OBO Academy - Monarch Training Series¶
Goal¶
The goal of this course is to provide ongoing training for the OBO community. As with previous tutorials, we follow the flipped classroom concept: as organisers, we provide you with materials to look at, and you will work through the materials on your own. During our biweekly meeting, we will answer your questions, provide you with additional demonstrations where needed and go into depth wherever you as a student are curious to learn more. This means that this course can only work if you are actually putting in the time to preparing the materials. That said, we nevertheless welcome anyone to just lurk or ask related questions.
You (Students)¶
- Join the Monarch Tutorials Mailing List
- Read the "Getting started" guide
- Check which lessons interest you in the upcoming schedule - just participate in the ones you care about
- Prepare the lessons (between 3 and 7 hours of preparation time)
- Prepare questions for the revision sessions (without questions, the revision sessions will be silent and awkward)
- Make detailed issues on our issue tracker when materials are broken, hard to follow or need more details - that is really important as we rely on you to help to improve our materials continuously.
- Request new course units from us using the issue tracker.
We (Tutors and Organisers)¶
- Nicole Vasilevsky, Critical Path Institute
- Nico Matentzoglu, Semanticly, Athens, Greece
- Sabrina Toro, University of North Carolina at Chapel Hill
- Sarah Gehrke, University of North Carolina at Chapel Hill
- Prepare the materials for each lesson and provide schedules
- Build new training materials where needed
- Organise the course and rooms
Schedule¶
Note: this is tentative and subject to change
| Date | Lesson | Presenter / Notes | Recordings |
|---|---|---|---|
| August to Sept 2025 | No Meeting | Enjoy Summer break! | |
| 2025/07/22 | TBD | ||
| 2025/06/24 | From Fuzzy to Clear: Writing Ontology Definitions That Work This is a tutorial for curators at any level. |
Sabrina Toro, UNC-Chapel Hill | here |
| 2025/06/09 | Using AI coding apps for ontology developers. Tutorial material | Chris Mungall, LBNL | Here |
| 2025/04/08 | Introduction to developing agentic workflows for semantic engineers. Tutorial material | Chris Mungall, LBNL | Here |
| 2025/02/04 | More! Hands On Workshop: OntoGPT | Harry Caufield, LBNL | |
| 2024/10/15 | Hands On Workshop: OntoGPT | Harry Caufield, LBNL | Here |
| July to Sept 2024 | No Meeting | Enjoy Summer break! | |
| 2024/06/25 | Structures and Instructors: Applying the Strengths of Large Language Models to Biomedical Informatics | Harry Caufield, LBNL | Here |
| 2024/05/14 | Introduction to the legendary Uberon Anatomy ontology | Damien Goutte-Gattat and Nico Matentzoglu | Here |
| 2024/04/30 | An Introduction to Synonyms in OBO Ontologies | Nicole Vasilevsky, C-Path | Here |
| 2024/04/16 | AI-assisted ontology editing workflows 2: Validation | Chris Mungall, LBNL | Here |
| 2024/04/02 | OBO Academy Phenomics Series: Phenotype data and the role of ontologies | James McLaughlin (EBML-EBI) and Nico Matentzoglu | Here |
| 2024/03/19 | No Meeting | ||
| 2024/03/05 | AI-assisted ontology editing workflows 1: generating and augmenting | Chris Mungall, LBNL | Here |
| 2024/02/20 | Ontology Metadata Standardisation | Anita Caron, EBI | Here |
| 2024/02/06 | Introduction to Open Source licenses | Seth Carbon, LBNL | |
| 2024/01/23 | Bridge2AI data standards: a practical introduction | Harry Caufield, LBNL | Here |
| 2024/01/09 | No Meeting | Enjoy Winter break! | |
| 2023/12/26 | No Meeting | Enjoy Winter break! | |
| 2023/12/12 | Introduction to DOSDP pattern design and workflows | Tutorial by Ray Stefancsik (Slides) | Here |
| 2023/11/28 | No Meeting | ||
| 2023/11/14 | Enhancing curation workflows with CurateGPT | Tutorial by Chris Mungall | Here |
| 2023/10/31 | No Meeting | ||
| 2023/10/17 | Using ontologies for data annotation and consequences for ontology development | Tutorial by Sabrina Toro | Here |
| 2023/10/03 | Units modeling in and around OBO | Tutorial by James Overton | Here |
| 2023/09/19 | Improving ontology interoperability with Biomappings | Tutorial by Charlie Hoyt | Here |
| 2023/09/05 | Modern prefix management with Bioregistry and curies |
Tutorial by Charlie Hoyt | Here |
| 2023/08/22 | How to determine if two entities are the same? | Tutorial by Nico Matentzoglu | Here |
