Ontology editors' manual

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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 5.6 setup

Installing and Using git

Ontology Editors Daily Workflow

Interpretation of Travis checks errors

Editing the Ontology

Ontology editing principles

Topic Status Last reviewed
General Gene Ontology Principles Draft
GO term guidelines- by aspect
* Molecular Function terms guidelines
* Binding terms guidelines
* Biological Process terms guidelines
* Cellular Component terms guidelines
*  Guidelines for Protein-containing complexes terms
Guidelines for GO textual definitions and definition cross references
Relations
Merging terms - deprecated
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
Synonyms
Adding a Term to a GO Subset (Slim)
Adding and Removing Taxon Restrictions
Updating EC mappings In progress 2023-03-23
Term obsoletion
Obsoleting an Existing Ontology Term
Restoring an Obsolete Ontology Term
Term merges
Merging Ontology Terms
Subsets
Adding and Removing GO Subsets (Slims)
GO import files
Adding Terms and Regenerating the Import Files

Automatically Generated Ontology Content

Some content included in the ontology is automatically generated. This includes:

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