Mondo Disease Ontology Highlights from 2024
By Sabrina Toro and Katie Mullen on behalf of the Mondo Team
This is the time of year when we reflect on the year coming to a close. Like elves the week before Christmas, the Mondo team has been very busy this year. We want to take the opportunity of this blog post to review some of our greatest achievements. As always, our biggest highlight is the strengthening of our ties with the community. We are extremely thankful to our Mondo community, users, experts, clinicians, and researchers, for their help and support.
Mondo milestone: 100th release!
This year, Mondo reached a major milestone and celebrated its 100th release in December. Over the year, we addressed and closed 653 GitHub issues from 110 contributors, 97 of whom were users. 2,078 new Mondo terms were created, 82 terms were merged (i.e., obsolete terms with replacement), and 34 terms were obsoleted.
Multiple workflows were created and/or updated to ensure that mappings and provenances for synonyms and SubclassOf annotations are kept up-to-date with external disease resources. We also hosted an epilepsy workshop to review and update the representation of epilepsy terms in Mondo. The following is a summary of some of this year’s highlights. At the end of this post, you can find additional resources. You can also reach out to any of the Mondo team members with questions.
Epilepsy workshop engages experts
We hosted workshops to align the representation of epilepsy diseases to ensure that the Mondo epilepsy classification is scientifically accurate, aligns with the current understanding of the disease features, and is maximally useful for the community’s needs. Our two-part workshop brought together clinicians, geneticists and patient advocates, and led to improvement of the representation of epilepsy disease entities in Mondo. To date, five new terms were created, and an additional 18 new terms will be added soon. We reviewed the classification of terms in specific areas including immune epilepsies, genetic epilepsies, generalized epilepsies and epilepsy syndromes. A summary of the workshops as well as recordings are available here.
We will host another workshop (Part 3, scheduled on Friday, January 17, 2025, 8–9:50am PT/11–12:50pm ET) to continue the discussions, including epilepsy syndromes, developmental and epileptic encephalopathies, and the representation of hereditary epilepsies. To join, please RSVP here.
Curate-athon closes the gap on GitHub open issues
In November 2024, the Mondo curation team attended a 3-day “curate-athon” during which we focused on addressing user requests. This curate-athon was extremely productive, and we were able to address 59 requests. We are learning from this successful event, and plan on organizing more curate-athons in 2025 to address user requests more efficiently and in a more timely manner. We thank each and every contributor and encourage all community members to submit issues on our GitHub issue tracker.
We need all of the species: Non-human animal diseases in Mondo
Last year, we started the expansion of the non-human animal disease representation in Mondo. We now have 2,744 non-human animal disease terms in Mondo. At the end of this year, we are nearing completion of the full representation of diseases from Online Mendelian Inheritance in Animals (OMIA). These are mainly genetic and hereditary diseases. We plan on continuing this work in 2025, by adding more common diseases from the Veterinary Nomenclature (VeNom).
For the community, by the community
Many members of the community already expertly curate disease information, including mappings between terminologies, links to curated resources, rare disease lists, etc. In addition, expert groups have preferred names for diseases; since these preferred names might be updated as time passes, it makes sense for these expert groups to maintain these preferred names themselves.
The Mondo team created simple workflows to get this “community-maintained” information directly from the expert groups. The information is maintained at the source as a simple spreadsheet, which is automatically uploaded and added into Mondo, assuming it passes our quality control checks. Using this workflow, we currently maintain rare disease information from National Organization for Rare Disorders (NORD) and Genetic and Rare Diseases Information Center (GARD) (see also our report from last year here), Mondo mappings to MedGen and Unified Medical Language System (UMLS) (from the MedGen team), Nanbyo Disease Ontology (NANDO) mappings (from the NANDO team), links to curated sources such as Clinical Genome Resource (ClinGen), and “preferred” disease names for ClinGen, NORD, and Experimental Factor Ontology (EFO).
In addition to facilitating the update of Mondo, this “community-maintained” content has improved re-use of work and limited effort duplication and strengthened the sense of community and conviviality. More details were presented on our September 20th 2024 outreach call (recording available here).
A standing ovation for the Mondo Outreach Call presenters
We are grateful for the Mondo Outreach call presenters and participants. We extend a special thank you to this year’s presenters: Sierra Moxon (LBL), Zoe Pendlington (Open Targets / EBI), Julie Tahraoui (Orphanet), Imke Tammen and Frank Nicolas (OMIA), Bryan Laraway (N3C), Brian Schilder (Imperial College London), Toyofumi Fujiwara (DBCLS), and Nicole Vasilevsky (Critical Path Institute).
New institutions, new connections
In April 2024, the Translational and Integrative Sciences Lab (TISLab), directed by Melissa Haendel and including many members of the Mondo and Monarch Initiative team, moved to the University of North Carolina at Chapel Hill (UNC) School of Medicine Department of Genetics. We appreciated everyone’s patience and understanding during the transition. We are all very excited about TISLab’s new institution and are grateful for the warm welcome we have received from the members of the Department. We are now closer to the Clinical Genome Resource (ClinGen) team (also at UNC), some of Mondo’s most active community members, and expect a lot of upcoming updates in the representation of genetic diseases in Mondo developed in collaboration with the ClinGen team.
We are thrilled to welcome Yousif Shwetar, a student at the UNC Medical Scientist Training Program (MSTP), who joined the TISLab and Mondo team. Yousif brings his medical expertise to the team and has a special interest in eye disorders. We are excited to have him on the team, and for the great contributions he has already made.
Plans for 2025: Continuing our Mondo Community Engagement
Several workshops are already in the works, including the Review of Epilepsy Diseases (workshop part 3, scheduled on Friday, January 17, 2025, 8–9:50am PT/11–12:50pm ET), retinal disorders, and immunological diseases. We invite the community at large to attend and participate in these workshops. Updates and logistics will be shared via our user mailing list. If you have not yet, make sure to sign up at https://groups.google.com/g/mondo-users
Once again we thank all members of our community for their constant support. We look forward to working with everyone this upcoming year.
Join the Mondo community
Mailing list:
mondo-users-subscribe@googlegroups.com
Please join our mailing list to receive monthly ontology release announcements, and invitations to events (e.g. outreach calls, workshops).
GitHub issue tracker:
https://github.com/monarch-initiative/mondo
Request changes in the ontology (e.g new terms or synonyms, changes in classifications) or report error(s) by submitting a GitHub issue.
Outreach calls:
https://mondo.monarchinitiative.org/pages/workshop/#outreach
These calls occur every four weeks on Fridays, at 9:00 AM PT / 12:00 PM ET. They are an opportunity:
- to hear from the Mondo team about the latest updates,
- to hear from users about their projects and use cases,
- and to ensure that Mondo improvements address the user use cases.
Everyone is invited to join the calls and present. Join our mailing list to receive invitations to these calls; contact info@monarchinitiative.org if you are interested in presenting your project.
Other resources
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.
