James P Balhoff | bioRxiv Science

bioRxiv2016

The Phenoscape Knowledgebase: tools and APIs for computing across phenotypes from evolutionary diversity and model organisms

I. Introduction I. Introduction II. Data ingestion and... III. Semantic similarity... IV. Web service interfaces V. Applications VI. Conclusion References The Phenoscape Knowledgebase (KB) is an ontology-driven database that combines existing phenotype annotations from model organism databases with new phenotype annotations from the evolutionary literature. Phenoscape curators have created phenotype annotations for more than 5,000 species and higher taxa, by defining computable phenotype concepts for more than 20,000 character states from over 160 published phylogenetic studies. These phenotype concepts are in the form of Entity-Quality (EQ) [1] compositions which incorporate terms from the Uberon anatomy ontology, the Biospatial Ontology (BSPO), and the Phenotype and T ...

Bioinformatics↗

bioRxiv2015

Using the Phenoscape Knowledgebase to relate genetic perturbations to phenotypic evolution

The abundance of phenotypic diversity among species can enrich our knowledge of development and genetics beyond the limits of variation that can be observed in model organisms. The Phenoscape Knowledgebase (KB) is designed to enable exploration and discovery of phenotypic variation among species. Because phenotypes in the KB are annotated using standard ontologies, evolutionary phenotypes can be compared with phenotypes from genetic perturbations in model organisms. To illustrate the power of this approach, we review the use of the KB to find taxa showing evolutionary variation similar to that of a query gene. Matches are made between the full set of phenotypes described for a gene and an evolutionary profile, the latter of which is defined as the set of phenotypes that are variable among the daughters of any node on the taxonomic tree. Phenoscapes semantic similarity interface allows the user to assess the statistical significance of each match and flags matches that may only result from differences in annotation coverage between genetic and evolutionary studies. Tools such as this will help meet the challenge of relating the growing volume of genetic knowledge in model organisms to the diversity of phenotypes in nature. The Phenoscape KB is available at http://kb.phenoscape.org.

Bioinformatics↗