ArticleNucleic acids research2019
Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources.
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Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 367 papers, 6 of them syntheses that pooled it.
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367citing papers in PubMed, 6 pooled it
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Who cites it
367 citing papers in PubMed, 6 syntheses or guidelines pooled it.
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- A systematic review and functional bioinformatics analysis of genes associated with Crohn's disease identify more than 120 related genes.BMC genomics · 2022Pooled it
- A meta-analysis of prognostic biomarkers in neonatal retinal hemorrhage.International ophthalmology · 2022Pooled 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
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- Brain region-resolved pharmacodynamics of an antisense oligonucleotide targeting human SNCA 3'UTR in BAC-hSNCA rats.Translational neurodegeneration · 2026Article
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- PubMind: literature-based genetic variant extraction and functional annotation using large language models.Nature communications · 2026Article
- RankVar: machine learning-based variant ranking and reinterpretation for rare genetic diseases.Genome medicine · 2026Article
- Cell type-specific contextualisation of the human phenome: towards the systematic treatment of all rare diseases.Genome medicine · 2026Article
- From presence to provenance: Building substantive infrastructure for China's rare disease ecosystem.Intractable & rare diseases research · 2026Review
- Alkamines reveal a hidden layer of steroid and drug metabolism.bioRxiv : the preprint server for biology · 2026Article
- A dataset of patients with isolated and syndromic optic neuropathies linked to RTN4IP1 genetic variants.Scientific data · 2026Article
- European Reference Networks - a flagship activity of the EU in the field of rare and complex diseases: from 2017 to 2025.Orphanet journal of rare diseases · 2026Review
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- Architects of the Developing Brain: Cytoskeleton-Organizing Molecules in Neurodevelopmental Disorders.Cells · 2026Review
- AProceedings of the National Academy of Sciences of the United States of America · 2026Article
307 more citing papers are in PubMed but not listed here.
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Authors and funding
69 authors.
Sebastian KöhlerCharité Centrum für Therapieforschung, Charité-Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany.
Leigh CarmodyMonarch Initiative, monarchinitiative.org.
Nicole VasilevskyMonarch Initiative, monarchinitiative.org.
Julius O B JacobsenMonarch Initiative, monarchinitiative.org.
Daniel DanisMonarch Initiative, monarchinitiative.org.
Jean-Philippe GourdineMonarch Initiative, monarchinitiative.org.
Michael GarganoMonarch Initiative, monarchinitiative.org.
Nomi L HarrisMonarch Initiative, monarchinitiative.org.
Nicolas MatentzogluMonarch Initiative, monarchinitiative.org.
Julie A McMurryMonarch Initiative, monarchinitiative.org.
David Osumi-SutherlandMonarch Initiative, monarchinitiative.org.
Valentina CiprianiMonarch Initiative, monarchinitiative.org.
James P BalhoffMonarch Initiative, monarchinitiative.org.
Tom ConlinMonarch Initiative, monarchinitiative.org.
Hannah BlauMonarch Initiative, monarchinitiative.org.
Gareth BaynamWestern Australian Register of Developmental Anomalies and Genetic Services of Western Australia, Department of Health, Government of Western Australia, WA, Australia.
Richard PalmerSpatial Sciences, Department of Science and Engineering, Curtin University, Perth, WA, Australia.
Dylan GratianWestern Australian Register of Developmental Anomalies and Genetic Services of Western Australia, Department of Health, Government of Western Australia, WA, Australia.
Hugh DawkinsThe Office of Population Health Genomics, Department of Health, Government of Western Australia, Perth, WA, Australia.
Michael SegalSimulConsult, Chestnut Hill, MA, USA.
Anna C JansenNeurogenetics Research Group, Vrije Universiteit Brussel, Brussels, Belgium.
Ahmed MuazMonarch Initiative, monarchinitiative.org.
Willie H ChangCentre for Computational Medicine, Hospital for Sick Children and Department of Computer Science, University of Toronto, Toronto, Canada.
Jenna BergersonNational Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Stanley J F LaulederkindRat Genome Database, Department of Biomedical Engineering, Medical College of Wisconsin & Marquette University, 8701 Watertown Plank Road Milwaukee, WI 53226, USA.
Zafer YükselBioscientia GmbH, Ingelheim, Germany.
Sergi BeltranCNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain.
Alexandra F FreemanNational Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Panagiotis I SergouniotisUniversity of Manchester & Manchester Royal Eye Hospital, Manchester, UK.
Daniel DurkinThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Andrea L StormICF, Rockville, MD, USA.
Marc HanauerINSERM, US14-Orphanet, Plateforme Maladies Rares, 75014 Paris, France.
Michael BrudnoCentre for Computational Medicine, Hospital for Sick Children and Department of Computer Science, University of Toronto, Toronto, Canada.
Susan M BelloThe Jackson Laboratory, Bar Harbor, ME, USA.
Murat SincanSanford Imagenetics, Sanford Health, Sioux Falls, SD, USA.
Kayli RagethSanford Imagenetics, Sanford Health, Sioux Falls, SD, USA.
Matthew T WheelerCenter for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA.
Renske OegemaDepartment of Genetics, University Medical Center Utrecht, the Netherlands.
Halima LourghiINSERM, US14-Orphanet, Plateforme Maladies Rares, 75014 Paris, France.
