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.
  • Mungall, C. J., Washington, N. L., Nguyen-Xuan, J., Condit, C., Smedley, D., Köhler, S., … Haendel, M. A. (2015). Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery. Human Mutation, 36(10), 979–84.
  • 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., Kohler, S., Oellrich, A., Wang, K., Mungall, C., Lewis, S. E., … Köhler, S. (2013). Improved exome prioritization of disease genes through cross species phenotype comparison. Genome Research.
  • 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.
  • Bone, W. P., Washington, N. L., Buske, O. J., Adams, D. R., Davis, J., Draper, D., … Smedley, D. (2015). Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency. Genetics in Medicine, in press(August), 1–10.