Ontology Development: Difference between revisions

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== Ontology editors==
== Ontology editors==
Karen Christie, Harold Drabkin, Raymond Lee, Pascale Gaudet
Pascale Gaudet, Raymond Lee, Edith Wong, Val Wood


==Software support==
==Software support==
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== Other group members==
== Other group members==
Peter D'Eustachio, Tanya Berardini, Kimberly VanAuken, David Hill, Chris Mungall, Paul Thomas
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).  
=== Agenda and Minutes ===
=== Agenda and Minutes ===
* [[Ontology editors' conference call minutes 2021|2021]]
* [[Ontology editors' conference call minutes 2023|2023]]
* Past Annotation 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]]
* 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]]
 
= Documentation=
==[[Protege5_5_setup_for_GO_Eds|Protégé 5.5 setup]]==
==[[Installing and Using git]]==
==[[Ontology Editors Daily Workflow]]==
==Editing the Ontology==
 
===Ontology editing principles===
 
{| class="wikitable"
!Topic
! Status
! Last reviewed
|-
|[[General Gene Ontology Principles]]
| Under review
|
|-
|'''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]]
|
|
|}
 
===How-to:Protégé instructions===
 
 
 
{| class="wikitable"
|-
! New terms
|-
|[[Guidelines for creating a GO term |GO term creation procedure]]
|-
|[[Guidelines for creating a Regulation Term|Procedure for creation of 'Regulation' terms]]
|-
|[[Guidelines for creating relationships between terms]] (being reviewed)
|-
|[[Guidelines for equivalence axioms]]  (being reviewed) ---  Also [[Logical_Definitions]] (being reviewed)
|-
|[[Disjoint_Documentation |Guidelines for creating disjoint terms]] (being reviewed)
|-
|[[Guidelines for using ChEBI terms]]
|-
!Term annotations
|-
|[[Adding or Deleting Asserted Subclasses]]
|-
|[[Adding Term Comments]]
|-
|[[Synonyms]]
|-
|[[Guidelines for 'database cross references' and 'definition database cross references']] (dbxrefs)
|-
|[[Adding a Term to a GO Subset (Slim)]]
|-
|[[Adding Taxon Restrictions| 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=
 
=[[Content Meeting Documentation|Guidance for organizing content meetings]]=
(old doc, but basic principles still apply)
 
 
=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]]
 
===Low priority===
*[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris, DavidOS)
*[[microbial ontology development and annotation]]


===Completed projects===
===GO ontology in GitHub===
*[[Adding missing CHEBI xps]]
* The Gene Ontology uses an issue tracker hosted on [https://github.com/geneontology GitHub] to record and track ontology issues.
*[[Cell cross-products]], [[Cell-type specific GO terms]] (Jane, Paola, Alex, Chris, DavidOS)
* The go-annotation repo on GitHub may be accessed [https://github.com/geneontology/go-ontology here].
*Addition of cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]
* 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]
*[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).


===Proposed content work===
===GO ontology on slack===
A list of topics that  we propose to address, but for which a timeline has not been set
*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].
 
* [[protein and peptidyl amino acid modification / protein processing]]
* [[Response to drug]]
* [[Polyketide synthases]]
 
=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==
* [[Release Pipeline]]
* [[Release Pipeline]]
* [http://current.geneontology.org/reports/gorule-report.html GO Rules rrrors reports]
'''TO BE REPLACED'''
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)




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

Revision as of 09:37, 8 March 2023

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