Maria G Della RoccaICF, Rockville, MD, USA.
Rachel ThompsonInstitute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.
Francisco CastellanosThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
James PriestDepartment of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
Charlotte Cunningham-RundlesMount Sinai School of Medicine, New York, NY, USA.
Ayushi HegdeThe Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
Ruth C LoveringInstitute of Cardiovascular Science, University College London, UK.
Catherine HajekSanford Imagenetics, Sanford Health, Sioux Falls, SD, USA.
Annie OlryINSERM, US14-Orphanet, Plateforme Maladies Rares, 75014 Paris, France.
Luigi NotarangeloNational Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Morgan SimilukNational Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Xingmin A ZhangMonarch Initiative, monarchinitiative.org.
David Gómez-AndrésChild Neurology Unit. Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.
Hanns LochmüllerCNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, Barcelona 08028, Spain.
Hélène DollfusCentre for Rare Eye Diseases CARGO, SENSGENE FSMR Network, Strasbourg University Hospital, Strasbourg, France.
Sergio RosenzweigImmunology Service, Department of Laboratory Medicine, NIH Clinical Center, Bethesda, MD, USA.
Shruti MarwahaCenter for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, USA.
Ana RathINSERM, US14-Orphanet, Plateforme Maladies Rares, 75014 Paris, France.
Kathleen SullivanDepartment of Pediatrics, Division of Allergy Immunology, The Children's Hospital of Philadelphia, University of Pennsylvania Perelman School of Medicine, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA.
Cynthia SmithThe Jackson Laboratory, Bar Harbor, ME, USA.
Joshua D MilnerNational Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Dorothée LerouxCentre for Rare Eye Diseases CARGO, SENSGENE FSMR Network, Strasbourg University Hospital, Strasbourg, France.
Cornelius F BoerkoelSanford Imagenetics, Sanford Health, Sioux Falls, SD, USA.
Amy KlionNational Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Melody C CarterNational Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
Tudor GrozaMonarch Initiative, monarchinitiative.org.
Damian SmedleyMonarch Initiative, monarchinitiative.org.
Melissa A HaendelMonarch Initiative, monarchinitiative.org.
Chris MungallMonarch Initiative, monarchinitiative.org.
Peter N RobinsonMonarch Initiative, monarchinitiative.org.
Funding
Mouse Genome DatabaseU41HG000330 · NHGRI · JACKSON LABORATORY · PI BLAKE, JUDITH A, BULT, CAROL J · 2011 to 2020
$45.5MRegulation of IgA class switching in the intestinal mucosaP01AI061093 · NIAID · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI CASANOVA, JEAN-LAURENT · 2004 to 2021
$29.8MCD2H - The National COVID Cohort Collaborative (N3C) IDeA CTR CollaborationU24TR002306 · NCATS · UNIVERSITY OF COLORADO DENVER · PI CHUTE, CHRISTOPHER G, EICHMANN, DAVID A. · 2017 to 2021
$28.9MStudies of Inherited Causes of Fungal SusceptabilityZIAAI001122 · NIAID · NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES · PI ROSENZWEIG, SERGIO · 2010 to 2025
$26.0MEosinophils and Eosinophil Activation in the Pathogenesis of Human DiseaseZIAAI001130 · NIAID · NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES · PI KLION, AMY · 2010 to 2025
$22.5MThe 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
$16.0MWhat comes next? Engaging stakeholders in governance of participant data and relationships during the sunset of large genomic medicine research initiativesU01HG010218 · NHGRI · STANFORD UNIVERSITY · PI ASHLEY, EUAN A, BERNSTEIN, JONATHAN ADAM · 2018 to 2022
$6.3MBiomedical Data Translator Technical Feasibility Assessment and Architecture DesignOT3TR002019 · NCATS · JOHNS HOPKINS UNIVERSITY · PI CHUTE, CHRISTOPHER G, HAENDEL, MELISSA A · 2016 to 2019
$5.7MAn Intelligent Concept Agent for Assisting with the Application of MetadataU01HG009453 · NHGRI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI MUNGALL, CHRISTOPHER J · 2016 to 2018
$1.7MForums for Integrative PhenomicsU13CA221044 · NCI · UNIVERSITY OF COLORADO DENVER · PI HAENDEL, MELISSA A, ROBINSON, PETER NICHOLAS · 2017 to 2019
$223kMutation Analysis Of Selected Lymphoid Immune DisordersZIACL010304 · CLC · CLINICAL CENTER · PI ROSENZWEIG, SERGIO · 2009 to 2025
$0kBritish Heart Foundation RG/13/5/30112NCATS NIH HHS OT3 TR002019NCATS NIH HHS U24 TR002306NCI NIH HHS U13 CA221044NHGRI NIH HHS U01 HG009453NHGRI NIH HHS U01 HG010218NHGRI NIH HHS U41 HG000330NIAID NIH HHS P01 AI061093NIH HHS R24 OD011883
Abstract
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-phenotype-ontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.
Indexed as
Biological OntologiesKnowledge BasesComputational BiologyCongenital AbnormalitiesDatabases, GeneticGenetic Predisposition to DiseaseGenetic VariationHumansInternetPhenotypeRare DiseasesWhole Genome Sequencing
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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.