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= 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.
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.


==Content Development ==
= Group Leader =
===Projects===
Pascale Gaudet (GO Central); GitHub: @pgaudet
====High Priority====
 
*[[Cell Cycle]] (Val, Pombe experts, GOEds)
== Ontology editors==
*Ongoing addition of cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]
Karen Christie, Harold Drabkin, Raymond Lee, Pascale Gaudet
**[[Cell cross-products]], [[Cell-type specific GO terms]] (Jane, Paola, Alex, Chris, DavidOS)
 
**[[Adding missing CHEBI xps]]
==Software support==
*[[Signaling |Signaling overhaul]] (Becky, signaling WG)
Jim Balhoff
*[[Virus terms|Virus-related term overhaul]], [[Virus_ontology_devt_July_2012|Phage Terms]] (Jane Lomax, Brenley McIntosh, Rebecca Foulger & others)
 
*[[Enzymes and EC mappings]]
== Other group members==
Peter D'Eustachio, Tanya Berardini, Kimberly VanAuken, David Hill, Chris Mungall, Paul Thomas


====Medium Priority====
=Communication=
*[[Non-symbiotic multi-organism processes]] (Jane)
==Editor's Conference calls==
*[[Neurobiology Project]] (David, Tanya, Jane, Paola, DavidOS)


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


====Recently completed projects====
* Calls are held weekly on Mondays, 12:00PM-1:00PM EST
*[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
* Calls are scheduled on the GO's Google calendar.  Please request access to the calendar if you don't have it.
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David) - 2012
* Reminder emails are sent out to the go-ontology mailing list (see [[Internal_email_lists]] to register).
*[[Kidney Physiology]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
*[[Cardiac conduction]] (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
*Rework disjoint terms as [http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F#Conclusion concluded in discussion on GO list] (Jane).
*[[:Category:Content MENGO|MENGO collaboration]] (Jane)


====Proposed content work====
A list of topics that  we propose to address, but for which a timeline has not been set


*Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology.
=== Agenda and Minutes ===
*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)
* [[Ontology editors' conference call minutes 2022|2022]]
* [[Recombination and DNA repair]]
* 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]]
* [[RNA processes]]
* [[Bile formation and secretion processes]]
* [[protein and peptidyl amino acid modification / protein processing]]
* [[Response to drug]]
* [[Polyketide synthases]]
* [[cell growth/proliferation/division]]
* [[oxidoreductases]]


==Guides, Training and 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.


*[[Content Meeting Documentation|Guidance for organizing content meetings]]
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.
*[[:Category:Curator Guides|Curator guides]]
*[[Editor_Guide]]
*[[Ontology Documentation Drafts]] - for working on documentation of ontology content that will become part of the web-based documentation
*[[New Ontology Editor Training]]
*[[Ontology Editing Examples|Ontology Editing Examples: Regulation of a pathway by regulation of enzyme activity]]


==Other Ontology Development Group Activities==
==[[Protege5_5_setup_for_GO_Eds|Protégé 5.5 setup]]==
===QC===
==[[Installing and Using git]]==
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)
==[[Ontology Editors Daily Workflow]]==
*[[Jenkins]]
==Editing the Ontology==


===TermGenie===
===Ontology editing principles===
*[[Template-able Requests Prior To TG]]


===Website===
{| class="wikitable"
*[[Editorial-type sections copied over from the GO website ontology documentation: MF]]
!Topic
! Status
! Last reviewed
|-
|[[General Gene Ontology Principles]]
| Under review
|
|-
! colspan="3" |'''Creating a new GO term - by aspect'''
|-
| * [[Guidelines for new Molecular Functions | New Molecular Functions]]
|
|
|-
|* [[Guidelines for new Binding terms | New Binding terms]]
|
|
|-
|* [[Guidelines for new Biological Processes | New Biological Processes]]
|
|
|-
|* [[Guidelines for new Cellular Components | New Cellular Components]]
|
|
|-
|[[Guidelines for GO textual definitions]]
|
|
|-
|[[Relations]]
|
|
|-
|[[Principles for merging terms|Merging terms ]]
|
|
|-
|[[Principles for term obsoletion|Obsoleting terms]]  
|
|
|-
|[[Guidelines for 'database cross references' and 'definition database cross references' |Database cross references and definition database cross references]] (dbxrefs)
|
|
|-
|[[External ontologies]]
|
|
|}


