Difference between revisions of "Ontology Development"

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With the help of the software team the group create rules to ensure the ontology's integrity.
 
With the help of the software team the group create rules to ensure the ontology's integrity.
  
= Group Leader =
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Pascale Gaudet (GOC); GitHub: @pgaudet
David Hill (MGI); GitHub: @ukemi
 
  
 
=Communication=
 
=Communication=
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=== Agenda and Minutes ===
 
=== Agenda and Minutes ===
* [[Ontology editors' conference call minutes 2019|2019]]
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* [[Ontology editors' conference call minutes 2020|2020]]
* Past Annotation Call Minutes: [[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]] |
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* 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]] |
  
 
= Documentation=
 
= Documentation=
==[[Protege_setup_for_GO_Eds|Setting up Protege for GO editors]]==
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==[[Protege5_5_setup_for_GO_Eds|Protégé 5.5 setup]]==
 
==[[Installing and Using git]]==
 
==[[Installing and Using git]]==
 
==[[Ontology Editors Daily Workflow]]==
 
==[[Ontology Editors Daily Workflow]]==
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!colspan="2" | New terms
 
!colspan="2" | New terms
 
|-
 
|-
|rowspan="7"|[[Principles for creating a GO term]] (being reviewed)
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|rowspan="10"|[[Principles for creating a GO term]] (being reviewed)
 
|[[Guidelines for creating a GO term]]
 
|[[Guidelines for creating a GO term]]
 
|-
 
|-
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|[[Guidelines for GO textual definitions]] (being reviewed)
 
|[[Guidelines for GO textual definitions]] (being reviewed)
 
|-
 
|-
|[[Guidelines for equivalence axioms]]  (being reviewed) --- Also [[Logical_Definitions]] (being reviewed)
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|[[Guidelines for equivalence axioms]]  (being reviewed) --- Also [[Logical_Definitions]] (being reviewed)
 
|-
 
|-
 
|[[Guidelines for new Molecular Functions]] (new)
 
|[[Guidelines for new Molecular Functions]] (new)
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|-
 
|-
 
|[[Guidelines for new Cellular Components]] (new)
 
|[[Guidelines for new Cellular Components]] (new)
 +
|-
 +
|[[Guidelines for 'database cross references' and 'definition database cross references']] (new)
 
|-
 
|-
 
!colspan="2" |Modifying existing terms
 
!colspan="2" |Modifying existing terms
 
|-
 
|-
|rowspan="4"|[[Principles for Modifying an Existing Ontology Term]] (to be reviewed)
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|rowspan="5"|[[Principles for Modifying an Existing Ontology Term]] (to be reviewed)
 
|[[Deleting Asserted Subclasses]]
 
|[[Deleting Asserted Subclasses]]
 
|-
 
|-
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|[[Adding a Term to a GO Subset (Slim)]]
 
|[[Adding a Term to a GO Subset (Slim)]]
 
|-
 
|-
|[[Adding Taxon Restrictions]]
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|[[Adding Taxon Restrictions| Adding and Removing Taxon Restrictions]]
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|-
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|[[Adding References to GitHub tickets]]
 
|-
 
|-
 
!colspan="2" |Term obsoletion
 
!colspan="2" |Term obsoletion
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*[[:Category:Content PAMGO|PAMGO collaboration]], phase 2 (as of Jan. 2007)
 
*[[:Category:Content PAMGO|PAMGO collaboration]], phase 2 (as of Jan. 2007)
 
*[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
 
*[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
*Autophagy (Paul D, Marc F, David H, Ruth, Paola and community experts) - [https://www.ncbi.nlm.nih.gov/pubmed/29455577 Denny et al 2018]
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*[[Autophagy 2015-2016]] (Paul D, Marc F, David H, Ruth, Paola and community experts) - [https://www.ncbi.nlm.nih.gov/pubmed/29455577 Denny et al 2018]
 
*[[ASCB 2009]]
 
*[[ASCB 2009]]
 
*[[Binding_terms_working_group|Binding]] discussion - mainly annotation issues, but with some ontology content points
 
*[[Binding_terms_working_group|Binding]] discussion - mainly annotation issues, but with some ontology content points
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A list of topics that  we propose to address, but for which a timeline has not been set
 
A list of topics that  we propose to address, but for which a timeline has not been set
  
*Peripheral nervous system development
 
*Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology.
 
*Overhaul [[translation]], similar to what's being done for transcription. [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1891512&group_id=36855| SF 1891512] is closed, but notes some issues for consideration. (midori 2010-10-04)
 
* [[Recombination and DNA repair]]
 
* [[RNA processes]]
 
 
* [[protein and peptidyl amino acid modification / protein processing]]
 
* [[protein and peptidyl amino acid modification / protein processing]]
 
* [[Response to drug]]
 
* [[Response to drug]]
 
* [[Polyketide synthases]]
 
* [[Polyketide synthases]]
* [[cell growth/proliferation/division]]
 
* [[oxidoreductases]]
 
  
 
=Quality Control=
 
=Quality Control=

Latest revision as of 23:37, 21 June 2020

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.

Pascale Gaudet (GOC); GitHub: @pgaudet

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

Protégé 5.5 setup

Installing and Using git

Ontology Editors Daily Workflow

Editing the Ontology

General Gene Ontology Principles
New terms
Principles for creating a GO term (being reviewed) Guidelines for creating a GO term
Guidelines for creating relationships between terms (being reviewed)
Guidelines for creating disjoint terms (to be written)
Guidelines for creating a Regulation Term
Guidelines for GO textual definitions (being reviewed)
Guidelines for equivalence axioms (being reviewed) --- Also Logical_Definitions (being reviewed)
Guidelines for new Molecular Functions (new)
Guidelines for new Biological Processes (new)
Guidelines for new Cellular Components (new)
Guidelines for 'database cross references' and 'definition database cross references' (new)
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 and Removing Taxon Restrictions
Adding References to GitHub tickets
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 Adding Terms and Regenerating the Import Files

Relations General Relations Documentation Draft 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

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