The Monarch Initiative 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.




Communication and Internal Docs


  • Mungall, C. J., McMurry, J. A., Köhler, S., Balhoff, J. P., Borromeo, C., Brush, M., … Haendel, M. A. (2016). The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.++ Nucleic Acids Research, gkw1128.
  • Haendel MA, McMurry JA, Relevo R, Mungall CJ, Robinson PN, Chute CG. A Census of Disease Ontologies. Annu Rev Biomed Data Sci [Internet]. Annual Reviews; 2018 Jul 20;1(1):305–331. Available from:
  • Vasilevsky NA, Foster ED, Engelstad ME, … Mungall C, Holm IA, Rageth K, Brownstein CA, Shefchek K, McMurry JA, Robinson PN, Köhler S, Haendel MA. Plain-language medical vocabulary for precision diagnosis. Nat Genet. 2018 Apr;50(4):474–476. PMCID: PMC6258202
  • Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine J-P, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Others. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. Oxford University Press; 2018;47(D1):D1018–D1027.
  • McMurry, J. A., Köhler, S., Washington, N. L., Balhoff, J. P., Borromeo, C., Brush, M., … Haendel, M. A. (2016). Navigating the Phenotype Frontier: The Monarch Initiative. Genetics, 203(4), 1491–5.
  • Robinson, P. N., Mungall, C. J., & Haendel, M. (2015). Capturing phenotypes for precision medicine. Molecular Case Studies, 1(1), a000372.
  • Mungall, C. J., Gkoutos, G., Smith, C., Haendel, M., Lewis, S., & Ashburner, M. (2010). Integrating phenotype ontologies across multiple species. Genome Biology, 11(1), R2.