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Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Journal Article · · Nucleic Acids Research
DOI:https://doi.org/10.1093/nar/gky1105· OSTI ID:1625571
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  1. Charité Centrum für Therapieforschung, Charité—Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Inst. of Health, Berlin (Germany); Einstein Center Digital Future, Berlin (Germany); Monarch Initiative (monarchinitiative.org); DOE/OSTI
  2. Monarch Initiative (monarchinitiative.org); The Jackson Lab. for Genomic Medicine, Farmington, CT (United States)
  3. Monarch Initiative (monarchinitiative.org); Oregon Health & Science Univ., Portland, OR (United States)
  4. Monarch Initiative (monarchinitiative.org); Queen Mary University of London (United Kingdom). Genomics England
  5. Monarch Initiative (monarchinitiative.org); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Environmental Genomics and Systems Biology
  6. Monarch Initiative (monarchinitiative.org); Wellcome Trust Genome Campus, Cambridge (United Kingdom). European Bioinformatics Institute (EMBL-EBI)
  7. Monarch Initiative (monarchinitiative.org); Oregon State Univ., Corvallis, OR (United States). Linus Pauling Inst.
  8. Monarch Initiative (monarchinitiative.org); Queen Mary Univ. College of London (United Kingdom). William Harvey Research Inst.; Univ. College of London (United Kingdom). UCL Genetics Inst.; University College of London (United Kingdom). UCL Inst. of Ophthalmology
  9. Monarch Initiative (monarchinitiative.org); Univ. of North Carolina, Chapel Hill, NC (United States). Renaissance Computing Inst.
  10. Government of Western Australia, Perth, WA (Australia). Dept. of Health. Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia and The Office of Population Health Genomics; Univ. of Western Australia, Perth, WA (Australia). School of Paediatrics and Telethon Kids Inst.; Murdoch Univ., WA (Australia). Inst. for Immunology and Infectious Diseases; Curtin Univ., Perth, WA (Australia). Dept. of Science and Engineering. Spatial Sciences
  11. Curtin Univ., Perth, WA (Australia). Dept. of Science and Engineering. Spatial Sciences
  12. Government of Western Australia, Perth, WA (Australia). Dept. of Health. Western Australian Register of Developmental Anomalies and Genetic Services of Western Australia and The Office of Population Health Genomics
  13. Government of Western Australia, Perth, WA (Australia). Dept. of Health. The Office of Population Health Genomics
  14. SimulConsult, Chestnut Hill, MA, (United States)
  15. Vrije Univ., Brussels (Belgium). Neurogenetics Research Group; UZ Brussels (Belgium). Dept. of Pediatrics. Pediatric Neurology Unit
  16. Monarch Initiative (monarchinitiative.org); Garvan Inst. of Medical Research, Sydney, NSW (Australia)
  17. Univ. of Toronto, ON (Canada). Centre for Computational Medicine. Hospital for Sick Children. Dept. of Computer Science
  18. National Institutes of Health (NIH), Bethesda, MD (United States). National Inst. of Allergy and Infectious Diseases
  19. Marquette Univ., Milwaukee, WI (United States). Medical College of Wisconsin. Dept. of Biomedical Engineering. Rat Genome Database
  20. Bioscientia GmbH, Ingelheim (Germany)
  21. Barcelona Institute of Science and Technology (BIST), Barcelona (Spain). CNAG-CRG, Centre for Genomic Regulation (CRG); Univ. Pompeu Fabra, Barcelona (Spain)
  22. Univ. of Manchester (United Kingdom). Manchester Royal Eye Hospital
  23. The Jackson Lab. for Genomic Medicine, Farmington, CT (United States)
  24. ICF, Rockville, MD, (United States); National Institutes of Health (NIH), Bethesda, MD (United States). National Center for Advancing Translational Sciences. Office of Rare Diseases Research
  25. Orphanet, Paris (France). Plateforme Maladies Rares. INSERM
  26. The Jackson Lab., Bar Harbor, ME (United States)
  27. Sanford Health, Sioux Falls, SD (United States). Sanford Imagenetics
  28. Stanford Univ., CA (United States). School of Medicine. Center for Undiagnosed Diseases
  29. Univ. of Utrecht (Netherlands). Univ. Medical Center. Dept. of Genetics
  30. Orphanet, Paris (France). Plateforme Maladies Rares. INSERM