===Protege===
*[[Protege workshop]] Jan. 2012
*[[Ontology_workshop_Jan_2013]]
*[[Protege Feature Requirements]]


[[Category:Ontology]]
{| class="wikitable"
! Guidelines for specific terms
! Status
! Last reviewed
|-
[[Principles for catalytic activity terms]]
| Draft
| 2022-05-16
|-
|
|
|
|}


===LEGO===
===How-to:Protégé instructions===
*[[Regulation]]


*[[Noctua_meeting_140929|Modelling complex annotations in LEGO/noctua - meeting 140929]]


===Annotation extensions===
{| class="wikitable"
*[[Terms that could be obsoleted if information was collected as annotation extension]]
!Topic
! Status
! Last reviewed
|-
! colspan="3" | New terms
|-
|[[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 relationships between terms]]
| Under review
|
|-
|[[Guidelines for equivalence axioms]]  (being reviewed) ---  Also [[Logical_Definitions]]
| Under review
|
|-
|[[Disjoint_Documentation |Guidelines for creating disjoint terms]]
| Under review
|
|-
|[[Guidelines for using ChEBI terms]]
|
|
|-
! colspan="3" |Term annotations
|-
|[[Adding or Deleting Asserted Subclasses]]
|
|
|-
|[[Adding Term Comments]]
|
|
|-
|[[Synonyms]]
|
|
|-
|[[Adding a Term to a GO Subset (Slim)]]
|
|
|-
|[[Adding Taxon Restrictions| Adding and Removing Taxon Restrictions]]
|
|
|-
! colspan="3" |Term obsoletion
|-
|[[Obsoleting an Existing Ontology Term]]
|
|
|-
|[[Restoring an Obsolete Ontology Term]]
|
|
|-
! colspan="3" |Term merges
|-
|[[Merging Ontology Terms]]
|
|
|-
! colspan="3" |Subsets
|-
|[[Adding and Removing GO Subsets (Slims)]]
|
|
|-
! colspan="3" |[[GO import files]]
|-
|[[Adding Terms and Regenerating the Import Files]]
|}


==Meetings==
=[[Identifiers]] To be reviewed=
===Cambridge Editors' meetings - weekly Tuesday 10-11 AM===


*[[CamEds Ontology meeting 2012-06-19|June 19]]
=[[Content Meeting Documentation|Guidance for organizing content meetings]]=
*[[CamEds Ontology meeting 2012-06-26|June 26]]
(old doc, but basic principles still apply)
*[[CamEds Ontology meeting 2012-07-3|July 3]]
*[[CamEds Ontology meeting 2012-07-17|July 17]]
*[[CamEds Ontology meeting 2012-07-31|July 31]]
*[[CamEds Ontology meeting 2012-08-31|August 7]]
*[[CamEds Ontology meeting 2012-10-24|October 24]]




===SourceForge Meetings: Fortnightly, Wednesdays, 4:30-5:15pm BST===
=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]]
* [[Protein_Complexes:_who,_what,_where]]


*[[SourceForge meeting 2013-07-24|July 24]]
===Low priority===
*[[SourceForge meeting 2013-09-04|Sept 4]]
*[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris, DavidOS)
*[[SourceForge meeting 2013-09-11|Sept 11]]
*[[microbial ontology development and annotation]]
*[[SourceForge meeting 2013-09-25|Sept 25]]
*[[SourceForge meeting 2013-10-09|Oct 9]]
*[[SourceForge meeting 2013-10-30|Oct 30]]
*[[SourceForge meeting 2013-12-11|Dec 11th]]
*[[SourceForge meeting 2014-01-29|Jan 29th]]
*[[SourceForge meeting 2014-02-12|Feb 12th]]
*[[SourceForge meeting 2014-02-26|Feb 26th]]
*[[SourceForge meeting 2014-04-23|Apr 23rd]]
*[[SourceForge meeting 2014-05-14|May 14th]]
*[[SourceForge meeting 2014-06-25|June 25th]]
*[[SourceForge meeting 2014-09-10|Sept 10th]]
*[[SourceForge meeting 2014-09-24|Sept 24th]]
*[[SourceForge meeting 2014-10-22|Oct 22nd]]


