Rare disease (RD) research is a field of medicine increasingly reliant on information technology. Low-cost whole-genome sequencing has revolutionized the discovery of genetic causes of disorders. The analysis of phenotypic abnormalities provides a translational bridge from genome-scale biology to a disease-centered view on human pathology. Detailed phenotype data, combined with ever-increasing amounts of genomic data, have an enormous potential to accelerate the identification of clinically actionable prognostic or therapeutic implications and to improve our understanding of RD. Harmonisation of phenomics information including disorders and phenotype traits that are stored in different supports (patient records, databases, registries) in a non-standardised way, is a cornerstone for the production of sound data necessary to foster research. This project builds on three resources largely adopted by the RD community: Orphanet, and its ontology ORDO, HPO and PhenoTips. It is aimed to provide the community with an integrated, RD-specific informatics ecosystem that will harmonize the way phenomics information is stored in databases and in patient files worldwide, and thereby contribute to interoperability. This ecosystem will consist of a suit of tools and ontologies, optimized to work together, and available to clinicians and scientists through commonly used software repositories. Additionally, the ecosystem will improve and streamline the interpretation of variants identified through exome and full genome sequencing by harmonizing the way phenotypic information is collected.