Dr. Melissa Haendel and the Ontology Development Group announce the first (sneak peak) release of the Monarch Initiative (http://monarchinitiative.org/). The Monarch Initiative Discovery System will contain a wealth of information about model organisms, in vitro models, genes, pathways, gene expression, protein and genetic interactions, orthology, disease, phenotypes, publications, and authors with semantic similarity calculations that suggest novel relationships based on the information content of data descriptions.
Why are we calling this a Sneak Peek? Because we plan to incrementally add functionality over the next few months based on user feedback.The Sneak Peek currently includes phenotype-genotype data from human, mouse, and zebrafish. The system allows comparison of phenotypic profiles (either a disease related set or a user-defined set) across organisms using a semantic similarity algorithm (the OWLsim algorithm) and a suite of integrated phenotype, anatomy, and disease ontologies. Functionality includes the ability to explore the relationships between models, diseases, genes, and phenotypes, including a visualization tool to review phenotypes across models to investigate the degree to which they recapitulate a disease.
Services include an API to retrieve the models most related to any given set of phenotypes, as well as an API call to determine the sufficiency of a phenotype annotation profile. These services are being used within PhenoTips and by the NIH Undiagnosed Disease Program to compare human undiagnosed disease phenotype profiles against model systems to ensure adequate annotation to aid prioritization of gene candidates.