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====
*[[Cell Cycle]] (Val, Pombe experts, GOEds)
*Ongoing 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)
*[[Enzymes and EC mappings]]


====Medium Priority====
== Ontology editors==
*[[Non-symbiotic multi-organism processes]] (Jane)
Pascale Gaudet, Raymond Lee, Val Wood
*[[Neurobiology Project]] (David, Tanya, Jane, Paola, DavidOS)


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


====Recently completed projects====
== Other group members==
*[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
Tanya Berardini, Peter D'Eustachio, Steven Marygold, Li Ni, Kimberly VanAuken
*[[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


*Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology.
=Communication=
*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)
==Editor's Conference calls==
* [[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]]


*[[Content Meeting Documentation|Guidance for organizing content meetings]]
===GO ontology in GitHub===
*[[:Category:Curator Guides|Curator guides]]
* The Gene Ontology uses an issue tracker hosted on [https://github.com/geneontology GitHub] to record and track ontology issues.
*[[Editor_Guide]]
* The go-annotation repo on GitHub may be accessed [https://github.com/geneontology/go-ontology here].
*[[Ontology Documentation Drafts]] - for working on documentation of ontology content that will become part of the web-based documentation
* 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]
*[[New Ontology Editor Training]]
*[[Ontology Editing Examples|Ontology Editing Examples: Regulation of a pathway by regulation of enzyme activity]]


==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]]
 
===LEGO===
*[[Regulation]]
 
*[[Noctua_meeting_140929|Modelling complex annotations in LEGO/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===
 
*[[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]]
 
 
[[Category:Ontology]]
[[Category:Meetings]]
 
===Editor's Conference calls-weekly NOW ON THURSDAYS, 8:30-9:15 AM PST===
 
*[[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|Jan-July 2014 minutes]]
 
*[[Ontology meeting 2015-01-06|Jan 6]] First call of 2015
 
==Useful Links==
*[[Completed ontology content work]]
*[[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]]

Latest revision as of 21:46, 19 April 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, Val Wood

Software support

Jim Balhoff

Other group members

Tanya Berardini, Peter D'Eustachio, Steven Marygold, Li Ni, 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

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