ReviewNucleic acids research2017
The Human Phenotype Ontology in 2017.
Abstract readReview
In one paragraph
Review in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 416 papers, 4 of them syntheses that pooled it.
0numbers the graph read from it
0cells of the map it votes in
416citing papers in PubMed, 4 pooled it
–field-weighted citation impact
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
416 citing papers in PubMed, 4 syntheses or guidelines pooled it.
- Matching heterogeneous cohorts by projected principal components reveals two novel Alzheimer's disease-associated genes in the Hispanic population.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2026Pooled it
- A critical assessment of Traditional Chinese Medicine databases as a source for drug discovery.Frontiers in pharmacology · 2024Pooled it
- Inherited metabolic disorders in adults: systematic review on patient characteristics and diagnostic yield of broad sequencing techniques (exome and genome sequencing).Frontiers in neurology · 2023Pooled it
- Curation and expansion of Human Phenotype Ontology for defined groups of inborn errors of immunity.The Journal of allergy and clinical immunology · 2022Pooled it
- Article
- The genotypic and phenotypic landscape of PDHA1-related pyruvate dehydrogenase complex deficiency.Brain : a journal of neurology · 2026Article
- CRONDEX: a web-based platform for exploring links between chromatin-related genes and neurodevelopmental disorders.Clinical epigenetics · 2026Article
- CNV-Hub: an integrated web-based platform for CNV classification and interpretation using multi-algorithm consensus.NAR genomics and bioinformatics · 2026Article
- Gene List Selection Matters: Missed Diagnoses in Prenatal Exome Sequencing-PanelApp R21 and HPO-Driven Versus OMIM-Based Gene Lists.Prenatal diagnosis · 2026Article
- Gene Portals: A Framework for Integrating Clinical, Functional, and Structural Evidence into Rare Disease Variant Classification.medRxiv : the preprint server for health sciences · 2026Article
- GA4GH phenopacket-driven characterization of genotype-phenotype correlations in Mendelian disorders.American journal of human genetics · 2026Article
- TWAS atlas 2.0: an updated data resource for transcriptome-wide association studies.Nucleic acids research · 2026Article
- Gene4Denovo2: an updated platform for human de novo mutations discovery and interpretation.Nucleic acids research · 2026Article
- A multimodal vision knowledge graph of cardiovascular disease.Nature cardiovascular research · 2026Article
- Genetic and clinical aspects of TMC1-related hearing loss in Iranian families: identification of two novel variants.Molecular biology reports · 2025Article
- Genetic Characterization of 128 Chinese Individuals with Neurodevelopmental Disorders via Whole-Exome Sequencing.Developmental neuroscience · 2025Article
- Matching Heterogeneous Cohorts by Projected Principal Components Reveals Two Novel Alzheimer's Disease-Associated Genes in the Hispanic Population.medRxiv : the preprint server for health sciences · 2025Article
- Diagnostic Yield of Exome Sequencing for Pregnancies With and Without Fetal Anomalies and for Stillbirth.Prenatal diagnosis · 2025Article
- Improving computational drug repositioning through multi-source disease similarity networks.Scientific reports · 2025Article
- Phenotypic similarity of adverse drug reactions and disease phenotypes is a bridge to mechanistic discovery.npj drug discovery · 2025Article
356 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
59 authors.
Sebastian KöhlerInstitute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany dr.sebastian.koehler@gmail.com.
Nicole A VasilevskyLibrary and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.ORCID 0000-0001-5208-3432
Mark EngelstadLibrary and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
Erin FosterLibrary and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
Julie McMurryLibrary and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
Ségolène AyméInstitut du Cerveau et de la Moelle épinière-ICM, CNRS UMR 7225-Inserm U 1127-UPMC-P6 UMR S 1127, Hôpital Pitié-Salpêtrière, 47, bd de l'Hôpital, 75013 Paris, France.
Gareth BaynamWestern Australian Register of Developmental Anomalies and Genetic Services of Western Australia, King Edward Memorial Hospital Department of Health, Government of Western Australia, Perth, WA 6008, Australia.
Susan M BelloThe Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA.
Cornelius F BoerkoelImagenetics Research, Sanford Health, PO Box 5039, Route 5001, Sioux Falls, SD 57117-5039, USA.
Kym M BoycottChildren's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada.
Michael BrudnoDepartment of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada.
Orion J BuskeDepartment of Computer Science, University of Toronto, Toronto, ON M5S 2E4, Canada Centre for Computational Medicine, Hospital for Sick Children, Toronto, ON M5G 1L7, Canada.
Patrick F ChinneryDepartment of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.
Valentina CiprianiUCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.
Laureen E ConnellCold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
Hugh J S DawkinsOffice of Population Health Genomics, Public Health Division, Health Department of Western Australia, 189 Royal Street, Perth, WA, 6004 Australia.
Laura E DeMareCold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
Andrew D DevereauGenomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
Bert B A de VriesDepartment of Human Genetics, Radboud University, University Medical Centre, Nijmegen, The Netherlands.
