Matching Phenotypes

This page discusses the method developed and implemented in late 2010 for search for, and scoring, phenotype matches between taxa (Phenoscape) and zebrafish mutants (ZFIN).

Purpose

An important goal for the Phenoscape project is to be able to suggest candidate genes that may have contributed to evolutionary change. The way that we have proposed to do this is to search for changes in phenotype that appear as the result of mutations in model organisms and also appear as phenotype changes on an evolutionary tree.

Selecting Phenotypes from Taxon Annotations

The matching process involves matching changes in phenotype, not directly matching phenotypes. For phenotypes associated with mutants of model organism mutants, it is understood that they vary with respect to the wild type. For taxa, however, this means looking for taxonomic nodes where variation in a phenotype is observed among the children of the node. For example, there are nine species within the genus Aspidoras with annotations for the shape of the opercle bone. Of these, eight exhibit opercle bones with round shape, but the ninth (A. pauciradiatus) is annotated with a triangular opercle. In contrast, all three annotated species of the related Hoplosternum are annotated with a triangular opercle. Thus there is detectable variation in opercle shape within the children of Aspidoras, but not within Hoplosternum - suggesting that change in opercle shape has occurred somewhere among the descendants of Aspidoras. Once changes are identified, they treated as variation in the affected entity at the level of the attribute parent of the qualities involved (e.g., shape).

Using attributes to limit the scope of quality comparisons

Each phenotype is linked to multiple entities via inheres_in_part_of relations.

Scoring matches of sets of phenotypes (phenotypic profiles) associated with a gene or taxon node

• maxIC
• ICCS
• simIC
• simJ