Ontology Development: Difference between revisions

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= Group Leader =
= Group Leader =
David Hill (MGI)
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=
=Communication=
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=== When ===
=== When ===
* Calls are held weekly on Mondays, 12:00PM-1:00PM EST
* 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.
* 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).  
* Reminder emails are sent out to the go-ontology mailing list (see [[Internal_email_lists]] to register).  
=== How to Join ===
* Recurring meeting URL: https://stanford.zoom.us/j/828418143
*to join via phone: enter Meeting ID 828418143# after dialing in
*from US: +1 646 558 8656 (US Toll) or +1 408 638 0968 (US Toll)
=== Agenda and Minutes ===
=== Agenda and Minutes ===
*[[Ontology editor's conference call minutes 2018|Ontology editor's conference call minutes 2018]]
* [[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]]
* 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]] |
 
= Documentation=
==[[Protege_setup_for_GO_Eds|Setting up Protege for GO editors]]==
==[[Installing and Using git]]==
==[[Ontology Editors Daily Workflow]]==
==Editing the Ontology==
 


{| class="wikitable"
===GO ontology in GitHub===
!colspan="2" | [[General Gene Ontology Principles]]
* 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].
!colspan="2" | New terms
* 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]
|-
|rowspan="7"|[[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|Disjoint_Documentation]] (being reviewed)
|-
|[[Guidelines for creating a Regulation Term]]
|-
|[[Guidelines for GO textual definitions]] (being reviewed)
|-
|[[Guidelines for equivalence axioms]] (being reviewed)
|-
|[[Guidelines for new Molecular Functions]] (new)
|-
|[[Guidelines for new Biological Processes]] (new)
|-
|[[Guidelines for new Cellular Components]] (new)
|-
!colspan="2" |Modifying existing terms
|-
|rowspan="4"|[[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 Taxon Restrictions]]
|-
!colspan="2" |Term obsoletion
|-
|rowspan="2" |[[Principles for term obsoletion]]
|[[Obsoleting an Existing Ontology Term]]
|-
|[[Restoring an Obsolete Ontology Term]]
|-
!colspan="2" |Term merges
|-
|[[Principles for merging terms]] (being reviewed)
|[[Merging Ontology Terms]]
|-
!colspan="2" |Subsets
|-
|Subset documentation (to add)
|[[Adding and Removing GO Subsets (Slims)]]
|-
!colspan="2" |Import Files
|-
| Principles for [[GO import files]]
|[[Adding Terms and Regenerating the Import Files]]
|}


==[[Relations]] General Relations Documentation Draft To be reviewed==
===GO ontology on slack===
 
*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].
==[[New Ontology Editor Training]] To be reviewed==
==Website - to be moved to the wiki?==
 
* [[http://www.geneontology.org/page/biological-process-ontology-guidelines  Biological-process-ontology-guidelines]]
 
=[[Identifiers]] To be reviewed=
 
=[[Content Meeting Documentation|Guidance for organizing content meetings]]=
(old doc, but basic principles still apply)
 
 
=Content Development =
==Projects==
===High Priority/Ongoing===
*[[Transcription 2018]] (Pascale, Ruth, Astrid, Marcio, Paul T)
*[[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===
*[[Non-symbiotic multi-organism processes]] (Jane, David OS)
 
===Low priority===
*[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris, DavidOS)
*[[microbial ontology development and annotation]]
 
===Recently completed projects===
*[[Uberon alignment]] (DavidH)
*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===
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]]
* [[Response to drug]]
* [[Polyketide synthases]]
* [[cell growth/proliferation/division]]
* [[oxidoreductases]]
 
===[[Completed ontology content work]]===
 
=Quality Control=
==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==
http://wiki.geneontology.org/index.php/Release_Pipeline
* [[Release Pipeline]]
Errors: http://current.geneontology.org/ontology/reports/index.html
 
'''TO BE REPLACED'''
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)


=Other Ontology Development Group Activities=


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

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