The Monarch Initiative: An integrative data and analytic platform connecting phenotypes to genotypes across species

Christopher J. Mungall; Julie A. McMurry; Sebastian Kohler; James P. Balhoff; Charles Borromeo; Matthew Brush; Seth Carbon; Tom Conlin; Nathan Dunn; Mark Engelstad; Erin Foster; J. P. Gourdine; Julius O.B. Jacobsen; Dan Keith; Bryan Laraway; Suzanna E. Lewis; Jeremy Nguyen Xuan; Kent Shefchek; Nicole Vasilevsky; Zhou Yuan; Nicole Washington; Harry Hochheiser; Tudor Groza; Damian Smedley; Peter N. Robinson; Melissa A. Haendel

doi:10.1093/nar/gkw1128

The Monarch Initiative: An integrative data and analytic platform connecting phenotypes to genotypes across species

Christopher J. Mungall, Julie A. McMurry, Sebastian Kohler, James P. Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, Tom Conlin, Nathan Dunn, Mark Engelstad, Erin Foster, J. P. Gourdine, Julius O.B. Jacobsen, Dan Keith, Bryan Laraway, Suzanna E. Lewis, Jeremy Nguyen Xuan, Kent Shefchek, Nicole Vasilevsky, Zhou YuanNicole Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N. Robinson, Melissa A. Haendel

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203 Scopus citations

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. Nonhuman 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.

Original language	English (US)
Pages (from-to)	D712-D722
Journal	Nucleic acids research
Volume	45
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkw1128
State	Published - Jan 1 2017

ASJC Scopus subject areas

Genetics

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Mungall, C. J., McMurry, J. A., Kohler, S., Balhoff, J. P., Borromeo, C., Brush, M., Carbon, S., Conlin, T., Dunn, N., Engelstad, M., Foster, E., Gourdine, J. P., Jacobsen, J. O. B., Keith, D., Laraway, B., Lewis, S. E., Xuan, J. N., Shefchek, K., Vasilevsky, N., ... Haendel, M. A. (2017). The Monarch Initiative: An integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic acids research, 45(D1), D712-D722. https://doi.org/10.1093/nar/gkw1128

Mungall, CJ, McMurry, JA, Kohler, S, Balhoff, JP, Borromeo, C, Brush, M, Carbon, S, Conlin, T, Dunn, N, Engelstad, M, Foster, E, Gourdine, JP, Jacobsen, JOB, Keith, D, Laraway, B, Lewis, SE, Xuan, JN, Shefchek, K, Vasilevsky, N, Yuan, Z, Washington, N, Hochheiser, H, Groza, T, Smedley, D, Robinson, PN & Haendel, MA 2017, 'The Monarch Initiative: An integrative data and analytic platform connecting phenotypes to genotypes across species', Nucleic acids research, vol. 45, no. D1, pp. D712-D722. https://doi.org/10.1093/nar/gkw1128

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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. Nonhuman 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.",

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The Monarch Initiative: An integrative data and analytic platform connecting phenotypes to genotypes across species

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