Investigating the importance of anatomical homology for cross-species phenotype comparisons using semantic similarity.

BioRxiv : the Preprint Server for Biology
Prashanti MandaTodd J Vision

Abstract

There is growing use of ontologies for the measurement of cross-species phenotype similarity. Such similarity measurements contribute to diverse applications, such as identifying genetic models for human diseases, transferring knowledge among model organisms, and studying the genetic basis of evolutionary innovations. Two organismal features, whether genes, anatomical parts, or any other inherited feature, are considered to be homologous when they are evolutionarily derived from a single feature in a common ancestor. A classic example is the homology between the paired fins of fishes and vertebrate limbs. Anatomical ontologies that model the structural relations among parts may fail to include some known anatomical homologies unless they are deliberately added as separate axioms. The consequences of neglecting known homologies for applications that rely on such ontologies has not been well studied. Here, we examine how semantic similarity is affected when external homology knowledge is included. We measure phenotypic similarity between orthologous and non-orthologous gene pairs between humans and either mouse or zebrafish, and compare the inclusion of real with faux homology axioms. Semantic similarity was preferentially increa...Continue Reading

Related Concepts

Vertebrates
Body Part
Part
Genes
Patient Transfer
Limb Structure
Fish <Chondrichthyes>
Fin
Zebrafish
Fish <Actinopterygii>

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