Ontology Curator Pathway: GO-Style

Note: There is no one single accepted way of doing ontology curation in the OBO-World, see here. This guide reflects the practice of the GO-style ontology curation, as it is used by GO, Uberon, CL, PATO and others.

Note: Work on this document is still in progress, items that are not linked are currently being worked on.

Getting Set-up

1. Download and install GitHub Desktop
2. Download and install Protege. See instructions on how to set up Protege here
3. Install ELK reasoner in protege
4. Setting up your ID range
5. Setting up ODK

Learning

Learning about Ontologies

1. Fundamentals of Ontologies

Learning Git and GitHub

1. Fundamentals of GitHub
2. Github issues
3. Cloning a Repo
4. Creating pull requests
5. Introduction into the command line

Learning protege

1. Protege interface
2. Browse and Search
3. DL query
4. Editing Terms
5. Creating New Terms
6. Adding disjointness
7. Logical axiomatization of classes & use of reasoning
8. Ontology Relations
9. Updating Imports with ODK
10. OBO-style term annotation
11. Obsoleting terms
12. Merging terms

General mindset

1. How to be a team open science player

Ontology Curator How To Collection

This section is a non-ordered collection of how to documents that a curator might needs

• Adding taxon restrictions
• Changing files in pull requests
• Cloning a repo
• Creating new terms
• Daily Workflow
• Fixing Conflicts
• Creating a github fork
• Creating a github pull request
• Setting up your ID range
• Setting up ELK reasoner in protege
• Obsoleting terms
• Merging terms
• Creating slims
• Setting up ODK
• Switching ontologies
• Updating Imports with ODK