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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.

Type Journal
ISBN 1362-4962 (Electronic) 0305-1048 (Linking)
Authors 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.; Keith, D.; Laraway, B.; Lewis, S. E.; NguyenXuan, J.; Shefchek, K.; Vasilevsky, N.; Yuan, Z.; Washington, N.; Hochheiser, H.; Groza, T.; Smedley, D.; Robinson, P. N.; Haendel, M. A.
Responsible Garvan Author (missing name)
Publisher Name NUCLEIC ACIDS RESEARCH
Published Date 2017-01-04
Published Volume 45
Published Issue D1
Published Pages D712-D722
Status Published in-print
DOI 10.1093/nar/gkw1128
URL link to publisher's version https://www.ncbi.nlm.nih.gov/pubmed/27899636
OpenAccess link to author's accepted manuscript version https://publications.gimr.garvan.org.au/open-access/14277