The Mondo Disease Ontology: Highlights from 2022
The Mondo Disease Ontology wouldn’t be what it is without our continuously growing Mondo community, for whom we are incredibly grateful. Our preprint on Mondo was published this year with almost 100 co-authors who have contributed to Mondo in various ways. This past year, new users and collaborators have joined our extensive community of experts, clinicians, researchers, and other users. We are very excited to welcome your help, support, and contributions.
Mondo Team Member Updates
The Mondo team is a collaborative effort between expert biocurators, semantic engineers, medical experts, and project managers, who were brought together to provide an integrated classification of disease entities.
We are thrilled to welcome a new Monarch team member and Mondo contributor: Katie Mullen. Katie recently joined the Translational and Integrative Sciences Lab at the University of Colorado (TISLab) as a veterinary informatics postdoctoral scholar. Katie is a burgeoning ontologist sharing her veterinary expertise to help us improve our modeling of non-human diseases in Mondo (more details below).
After 12 years with the TISLab, Nicole Vasilevsky will transition to a new role as Associate Director of Data Science at the Critical Path Institute starting on January 09, 2023. Nicole’s new position will allow her to continue to lead the Mondo curation efforts, albeit at a lower capacity. We thank you for your patience with any delays in addressing requests for changes to Mondo during this transition time. And we are sending Nicole huge congratulations on the new role!
Mondo development highlights
Focus on ‘non-human animal diseases’
Veterinary data offers a wealth of information that can be leveraged to understand better underlying mechanisms of disease processes in animals and how they apply to human health. Most of this data is currently collected in an unstructured format, making applying bioinformatics applications and analyses difficult. A recent goal of the Monarch Initiative is to standardize and harmonize this existing data (see our recent blog post about our Comparative Veterinary Informatics Workshop). Towards this end, the Mondo team is restructuring the ‘non-human animal’ branch in Mondo. We reclassified human and non-human animal diseases into separate branches in the ontology. We included information about the species affected by the disease (e.g., feline) and the analogous human disease (feline leukemia is analogous to human leukemia). These semantics will not only ensure a similar classification of diseases in human and non-human animals but also facilitate cross-species disease data comparison. We are expanding the representation of these non-human diseases in Mondo by adding new terms, including neoplasm terms for additional species (such as dog, cat, horse, cattle, etc.). We plan to add other diseases, working in collaboration with veterinary experts. Sabrina Toro highlighted related work in a talk at the International Conference on Biomedical Ontology (ICBO) in Ann Arbor this fall, focused on the complementary ontology, Vertebrate Breed Ontology (see the conference paper here) and will present this work at the upcoming Rocky Bioinformatics Conference.
Improved Classifications in Mondo
Mondo is iteratively developed and continually updated. We finalized improvements to our upper-level classifications in Mondo, which can be viewed in the Ontology Lookup Service and is pictured below. In addition, significant effort was made towards obsoleting classes deemed out of scope for Mondo. We created detailed descriptions documenting our reasoning for excluding specific terms, whether it is because they do not represent actual diseases or represent grouping terms that are out of scope in Mondo.
We added 850 new terms to Mondo this year and are grateful for all the new terms requests from our broad user community. We want to highlight some specific contributions:
- Many thanks to the ClinGen Expert Working Groups for their continued improvement of Mondo by adding new terms and recommended reclassifications.
- We are grateful to pulmonary experts Matthias Griese and Christina Rapp, who helped add approximately 60 new subclasses of lung disease to Mondo, including several recently described new monogenic disorders.
- We welcome our new user, Lewis Fermaglich, from the FDA Office of Orphan Products Development, to the Mondo community, who is helping extend the representation of terms needed for annotations of rare diseases.
- We have improved the classification of classes representing susceptibility to specific diseases, represented in the ‘inherited disease susceptibility’ branch in Mondo.
- Sabrina Toro finalized the effort to reclassify and axiomatize chromosomal abnormalities in Mondo, which aids in annotating and structuring Down Syndrome data in the INCLUDE Data Hub.
- Our direct collaboration with Ada Hamosh and the OMIM team has included entertaining discussions and led to invaluable improvements and alignments with the OMIM Mendialn Disease resource.
- Lastly, we’d like to acknowledge Megan Kane and Donna Maglott from the MedGen team for their meticulous and detailed reporting of issues, including database cross-reference alignments.
All of these efforts and the other user-reported issues have contributed significantly to the improvement of the resource. Community contributions are what make Mondo what it is today.
Synchronization with External Resources
The technical team revamped our ingest pipeline that will keep the external sources harmonized in Mondo and up to date, with an initial focus on synchronizing with OMIM, Orphanet, Disease Ontology, and the NCI Thesaurus. Work is underway to update our mappings to external sources in Mondo, with a significant push to update the ICD10 mapping to Mondo terms.
Community Opportunities
We aim to host community workshops in the new year addressing specific topic areas and branches in Mondo. Several areas are on our radar, including agreeing upon disease naming conventions amongst the community, improving the classification of infectious diseases in Mondo, addressing psychiatric disease classification, and others. Please let us know if there is a specific topic area of interest to you. Monarch Project Manager Sarah Gehrke and curator Sabrina Toro coordinate the workshops. Please ensure you are signed up for our mailing list to hear about and join upcoming workshops. As always, please continue to add any issues and requests on our GitHub tracker, and we’ll respond as quickly as possible.
Past Workshops + presentations in 2022
- Using the Mondo Disease Ontology to Standardize Rare Disease Nomenclature, (September 21, 2022, FDA Office of Orphan Products Development, Virtual.
- Using the Mondo Disease Ontology for Disease Data Curation (June 08, 2022): https://mondo.monarchinitiative.org/pages/workshop/#june-2022
- 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
Preprint
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
Contribute to Mondo
GitHub issue tracker: Submitting a GitHub ticket is the best way to inform the Mondo team about issues you’ve encountered, requests for new terms or synonyms, or suggestions.
Community calls: There are Mondo curator calls every Thursday at 10 am P.T./1 pm E.T., and all are welcome to join to listen in or bring up any issues. Contact Sabrina Toro (sabrina@tislab.org) for an invitation.
Resources
Mondo website: https://mondo.monarchinitiative.org/
Mondo GitHub: https://github.com/monarch-initiative/mondo
Mondo Discussion Board: https://github.com/monarch-initiative/mondo/discussions
Mondo users mailing list: mondo-users-subscribe@googlegroups.com (subscribe to the mailing list to get updates about releases, obsoletion candidates, and pet pictures)
Generic slide deck on the Mondo Disease Ontology: Generic_Mondo_Slides. This is available for reuse with attribution.
Contact: Nicole Vasilevsky, nicole@tislab.org or Sabrina Toro, sabrina@tislab.org
Funding
Mondo is generously supported by an NIH Office of the Director Grant #5R24OD011883 and NIH-UDP: HHSN268201350036C, HHSN268201400093P, NCI/Leidos #15X143, and Phenomics First, NIH-NHGRI: 1 RM1 HG010860–01.
