GO OWL/Protege Tutorial 2017

Welcome! This repository contains material for GO editors course to be held at Berkeley Lab August 2017

Most of the material here is recycled from a course held at EBI in 2013 and led by David Osumi-Sutherland, Simon Jupp and Chris Mungall. This 2017 course will be led by Chris Mungall and David Osumi-Sutherland.

Tutorial

go-protege-tutorial on Read The Docs

Quick Start

Pre-meeting Preparation

1. Download Protege from http://protege.stanford.edu (you should have 5.1.0 for this course)
2. Install plugins
   • http://wiki.geneontology.org/index.php/Protege_setup_for_GO_Eds (a bit out of date)
   • http://wiki.geneontology.org/index.php/Ontology_editor_plugins
3. Do some light reading (see below)

Readling List

Mungall, C. J., Dietze, H., & Osumi-Sutherland, D. (2014). Use of OWL within the Gene Ontology. In M. Keet & V. Tamma (Eds.), Proceedings of the 11th International Workshop on OWL: Experiences and Directions (OWLED 2014) (pp. 25–36). Riva del Garda, Italy, October 17-18, 2014. http://doi.org/10.1101/010090

Pizza Tutorial http://owl.cs.manchester.ac.uk/publications/talks-and-tutorials/protg-owl-tutorial/ (this is an excellent general purpose intro, some of our material is inspired by this)

OWL Primer (advanced) https://www.w3.org/TR/owl-primer/

Instructions

We will work through the examples in this directory. Each section introduces new constructs and/or concepts.

For each section, the instructor will first demonstrate some examples. The students will then follow the instructions in the README file for the section. After completion, the students can exchange OWL files and review one another's work.

Introductory material can be found in each section of the go-protege-tutorial

Suggested Order:

• basic-subclass

  Task: build a basic hierarchy Constructs: SubClass, annotations Uses reasoner: None Ontology: cell component (subset)

• basic-disjoint

  Task: find problems in ontology Constructs: DisjointWith Uses reasoner: Elk Ontology: cell component (subset)

• basic-restriction

  Task: add part_of restrictions to ontology Constructs: SubClass, ObjectProperty, "some" (existential restriction) Uses reasoner: None Ontology: cell component (subset)

• basic-dl-query

  Task: perform queries using class expressions Constructs: and, some Uses reasoner: Elk Ontology: cell component (subset)

• basic-classification

  Task: use reasoner to build hierarchy Constructs: SubClass, "some", Equivalence, "and" (intersection) Uses reasoner: Elk Ontology: cell component (subset)

• taxon-union

  Task: create taxonomic grouping classes Constructs: or, not Uses reasoner: Hermit Ontology: NCBITaxon (subset)

• regulation-classification

  Task: examine how to compose relations to get desired inferences Constructs: property chains Uses Reasoner: Hermit Ontology: BP (subset)

• response-to-stimulus

  Task: use an external ontology for classification Constructs: owl:imports Uses Reasoner: Hermit Ontology: BP (Subset) and import of Stimulus ontology

• advanced-metabolism

  Note: We may skip this one until day 2 Task: use an external ontology for classification, together with helper axioms Constructs: owl:imports, property chains Uses Reasoner: Hermit or Elk Ontology: BP (Subset) and import of Chebi plus extras

• disjoint-expressions

  Note: the instructor may use this one as an example Task: create spatial disjointness axioms without the use of helper "X part" classes Constructs: General Axioms Uses Reasoner: Hermit

Acknowledgements and Rights

This tutorial was developed by:

• David Osumi-Sutherland
• Simon Jupp
• Chris Mungall

It is available under a CC-BY license, please credit the authors if you reuse. You can also cite the following DOI: