Ontology editors' manual

From GO Wiki
Jump to navigation Jump to search

Useful references

On becoming an OBO Semantic Engineer, by James Overton, Becky Jackson, Nicole Vasilevsky, Nicolas Matentzoglu, and Shawn Tan.

This book provides best practices as recommended by OBO Foundry. Note that some parts of this book may be more general than the documentation presented in this wiki.

Protégé 5.5 setup

Protégé 5.6 setup

Installing and Using git

Ontology Editors Daily Workflow

Editing the Ontology

Ontology editing principles

Topic Status Last reviewed
General Gene Ontology Principles Draft
Creating a new GO term - by aspect
*  New Molecular Functions
*  New Binding terms
*  New Biological Processes
*  New Cellular Components
Guidelines for GO textual definitions and definition cross references
Merging terms
Obsoleting terms
Guidelines for database cross references (dbxrefs)
 RHEA and EC dbxrefs
External ontologies used in GO

How-to:Protégé instructions

Topic Status Last reviewed
New terms
GO term creation procedure  Current 2022-05-17
Procedure for creation of 'Regulation' terms
Guidelines for creating relationships between terms Under review
Guidelines for logical definitions Under review
Guidelines for creating disjoint terms Under review
Guidelines for using ChEBI terms
Term annotations
Adding or Deleting Asserted Subclasses (or parents terms)
Adding Term Comments
Adding a Term to a GO Subset (Slim)
Adding and Removing Taxon Restrictions
Term obsoletion
Obsoleting an Existing Ontology Term
Restoring an Obsolete Ontology Term
Term merges
Merging Ontology Terms
Adding and Removing GO Subsets (Slims)
GO import files
Adding Terms and Regenerating the Import Files

Identifiers To be reviewed

Guidance for organizing content meetings

(old doc, but basic principles still apply)

Content Development

Ongoing Projects

Low priority

Completed projects

Proposed content work

A list of topics that we propose to address, but for which a timeline has not been set