Frequently Asked Questions

What is PhenomeNet?

PhenomeNet is a cross-species phenotype similarity network. It contains the experimentally observed phenotypes of multiple species as well as the phenotypes of human diseases. PhenomeNet provides a measure of phenotypic similarity between the phenotypes it contains.

What is phenotypic similarity?

To compute phenotypic similarity between two sets of phenotypes, we use a weighted Jaccard index. First, phenotype ontologies are used to infer all the implications of a phenotype observation using several phenotype ontologies. As a second step, the information content of each phenotype is computed and used as a weight in the Jaccard index.

What can I do with PhenomeNet?

Phenotypic similarity is useful in several ways. Phenotypic similarity between a phenotype resulting from a genetic mutation and a disease can be used to suggest candidate genes for a disease. Phenotypic similarity can also identify genes in a same pathway or orthologous genes.

How does the comparison of phenotypes across species work?

PhenomeNet uses the axioms in multiple species-dependent phenotype ontologies to infer equivalent and related phenotypes across species. For this purpose, phenotype ontologies and phenotype annotations are integrated in a single ontology, and automated reasoning is used to infer equivalences. Specifically, for every phenotype, PhenomeNet infers the related mammalian phenotype and uses the Mammalian Phenotype Ontology for computing phenotypic similarity.

How do I cite PhenomeNet?

If you use PhenomeNet in your research, please cite

Robert Hoehndorf, Paul N. Schofield and Georgios V. Gkoutos. PhenomeNET: a whole-phenome approach to disease gene discovery. Nucleid Acids Research, 2011.

I want to use PhenomeNet, or parts of PhenomeNet, for my own project. Can I get the source code and raw data?

Yes. We make our source code and all data freely available on If you have any questions, please contact us.

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