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The HPO is the clinical window of the Monarch Initiative which is an NIH supported project that integrates, aligns, and re-distributes cross-species gene, genotype, variant, disease, and phenotype data. The Monarch Browser allows users to browse not only human diseases but to see their links to other organisms, genes, phenotypes, and pathways, which may be of especial interest to translational researchers.

Am I allowed to change the contents of HPO?

The HPO is a community-driven project. We request that all proposed changes be suggested on our GitHub tracker so that they will be of use to all users of the HPO.

What is the medical focus of the Human Phenotype Ontology?

The medical focus of the HPO in its initial decade (2007-2017) was on rare, mainly Mendelian diseases. The construction of the initial version of the HPO in 2007/2008 was performed by generating an ontology based on descriptions in the Clinical Synopsis of the Online Mendelian Inheritance in Man (OMIM) database. Since the initial publication of the HPO in 2008, the HPO team has held regular workshops with clinicians to refine and extend the clinical terminology of the HPO in specific areas such as cardiology or immunology. We have added textual definitions, computational logical definitions, and many thousands of new terms since then. The HPO is currently being extended to other areas of medicine.

## What is an ontology?

A terminology contains a list of items (often called "terms") that represent the concepts of a domain. An ontology is a terminology that additionally specifies formal semantic relationships of concepts. For instance, a terminology of wines would include a list of items such as Chardonnay, Cabernet Sauvignon, Rioja, Riesling, Sauvignon blanc, etc., but an ontology of wine might have a term for "red wine" and "Rioja"; It also can specify that "Rioja" is a type of "red wine". Ontologies and terminologies can be used as tools for standardizing and exchanging data. Ontologies such as the HPO typically enable sophisticated computational algorithms that exploit the semantic relations between terms.