Helen V FirthWellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
Kathleen FresonDepartment of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium.
Daniel GreeneDepartment of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.
Ada HamoshMcKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Ingo HelbigDivision of Neurology, The Children's Hospital of Philadelphia, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA.
Courtney HumCentre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1H3, Canada.
Johanna A JähnDepartment of Neuropediatrics, University Medical Center Schleswig-Holstein (UKSH), Kiel, Germany.
Roger JamesNIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.
Roland KrauseLuxembourgCentre for Systems Biomedicine, University of Luxembourg, 7, avenue des Hauts-Fourneaux, L-4362 Esch-sur-Alzette, Luxembourg.
Stanley J F LaulederkindHuman and Molecular Genetics Center, Medical College of Wisconsin, USA.ORCID 0000-0001-5356-4174
Hanns LochmüllerJohn Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
Gholson J LyonStanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, New York, NY 11797, USA.
Soichi OgishimaDept of Bioclinical Informatics, Tohoku Medical Megabank Organization, Tohoku University, Tohoku Medical Megabank Organization Bldg 7F room #741,736, Seiryo 2-1, Aoba-ku, Sendai Miyagi 980-8573 Japan.
Annie OlryOrphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France.
Willem H OuwehandMedical Research Council Biostatistics Unit, Cambridge Institute of Public Health, Cambridge Biomedical Campus, Cambridge, UK.
Nikolas PontikosUCL Institute of Ophthalmology, Department of Ocular Biology and Therapeutics, 11-43 Bath Street, London EC1V 9EL, UK.
Ana RathOrphanet-INSERM, US14, Plateforme Maladies Rares, 96 rue Didot, 75014 Paris, France.
Franz SchaeferDivision of Pediatric Nephrology and KFH Children's Kidney Center, Center for Pediatrics and Adolescent Medicine, 69120 Heidelberg, Germany.
Richard H ScottGenomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
Michael SegalSimulConsult Inc., 27 Crafts Road, Chestnut Hill, MA 02467, USA.
Panagiotis I SergouniotisManchester Royal Eye Hospital & University of Manchester, Manchester M13 9WL, UK.
Richard SeverCold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, USA.
Cynthia L SmithThe Jackson Laboratory, 600 Main St, Bar Harbor, ME 04609, USA.
Volker StraubJohn Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
Rachel ThompsonJohn Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
Catherine TurnerJohn Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, UK.
Ernest TurroDepartment of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.
Marijcke W M VeltmanNIHR Rare Diseases Translational Research Collaboration, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.
Tom VulliamyBlizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London E1 2AT, UK.
Jing YuNuffield Department of Clinical Neurosciences, University of Oxford, Level 6, West Wing, John Radcliffe Hospital, Oxford OX3 9DU, UK.
Julie von ZiegenweidtDepartment of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Long Road, Cambridge CB2 0PT, UK.
Andreas ZanklDiscipline of Genetic Medicine, Sydney Medical School, The University of Sydney, Australia.
Stephan ZüchnerJD McDonald Department of Human Genetics and Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA.
Tomasz ZemojtelInstitute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
Julius O B JacobsenGenomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
Tudor GrozaGarvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.
Damian SmedleyGenomics England, Queen Mary University of London, Dawson Hall, Charterhouse Square, London EC1M 6BQ, UK.
Christopher J MungallEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA.
Melissa HaendelLibrary and Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, OR 97239, USA.
Peter N RobinsonThe Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA peter.robinson@jax.org.
Funding
Mouse Genome DatabaseU41HG000330 · NHGRI · JACKSON LABORATORY · PI BLAKE, JUDITH A, BULT, CAROL J · 2011 to 2020
$45.5MThe Monarch Initiative: Linking Diseases to Model Organism ResourcesR24OD011883 · OD · UNIV OF NORTH CAROLINA CHAPEL HILL · PI HAENDEL, MELISSA A, MUNGALL, CHRISTOPHER J · 2012 to 2024
$16.0MAn Intelligent Concept Agent for Assisting with the Application of MetadataU01HG009453 · NHGRI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI MUNGALL, CHRISTOPHER J · 2016 to 2018
$1.7MVASCULAR REFLEX MECHANISMS IN EXERCISE AND HEART FAILUREF32HL009012 · NHLBI · PENNSYLVANIA STATE UNIV HERSHEY MED CTR · PI SILBER, DAVID H · 1994 to 1996
–British Heart Foundation RG/09/012/28096Department of Health RP-PG-0310-1002Medical Research Council G1002274Medical Research Council MC_UP_1501/2NHGRI NIH HHS U01 HG009453NHGRI NIH HHS U41 HG000330NIH HHS R24 OD011883
Abstract
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 Phenotype Ontology (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.
Indexed as
Biological OntologiesComputational BiologyGenomicsPhenotypeAlgorithmsGenetic Association StudiesHumansPrecision MedicineRare DiseasesSoftwareTranslational Research, Biomedical
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.