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OBO Academy - Monarch Training Series


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)

  • 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


Note: this is tentative and subject to change

Date Lesson Notes Recordings
August 2024 No Meeting Enjoy Summer break!
July 2024 No Meeting Enjoy Summer break!
2024/06/25 Structures and Instructors: Applying the Strengths of Large Language Models to Biomedical Informatics Harry Caufield 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


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.