Fig. 1

An overview of the data sources and strategies used to generate the PhenomeNET ontologies. On one side, we use mappings between HP, MP, DO, and ORDO, generated using the AML ontology matching system; on the other side, we use the axioms used to define classes in HP and MP together with the background knowledge in other ontologies to generate mappings formally. Using the ELK reasoner, we generate a hierarchical ontology structure (i.e., a taxonomy) from which we derive equivalent class, sub-class, and super-class mappings. The PhenomeNET-Full ontology is based on a combination of all these mapping approaches, while PhenomeNET-Map uses only the AML-generated mappings between HP and MP. PhenomeNET-Plain does not use any of the AML-generated mappings but solely relies on the axioms and background knowledge