Mondo Disease Ontology Workshops and Outreach Calls
Details and summaries for upcoming and past Mondo workshops.
Workshops and Outreach Calls
- Mondo Epilepsy Workshop (Part 1: October 25, 2024, Part 2: November 22, 2024)
- Mondo Outreach Calls
- Mondo Workshop (February 01, 2023)
- Using the Mondo Disease Ontology for Disease Data Curation (June 08, 2022)
- Mondo Clinical Reclassification Workshop Part 2 (November 17, 2021)
- Mondo Clinical Reclassification Workshop Part 2 (November 17, 2021)
- Renal Disease and Phenotype Workshop (July 14, 2021)
- ClinGen Virtual Retreat 2021 (June 24, 2021)
- Mondo Upper Level Reclassification Workshop (April 05, 2021)
- Mondo Introductory Workshop (November 2018)
Mondo Epilepsy Workshop
Description
The goal of this workshop series is to review the classification of terms in Mondo based on your expert opinions, to ensure that the epilepsy branch is scientifically accurate, aligns with the current understanding of the disease features, and is maximally useful for your projects.
Date and Time
- Part 1: October 25, 2024 (Friday) from 8-10 AM (see your local time here)
- Part 2: November 22, 2024 (Friday) from 8-9:50 AM (see your local time here)
- Part 3: January 17, 2025 (Friday) from 8-9:50 AM (see your local time here)
Agenda
The emerging agenda is available here. To RSVP, please fill out this form.
Recordings
- Part 1 recording here
- Part 2 recording here
Funding
Funded by NHGRI Phenomics First (1RM1HG010860-01) and the Critical Path Institute.
Mondo Outreach Calls
The goal of the Mondo Outreach Calls is to bring together stakeholders and clinical terminology experts with the goal of discussing specific use cases and requirements, and improving Mondo with a focus of our user needs in mind. Every month we plan to invite a group to present their use case (not necessarily directly related to Mondo), and learn if there is anything we can do from the Mondo technical side to better support them. During the call, the Mondo technical team will give an overview of the latest developments and followed by a ~20 minute talk + discussion from specific users where we’ll discuss paths forward on how we can work together.
Notes are available here.
| Date | Time | Presenter (Organization) | Topic | Recording |
|---|---|---|---|---|
| Dec 13 | 9AM PT/12PM ET | Nicole Vasilevsky (Critical Path Institute) | Epilepsy Workshop Summary | |
| Sep 20 | 9AM PT/12PM ET | Sabrina Toro and Trish Whetzel (Monarch Initiative) | Externally managed metadata in Mondo | Here |
| June 28 | 9AM PT/12PM ET | Toyofumi Fujiwara (DBCLS) | Enhancing Interoperability of Biomedical Resources Using Ontologies | Here |
| May 31 | 9AM PT/12PM ET | Brian Schilder (Imperial College London) | Navigating the Phenomic Landscape: Systematic characterisation of the latent genomic space underlying all traits and diseases | Here |
| May 3 | 9 AM PT/12 PM ET | Bryan Laraway(N3C) | Mondo to identify rare disease cohorts within N3C | Here |
| Apr 5 | 9 AM PT/12 PM ET | Imke Tammen and Frank Nicolas (OMIA) | Online Mendelian Inheritance in Animals (OMIA) | Here |
| Mar 8 | 9 AM PT/12 PM ET | Julie Tahraoui (Orphanet) | Orphanet mapping practices | Here |
| Feb 9 | 9 AM PT/12 PM ET | Zoe Pendlington (Open Targets / EBI) | Open Targets and the Experimental Factor Ontology (EFO) | Here |
| Jan 12 | 9 AM PT/12 PM ET | Sierra Moxon | Use of Mondo in NCATS Translator | Here |
| Dec 15 | 9 AM PT/12 PM ET | Kevin Schaper (Monarch Initiative) | Use of Mondo in Monarch | Here |
| Nov 17 | 9 AM PT/12 PM ET | Sabrina Toro and Trish Whetzel (Monarch Initiative) | Overview of Mondo reclassification efforts | Here |
| Oct 20 | 9 AM PT/12 PM ET | Emily Hartley and Ian Braun (Critical Path Institute) | RDCA-DAP: Ontology Applications in Rare Diseases | Here |
| Sept 22 | 9 AM PT/12 PM ET | Daniel Himmelstein (Related Sciences), Eric Czech (Related Sciences), and Daniel Korn (Every Cure) | Classifying EFO/MONDO diseases as areas, roots, or subtypes; Slides are here | Here |
| Aug 25 | 9 AM PT/12 PM ET | Courtney Thaxton (ClinGen) | ClinGen Variant Curation | Here |
| July 28 | 9 AM PT/12 PM ET | Megan Kane (MedGen) | MedGen curation workflows | Here |
| June 30 | 9 AM PT/12 PM ET | Eric Sid and Qian Zhu (NCATS) | Use of Disease Ontologies and Knowledge in Addressing Translation Science in Rare Diseases | Here |
| June 02 | 9 AM PT/12 PM ET | Gioconda Alyea, Sean Roberts, and Marybeth McAfee (NORD) | Rare Diseases in NORD | Here |
Mondo Workshops
Description
The goal of this workshop was to bring together the Mondo team members to define our objectives and highest priorities for the upcoming year (and beyond) and develop a plan, with a timeline and assignments, for actionable tasks. These included but were not limited to 1) aligning with the foundations of ICD11 and 2) improving the Mondo design philosophy.
