Relevant Publications

Cite Mondo

  • Mondo: Unifying diseases for the world, by the world, Nicole A Vasilevsky, Nicolas A Matentzoglu, Sabrina Toro, Joe E Flack, Harshad Hegde, Deepak R Unni, Gioconda Alyea, Joanna S Amberger, Larry Babb, James P Balhoff, Taylor I Bingaman, Gully A Burns, Tiffany J Callahan, Leigh C Carmody, Lauren E Chan, George S Chang, Michel Dumontier, Laura E Failla, May J Flowers, H A Garrett, Dylan Gration, Tudor Groza, Marc Hanauer, Nomi L Harris, Ingo Helbig, Jason A Hilton, Daniel S Himmelstein, Charles T Hoyt, Megan S Kane, Sebastian Köhler, David Lagorce, Martin Larralde, Antonia Lock, Irene López Santiago, Donna R Maglott, Adriana J Malheiro, Birgit HM Meldal, Julie A McMurry, Moni Munoz-Torres, Tristan H Nelson, David Ochoa, Tudor I Oprea, David Osumi-Sutherland, Helen Parkinson, Zoë M Pendlington, Ana Rath, Heidi L Rehm, Lyubov Remennik, Erin R Riggs, Paola Roncaglia, Justyne E Ross, Marion F Shadbolt, Kent A Shefchek, Morgan N Similuk, Nicholas Sioutos, Rachel Sparks, Ray Stefancsik, Ralf Stephan, Doron Stupp, Jagadish Chandrabose Sundaramurthi, Imke Tammen, Courtney L Thaxton, Eloise Valasek, Alex H Wagner, Danielle Welter, Patricia L Whetzel, Lori L Whiteman, Valerie Wood, Colleen H Xu, Andreas Zankl, Xingmin A Zhang, Christopher G Chute, Peter N Robinson, Christopher J Mungall, Ada Hamosh, Melissa A Haendel, medRxiv 2022.04.13.22273750; doi: https://doi.org/10.1101/2022.04.13.22273750

Manuscripts

  • The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species. Tim E Putman, Kevin Schaper, Nicolas Matentzoglu, Vincent P Rubinetti, Faisal S Alquaddoomi, Corey Cox, J Harry Caufield, Glass Elsarboukh, Sarah Gehrke, Harshad Hegde, Justin T Reese, Ian Braun, Richard M Bruskiewich, Luca Cappelletti, Seth Carbon, Anita R Caron, Lauren E Chan, Christopher G Chute, Katherina G Cortes, Vinícius De Souza, Tommaso Fontana, Nomi L Harris, Emily L Hartley, Eric Hurwitz, Julius O B Jacobsen, Madan Krishnamurthy, Bryan J Laraway, James A McLaughlin, Julie A McMurry, Sierra A T Moxon, Kathleen R Mullen, Shawn T O’Neil, Kent A Shefchek, Ray Stefancsik, Sabrina Toro, Nicole A Vasilevsky, Ramona L Walls, Patricia L Whetzel, David Osumi-Sutherland, Damian Smedley, Peter N Robinson, Christopher J Mungall, Melissa A Haendel, Monica C Munoz-Torres. (2024) Nucleic Acids Research. 52(D1):D938-D949. doi: 10.1093/nar/gkad1082.
  • Axiomatization and refactoring of the ‘chromosomal disorder’ branch of Mondo. Sabrina Toro, Nicole Vasilevsky, Nicolas Matentzoglu, Peter N. Robinson, & Christopher Mungall. (2022) Zenodo. https://doi.org/10.5281/zenodo.6612070
  • New view of the Mondo Disease Ontology High-level Classification According to Harrison’s Principles of Internal Medicine textbook. Sabrina Toro, Ada Hamosh, Nico Matentzoglu, Monica Munoz-Torres, Lauren Chan, Courtney Thaxton, Gioconda Alyea, Melissa Haendel, Chris Mungall, Peter N Robinson, & Nicole Vasilevsky. (2021) Zenodo. https://doi.org/10.5281/zenodo.5273598
  • How many rare diseases are there? Melissa Haendel, Nicole Vasilevsky, Deepak Unni, Cristian Bologa, Nomi Harris, Heidi Rehm, Ada Hamosh, Gareth Baynam, Tudor Groza, Julie McMurry, Hugh Dawkins, Ana Rath, Courtney Thaxon, Giovanni Bocci, Marcin P. Joachimiak, Sebastian Köhler, Peter N. Robinson, Chris Mungall & Tudor I. Oprea. (2019) Nature Reviews Drug Discovery.
  • The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. Kent A Shefchek, Nomi L Harris, Michael Gargano, Nicolas Matentzoglu, Deepak Unni, Matthew Brush, Daniel Keith, Tom Conlin, Nicole Vasilevsky, Xingmin Aaron Zhang, James P Balhoff, Larry Babb, Susan M Bello, Hannah Blau, Yvonne Bradford, Seth Carbon, Leigh Carmody, Lauren E Chan, Valentina Cipriani, Alayne Cuzick, Maria Della Rocca, Nathan Dunn, Shahim Essaid, Petra Fey, Chris Grove, Jean-Phillipe Gourdine, Ada Hamosh, Midori Harris, Ingo Helbig, Maureen Hoatlin, Marcin Joachimiak, Simon Jupp, Kenneth B Lett, Suzanna E Lewis, Craig McNamara, Zoë M Pendlington, Clare Pilgrim, Tim Putman, Vida Ravanmehr, Justin Reese, Erin Riggs, Sofia Robb, Paola Roncaglia, James Seager, Erik Segerdell, Morgan Similuk, Andrea L Storm, Courtney Thaxon, Anne Thessen, Julius O B Jacobsen, Julie A McMurry, Tudor Groza, Sebastian Köhler, Damian Smedley, Peter N Robinson, Christopher J Mungall, Melissa A Haendel, Monica C Munoz-Torres, David Osumi-Sutherland. (2020) Nucleic Acids Research, gkz997, https://doi.org/10.1093/nar/gkz997.
  • k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction. Christopher J. Mungall, Sebastian Koehler, Peter Robinson, Ian Holmes, Melissa Haendel. (2019) bioRxiv 048843; doi: https://doi.org/10.1101/048843
  • A Census of Disease Ontologies. Melissa A. Haendel, Julie A. McMurry, Rose Relevo, Christopher J. Mungall, Peter N. Robinson, and Christopher G. Chute (2018) Annual Review of Biomedical Data Science Vol. 1:305-331
  • The Monarch Initiative: An Integrative Data and Analytic Platform Connecting Phenotypes to Genotypes across Species. Christopher J. Mungall, Julie A. McMurry, Sebastian Köhler, 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 NguyenXuan, Kent Shefchek, Nicole Vasilevsky, Zhou Yuan, Nicole Washington, Harry Hochheiser, Tudor Groza, Damian Smedley, Peter N. Robinson, Melissa A. Haendel. (2017) Nucleic Acids Research 45 (D1): D712–22.

Relevant Publications

Blogs

Relevant Presentations

Analyses

Rare Disease analysis in Mondo: This analysis is intended to answer the question of ‘How many rare diseases are there?’ we analyzed terms in Mondo to get a total count of Rare Diseases as defined in Mondo Disease Ontology (Mondo).

Ontology Development Tools

  • Protege: An ontology development software application
  • Ontology Development Kit: A toolkit to initialize an OBO library repository and associated files.
  • ROBOT: ROBOT is a an tool for working with Open Biomedical Ontologies.