Protege-OWL Berkeley Training 2017 Agenda
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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- Install plugins - Protege_setup_for_GO_Eds (a bit out of date) and Ontology_editor_plugins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
- Merging terms
- Taxon restrictions
- Adding new terms
- Real-world ontology editing
- Build failures and how to cope with them
- Discussion
- Project Planning-priorities and personel