  31. Newcastle Univ., Newcastle upon Tyne (United Kingdom). Inst. of Genetic Medicine
  32. Stanford Univ., CA (United States). School of Medicine. Dept. of Pediatrics
  33. Icahn School of Medicine at Mount Sinai, New York, NY (United States)
  34. Univ. College London (United Kingdom). Inst. of Cardiovascular Science
  35. Vall d’Hebron Research Inst. (VHIR), Barcelona (Spain). Hospital Universitari Vall d’Hebron. Child Neurology Unit
  36. Barcelona Institute of Science and Technology (BIST), Barcelona (Spain). CNAG-CRG, Centre for Genomic Regulation (CRG); Univ. of Freiburg (Germany). Medical Center. Faculty of Medicine. Dept. of Neuropediatrics and Muscle Disorders; Univ. of Ottawa (Canada). Children’s Hospital of Eastern Ontario Research Inst.; The Ottawa Hospital, Ottawa (Canada). Dept. of Medicine. Division of Neurology
  37. Strasbourg Univ. Hospital, Strasbourg (France). SENSGENE FSMR Network. Centre for Rare Eye Diseases CARGO
  38. National Institutes of Health (NIH), Bethesda, MD (United States). Clinical Center. Dept. of Lab. Medicine. Immunology Service
  39. Univ. of Pennsylvania, Philadelphia, PA (United States). Perelman School of Medicine. The Children’s Hospital of Philadelphia. Dept. of Pediatrics. Division of Allergy Immunology
  40. Monarch Initiative (monarchinitiative.org); The Jackson Lab. for Genomic Medicine, Farmington, CT (United States); Univ. of Connecticut, Farmington, CT (United States). Inst. for Systems Genomics
+ Show Author Affiliations
The Human Phenotype Ontology (HPO)––a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases––is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO’s interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotypeontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.
Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1625571
Journal Information:
Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: D1 Vol. 47; ISSN 0305-1048
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English

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New models for human disease from the International Mouse Phenotyping Consortium journal May 2019
Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions journal January 2020
Human and mouse essentiality screens as a resource for disease gene discovery journal January 2020
Genetic landscape of autism spectrum disorder in Vietnamese children journal March 2020
Semantic integration of clinical laboratory tests from electronic health records for deep phenotyping and biomarker discovery journal May 2019
VCF/Plotein: visualization and prioritization of genomic variants from human exome sequencing projects journal June 2019
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language journal January 2019
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery journal January 2019
g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update) journal May 2019
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species journal November 2019
PAWER: protein array web exploreR journal September 2020
Genome analysis and knowledge-driven variant interpretation with TGex journal December 2019
Artificial intelligence in clinical and genomic diagnostics journal November 2019
RegulationSpotter: annotation and interpretation of extratranscriptic DNA variants text January 2019
Identifying Disease-Gene Associations With Graph-Regularized Manifold Learning journal April 2019
Expanding Clinical Presentations Due to Variations in THOC2 mRNA Nuclear Export Factor journal February 2020
Uncovering Missing Heritability in Rare Diseases journal April 2019
The Hearing Impairment Ontology: A Tool for Unifying Hearing Impairment Knowledge to Enhance Collaborative Research journal November 2019
Evaluating Face2Gene as a Tool to Identify Cornelia de Lange Syndrome by Facial Phenotypes journal February 2020
Additional file 1 of Genomic insights into body size evolution in Carnivora support Peto’s paradox dataset January 2021
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Additional file 7 of Genomic insights into body size evolution in Carnivora support Peto’s paradox dataset January 2021
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