Data from: A logical model of homology for comparative biology

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 vertebrate fins and limbs
from the Phenoscape Knowledgebase (KB). Using seven competency questions,
we evaluated the reasoning ramifications of two logical models: the
Reciprocal Existential Axioms Homology Model (REA) and the Ancestral Value
Axioms Homology Model (AVA). Both models returned the user-expected
results for all but one historical homology query and one serial homology
query. Additionally, for each competency question, the AVA model returns
the search term and any subtypes. 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.