The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.

Algorithms Animals Biological Ontologies Computational Biology / methods Databases, Genetic Exome Genetic Association Studies Genetic Variation Genomics Genotype Humans Internet Phenotype Software Translational Research, Biomedical User-Computer Interface

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
08 01 2020
Historique:
accepted: 14 10 2019
revised: 09 10 2019
received: 20 09 2019
pubmed: 9 11 2019
medline: 28 5 2020
entrez: 9 11 2019
Statut: ppublish

Résumé

In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may not match known diseases, candidate variants may be in genes that haven't been characterized, research organisms may not recapitulate human or veterinary diseases, environmental factors affecting disease outcomes are unknown or undocumented, and many resources must be queried to find potentially significant phenotypic associations. The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search. We develop many widely adopted ontologies that together enable sophisticated computational analysis, mechanistic discovery and diagnostics of Mendelian diseases. Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research. Launched in 2015, Monarch has grown with regards to data (new organisms, more sources, better modeling); new API and standards; ontologies (new Mondo unified disease ontology, improvements to ontologies such as HPO and uPheno); user interface (a redesigned website); and community development. Monarch data, algorithms and tools are being used and extended by resources such as GA4GH and NCATS Translator, among others, to aid mechanistic discovery and diagnostics.

Identifiants

DOI: 10.1093/nar/gkz997 PMID: 31701156 PMC: PMC7056945
pubmed: 31701156
pii: 5614574
doi: 10.1093/nar/gkz997
pmc: PMC7056945
doi:

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

D704-D715

Subventions

Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/I000488/1
Pays : United Kingdom
Organisme : NHGRI NIH HHS
ID : U41 HG000330
Pays : United States
Organisme : NIH HHS
ID : R24 OD011883
Pays : United States

Informations de copyright

© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Auteurs

Kent A Shefchek (KA)

Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA.

Nomi L Harris (NL)

Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA.

Michael Gargano (M)

The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA.

Nicolas Matentzoglu (N)

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Deepak Unni (D)

Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA.

Matthew Brush (M)

Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA.

Daniel Keith (D)

Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA.

Tom Conlin (T)

Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA.

Nicole Vasilevsky (N)

Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA.

Xingmin Aaron Zhang (XA)

The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA.

James P Balhoff (JP)

Renaissance Computing Institute at UNC, Chapel Hill, NC 27517, USA.

Larry Babb (L)

Broad Institute, Cambridge, MA 02142, USA.

Susan M Bello (SM)

The Jackson Laboratory, Bar Harbor, ME 04609, USA.

Hannah Blau (H)

The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA.

Yvonne Bradford (Y)

Institute of Neuroscience, University of Oregon, Eugene, OR 97401, USA.

Seth Carbon (S)

Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA.

Leigh Carmody (L)

The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA.

Lauren E Chan (LE)

College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA.

Valentina Cipriani (V)

William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.

Alayne Cuzick (A)

Rothamsted Research, Harpenden AL5 2JQ, UK.

Maria Della Rocca (M)

Office of Rare Diseases Research (ORDR), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD 20892, USA.

Nathan Dunn (N)

Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA.

Shahim Essaid (S)

Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA.

Petra Fey (P)

dictyBase, Center for Genetic Medicine, Northwestern University, Chicago, IL 60611, USA.

Chris Grove (C)

California Institute of Technology, Pasadena, CA 91125, USA.

Jean-Phillipe Gourdine (JP)

Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA.

Ada Hamosh (A)

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.

Midori Harris (M)

University of Cambridge, Cambridge CB2 1TN, UK.

Ingo Helbig (I)

Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.
Department of Neuropediatrics, Christian-Albrechts-University of Kiel, 24105 Kiel, Germany.
Department of Neurology, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA 19104, USA.

Maureen Hoatlin (M)

Department of Biochemistry and Molecular Biology, Oregon Health & Science University, Portland, OR 97239, USA.

Marcin Joachimiak (M)

Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA.

Simon Jupp (S)

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Kenneth B Lett (KB)

Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA.

Suzanna E Lewis (SE)

Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA.

Craig McNamara (C)

Pryzm Health, 4215 Queensland, Australia.

Zoë M Pendlington (ZM)

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

Clare Pilgrim (C)

University of Cambridge, Cambridge CB2 1TN, UK.

Tim Putman (T)

Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA.

Vida Ravanmehr (V)

The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA.

Justin Reese (J)

Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA.

Erin Riggs (E)

Autism & Developmental Medicine Institute, Geisinger, Danville, PA 17837, USA.

Sofia Robb (S)

Stowers Institute for Medical Research, Kansas City, MO 64110, USA.

Paola Roncaglia (P)

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

James Seager (J)

Rothamsted Research, Harpenden AL5 2JQ, UK.

Erik Segerdell (E)

Xenbase, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA.

Morgan Similuk (M)

National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Andrea L Storm (AL)

Office of Rare Diseases Research (ORDR), National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Bethesda, MD 20892, USA.

Courtney Thaxon (C)

University of North Carolina Medical School, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA.

Anne Thessen (A)

Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA.

Julius O B Jacobsen (JOB)

William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.

Julie A McMurry (JA)

College of Public Health and Human Sciences, Oregon State University, Corvallis, OR 97331, USA.

Tudor Groza (T)

Pryzm Health, 4215 Queensland, Australia.

Sebastian Köhler (S)

Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.

Damian Smedley (D)

William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.

Peter N Robinson (PN)

The Jackson Laboratory For Genomic Medicine, Farmington, CT 06032, USA.

Christopher J Mungall (CJ)

Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94710, USA.

Melissa A Haendel (MA)

Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA.
Oregon Clinical and Translational Research Institute, Oregon Health & Science University, Portland, OR 97239, USA.

Monica C Munoz-Torres (MC)

Center for Genome Research and Biocomputing, Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR 97331, USA.

David Osumi-Sutherland (D)

European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Algorithmes › The Monarch Initiative in 2019: an integrative...
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questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Exome › The Monarch Initiative in 2019: an integrative...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Études d'associations génétiques › The Monarch Initiative in 2019: an integrative...
questionsmedicales.fr › Phénomènes génétiques › Variation génétique › The Monarch Initiative in 2019: an integrative...
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