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The Human Phenotype Ontology in 2017

Journal Article · · Nucleic Acids Research
DOI:https://doi.org/10.1093/nar/gkw1039· OSTI ID:1408411
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  1. Charite-Universitatsmedizin, Berlin (Germany)
  2. Oregon Health and Science Univ., Portland, OR (United States)
  3. Institut du Cerveau et de la Moelle epiniere, Paris (France)
  4. Univ. of Western Australia, Perth, WA (Australia); King Edward Memorial Hospital Department of Health, Perth, WA (Austrailia)
  5. The Jackson Laboratory, Bar Harbor, ME (United States)
  6. Sanford Health, Sioux Falls, SD (United States)
  7. Univ. of Ottawa, ON (Canada)
  8. Univ. of Toronto, ON (Canada); Hospital for Sick Children, Toronto, ON (Canada)
  9. Univ. of Cambridge (United Kingdom); Cambridge Biomedical Campus, Cambridge (United Kingdom)
  10. Univ. College London, London (United Kingdom)
  11. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY (United States)
  12. Health Department of Western Australia, Perth, WA (Australia)
  13. Queen Mary Univ. of London (United Kingdom)
  14. Radboud Univ., Nijmegen (Netherlands)
  15. Wellcome Genome Campus, Hinxton, Cambridge (United Kingdom)
  16. Univ. of Leuven (Belgium)
  17. Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States)
  18. The Children's Hospital of Philadelphia, PA (United States); Univ. Medical Center Schleswig-Holstein (UKSH), Kiel (Germany)
  19. Univ. Medical Center Schleswig-Holstein (UKSH), Kiel (Germany
  20. Univ. of Luxembourg (Luxembourg)
  21. Medical College of Wisconsin, Milwaukee, WI (United States)
  22. Univ. of Newcastle, Newcastle upon Tyne (United Kingdom)
  23. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY (United States)
  24. Tohoku Univ., Sendai (Japan)
  25. Orphanet, Paris (France)
  26. Cambridge Biomedical Campus, Cambridge (United Kingdom)
  27. Center for Pediatrics and Adolescent Medicine, Heidelberg (Germany)
  28. SimulConsult Inc., Chestnut Hill, MA (United States)
  29. Univ. of Manchester (United Kingdom)
  30. Univ. of Oxford (United Kingdom)
  31. Univ. of Cambridge (United Kingdom)
  32. Univ. of Sydney, NSW (Australia); Sydney Childrens Hospitals Network, Sydney, NSW (Australia)
  33. Univ. of Miami, FL (United States)
  34. Garvan Inst. of Medical Research, Sydney, NSW (Australia); St. Vincent's Clinical School, Sydney, NSW (Australia)
  35. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  36. Univ. of Connecticut, Farmington, CT (United States); The Jackson Lab. for Genomic Medicine, Farmington, CT (United States)
+ Show Author Affiliations
Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human PhenotypeOntology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1408411
Journal Information:
Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 45; ISSN 0305-1048
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English

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Network pharmacology to dissect the mechanisms of Yinlai Decoction for pneumonia journal June 2020
Pathway networks generated from human disease phenome journal September 2018
The Italian neuromuscular registry: a coordinated platform where patient organizations and clinicians collaborate for data collection and multiple usage journal October 2018
From scientific discovery to treatments for rare diseases – the view from the National Center for Advancing Translational Sciences – Office of Rare Diseases Research journal November 2018
A nomenclature and classification for the congenital myasthenic syndromes: preparing for FAIR data in the genomic era journal November 2018
An ontological foundation for ocular phenotypes and rare eye diseases journal January 2019
Can a decision support system accelerate rare disease diagnosis? Evaluating the potential impact of Ada DX in a retrospective study journal March 2019
OPA1: 516 unique variants and 831 patients registered in an updated centralized Variome database journal September 2019
Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns journal October 2017
Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants journal December 2019
Matching disease and phenotype ontologies in the ontology alignment evaluation initiative journal December 2017
Disease Ontology: improving and unifying disease annotations across species journal February 2018
A FAIR guide for data providers to maximise sharing of human genomic data journal March 2018
VarWatch—A stand-alone software tool for variant matching journal April 2019
Revisiting biomarker discovery by plasma proteomics journal September 2017
Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium journal September 2018
OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants. text January 2018
Precision global health and comorbidity: a population-based study of 16 357 people in rural Uganda. text January 2018
An ontological foundation for ocular phenotypes and rare eye diseases. text January 2019
Disease model discovery from 3,328 gene knockouts by The International Mouse Phenotyping Consortium. text January 2017
DDIEM: drug database for inborn errors of metabolism text January 2020
The anatomy of phenotype ontologies: principles, properties and applications text January 2017
SpainUDP: The Spanish Undiagnosed Rare Diseases Program journal June 2018
Computational Drug Repurposing: Current Trends journal October 2019
Identifying Clinical Terms in Medical Text Using Ontology-Guided Machine Learning journal January 2019
Bradykinin-Mediated Angioedema: An Update of the Genetic Causes and the Impact of Genomics journal September 2019
Artificial Intelligence and Integrated Genotype–Phenotype Identification journal December 2018
Biological Network Approaches and Applications in Rare Disease Studies journal October 2019
SpainUDP: The Spanish Undiagnosed Rare Diseases Program
  • López-Martín, Estrella; Martínez-Delgado, Beatriz; Bermejo-Sánchez, Eva
  • International Journal of Environmental Research and Public Health, Vol. 15, Issue 8 https://doi.org/10.3390/ijerph15081746
journal August 2018
Meeting Patients’ Right to the Correct Diagnosis: Ongoing International Initiatives on Undiagnosed Rare Diseases and Ethical and Social Issues journal September 2018
Text-based phenotypic profiles incorporating biochemical phenotypes of inborn errors of metabolism improve phenomics-based diagnosis text January 2018
DISNET: a framework for extracting phenotypic disease information from public sources journal January 2020

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59 BASIC BIOLOGICAL SCIENCES