| 2023/08/08 | No Meeting | Enjoy Summer break! | |
| July 2023 | No Meeting | Enjoy Summer break! | |
| 2023/06/27 | No Meeting | Enjoy Summer break! | |
| 2023/06/13 | Modelling with Subclass and Equivalent class statements | Tutorial by Henriette Harmse | slides |
| 2023/05/30 | First steps with ChatGPT for semantic engineers and curators | Led by Sierra Moxon and Nico Matentzoglu | N/A |
| 2023/05/16 | Cancelled: Monarch/C-Path workshop | ||
| 2023/05/02 | Cancelled: No meeting week | ||
| 2023/04/18 | Overview of Protege 5.6 - the latest features | Tutorial by Damien Goutte-Gattat (slides) | Here |
| 2023/04/04 | Introduction to Exomiser | Tutorial by Valentina, Yasemin and Carlo from QMUL | Here |
| 2023/03/21 | Introduction to Wikidata | Tutorial by Andra Waagmeester and Tiago Lubiana | Here |
| 2023/03/07 | OAK for the Ontology Engineering community | Tutorial by Chris Mungall | Here |
| 2023/02/21 | OBO Academy Clinic | Bring your ontology issues and questions to discuss with Sabrina and Nico! Attend the Ontology Summit Seminars instead! | |
| 2023/02/07 | Querying the Monarch KG using Neo4J | Tutorial by Kevin Schaper | Here |
| 2023/01/24 | OBO Academy Clinic | Bring your ontology issues and questions to discuss with Sabrina and Nico! | |
| 2023/01/10 | Modeling with taxon constraints | Tutorial by Jim Balhoff | Here |
| 2022/12/27 | No Meeting | Enjoy the Holidays! | |
| 2022/12/13 | Introduction to Semantic Entity Matching | Slides | Here |
| 2022/11/29 | OBO Academy hackathon | Work on open tickets together. | |
| 2022/11/15 | Contributing to OBO ontologies - Part 2 | Here | |
| 2022/11/01 | Contributing to OBO ontologies - Part 1 | Here | |
| 2022/10/18 | Introduction to Medical Action Ontology (MAxO) | Here | |
| 2022/10/04 | No Meeting | ISB virtual conference: register here | |
| 2022/09/20 | How to be an open science ontologist | Here | |
| 2022/09/06 | Pull Requests: Part 2 | Here | |
| 2022/07/26 | Pull Requests: Part 1 | Here | |
| 2022/07/12 | Basic introduction to the CLI: Part 2 | Due to intermitent connection issues, the first few minutes of this recording are not included. Refer to the Tutorial link for the initial directions. | Here |
| 2022/06/28 | Basic introduction to the CLI: Part 1 | Here | |
| 2022/06/14 | Application/project ontologies | Here | |
| 2022/05/31 | Contributing to ontologies: annotation properties | Here | |
| 2022/05/17 | Introduction to managing mappings with SSSOM | Here | |
| 2022/05/03 | No meeting | ||
| 2022/04/19 | Disjointness and Unsatisfiability | Here | |
| 2022/04/05 | No meeting | ||
| 2022/03/22 | Creating an ontology from scratch | Here | |
| 2022/03/08 | Obsoletions in OBO ontologies | Review Obsoleting an Existing Ontology Term and Merging Ontology Terms. Slides are here. | Here |
| 2022/02/22 | SPARQL for OBO ontology development | Here | |
| 2022/02/07 | ODK/DOSDPs | Here | |
| 2022/01/25 | Contributing to OBO ontologies | This is not new content but we'll start at the beginning again with our previous lessons. | Here |
| 2022/01/11 | Office hours with Nicole and Sabrina - no formal lesson | Bring any open questions. | |
| 2021/12/14 | Lessons learned from troubleshooting ROBOT | Open discussion, no advance preparation is needed. | |
| 2021/11/30 | Semantics of object properties (including Relations Ontology) | ||
| 2021/11/16 | SPARQL for OBO ontology development | Here | |
| 2021/11/02 | Templating: DOSDPs and ROBOT | ||
| 2021/10/19 | Ontology Design | ||
| 2021/10/05 | Cancelled due to overlap with ISB conference | ||
| 2021/09/21 | Ontology Pipelines with ROBOT 2 | ||
| 2021/09/08 | Migrating legacy ontology systems to ODK | ||
| 2021/09/07 | Ontology Pipelines with ROBOT | ||
| 2021/09/01 | Manage dynamic imports the ODK | ||
| 2021/08/25 | Ontology Release Management with the ODK | Here | |
| 2021/08/24 | Contributing to OBO ontologies 2 | Here | |
| 2021/08/17 | Contributing to OBO ontologies |
Notes¶
Most of materials used by this course were developed by James Overton, Becky Jackson, Nicole Vasilevsky and Nico Matentzoglu as part of a project with the Critical Path Institute (see here). The materials are improved as part of an internal training program (onboarding and CPD) for the Phenomics First project (NIH / NHGRI #1RM1HG010860-01).
Thanks to Sarah Gehrke for her help with project management.