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 5.5 setup

Installing and Using git

Ontology Editors Daily Workflow

Editing the Ontology

Ontology editing principles

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


Guidelines for specific terms Status Last reviewed
 Principles for catalytic activity terms  Draft 2022-05-16

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 equivalence axioms (being reviewed) --- Also 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
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

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

Quality Control

SPARQL checks on the ontology

SPARQL checks on the ontology

Ontology release pipeline

TO BE REPLACED