The Mondo Disease Ontology: Highlights from 2023
By Sabrina Toro, Nicole Vasilevsky, Sarah Gehrke, Monica Munoz-Torres
This year has once again demonstrated how wonderful our Mondo community is and how grateful we are for all the help and support we receive from users, experts, clinicians, and researchers. Every year, our community grows, and this past year is no exception!
Mondo Team Updates
We are delighted to welcome a new Mondo team member: Trish Whetzel! Trish is an Assistant Research Professor at the University of Colorado and a member of the Translational and Integrative Sciences Lab. She brings her expertise in ontology and software development, and we are excited for her to be part of the team. Welcome, Trish!
As we enter 2024, the Mondo team is restructuring to accommodate new roles and efforts.
- Dr. Nicole Vasilevsky’s leadership has been foundational to the success of the Mondo ontology and the thriving community around it. As she fully steps into her new role as Associate Director of Data Science role at the Critical Path Institute, Nicole steps down as our lead and will continue to contribute to Mondo as a curator.
- Dr. Sabrina Toro has been appointed as the new Lead Mondo Curator.
- On the technical side, Dr. Nicolas Matentzoglu is stepping back some of his responsibilities and Dr. Trish Whetzel will assume the role of Mondo Technical Lead in January of 2024.
- In the new year, Sarah Gehrke will support Mondo as project manager.
- Drs. Monica Munoz-Torres, Chris Mungall, and Melissa Haendel will continue in their strategic leadership roles on the project.
We appreciate your patience and understanding while we settle into this new structure and new roles. These changes will allow us to continue to grow and support the Mondo community well into the future.
Mondo development highlights
We made some major improvements to Mondo this year. Here are some of our accomplishments.
Mondo rare disease subset
Mondo has been at the center of rare disease data integration in the Monarch Initiative and many other resources. What is considered a “rare” disease varies between sources and geographical locations, making reconciliation between rare disease resources difficult. Mondo recognizes these impediments and differences of view. As a result, we worked with rare disease authorities such as NORD, GARD, and Orphanet to create the Mondo Rare Disease Subset. This subset represents diseases considered “rare,” according to the rare disease authorities. Metadata allows users to filter these diseases according to the rare disease authority of their choice. More details can be found in our Rare Disease Subset documentation and in our upcoming publication.
Mondo Strategic Refinement
Mondo was originally created by integrating disease terms from external disease terminologies. Some of these disease terms represented “grouping terms”, i.e., terms that do not represent actual diseases but instead have the purpose of grouping disease entities together. Mondo’s disease classification philosophy continues to be guided by clinical experts and mainly focuses on affected structures and systems.
Earlier this year, we identified that some of the grouping classes originally integrated into Mondo do not follow our current disease classification philosophy. For example, disease entities were grouped based on their “similarities” (e.g., ‘Duchenne and Becker muscular dystrophy’ — MONDO:0016899) or based on phenotypic features (e.g., ‘dysostosis with predominant craniofacial involvement’ — MONDO:0800085). These created incorrect inferences in the Mondo ontology: for example, the grouping term “connective tissue disease with eye involvement” (MONDO:0020272) classified ”Marfan syndrome” (MONDO:0007947) as an “eye disorder.” We identified these problematic grouping terms and obsoleted the terms. Children of these obsoleted terms were reviewed to ensure that their classification was correct in the ontology. More details on this process can be found in our Strategic Refinement documentation.
The Mondo community has been a key partner in this refinement process. We want to thank everyone who served as expert reviewers. Your input was extremely helpful and gave us a lot of good information that we will process and incorporate into Mondo going forward.
Non-human animal diseases
The wealth of data in the veterinary health records could be leveraged to improve disease diagnosis of both non-human and human patients. A current effort is to standardize veterinary data, including non-human animal diseases. We are expanding the non-human animal disease branch of the ontology, currently focusing on adding diseases reported in the Online Mendelian Inheritance in Animals (OMIA). A relationship between non-human diseases is added to the human counterpart, supporting the comparison of human and non-human animal data. We are dedicated to supporting the needs of the veterinary community, and we encourage interested individuals to reach out, share their use cases, and attend our Mondo outreach calls (see below).
Mondo Community Engagement
This year we launched the new Mondo outreach call series, taking place every four weeks. We bring together Mondo users and clinical terminology experts to provide a forum to discuss specific use cases and requirements, with the goal of improving Mondo with the users’ needs in mind. These calls have been enlightening, and have informed the Mondo team on priorities and improvements that benefit the community at large.
We want to take the opportunity to thank everyone who presented and participated in these outreach calls, specifically Gioconda Alyea and Sean Roberts (NORD), Eric Sid and Qian Zhu (NCATS), Megan Kane (MedGen), Courtney Thaxton (ClinGen), Daniel Himmelstein (Related Sciences), Eric Czech (Related Sciences), and Daniel Korn (Every Cure), Emily Hartley and Ian Braun (Critical Path Institute), and Kevin Schaper (the Monarch Initiative).
Your input and community contributions are invaluable to the success and continued growth of Mondo. We encourage all users to participate in these outreach calls and sign up to present. Find up-to-date information, including the schedule, here.
Looking forward
In addition to our ongoing efforts to improve and update our mappings to external disease terminologies, we started discussions to include new references to disease resources. We have been working closely with the teams at NORD, MedGen, GARD, ClinGen, and OMIA to add reference to these resources in Mondo.
Additionally, diseases can have multiple names, and each community has its own preferred disease names. We are looking for solutions to add ways for users to be able to tag their preferred terms label in Mondo to use in their system.
We look forward to another year filled with collaboration and many other projects, making Mondo an invaluable resource! Please continue to submit requests on our GitHub issue tracker, and contact us anytime with questions.
Contribute to Mondo
GitHub issue tracker: Submitting a GitHub ticket is the best way to inform the Mondo team about issues you’ve encountered, request new terms or synonyms, ask questions, or make suggestions.
Outreach calls: Fridays, every four weeks, at 9:00 AM PT / 12:00 PM ET. All are welcome to join to listen in or present. 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)
Contact: Sabrina Toro, sabrina@tislab.org; Trish Whetzel, trish@tislab.org
Funding
Mondo is generously supported by an NIH Office of the Director Grant #5R24OD011883, as well as by NIH-UDP: HHSN268201350036C, HHSN268201400093P, NCI/Leidos #15X143 and Phenomics First, NIH-NHGRI: 1 RM1 HG010860–01.
