Ontology editors' manual: Difference between revisions

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= Useful references=
= Useful references=
[https://oboacademy.github.io/obook/ On becoming an OBO Semantic Engineer], by James Overton, Becky Jackson, Nicole Vasilevsky, Nicolas Matentzoglu, and Shawn Tan.
* [https://oboacademy.github.io/obook/ 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.
* [https://go-protege-tutorial.readthedocs.io/en/latest/ GO Protege tutorial]


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.
=[[Protege5_5_setup_for_GO_Eds|Protégé 5.5 setup]]=
=[[Protege5_6_setup_for_GO_Eds|Protégé 5.6 setup]]=
=[[Protege5_6_setup_for_GO_Eds|Protégé 5.6 setup]]=
=[[Installing and Using git]]=
=[[Installing and Using git]]=
=[[Ontology Editors Daily Workflow]]=
=[[Ontology Editors Daily Workflow]]=
===[[Interpretation of Travis checks errors]]===
==Editing the Ontology==
==Editing the Ontology==


===Ontology editing principles===
===Ontology editing principles===
* [[Creating new GO terms]]


{| class="wikitable"
{| class="wikitable"
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|-
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! colspan="3" |'''Creating a new GO term - by aspect'''
! colspan="3" |'''GO term guidelines- by aspect'''
|-
|-
| * [[Guidelines for new Molecular Functions | New Molecular Functions]]
| * [[Guidelines_for_new_Molecular_Functions | Molecular Function terms guidelines]]
|  
|  
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|-
|-
|* [[Guidelines for new Binding terms | New Binding terms]]
|* [[Guidelines for new Binding terms | Binding terms guidelines]]
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|-
|-
|* [[Guidelines for new Biological Processes | New Biological Processes]]  
|* [[Guidelines for new Biological Processes | Biological Process terms guidelines]]  
|  
|  
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|-
|-
|* [[Guidelines for new Cellular Components | New Cellular Components]]
|* [[Guidelines for new Cellular Components | Cellular Component terms guidelines]]
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|-
|-
|[[Guidelines for GO textual definitions]] and definition cross references
|* [[Protein_complexes | Protein-containing complexes terms guidelines]]
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|-
|[[Guidelines_for_GO_textual_definitions | Textual definitions and definition cross references guidelines]]
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|-
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|[[Principles for merging terms|Merging terms ]]
|[[Principles for merging terms|Merging terms - deprecated]]
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|[[Guidelines for creating a GO term |GO term creation procedure]]
|[[Guidelines for creating a GO term |GO term creation procedure]]
| Current
| Current
| 2022-05-17
| 2024-04-12
|-
|[[Guidelines for creating a Regulation Term|Procedure for creation of 'Regulation' terms]]
|
|
|-
|-
|[[Guidelines for creating relationships between terms]]  
|[[Guidelines for creating relationships between terms]]  
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|[[Adding a Term to a GO Subset (Slim)]]
|[[Adding a Term to a GO Subset (Slim)]]
|  
|  
|
|  
|-
|-
|[[Adding Taxon Restrictions| Adding and Removing Taxon Restrictions]]
|[[Adding Taxon Restrictions| Adding and Removing Taxon Restrictions]]
|  
|  
|
|
|-
|[[Updating EC mappings| Updating EC mappings]]
| In progress
| 2023-03-23
|-
|-
! colspan="3" |Term obsoletion
! colspan="3" |Term obsoletion
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|-
|-
|[[Adding and Removing GO Subsets (Slims)]]
|[[Adding and Removing GO Subsets (Slims)]]
|
|
|-
|[[Procedure to check subset coverage]]
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|  
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|[[Adding Terms and Regenerating the 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=
=[[Identifiers]] To be reviewed=
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=[[Content Meeting Documentation|Guidance for organizing content meetings]]=
=[[Content Meeting Documentation|Guidance for organizing content meetings]]=
(old doc, but basic principles still apply)
(old doc, but basic principles still apply)




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*[[Non-symbiotic multi-organism processes]] (Jane, David OS)
*[[Non-symbiotic multi-organism processes]] (Jane, David OS)
* Signaling: [[2017 Cambridge GOC Signalling Workshop]]
* Signaling: [[2017 Cambridge GOC Signalling Workshop]]
* [[Protein_Complexes:_who,_what,_where]]


===Low priority===
===Low priority===
*[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris, DavidOS)
*[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris, DavidOS)
*[[microbial ontology development and annotation]]


===Completed projects===
===Completed projects===

Latest revision as of 01:47, 12 April 2024

Useful references

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
*  Protein-containing complexes terms guidelines
 Textual definitions and definition cross references guidelines
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 2024-04-12
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)
Procedure to check subset coverage
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

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