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
- Axiomatization and refactoring of the ‘chromosomal disorder’ branch of Mondo. Toro, Sabrina, Vasilevsky, Nicole, Matentzoglu, Nicolas, Robinson, Peter N., & Mungall, Christopher. (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. 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. Nature Reviews Drug Discovery, 05 November 2019
- 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, et al. 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. Mungall C, et al. (2019) 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. Mungall, Christopher J., Julie A. McMurry, Sebastian Köhler, James P. Balhoff, Charles Borromeo, Matthew Brush, Seth Carbon, et al. 2017. Nucleic Acids Research 45 (D1): D712–22.
Relevant Publications
- Response to Biesecker et al. By Ada Hamosh et. al (2021)
- Disease Naming in Mondo
Blogs
- Mondo Disease Ontology Highlights from 2021 By Sabrina Toro and Nicole Vasilevsky - Published December 01, 2021, Monarch Initiative
- The Mondo ‘Cat’-a-log and Mondo Highlights from 2020 by Nicole Vasilevsky - Published December 18, 2020, Monarch Intiative
- New release of Mondo Disease Ontology - Published June 13, 2019, Monarch Initiative
- Monkeying around with OWL: Musings on building and using ontologies. Posts by Chris Mungall
Relevant Presentations
- Standardizing Rare Disease Data Collection: It Takes an (Ontology) Village. Vasilevsky N. [Keynote address]. 4th U.S. Semantic Technologies Symposium, East Lansing, MI, USA, September 29, 2022.
- Using the Mondo Disease Ontology to Standardize Rare Disease Nomenclature. Nicole Vasilevsky. FDA Office of Orphan Products Development, Virtual, September 21, 2022
- Standardization of Cancer Terminology in the Mondo Disease Ontology. Nicole Vasilevsky, Nico Matentzoglu, Sabrina Toro, Joe Flack, Ada Hamosh, Peter Robinson, Melissa Haendel, Chris Mungall. [Poster presentation] Cancer Genomics Consortium 2022 Annual Meeting. Virtual. August 01, 2022.
- Mondo Disease Ontology: Building a Community-Based Disease Resource. Nicole Vasilevsky, Sabrina Toro, Nico A. Matentzoglu, Dazhi Jiao, Nomi L. Harris, Melissa A. Haendel, Peter N. Robinson, Chris Mungall. [Conference session]. AMIA 2022 Informatics Summit, Chicago, IL,, USA. March 23, 2022
- The Mondo Disease Ontology. Vasilevsky, NA. NHGRI Centers For Excellence In Genomic Science, Virtual, October 15, 2021
- Reclassification and Axiomatization of Chromosomal Anomaly Diseases in the Mondo Ontology. Sabrina Toro, Nico Matentzoglu, Melissa Haendel, Chris Mungall, Nicole Vasilevsky. [Poster presentation], Biocuration 2021, October 05, 2021
- Reclassification of Infectious Disease in the Mondo Disease Ontology. Nicole Vasilevsky, Sabrina Toro, Nicolas Matentzoglu, Dazhi Jiao, Melissa Haendel, Peter Robinson and Chris Mungall. [Flash talk and Poster presentation], International Conference on Biomedical Ontology (ICBO), September 17, 2021.
- Mondo Disease Ontology: harmonizing disease concepts across the world. Nicole Vasilevsky, Nico Matentzoglu, Dazhi Jiao, Melissa Haendel, Peter Robinson, Chris Mungall. (2021) [Poster presentation and Lightning Talk] Curating the Clinical Genome (virtual). May 12, 2021. Recording here.
- Aligning Design Patterns Across Multiple Ontologies in the Life Sciences by Chris Mungall, Keynote at 11th Workshop on Ontology Design and Patterns - WOP2020. Recording here. Meeting info here.
- How Many Rare Diseases Are There? How Good Identifier Provisioning Can Help Answer This Question by Melissa Haendel, PIDapalooza 2021.
- Modeling and making computable the complex interplay between environmental and genetic causes and phenotypic outcomes by Melissa Haendel. Kohane Journal Club 2021.
- Mondo: The world’s disease concepts, unified by Nicole Vasilvsky, ClinGen Biocurators Working Group meeting, October 22, 2020.
- Mondo Disease Ontology: harmonizing disease concepts across the world by Nicole Vasilevsky, Shahim Essaid, Nico Matentzoglu, Nomi L. Harris, Melissa Haendel, Peter Robinson, Christopher J. Mungall. Poster presentation at International Conference on Biomedical Ontology (ICBO), Virtual conference. Poster here
- Mondo: a unified disease resource connecting clinical and translational research by Chris Mungall, Pistoia Alliance, July 2020. Recording here
- Mondo: The world’s disease concepts, unified by Chris Mungall and Nicole Vasilevsky, GAG4H Meeting, June 18, 2020. Recording here
- Semantic integration across species for rare disease diagnostics, presentation by Melissa Haendel, Michigan CTSA, 2019.
- Mondo Disease Ontology: harmonizing disease concepts around the world, poster presentation by Nicole Vasilevsky, Childhood Cancer Data Initiative Symposium, July 2019.
- Introduction to Mondo, presentation by Chris Mungall, VICC Disease Harmonization call, May 2019.
- A comprehensive disease ontology for human disease curation, presentation by Nicole Vasilevsky at the Biocuration 2018 conference
- OBO Tools and Workflows, presentation by Chris Mungall at ICBO 2017
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.