Annotation Resource: Human Phenotype Ontology - bcb420-2025/Clare_Gillis GitHub Wiki

Human Phenotype Ontology (HPO)

1. What sort of data is it? What sort of information does it offer us?

  • HPO provides a standardized library of phenotypic abnormalities associated with genes. The dataset contains genes (denoted by an NCBI gene identifier and a HUGO gene symbol,) phenotypic abnormalities (denoted by a term identifier and name,) and diseases (denoted by a disease identifier and name.) Users can search by gene, phenotype, or disease to find genes, phenotypes, or diseases associated with their search term (ex. phenotypes and diseases associated with a gene.)

2. When and where was is published?

Robinson, P. N., Köhler, S., Bauer, S., Seelow, D., Horn, D., & Mundlos, S. (2008). The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease. American journal of human genetics, 83(5), 610–615. https://doi.org/10.1016/j.ajhg.2008.09.017

Gargano, M. A., Matentzoglu, N., Coleman, B., Addo-Lartey, E. B., Anagnostopoulos, A. V., Anderton, J., Avillach, P., Bagley, A. M., Bakštein, E., Balhoff, J. P., Baynam, G., Bello, S. M., Berk, M., Bertram, H., Bishop, S., Blau, H., Bodenstein, D. F., Botas, P., Boztug, K., Čady, J., … Robinson, P. N. (2024). The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic acids research, 52(D1), D1333–D1346. https://doi.org/10.1093/nar/gkad1005

3. Is this annotation set updated regularly or is it a static source?

  • This dataset is updated regularly - every few months they release updates to their terms, annotations, and API.

4. Where can I find this data?

5. How is the data formatted and released? Does it exist in some sort of standard file format?

  • Phenotype info is stored in HPOA format (a specific file format meant to hold HPO phenotype data) and associations (genes_to_phenotype, phenotype_to_genes, etc) are stored in TXT files. More info about these formats can be found here
  • Ontology data can be downloaded in OBO (human readable), OWL (computer readable), or JSON (lightweight, computer readable) formats.

6. What identifiers are associated with these annotations?