Human Phenotype Ontology

Downloads

Ontology

In general, users should always use the PURL (persistent URL) to access the HPO-data, i.e.

This currently re-directs you to our Hudson/Jenkins page. Hudson/Jenkins are continuous integration systems, that will provide stable releases.

Annotations

The annotation files (e.g. phenotype_annotation.tab) from our Hudson/Jenkins page. The format of the annotation file is explained under Documentation.

  • phenotype_annotation.tab: contains annotations from the HPO-team (mostly referring to OMIM), Orphanet, and DECIPHER
  • phenotype_annotation_hpoteam.tab: contains annotations the HPO-team (mostly referring to OMIM)
  • negative_phenotype_annotation.tab: contains negative annotations (i.e. a disease is NOT associated with this HPO-term)

Chinese HPO

A Chinese version of the HPO can be downloaded from the CHPO Website.

Database

The HPO can also be obtained in the form of a database. The most recent dump of this DB can be obtained from here. There are also some Documentation-files available. If you have problems or questions related to the database version of the HPO, contact Sebastian.

Genes

Furthermore, we provide two files (genes_to_phenotype.txt and phenotype_to_genes.txt) to link between genes and HPO-terms. These files will be updated at regular intervals (once every month). The links are generated using the information about the phenotypes of a particular syndrome and the corresponding genes that are known to cause this syndrome when mutated. Questions and further requests can be sent to Sebastian.

Translation of the HPO

We do have translations of the HPO labels into spanish (¡Muchas gracias! to Pablo Lapunzina M.D., Ph.D. and colleagues) and italian. We are working with several people to translate more content of HPO into a multitude of languages. Several translations are being actively developed at the moment (e.g. german). Chinese and Japanese translations are also already finished (e.g. CHPO project)

The translations are considered a project coordinated by the HPO team and is hosted on GitHub. We kindly ask you to not start translating HPO content without contacting us beforehand. This might cause duplicated translations and other problems. Please contact us here.

Mappings

The HPO team (Sandra, Peter, Sebastian) has developed a mapping between the categories of the London Dysmorphology Database (LDDB), which is an important resource used by many clinical geneticists to help in the differential diagnosis. The mapping is provided so that users will be able to convert phenotypic data encoded with LDDB categories into HPO terms. We also have created mappings to MEDDRA and Orphanet. Note that we are partnering with Orphanet and they are now re-annotating all their disease entries with HPO terms.

The UMLS has now completely incorporated HPO. In order to make access to this mapping easier, the HPO ontology files contain all cross-references that UMLS created. In the OBO-version you will find e.g. “xref: SNOMEDCT_US:32659003” and “xref: UMLS:C0266295”.

Please contact us here if you need more information or would like to contribute to our mapping efforts.