Ontology editors' manual
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 | ||
| 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:
- Taxon constraints axioms
- Links to Molecular Function reaction participants
Identifiers To be reviewed
Guidance for organizing content meetings
(old doc, but basic principles still apply)
Content Development
Ongoing Projects
- Transcription 2018 (Pascale, Ruth, Astrid, Marcio, Paul T)
- Cell Cycle (Val, Pombe experts, GOEds)
- Enzymes and EC mappings
- Non-symbiotic multi-organism processes (Jane, David OS)
- Signaling: 2017 Cambridge GOC Signalling Workshop
Low priority
- Neuro Behaviour Ontology (NBO)-GO alignment (Jane, George Gkoutos, Chris, DavidOS)
Completed projects
- Adding missing CHEBI xps
- Cell cross-products, Cell-type specific GO terms (Jane, Paola, Alex, Chris, DavidOS)
- Addition of cross-products - see Category:Cross_Products and Cross_Product_Guide
- Uberon alignment (DavidH)
- MENGO collaboration (Jane)
- PAMGO collaboration (Jane)
- PAMGO collaboration, phase 1
- PAMGO collaboration, phase 2 (as of Jan. 2007)
- Apoptosis (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
- Autophagy (Paul D, Marc F, David H, Ruth, Paola and community experts) - Denny et al 2018
- ASCB 2009
- Binding discussion - mainly annotation issues, but with some ontology content points
- Cardiac conduction (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
- Cardiovascular physiology/development - implemented Oct 2007
- Cellular component processes (Jane, David, Midori, Val, ad hoc others) - started summer 2008
- Central Nervous System Development
- Chaperones(completed by working group at Cambridge GOC meeting Sept. 2009)
- Ciliary components and processes (Paola, Karen Christie, SYSCILIA experts) Roncaglia et al 2017
- Collaboration with MIT GO-Engineering - Manuscript written
- Electron transport
- Extracellular RNA-containing vesicles (Paola, Aleks and community experts) Cheung et al 2016
- regulates links between function and process (David, Tanya)
- Gene expression (SF 1418820)
- Function-Process Links
- Heart Development (David, Ruth, Varsha, Doug, Susan, Yasmin, Becky)
- Lung_Development (David, Jen, community experts)
- Immunology Revisions
- is_a complete biological process
- Kidney Development (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
- Kidney Physiology (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
- Morphogenesis (David, Tanya)
- Muscle Biology - Started Feb. 2007; meeting July 2007; Done Oct 2007
- Neurobiology Project (David, Tanya, Jane, Paola, DavidOS)
- Plant_term - March 28, 2007
- plasma lipoprotein particle ontology - done Sept. 2010
- Peptidase & protease activity overhaul begun June 2008; essentially completed August 2008
- Regulation Main Page live March 2008
- Regulator, activator and inhibitor MF terms (David, Tanya)
- RNA processing
- SDB 2009
- Sensu revamp
- Signaling overhaul (Becky, signaling WG)
- Synapse project (Synapse experts, DavidOS, Becky Foulger) - completed 2018
- Transcription & transcription factor activity overhaul (Karen, David) - 2012
- Transporters (Jen and community experts) - Started Feb. 2007
- Utilization - done March 2010
- Virus-related term overhaul, Phage Terms (Jane Lomax, Brenley McIntosh, Rebecca Foulger & others)
- Generic GO slim overhaul (Jane & Val)
- Make cc part_of tree complete (i.e. find homes for the children of 'unlocalized protein complex')
- regulates links- Dec 2008 (David, Tanya)
- Correct disjointness violations
- Rework disjoint terms as concluded in discussion on GO list (Jane).
Proposed content work
A list of topics that we propose to address, but for which a timeline has not been set