Ontology Development: Difference between revisions

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=== Agenda and Minutes ===
=== Agenda and Minutes ===
* [[Ontology editors' conference call minutes 2021|2021]]
* [[Ontology editors' conference call minutes 2022|2022]]
* Past Annotation Calls: [[Ontology Development reports 2005-2010|2005-2010]] |  [[Ontology editor's conference call minutes 2011|2011]] | [[Ontology editor's conference call minutes 2012|2012]] | [[Ontology editor's conference call minutes 2013|2013]] | [[Ontology editor's conference call minutes 2014|2014]] |  [[Ontology editor's conference call minutes 2015|2015]] | [[Ontology editor's conference call minutes 2016|2016]] | [[Ontology editor's conference call minutes 2017|2017]] | [[Ontology editor's conference call minutes 2018|2018]] | [[Ontology editors' conference call minutes 2019|2019]] | [[Ontology editors' conference call minutes 2020|2020]]
* Past Ontology Editors' Calls: [[Ontology Development reports 2005-2010|2005-2010]] |  [[Ontology editor's conference call minutes 2011|2011]] | [[Ontology editor's conference call minutes 2012|2012]] | [[Ontology editor's conference call minutes 2013|2013]] | [[Ontology editor's conference call minutes 2014|2014]] |  [[Ontology editor's conference call minutes 2015|2015]] | [[Ontology editor's conference call minutes 2016|2016]] | [[Ontology editor's conference call minutes 2017|2017]] | [[Ontology editor's conference call minutes 2018|2018]] | [[Ontology editors' conference call minutes 2019|2019]] | [[Ontology editors' conference call minutes 2020|2020]] | [[Ontology editors' conference call minutes 2021|2021]]


= Documentation=
= Documentation=
Useful reference: [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.
==[[Protege5_5_setup_for_GO_Eds|Protégé 5.5 setup]]==
==[[Protege5_5_setup_for_GO_Eds|Protégé 5.5 setup]]==
==[[Installing and Using git]]==
==[[Installing and Using git]]==
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|'''Creating a new GO term - by aspect'''
! colspan="3" |'''Creating a new GO term - by aspect'''
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| * [[Guidelines for new Molecular Functions | New Molecular Functions]]
| * [[Guidelines for new Molecular Functions | New Molecular Functions]]
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||[[Guidelines for GO textual definitions]]  
|[[Guidelines for GO textual definitions]]  
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| [[Principles for merging terms |Merging terms ]]
|[[Principles for merging terms|Merging terms ]]
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|-  
| [[Principles for term obsoletion |Obsoleting terms]]  
|[[Principles for term obsoletion|Obsoleting terms]]  
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|[[Guidelines for 'database cross references' and 'definition database cross references' |Database cross references and definition database cross references]] (dbxrefs)
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|[[External ontologies]]
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{| class="wikitable"
! Guidelines for specific terms
! Status
! Last reviewed
|-
| [[Principles for catalytic activity terms]]
| Draft
| 2022-05-16
|-
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|  
|  
|  
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===How-to:Protégé instructions===
===How-to:Protégé instructions===




{| class="wikitable"
{| class="wikitable"
!Topic
! Status
! Last reviewed
|-
|-
! New terms
! colspan="3" | New terms
|-
|-
|> [[Guidelines for creating a GO term |GO term creation procedure]]
|[[Guidelines for creating a GO term |GO term creation procedure]]
| Current
| 2022-05-17
|-
|-
|>>[[Guidelines for creating a Regulation Term|* Procedure for creation of 'Regulation' terms]]
|[[Guidelines for creating a Regulation Term|Procedure for creation of 'Regulation' terms]]
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|-
|-
|> [[Guidelines for creating relationships between terms]] (being reviewed)
|[[Guidelines for creating relationships between terms]]  
| Under review
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|-
|-
|>> [[Guidelines for equivalence axioms]]  (being reviewed) ---  Also [[Logical_Definitions]] (being reviewed)
|[[Guidelines for equivalence axioms]]  (being reviewed) ---  Also [[Logical_Definitions]]  
| Under review
|
|-
|-
|> [[Disjoint_Documentation |Guidelines for creating disjoint terms]] (being reviewed)
|[[Disjoint_Documentation |Guidelines for creating disjoint terms]]  
| Under review
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|-
|> [[Guidelines for using ChEBI terms]]
|[[Guidelines for using ChEBI terms]]
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|-
!Term annotations
! colspan="3" |Term annotations
|-
|-
|[[Adding or Deleting Asserted Subclasses]]
|[[Adding or Deleting Asserted Subclasses]]
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|-
|-
|[[Adding Term Comments]]
|[[Adding Term Comments]]
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|-
|-
|[[Synonyms]]
|[[Synonyms]]
|-
|  
|[[Guidelines for 'database cross references' and 'definition database cross references']] (dbxrefs)
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|-
|[[Adding a Term to a GO Subset (Slim)]]
|[[Adding a Term to a GO Subset (Slim)]]
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|-
|-
|[[Adding Taxon Restrictions| Adding and Removing Taxon Restrictions]]
|[[Adding Taxon Restrictions| Adding and Removing Taxon Restrictions]]
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|-
!Term obsoletion
! colspan="3" |Term obsoletion
|-
|-
|[[Obsoleting an Existing Ontology Term]]
|[[Obsoleting an Existing Ontology Term]]
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|-
|-
|[[Restoring an Obsolete Ontology Term]]
|[[Restoring an Obsolete Ontology Term]]
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|-
!Term merges
! colspan="3" |Term merges
|-
|-
|[[Merging Ontology Terms]]
|[[Merging Ontology Terms]]
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|-
!Subsets
! colspan="3" |Subsets
|-
|-
|[[Adding and Removing GO Subsets (Slims)]]
|[[Adding and Removing GO Subsets (Slims)]]
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|-
! [[GO import files]]
! colspan="3" |[[GO import files]]
|-
|-
|[[Adding Terms and Regenerating the Import Files]]
|[[Adding Terms and Regenerating the Import Files]]

Revision as of 08:09, 30 June 2022

Group's focus

This group's purpose is to ensure that the Gene Ontology represents biology in a way that is useful for gene product annotation of reference genomes and other MODs using the GO for annotation. The group serves as the link between biological knowledge that is gained from wet-bench scientists and the representation of that knowledge in the GO. Members of the group are responsible for reporting areas of the GO that need development and for suggesting changes and additions to the GO as needs arise. Members of the group serve as biological experts in domains that are covered by their organism. They are responsible for reviewing changes to be sure that they accurately reflect our current understanding of biology. With the help of the software team the group create rules to ensure the ontology's integrity.

Group Leader

Pascale Gaudet (GO Central); GitHub: @pgaudet

Ontology editors

Karen Christie, Harold Drabkin, Raymond Lee, Pascale Gaudet

Software support

Jim Balhoff

Other group members

Peter D'Eustachio, Tanya Berardini, Kimberly VanAuken, David Hill, Chris Mungall, Paul Thomas

Communication

Editor's Conference calls

When

  • Calls are held weekly on Mondays, 12:00PM-1:00PM EST
  • Calls are scheduled on the GO's Google calendar. Please request access to the calendar if you don't have it.
  • Reminder emails are sent out to the go-ontology mailing list (see Internal_email_lists to register).


Agenda and Minutes

Documentation

Useful reference: 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
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