Human Phenotype Ontology

The Human Phenotype Ontology is a formal ontology of human phenotypes.[1][2][3][4] Developed in collaboration with members of the Open Biomedical Ontologies Foundry, the ontology contains over 10,000 terms describing clinical phenotypic abnormalities. Data from Online Mendelian Inheritance in Man and medical literature were used to generate the terms currently in the HPO. The ontology contains over 50,000 annotations between phenotypes and hereditary disease.

Motivation

The Human Phenotype Ontology (HPO) was created to serve as a standardized vocabulary of phenotypic abnormalities that have been seen in human disease. Applications for the data in the ontology include clinical diagnostics, mapping between phenotypes of model organisms, and as a standard vocabulary for clinical databases. Clinical annotations within the HPO are sought from the medical and genetics community to improve the ontology.

Automatic Entity Recognition

Using manually annotated corpus with 228 abstracts, the Named-entity recognition tools NCBO Annotator, OBO Annotator and Bio-LarK CR obtained a F-score of 0.45, 0.54 and 0.56, respectively.[5] A Machine learning approach obtained a F-score of 0.65 in the same corpus and 0.86 in an updated version of the corpus.[6]

See also

References

  1. ↑ Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, et al. (January 2014). "The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data". Nucleic Acids Research. 42 (Database issue): D966–74. doi:10.1093/nar/gkt1026. PMC 3965098. PMID 24217912.
  2. ↑ Robinson PN, Köhler S, Bauer S, Seelow D, Horn D, Mundlos S (November 2008). "The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease". American Journal of Human Genetics. 83 (5): 610–5. doi:10.1016/j.ajhg.2008.09.017. PMC 2668030. PMID 18950739.
  3. ↑ Robinson PN, Mundlos S (June 2010). "The human phenotype ontology". Clinical Genetics. 77 (6): 525–34. doi:10.1111/j.1399-0004.2010.01436.x. PMID 20412080.
  4. ↑ Köhler S, Doelken SC, Rath A, Aymé S, Robinson PN (September 2012). "Ontological phenotype standards for neurogenetics". Human Mutation. 33 (9): 1333–9. doi:10.1002/humu.22112. PMID 22573485.
  5. ↑ Groza T, Köhler S, Doelken S, Collier N, Oellrich A, Smedley D, Couto FM, Baynam G, Zankl A, Robinson PN (2015). "Automatic concept recognition using the human phenotype ontology reference and test suite corpora". Database. 2015. doi:10.1093/database/bav005. PMC 4343077. PMID 25725061.
  6. ↑ Lobo M, Lamurias A, Couto FM (2017). "Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules". BioMed Research International. 2017: 8565739. doi:10.1155/2017/8565739. PMC 5700471. PMID 29250549.
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