Date
February 01, 2023
Using the Mondo Disease Ontology for Disease Data Curation
Presenters
Sabrina Toro, Nicole Vasilevsky, Nico Matentzoglu
Description
This workshop was presented at the virtual Curating the Clinical Genome conference. 31 participants attended. We introduced participants to Mondo, its advantages, and how it relates to other disease terminologies. The focus will be on disease curation best practices, how to use Mondo to annotate disease data, where to find disease terms, what to do if required terms do not exist in Mondo, and how to request changes or improvements. Mondo is a collaborative and community-developed resource; workshop attendees will learn how to contribute to Mondo. This workshop also introduced the Mondo ontology curation workflow, including new term creation, and how different user requests are reconciled (e.g. disease naming), term obsoletions and merges, and ontology releases. In addition, technical aspects of Mondo, including quality control and automated pipelines, were discussed.
Participants were polled at the beginning of the workshop about their usage and familiarity with Mondo. Participants were either very familiar with ontologies (8 respondents, 50%), or had heard about ontologies but didn’t understand what they were (7 respondents, 44%); one respondent (6%) did not know what ontology is. Half of the respondents use ontologies for curation anytime possible (8 respondents, 50%), while the other half either occasionally use ontologies for curation (4 respondents, 25%) or do not use ontology for data curation (4 respondents, 25%).
Most respondents used Mondo for disease curation (7 respondents, 39%) or knew about Mondo but did not use it (7 respondents, 39%). 2 respondents used Mondo for disease annotations and active members of the Mondo community, 2 respondents were Mondo users for reasons other than curation, and 1 respondent had never heard of Mondo.
Most respondents (13, 72%) had never requested changes to Mondo; the other respondents had either created GitHub issues (4 respondents) and/or contracted the Mondo team (3 respondents).
Date and Time
June 08, 2022
9-10:30am PT / 12-1:30pm EST / 5-6:30pm UK / 6-7:30pm Europe
Slides
- Slides are available here
Mondo Clinical Reclassification Workshop Part 2
Description
This workshop is a follow-up to the Mondo Clinical Reclassification Workshop (April 2021). Mondo was reclassified to create a clinical-centric view (see description here), however, many clinically useful terms are still difficult to find as they are subClasses of general grouping terms such as “disease of anatomical system”. In this workshop, we will propose an updated top-level classification of Mondo which more closely resembles the clinical view of diseases. We will gather stakeholders and community members for their comments, requests, and input.
Date and Time
November 17th, 2021
12-2pm PST / 3-5pm EST / 8-10pm UK / 9pm-11pm Europe
Funding:
NHGRI Phenomics First (1RM1HG010860-01)
Renal Disease and Phenotype Workshop
Description
This workshop was hosted by Nicole Vasilevsky (Mondo) and Peter Robinson (Human Phenotype Ontology), and brought together experts in kidney disease clinical care. We discussed improvements to classification of the ‘kidney disease’ (MONDO:0005240) hierarchy in Mondo. As an outcome of this meeting, the kidney disease hiearchy will be revised in accordance to the classifications described in Brenner and Rector’s The Kidney textbook. See GitHub ticket for more details.
Date and Time
July 14, 2021
2-3pm PT
Funding:
NHGRI Phenomics First (1RM1HG010860-01)
ClinGen Virtual Retreat 2021
Presentation Title
Mondo Disease Ontology (How ClinGen curators work with the Mondo Disease Ontology, which aims to harmonize disease definitions across the world)
Presenter
Nicole Vasilevsky
Description
ClinGen hosted a virtual retreat for all ClinGen contributors June 24-25, 2021. The retreat provided the ClinGen community and collaborators with an event to learn about and share new and existing work, as well as best practices across ClinGen. This presentation discussed the Mondo Disease Ontology, which is used for gene-disease annotations by ClinGen curators. The retreat agenda is available here.
Date and Time
June 24, 2021
3:40 - 5:10pm Eastern
Slides & Recording
Funding:
NHGRI Phenomics First (1RM1HG010860-01)
Mondo Clinical Reclassification Workshop
Description:
A workshop with invited members of the community to work on the top-level classification of Mondo. The workshop focused on semantic modeling of disease and defining ontology patterns. There is a great need for expert clinicians to define clinically relevant navigational grouping classes. These top down and bottom up approaches need to meet in the middle harmoniously. This workshop included clinicians and ontologists, as well as expert curators working on genes for clinical utility. As an outcome of this meeting, the Mondo hierarchy was revised in accordance to the classifications described in Harrison’s Principles of Internal Medicine textbook. See GitHub tickets for more details.
Date and Time
April 05, 2021, Monday
8am-11am PT / 11am-2pm ET / 4pm-7pm UK / 5pm-8pm Europe
Slides, Recording, Report
- Slides are available here.
- Recording is available here.
- A report with a full description of the workshop and outcomes is available here
Funding:
NHGRI Phenomics First (1RM1HG010860-01)
Mondo Introductory Workshop
Description:
The workshop focused on defining ontology patterns and community development processes for ontological disease descriptions. Specifically, there was a need to provision multiple attributes to a disease for computational classification. The attributes need to take into account penetrance, expressivity, genetic variation, histology, biomarkers, temporality, somatic and mosaic characteristics, environmental interactions, etc. There was a need to enable expert curation groups such as in ClinGen, EBI, Orphanet, GARD, MedGen, and OMIM to create disease definitions on the fly, capture the provenance and evidence robustly, and have an identifier for use immediately. This workshop included invited curators, clinicians and ontologists and provided an opportunity to get an overview of Mondo and the source terminologies, as well as networking opportunities. See more details here.
Date and Location
Date: November, 2018
Location: Broad Institute, Cambridge MA
Slides
Slides are available here.
Funding:
Phenomics BD2K Forums for Integrative Phenomics (1 U13 CA221044-01)