ICBO OBO Tutorial 2022: Using and Reusing Ontologies¶
September 26, 2022, 9:00 am – 12:30 pm ET
We'd love any feedback on this tutorial via this short survey.
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 2022 we will host a half-day OBO tutorial consisting of two parts, with a unifying theme of ontology term reuse.
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. The focus will be on making best use of OBO community open source software. We will introduce ROBOT, the command-line tool and library for automating ontology development tasks. We will show how the Ontology Development Kit (ODK) is used to standardize ontology projects with a wide range of best practices. The special emphasis of this year's tutorial will be ontology reuse, and specifically on how ROBOT and ODK can be used to manage imports from other ontologies and overcome a number of challenges to term reuse.
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.
As an outcome of this workshop, we expect that new ontologists will have a clearer understanding of why we need and use ontologies, how to find ontology terms and contribute to ontologies and make basic edits using Protege. Our more advanced participants should be able to apply OBO tools and workflows to their own ontology development practices.
Organizers¶
- James A. Overton, Knocean Inc.
- Becky Jackson, Bend Informatics
- Chris Mungall, Lawrence Berkeley National Laboratory
- Nicole Vasilevsky, University of Colorado Anschutz Medical Campus
- Nico Matentzoglu, Semanticly, Athens, Greece
- Randi Vita, La Jolla Institute for Allergy & Immunology
Agenda¶
| Time | Topic | Presenter |
|---|---|---|
| 09:00 am ET | Introduction to OBO, its community, principles, resources, and best practices | James Overton |
| 09:20 am ET | Hands-on lesson in basic tools: see details below | Nicole Vasilevsky |
| 10:15 am ET | Coffee break | |
| 10:30 am ET | Introduction to ROBOT | Becky Jackson |
| 11:30 pm ET | Introduction to the Ontology Development Kit (ODK) and Core Workflows | Nico Matentzoglu |
| 12:15 pm ET | How to be an open science ontologist (Slides are here) | Nico Matentzoglu |
Hands on lesson in basic tools¶
Instructor: Nicole Vasilevsky
Outline¶
- Protege ontology editor
- Protege basic functionality
- Plugins. See guide on installing ELK reasoner.
- How to contribute to ontologies via GitHub
Example: We will work on this ticket.