Example applications and input files for OntoFUNC

1. Prioritization of candidate genes for genetic diseases

Description: Animal models may provide insights into the pathobiology underlying human disease. If a mutation in an animal model results in phenotypes similar to a human disease phenotype, the animal model may be a good candidate for a disease model.

Original dataset: HPO annotations of OMIM diseases and MP annotated mouse models

Protocol: The Human Phenotype Ontology and Mammalian Phenotype Ontology are integrated across species based on the PhenomeNET system (also described here).

OntoFUNC input file: omim-mgi.txt

2. Functional similarity of proteins

Description: GO functional similarity between proteins can be used as indicator that two proteins interact. Several studies applied semantic similarity over GO to predict protein-protein interactions and evaluated the results (e.g., this study.

Original dataset: Gene Ontology Annotations of organisms from the Gene Ontology Annotation project.

Protocol: All GO functional annotations of C. elegans proteins are obtained from the GOA website and used directly for computation of functional similarity.

OntoFUNC input file: wbsim.txt