Ontology Development

From GO Wiki
Jump to navigation Jump to search

Documentation

Setting up Protege for GO editors

Installing and Using git

Ontology Editors Daily Workflow

Editing the Ontology

New terms
Principles for creating a GO term (being reviewed) Guidelines for creating a GO term
Guidelines for creating a Regulation Term
Guidelines for GO term definitions (being reviewed)
Modifying existing terms
Principles for Modifying an Existing Ontology Term (to be reviewed) Deleting Asserted Subclasses
Adding Term Comments
Adding a Term to a GO Subset (Slim)
Adding Taxon Restrictions
Term obsoletion
Principles for term obsoletion Obsoleting an Existing Ontology Term
Restoring an Obsolete Ontology Term
Term merges
Principles for merging terms (being reviewed) Merging Ontology Terms
Subsets
Subset documentation (to add) Adding and Removing GO Subsets (Slims)
Import Files
Principles for GO import files (to write; see Editor_file_guide) Adding Terms and Regenerating the Import Files

General Gene Ontology Principles

Editor Guide to has part To be reviewed

Editor Guide to Regulates To be reviewed

Guidelines for equivalence axioms To be reviewed

Curator Guide: Enzymes and Reactions To be reviewed

Notes on specific terms To be reviewed

Requesting a New Complex ID from IntAct

Editor file guide To be reviewed

Ontology Documentation Drafts To be reviewed

for working on documentation of ontology content that will become part of the web-based documentation

Ontology Editing Examples: Regulation of a pathway by regulation of enzyme activity To be reviewed

New Ontology Editor Training To be reviewed

Website - to be moved to the wiki?

Identifiers To be reviewed

Guidance for organizing content meetings

(old doc, but basic principles still apply)


Content Development

Projects

High Priority/Ongoing

  • Transcription 2018 (Pascale, Ruth, Astrid, Marcio, Paul T)
  • Cell Cycle (Val, Pombe experts, GOEds)
  • Enzymes and EC mappings
  • Synapse project (Synapse experts, DavidOS, Becky Foulger)
  • Extracellular RNA-containing vesicles (Paola, Aleks and community experts)
  • Ciliary components and processes (Paola, Karen Christie, SYSCILIA experts)
  • Autophagy (Paul D, Marc F, David H, Ruth, Paola and community experts)

Medium Priority

Low priority

Recently completed projects

Proposed content work

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

Completed ontology content work

Quality Control

SPARQL checks on the ontology

[|SPARQL checks on the ontology]

Ontology release pipeline

http://wiki.geneontology.org/index.php/Release_Pipeline Errors: http://current.geneontology.org/ontology/reports/index.html

TO BE REPLACED

Other Ontology Development Group Activities