Protege-OWL Berkeley Training 2017 Agenda

Logistics here: Protege-OWL_Berkeley_Training_2017_Logistics

Meeting material can be found in [geneontology/protege-tutorial](https://github.com/geneontology/protege-tutorial)

Pre-meeting preparation

Computer setup

We assume you will be bringing your normal work laptop. Ideally this will have 8G of memory or more and be a macbook (or PC with linux). Let Chris know if this is *not* the case

• make sure you are on the go-ontology list
• get a github account and ensure you are in users.yaml https://github.com/geneontology/go-site/blob/master/metadata/users.yaml
• Install a github client
• Download Protege from http://protege.stanford.edu (you should have 5.1.0 for this course)
• Install plugins - Protege_setup_for_GO_Eds (a bit out of date) and Ontology_editor_plugins
• Do some light reading (see below)

Reading List (optional)

• 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/

Agenda

Wednesday 2017-02-22

am

• Git and GitHub
• OWL Concepts

pm

• Walkthrough and exercises [geneontology/protege-tutorial](https://github.com/geneontology/protege-tutorial)
  • Basic Editing Guide
  • Using the reasoner
• external ontologies
• continuous integration: travis, jenkins and automated checks

Thursday 2017-02-23

am

• MF refactor?
• Design Patterns: what are they are how they can help you
• How TermGenie works; limitations and why we're switching
• Editing parts of the ontology as tables

pm

• further exercises
• advanced ontology debugging

Friday 2017-02-24

• Exercises
  • Adding new terms
    • term names
    • term definitions
    • term synonyms
    • xrefs
    • term relationships
  • Obsoleting terms
    • obsolete GO:0042964 thioredoxin biosynthetic process & GO:0042965 Glutaredoxin biosynthetic process #12923
  • Merging terms
    • MP: GO:0005945 6-phosphofructokinase complex -> high level protein complex/macromolecular complex term #12782
  • Taxon restrictions
• Real-world ontology editing
• Build failures and how to cope with them
• Discussion
  • Project Planning-priorities and personel