ICBO OBO Tutorial 2023: Using and Reusing Ontologies¶
Conference website: https://icbo-conference.github.io/icbo2023/
ICBO Workshops details: https://www.icbo2023.ncor-brasil.org/program.html#workshops
Date: August 28, 2023 13:30-15:00 (Part 1) and 15:30-17:15 (Part 2)
Tutorial recordings:
- part 1: https://www.youtube.com/watch?v=83lI3u7KX0g
- part 2: https://www.youtube.com/watch?v=m2khZcJVKU0)
Table of content:
Overview¶
The Open Biological and Biomedical Ontologies (OBO) community includes hundreds of open source scientific ontology projects, committed to shared principles and practices for interoperability and FAIR data. An OBO tutorial has been a regular feature of ICBO for a decade, introducing new and experienced ontology users and developers to ontologies in general, and to current OBO tools and techniques specifically. While ICBO attracts many ontology experts, it also includes an audience of ontology beginners, and of ontology users looking to become ontology developers or to further refine their skills. Our OBO tutorial will help beginner and intermediate ontology users with a combination of theory and hands-on practice.
For ICBO 2023 we will host a half-day OBO tutorial consisting of two parts.
The first part of our tutorial will be introductory, aimed at an audience that is new to ontologies and to the OBO Foundry. We will introduce OBO, its community, principles, resources, and best practices. We will finish the first part with a hands-on lesson in basic tools: ontology browsers, how to contribute to ontologies via GitHub (creating issues and making Pull Requests), and the Protege ontology editor.
The second part will build on the first, addressing an audience that is familiar with ontologies and OBO, and wants to make better use of OBO workflows and tools in their own projects.
This material for this year's OBO Tutorial will build on the content here in the OBO Academy. The OBO Academy offers free, open, online resources with self paced learning materials covering various aspects of ontology development and curation and OBO. Participants are encouraged to continue their learning using this OBO Academy website, and contribute to improving the OBO documentation.
Organizers¶
- Nicole Vasilevsky, Critical Path Institute, Tucson, AZ, USA (Based in Portland, OR, USA)
- Nico Matentzoglu, Semanticly, Athens, Greece
- Tiago Lubiana, Universidade de São Paulo, São Paulo, SP, Brazil
Advance preparation¶
The tutorial is designed to be 'show and tell' format, but you are welcome to install the following software on your machine in advance, if you'd like to follow along in real time:
Agenda¶
Time are in UTC - 3:00, Brasilia, Brazil
THE REAL SCHEDULE (updated LIVE) can be found here.
| Time | Topic | Presenter | Duration |
|---|---|---|---|
| 13:30 pm | Welcome | Tiago Lubiana | 10 min |
| 13:40 pm | Introduction to OBO, its community, principles, resources, and best practices | Darren Natale | 20 min |
| 14:00 pm | Hands-on lesson in basic tools | Sabrina Toro | 40 min |
| 14:40 pm | Protege updates and new features | Damien Goutte-Gattat | 20 min |
| 15:00 pm | Break | 15 min | |
| 15:15 pm | Overview of OBO Dashboard | Anita Caron | 20 min |
| 15:35 pm | Introduction to ROBOT | Becky Jackson | 45 min |
| 16:20 pm | Role of ChatGPT in OBO Ontology Development | Sierra Moxon | 20 min |
| 16:40 pm | On Becoming An Open Science Engineer | Nico Matentzoglu | 20 min |
| 17:00 pm | Extended Question and Answers | Tiago Lubiana | 30 min |
| 17:30 pm | Adjourn |