Dr. Sebastian Köhler On The Future of the Human Phenotype Ontology Resource

Sebastian Köhler, a founder of the Human Phenotype Ontology (HPO), discusses the future of this widely adopted standardized vocabulary for phenotypic abnormalities.

I think one of the major goals should be to focus on the molecular level and try to describe in more detail which phenotypic differences are caused by different variants in different genes that are all linked to the same syndrome, in order to be able to better stratify patients and make big steps towards personalisation of healthcare.

Sebastian Köhler, Co-Founder of the Human Phenotype Ontology.

The Human Phenotype Ontology (HPO) is a standardized, structured, vocabulary that describes phenotypic abnormalities encountered in human disease. With over 13,000 terms and over 156,000 annotations to hereditary diseases, the HPO can be leveraged as a powerful tool for phenotype-driven differential diagnostics, genomic diagnostics, precision medicine, and translational research. The HPO is increasingly adopted as a standard for phenotypic abnormalities, used by international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools like PhenoTips. Its widespread adoption contributes towards efforts in global data exchange that advance the identification of disease etiologies, with unparalleled benefits for rare diseases.

PhenoTips’ core software enables deep phenotyping with the HPO

Natural Language Processing, a simple and predictive term search, and gene and diagnosis suggestions based on HPO profiles, all at your fingertips.

Following our Speaker Series “The Importance of Deep Phenotyping in Precision Medicine” in which HPO founder Prof. Dr. Peter Robinson discussed the HPO’s applications in genomic analysis and precision medicine, PhenoTips spoke with HPO founder Dr. Sebastian Köhler about the future of the HPO.

Over the past decade the HPO has grown in both application and annotations, with thousands of new HPO terms added in the last year alone. The majority of these applications focus on rare disease, and Dr. Köhler foresees that rare disease would continue to be the focus in the coming years, with knowledge from rare disease research applied to more common conditions.

“From what I hear from the rare disease community in Europe, people are very interested in supporting newborn screening,” says Dr. Köhler. “I think that structured data like encoded HPO or SNOMED, or whatever standard is en vogue, will play a key role [in newborn screening]. But to be honest, I’m rather sure it is especially going to be HPO because only HPO has the built-in feature to act as a bridge between the clinical features and the molecular genetics knowledge.”

About Dr. Sebastian Köhler:Currently Senior Information Architect at Ada Health, Dr. Köhler is the author of over 60 publications in digital health, rare diseases, genomics, and knowledge representation. He has been developing machine learning tools for clinical, phenotype-driven interpretation of next generation sequencing results, such as PhenIX and ExomeWalker. He currently focuses on interoperability and semantic standards to build semantic knowledge graphs for AI and data analysis. Dr. Köhler’s latest paper, The Human Phenotype Ontology in 2021, summarizes recent advances in the HPO’s development and utilization.


Learn more about the Human Phenotype Ontology.

For more information on the HPO and its applications, watch the presentation by HPO co-founder Dr. Peter Robinson.

Watch the presentation