Difference between revisions of "Ontology Development"

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m (Group's focus)
 
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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 =
+
= Group's manager =
David Hill (MGI)  
+
Pascale Gaudet (GO Central); GitHub: @pgaudet
  
 
=Communication=
 
=Communication=
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=== Agenda and Minutes ===
 
=== Agenda and Minutes ===
* [[Ontology editors' conference call minutes 2019|2019]]
+
* [[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]] |
+
* 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]]==
+
==[[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)
+
|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)
+
|[[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)
+
|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]]
+
|[[Adding Taxon Restrictions| Adding and Removing Taxon Restrictions]]
 +
|-
 +
|[[Adding References to GitHub tickets]]
 
|-
 
|-
 
!colspan="2" |Term obsoletion
 
!colspan="2" |Term obsoletion
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=Content Development =
 
=Content Development =
==Projects==
+
==Ongoing Projects==
===High Priority/Ongoing===
 
 
*[[Transcription 2018]] (Pascale, Ruth, Astrid, Marcio, Paul T)
 
*[[Transcription 2018]] (Pascale, Ruth, Astrid, Marcio, Paul T)
 
*[[Cell Cycle]] (Val, Pombe experts, GOEds)
 
*[[Cell Cycle]] (Val, Pombe experts, GOEds)
 
*[[Enzymes and EC mappings]]
 
*[[Enzymes and EC mappings]]
*[https://github.com/geneontology/synapse 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===
 
 
*[[Non-symbiotic multi-organism processes]] (Jane, David OS)
 
*[[Non-symbiotic multi-organism processes]] (Jane, David OS)
 +
* Signaling: [[2017 Cambridge GOC Signalling Workshop]]
 +
* [[Protein_Complexes:_who,_what,_where]]
  
 
===Low priority===
 
===Low priority===
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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 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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*[[Central Nervous System Development]]
 
*[[Central Nervous System Development]]
 
*[[Chaperones]](completed by working group at Cambridge GOC meeting Sept. 2009)
 
*[[Chaperones]](completed by working group at Cambridge GOC meeting Sept. 2009)
 +
*Ciliary components and processes (Paola, Karen Christie, SYSCILIA experts) [https://www.ncbi.nlm.nih.gov/pubmed/29177046 Roncaglia et al 2017]
 
*[[Collaboration with MIT GO-Engineering]] - Manuscript written
 
*[[Collaboration with MIT GO-Engineering]] - Manuscript written
 
*[[Electron transport]]
 
*[[Electron transport]]
 +
*Extracellular RNA-containing vesicles (Paola, Aleks and community experts) [https://www.ncbi.nlm.nih.gov/pubmed/27076901 Cheung et al 2016]
 
*[[FP-regulates| regulates links between function and process]] (David, Tanya)
 
*[[FP-regulates| regulates links between function and process]] (David, Tanya)
 
*Gene expression ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1418820&group_id=36855| SF 1418820])
 
*Gene expression ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1418820&group_id=36855| SF 1418820])
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*[[Muscle Biology]] - Started Feb. 2007; meeting July 2007; Done Oct 2007
 
*[[Muscle Biology]] - Started Feb. 2007; meeting July 2007; Done Oct 2007
 
*[[Neurobiology Project]] (David, Tanya, Jane, Paola, DavidOS)
 
*[[Neurobiology Project]] (David, Tanya, Jane, Paola, DavidOS)
 +
*[[Plant_term]] - March 28, 2007
 
*[[plasma lipoprotein particle ontology]] - done Sept. 2010
 
*[[plasma lipoprotein particle ontology]] - done Sept. 2010
 
*[[Proteases |Peptidase & protease activity overhaul]] begun June 2008; essentially completed August 2008
 
*[[Proteases |Peptidase & protease activity overhaul]] begun June 2008; essentially completed August 2008
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*[[Sensu Main Page|Sensu revamp]]
 
*[[Sensu Main Page|Sensu revamp]]
 
*[[Signaling |Signaling overhaul]] (Becky, signaling WG)
 
*[[Signaling |Signaling overhaul]] (Becky, signaling WG)
 +
*[https://github.com/geneontology/synapse Synapse project] (Synapse experts, DavidOS, Becky Foulger) - completed 2018
 
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David) - 2012
 
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David) - 2012
 
*[[Transporters]] (Jen and community experts) - Started Feb. 2007
 
*[[Transporters]] (Jen and community experts) - Started Feb. 2007
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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]]
 
* [[Bile formation and secretion 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=
 
==SPARQL checks on the ontology==  
 
==SPARQL checks on the ontology==  
[[https://github.com/rctauber/robot/tree/reporting/robot-core/src/main/resources/queries |SPARQL checks on the ontology]]
+
[https://github.com/rctauber/robot/tree/reporting/robot-core/src/main/resources/queries SPARQL checks on the ontology]
  
 
==Ontology release pipeline==
 
==Ontology release pipeline==

Latest revision as of 02:01, 21 September 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.

Group's manager

Pascale Gaudet (GO Central); 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