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. Monarch encompasses multiple components: interface, data, ontologies, software and algorithms. These are listed, with links, on this page.

Ontologies created or maintained by Monarch



Communication and internal docs for team members


  • Köhler S, Gargano M, Matentzoglu N, Carmody LC, Lewis-Smith D, Vasilevsky NA, Danis D, …, Yüksel Z, Helbig I, Mungall CJ, Haendel MA, Robinson PN. The Human Phenotype Ontology in 2021. Nucleic Acids Res. 2021 Jan 8;49(D1):D1207–D1217. PMCID: PMC7778952
  • Thessen AE, Walls RL, Vogt L, Singer J, Warren R, Buttigieg PL, Balhoff JP, Mungall CJ, McGuinness DL, Stucky BJ, Yoder MJ, Haendel MA. Transforming the study of organisms: Phenomic data models and knowledge bases. PLoS Comput Biol. 2020 Nov;16(11):e1008376. PMID: 33232313

  • Rubinstein YR, Robinson PN, Gahl WA, Avillach P, Baynam G, Cederroth H, Goodwin RM, Groft SC, Hansson MG, Harris NL, Huser V, Mascalzoni D, McMurry JA, Might M, Nellaker C, Mons B, Paltoo DN, Pevsner J, Posada M, Rockett-Frase AP, Roos M, Rubinstein TB, Taruscio D, van Enckevort E, Haendel MA. The case for open science: rare diseases. Jamia Open. Oxford University Press; 2020 Sep 11;

  • Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Rocca MD, Dunn N, Essaid S, Fey P, Grove C, Gourdine J-P, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. The Monarch Initiative in 2019: An integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 2019 Nov 8; PMID: 31701156
  • 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 (2018). Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. Oxford University Press; 2018;47(D1):D1018–D1027.
  • 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.
  • 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.