Ontology Development: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
 
(573 intermediate revisions by 13 users not shown)
Line 1: Line 1:
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 <span class="plainlinks">[http://thebeginnerslens.com/ <span style="color:black;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">iphone photography</span>] 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 <span class="plainlinks">[http://www.bestpills4weightloss.com/ <span style="color:black;font-weight:normal; text-decoration:none!important; background:none!important; text-decoration:none;">weight loss pills</span>] 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.
= 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.


==Content Development ==
= Group Leader =
===Priority ranking===
Pascale Gaudet (GO Central); GitHub: @pgaudet
====High Priority====
*Cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]
**[[Cell cross-products]] (Jane, Alex, Chris, others?)
**[[XP:biological_process_xp_chebi |Chebi cross-products]] (David, Jane, Tanya, Chris, Harold, Midori)
*[[Function-Process Links]]
*[[Chemical terms in GO]](Part of the CHEbi alignment process)
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David)
*[[Virus terms|Virus-related term overhaul]] (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh, Alexander Diehl & others)
*[[Apoptosis]]


====Medium Priority====
== Ontology editors==
*[[Non-symbiotic multi-organism processes]]
Pascale Gaudet, Raymond Lee, Edith Wong, Val Wood
*[[Neurobiology Project]] (David, Tanya, Jane, Paola)
*[[:Category:Content MENGO|MENGO collaboration]] (Jane)
*[[Signaling |Signaling overhaul]] (Becky, signaling WG)
*[[Kidney Physiology]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
*[[Cardiac conduction]] (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
*[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris)


====Low priority====
==Software support==
*Peripheral nervous system development
Jim Balhoff
*[[Uberon alignment]]


===Timeline===
== Other group members==
Tanya Berardini, Karen Christie, Peter D'Eustachio, David Hill, Kimberly VanAuken


[[2010 Timeline]]
==PIs==
Chris Mungall, Paul Thomas


[[2011 Timeline]]
=Communication=
==Editor's Conference calls==


[[2012 Timeline]]
=== 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]]


===Proposed content work===
===GO ontology in GitHub===
A list of topics that we propose to address, but for which a timeline has not been set
* The Gene Ontology uses an issue tracker hosted on [https://github.com/geneontology GitHub] to record and track ontology issues.
* The go-annotation repo on GitHub may be accessed [https://github.com/geneontology/go-ontology here].
* 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]


*Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology.
===GO ontology on slack===
*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].
*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].
*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]]
* [[multi-organism processes v/s cellular processes]]
* [[protein and peptidyl amino acid modification / protein processing]]
* [[Response to drug]]
* [[Polyketide synthases]]
* [[cell growth/proliferation/division]]
* [[oxidoreductases]]


===[[Completed ontology content work]]===
==Ontology release pipeline==
* [[Release Pipeline]]


==Other Ontology Development Group Activities==
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)
*[[Tracker wishlist]]
*[[Content Meeting Documentation]]
**[http://wiki.geneontology.org/index.php/Content_Meeting_Participants_Information|Content meeting participants' information]
*[[:Category:Curator Guides|Curator guides]]
*[[Ontology Documentation Drafts]] - for working on documentation of ontology content that will become part of the web-based documentation
*[[microbial ontology development and annotation]]
*[[New Ontology Editor Training]]
*[[Cell-type specific GO terms]]
*[[Ontology_Development_Reports|Reports]]


==Editor's Conference calls-weekly 7-7.30 AM PST==
[[Category:Ontology]][[Category:GO Editors]]
*[[July 6]]
*[[July 20]]
*[[Aug 3]]
*[[Aug 17]]
*[[Aug 31]]
*[[Ontology meeting 2011-09-14|Sept 14]]
*[[Ontology meeting 2011-09-28|Sept 28]]
*[[Ontology meeting 2011-10-05|Oct 5]]
*[[Ontology meeting 2011-10-12|Oct 12]]
*[[Ontology meeting 2011-10-19|Oct 19]]
*[[Ontology meeting 2011-10-26|Oct 26]]
*[[Ontology meeting 2011-11-02|Nov 2]]
*[[Ontology meeting 2011-11-16|Nov 16]]
*[[Ontology meeting 2011-11-23|Nov 23]]
*[[Ontology meeting 2011-11-30|Nov 30]]
*[[Ontology meeting 2011-12-7|Dec 7]]
*[[Ontology meeting 2011-12-14|Dec 14]]
*[[Ontology meeting 2011-12-21|Dec 21]]
 
==Administrative==
*[[Ontology Development group summary]]
*[[Meeting_minutes:_general_topics|Miscellaneous meeting minutes]]
 
[[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