Abstract
The Human Phenotype Ontology (HPO)—a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases—is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO’s interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotype-ontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.
Highlights
A cornerstone of differential diagnostics and translational research is deep phenotyping: the computational analysis of detailed, individual clinical abnormalities [1,2]
We reported on a range of algorithms that had been developed by our group and others to support phenotype-driven genomic diagnostics [12]
As a result of the meeting, representatives of all the phenotypes ontologies have committed to an ongoing collaboration to align their respective ontologies by developing sets of common design patterns and using these to define terms in their ontologies. The outcome of these community efforts will be an integrated ecosystem of phenotype ontologies that can be leveraged in Human Phenotype Ontology (HPO)-based clinical diagnostics and disease mechanism discovery
Summary
A cornerstone of differential diagnostics and translational research is deep phenotyping: the computational analysis of detailed, individual clinical abnormalities [1,2]. To support the use of model organisms to further human health research, developers of the Mammalian Phenotype (MP) ontology [54] have collaborated with the HPO team to develop compatible logical definitions, but these efforts were restricted to comparison of individual definitions and resulted in manual changes to the respective ontologies.
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