W02: A how-to guide to create, manage, and release an OBO ontology (Ontology 101)

Submitted by pankaj on

ICBO2018 Workshop-W02

Date: Tuesday, August 07, 2018
Time: 10:30-12:30pm and 1:30-3:30pm
Location: Cascade Ballroom 110ABC

See program here.

Workshop materials:

Organizer(s):

  • Nicole Vasilevsky
  • James A. Overton
  • Melissa Haendel
  • Chris Mungall
  • Rebecca Tauber

Workshop type:

  • Ontology 101

Workshop Abstract

Starting your first ontology can be a daunting task. Even for those that have already developed ontologies, managing and releasing them according to best practices with a minimal amount of effort can be challenging. This how-to tutorial will help guide learners at beginner or moderate levels of experience in using OBO Foundry (http://www.obofoundry.org/) best practices and tools to develop scientifically accurate, logically well-formed, and interoperable ontologies. We will provide an interactive, hands-on training for ontologists, biocurators, researchers and students. The proposed format is as follows:

  • Introduction to the OBO Foundry, OWL, and OWL reasoning. We will introduce participants to the foundations and principles ontology development, logical construction, best practices defined within the OBO Foundry, and tips and strategies for community ontology development.
  • Tools and workflows for ontology development and release. Standard workflows exist in the OBO Foundry for managing various portions of an ontology project. We will provide an interactive tutorial to guide participants through the process of creation and releasing an ontology in a standardized way. This will include instruction on the basics of various ontology-editing tools such as Protégé, the Ontology Starter Kit (https://github.com/INCATools/ontology-starter-kit), ROBOT (http://robot.obolibrary.org), and the new language and tool, Knotation (https://knotation.org).

Participants will be asked to bring laptops with the following tools and software installed: a GitHub (https://github.com) account, Protégé 5.1 (available here: https://protege.stanford.edu/products.php), and the latest ROBOT release (https://github.com/ontodev/robot/releases).

Rational:

The objective of this tutorial is to increase awareness and skills in the basics of community ontology development in a hands-on, interactive format. As an outcome of this tutorial, participants will understand the foundations and principles of the OBO Foundry, learn basic editing workflows using currently available ontology editing tools such as Protégé, the Ontology Starter Kit, ROBOT, and new tools such as Knotation (currently under development); workflows for releasing OWL ontologies and best practices for contributing to community ontologies.

This workshop will provide an opportunity for beginner-level ontology developers to learn about best practices and workflows from expert-ontologists in a hands-on format, which would not otherwise be offered as part of the main conference program. It also provides an opportunity for moderate-experience level participants to learn to use the latest tools to support improved workflows, ontology management, and provenance and attribution.

The workshop organizers are actively involved in many OBO community projects. We will advertise this workshop through our various communities and expect to attract a diverse group of participants.

Funding:
NIH grant 1 U24 TR002306-01, “A National Center for Digital Health Informatics Innovation” to M. Haendel.
NIH grant 1 R24 HG010032-01, “Services to support the OBO foundry standards” to C. Mungall and B. Peters.