===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]]
*[http://wiki.geneontology.org/index.php/Extensions/x-metazoan-anatomy Uberon alignment] (DavidH)
*[[:Category:Content MENGO|MENGO collaboration]] (Jane)
*[[:Category:Content PAMGO|PAMGO collaboration]] (Jane)
*[[:Category:Content PAMGO|PAMGO collaboration]], phase 1
*[[:Category:Content PAMGO|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) - [https://www.ncbi.nlm.nih.gov/pubmed/29455577 Denny et al 2018]
*[[ASCB 2009]]
*[[Binding_terms_working_group|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) [https://www.ncbi.nlm.nih.gov/pubmed/29177046 Roncaglia et al 2017]
*[[Collaboration with MIT GO-Engineering]] - Manuscript written
*[[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)
*Gene expression ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1418820&group_id=36855| SF 1418820])
*[[Function-Process Links]]
*[[Heart_Development_workshop|Heart Development]] (David, Ruth, Varsha, Doug, Susan, Yasmin, Becky)
*[[Lung_Development]] (David, Jen, community experts)
*[[Immunology Revisions]]
*[[Isa-complete_BP|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
*[[Proteases |Peptidase & protease activity overhaul]] begun June 2008; essentially completed August 2008
*[[Regulation Main Page]] live March 2008
*[[Regulators |Regulator, activator and inhibitor MF terms]] (David, Tanya)
*[[RNA processing]]
*[[SDB 2009]]
*[[Sensu Main Page|Sensu revamp]]
*[[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
*[[Transporters]] (Jen and community experts) - Started Feb. 2007
*[[Utilization]] - done March 2010
*[[Virus terms|Virus-related term overhaul]], [[Virus_ontology_devt_July_2012|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 [http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F#Conclusion concluded in discussion on GO list] (Jane).


[[Category:Ontology]]
===Proposed content work===
[[Category:Meetings]]
A list of topics that  we propose to address, but for which a timeline has not been set


===Editor's Conference calls-weekly NOW ON THURSDAYS, 8:30-9:15 AM PST===
* [[protein and peptidyl amino acid modification / protein processing]]
* [[Response to drug]]
* [[Polyketide synthases]]


*[[Ontology editor's conference call minutes 2011|2011 minutes]]
=Quality Control=
*[[Ontology editor's conference call minutes Jan-June 2012|Jan-June 2012 minutes]]
==SPARQL checks on the ontology==
*[[Ontology editor's conference call minutes July-Dec 2012|July-Dec 2012 minutes]]
[https://github.com/rctauber/robot/tree/reporting/robot-core/src/main/resources/queries SPARQL checks on the ontology]
*[[Ontology editor's conference call minutes Jan-June 2013|Jan-June 2013 minutes]]
*[[Ontology editor's conference call minutes July-Dec 2013|July-Dec 2013 minutes]]
*[[Ontology editor's conference call minutes Jan-June 2014|Jan-June 2014 minutes]]
*[[Ontology editor's conference call minutes July-Dec 2014|July-Dec 2014 minutes]]


*[[Ontology meeting 2015-01-06|Jan 6]] First call of 2015
==Ontology release pipeline==
* [[Release Pipeline]]
* [http://current.geneontology.org/reports/gorule-report.html GO Rules rrrors reports]


==Useful Links==
'''TO BE REPLACED'''
*[[Completed ontology content work]]
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)
*[[SF + TG Rota for Gene Ontology requests]]
*[[Ontology_Development_Reports|Ontology Development Reports]] (discontinued Nov 2010)


[[Category:Ontology]]


==Administrative==
*[[Ontology Development group summary]]
*[[Meeting_minutes:_general_topics|Miscellaneous meeting minutes]]


[[Category:Ontology]]
[[Category:Ontology]][[Category:GO Editors]]

Latest 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