title: The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.
abstract: The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype-phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms. Advanced informatics tools can identify phenotypically relevant disease models in research and diagnostic contexts. Large-scale integration of model organism and clinical research data can provide a breadth of knowledge not available from individual sources and can provide contextualization of data back to these sources. The Monarch Initiative (monarchinitiative.org) is a collaborative, open science effort that aims to semantically integrate genotype-phenotype data from many species and sources in order to support precision medicine, disease modeling, and mechanistic exploration. Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species.
authors.affiliation: Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Mungall
authors.affiliation: Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA.
authors.forename: Julie A
authors.initials: JA
authors.lastname: McMurry
authors.affiliation: Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Köhler
authors.affiliation: RTI International, Research Triangle Park, NC, 27709, USA.
authors.forename: James P
authors.initials: JP
authors.lastname: Balhoff
authors.affiliation: Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
authors.forename: Charles
authors.initials: C
authors.lastname: Borromeo
authors.affiliation: Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA.
authors.forename: Matthew
authors.initials: M
authors.lastname: Brush
authors.affiliation: Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
authors.forename: Seth
authors.initials: S
authors.lastname: Carbon
authors.affiliation: Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA.
authors.forename: Tom
authors.initials: T
authors.lastname: Conlin
authors.affiliation: Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
authors.forename: Nathan
authors.initials: N
authors.lastname: Dunn
authors.affiliation: Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Engelstad
authors.affiliation: Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA.
authors.forename: Erin
authors.initials: E
authors.lastname: Foster
authors.affiliation: Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA.
authors.forename: J P
authors.initials: JP
authors.lastname: Gourdine
authors.affiliation: William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
authors.forename: Julius O B
authors.initials: JO
authors.lastname: Jacobsen
authors.affiliation: Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA.
authors.forename: Dan
authors.initials: D
authors.lastname: Keith
authors.affiliation: Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA.
authors.forename: Bryan
authors.initials: B
authors.lastname: Laraway
authors.affiliation: Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
authors.forename: Suzanna E
authors.initials: SE
authors.lastname: Lewis
authors.affiliation: Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: NguyenXuan
authors.affiliation: Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA.
authors.forename: Kent
authors.initials: K
authors.lastname: Shefchek
authors.affiliation: Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA.
authors.forename: Nicole
authors.initials: N
authors.lastname: Vasilevsky
authors.affiliation: Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
authors.forename: Zhou
authors.initials: Z
authors.lastname: Yuan
authors.affiliation: Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
authors.forename: Nicole
authors.initials: N
authors.lastname: Washington
authors.affiliation: Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
authors.forename: Harry
authors.initials: H
authors.lastname: Hochheiser
authors.affiliation: Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
authors.forename: Tudor
authors.initials: T
authors.lastname: Groza
authors.affiliation: William Harvey Research Institute, Barts & The London School of Medicine & Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
authors.forename: Damian
authors.initials: D
authors.lastname: Smedley
authors.affiliation: Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.|The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032mUSA.
authors.forename: Peter N
authors.initials: PN
authors.lastname: Robinson
authors.affiliation: Department of Medical Informatics and Clinical Epidemiology and OHSU Library, Oregon Health & Science University, Portland, OR, 97239, USA Haendel@ohsu.edu.
authors.forename: Melissa A
authors.initials: MA
authors.lastname: Haendel
mesh_terms: D000818:Animals; D005075:Biological Evolution; D019295:Computational Biology / Q000379:methods; D066289:Data Curation; D030541:Databases, Genetic; D056726:Genetic Association Studies / Q000379:methods*; D005838:Genotype; D006801:Humans; D010641:Phenotype; D057386:Search Engine; D012984:Software; D013045:Species Specificity; D014584:User-Computer Interface; D064878:Web Browser