of millions of years of evolution. This has been aided considerably by computer-based analysis, which is enabled by the standardization of genomic data. The complexity of anatomical data, has been an impediment to standardization and computation, and many of the critical tasks rely on manual inspection of the data and human judgment [1] Advances in this area have been made using semantic reasoning, but these have not explicitly incorporated nor evaluated homology reasoning. We formalize the biological expectations for homology reasoning and evaluate the consequences of applying formal homology relationships between anatomical structures in an anatomy ontology

Methods

Results

Conclusion