Ontology Development: Difference between revisions

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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/Ongoing====
*[[Cell Cycle]] (Val, Pombe experts, GOEds)
*[[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====
== Ontology editors==
*[[Non-symbiotic multi-organism processes]] (Jane, David OS)
Pascale Gaudet, Raymond Lee, Edith Wong, Val Wood


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


====Recently completed projects====
== Other group members==
*[[Uberon alignment]] (DavidH)
Tanya Berardini, Karen Christie, Peter D'Eustachio, David Hill, Kimberly VanAuken
*Addition of cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]
**[[Cell cross-products]], [[Cell-type specific GO terms]] (Jane, Paola, Alex, Chris, DavidOS)
**[[Adding missing CHEBI xps]]
*[[Signaling |Signaling overhaul]] (Becky, signaling WG)
*[[Virus terms|Virus-related term overhaul]], [[Virus_ontology_devt_July_2012|Phage Terms]] (Jane Lomax, Brenley McIntosh, Rebecca Foulger & others)
*[[Neurobiology Project]] (David, Tanya, Jane, Paola, DavidOS)
*[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David) - 2012
*[[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====
==PIs==
A list of topics that  we propose to address, but for which a timeline has not been set
Chris Mungall, Paul Thomas


*Peripheral nervous system development
=Communication=
*Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology.
==Editor's Conference calls==
*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]]
* [[Response to drug]]
* [[Polyketide synthases]]
* [[cell growth/proliferation/division]]
* [[oxidoreductases]]


==Guides, Training and Documentation==
=== 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 ===
* [[Ontology editors' conference call minutes 2024|2024]]
* 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]] | [[Ontology editors' conference call minutes 2022|2022]] | [[Ontology editors' conference call minutes 2023|2023]]


*[[:Category:Curator Guides|Curator guides]]
===GO ontology in GitHub===
*[[Editor_Guide]]
* The Gene Ontology uses an issue tracker hosted on [https://github.com/geneontology GitHub] to record and track ontology issues.
*[[Editor_file_guide]]
* The go-annotation repo on GitHub may be accessed [https://github.com/geneontology/go-ontology here].
*[[Protege_setup_for_GO_Eds|Protege setup for GO Eds]]
* Contact information for each group that contributes to the consortium is available [https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv here]
*[[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]]
*[[Guidelines on 'protein complex' terms]]
*[[Content Meeting Documentation|Guidance for organizing content meetings]] (old doc, but basic principles still apply)


==Other Ontology Development Group Activities==
===GO ontology on slack===
===QC===
*The GO consortium uses [https://geneontologyworkspace.slack.com/home GO Slack] as an informal chat service: [https://app.slack.com/client/T01NYRYPN6T/C01PAGWQM7X go-ontology slack channel].
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)
*[[Jenkins]]


===TermGenie===
==Ontology release pipeline==
*[[Template-able Requests Prior To TG]]
* [[Release Pipeline]]


===Website===
*[[Editorial-type sections copied over from the GO website ontology documentation: MF]]


===Protege===
[[Category:Ontology]][[Category:GO Editors]]
*[[Protege workshop]] Jan. 2012
*[[Ontology_workshop_Jan_2013]]
*[[Protege Feature Requirements]]
 
[[Category:Ontology]]
 
===Complex Modeling===
*[[Regulation]]
 
*[[Noctua_meeting_140929|Modelling complex annotations in noctua - meeting 140929]]
 
===Annotation extensions===
*[[Terms that could be obsoleted if information was collected as annotation extension]]
 
==Meetings==
===Cambridge Editors' meetings - weekly Tuesday 10-11 AM===
 
*[[CamEds Ontology meeting 2012-06-19|June 19]]
*[[CamEds Ontology meeting 2012-06-26|June 26]]
*[[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 - now fortnightly, Mondays, 4-5pm BST===
 
*[[SourceForge meeting 2013-07-24|July 24]]
*[[SourceForge meeting 2013-09-04|Sept 4]]
*[[SourceForge meeting 2013-09-11|Sept 11]]
*[[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]]
*[[SourceForge meeting 2015-02-11|Feb 11th]]
*[[SourceForge meeting 2015-02-25|Feb 25th]]
*[[SourceForge meeting 2015-03-11|Mar 11th]]
*[[SourceForge meeting 2015-03-25|Mar 25th]]
*[[SourceForge meeting 2015-04-22|Apr 22nd]]
*[[SourceForge meeting 2015-04-29|Apr 29th]]
*[[SourceForge meeting 2015-06-22|Jun 22nd]]
*[[SourceForge meeting 2015-12-14|Dec 14th]]
 
 
 
[[Category:Ontology]]
[[Category:Meetings]]
 
===Editor's Conference calls-weekly NOW ON MONDAYS, 12:00PM-1:00PM EST===
 
*[[Ontology editor's conference call minutes 2011|2011 minutes]]
*[[Ontology editor's conference call minutes Jan-June 2012|Jan-June 2012 minutes]]
*[[Ontology editor's conference call minutes July-Dec 2012|July-Dec 2012 minutes]]
*[[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 editor's conference call minutes Jan-June 2015|Jan-June 2015 minutes]]
*[[Ontology editor's conference call minutes July-Dec 2015|July-Dec 2015 minutes]]
*[[Ontology editor's conference call minutes Jan-June 2016|Jan-June 2016 minutes]]
*[[Ontology editor's conference call minutes July-Dec 2016|July-Dec 2016 minutes]]
*[[Ontology editor's conference call minutes Jan-June 2017|Jan-June 2017 minutes]]
*[[Ontology editor's conference call minutes July-Dec 2017|July-Dec 2017 minutes]]
*[[Ontology editor's conference call minutes Jan-June 2018|Jan-June 2018 minutes]]
 
==Useful Links==
*[[Completed ontology content work]]
*[[SF + TG Rota for Gene Ontology requests|Github and TermGenie Rota for Ontology Requests]]
*[[Ontology_Development_Reports|Ontology Development Reports]] (discontinued Nov 2010)
 
[[Category:Ontology]]
 
==Administrative==
*[[Ontology Development group summary]]
 
 
[[Category:Ontology]]

Latest revision as of 09:59, 8 January 2024

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

Pascale Gaudet, Raymond Lee, Edith Wong, Val Wood

Software support

Jim Balhoff

Other group members

Tanya Berardini, Karen Christie, Peter D'Eustachio, David Hill, Kimberly VanAuken

PIs

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

GO ontology in GitHub

  • The Gene Ontology uses an issue tracker hosted on GitHub to record and track ontology issues.
  • The go-annotation repo on GitHub may be accessed here.
  • Contact information for each group that contributes to the consortium is available here

GO ontology on slack

Ontology release pipeline