Ontology Development: Difference between revisions

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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.
= 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.


==Administrative==
Pascale Gaudet (GOC); GitHub: @pgaudet
*[[Ontology Development group summary]]
*[[Meeting_minutes:_general_topics|Miscellaneous meeting minutes]]


==Content Development ==
=Communication=
===Priority ranking===
==Editor's Conference calls==
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)
 
*High Priority
=== When ===
**Cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]
 
***[[Cell cross-products]] (Jane, Alex, Chris, others?)
* Calls are held weekly on Mondays, 12:00PM-1:00PM EST
***[[XP:biological_process_xp_chebi |Chebi cross-products]] (David, Jane, Tanya, Chris, Harold, Midori)
* Calls are scheduled on the GO's Google calendar.  Please request access to the calendar if you don't have it.
**[[Function-Process Links]]
* Reminder emails are sent out to the go-ontology mailing list (see [[Internal_email_lists]] to register).
***part_of links between function and process (David, Tanya)
 
***has_part links between function and process (Harold, Jen)
 
**Generic [[GO slim overhaul]] (Jane & Val)
=== Agenda and Minutes ===
**[[Chemical terms in GO]](Part of the CHEbi alignment process)
* [[Ontology editors' conference call minutes 2020|2020]]
**[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David)
* 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]] |
**[[Virus terms|Virus-related term overhaul]] (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh, Alexander Diehl & others)
 
**[[Apoptosis]]
= Documentation=
*Medium Priority
==[[Protege5_5_setup_for_GO_Eds|Protégé 5.5 setup]]==
**[[Neurobiology Project]] (David, Tanya, Jane, Paola)
==[[Installing and Using git]]==
**[[:Category:Content PAMGO|PAMGO collaboration]] (Jane)
==[[Ontology Editors Daily Workflow]]==
**[[:Category:Content MENGO|MENGO collaboration]] (Jane)
==Editing the Ontology==
**[[Signaling |Signaling overhaul]] (Becky, signaling WG)
 
**[[Kidney Development]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
 
**[[Kidney Physiology]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
{| class="wikitable"
**[[protein and peptidyl amino acid modification / protein processing]]
!colspan="2" | [[General Gene Ontology Principles]]
**[[Cardiac conduction]] (David, Ruth, Doug, Tanya, Becky, Paola, Stan)  
|-
*Low priority
!colspan="2" | New terms
**[[Response to drug]] (Jen)
|-
**Peripheral nervous system development
|rowspan="10"|[[Principles for creating a GO term]] (being reviewed)
**[[Polyketide synthases]]
|[[Guidelines for creating a GO term]]
**[[cell growth/proliferation/division]]
|-
**[[oxidoreductases]]
|[[Guidelines for creating relationships between terms]] (being reviewed)
**[[Uberon alignment]]
|-
|[[Guidelines for creating disjoint terms]] (to be written)
|-
|[[Guidelines for creating a Regulation Term]]
|-
|[[Guidelines for GO textual definitions]] (being reviewed)
|-
|[[Guidelines for equivalence axioms]] (being reviewed) ---  Also [[Logical_Definitions]] (being reviewed)
|-
|[[Guidelines for new Molecular Functions]] (new)
|-
|[[Guidelines for new Biological Processes]] (new)
|-
|[[Guidelines for new Cellular Components]] (new)
|-
|[[Guidelines for 'database cross references' and 'definition database cross references']] (new)
|-
!colspan="2" |Modifying existing terms
|-
|rowspan="5"|[[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| Adding and Removing Taxon Restrictions]]
|-
|[[Adding References to GitHub tickets]]
|-
!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==
 
==Website - to be moved to the wiki?==


===Timeline===
* [http://www.geneontology.org/page/biological-process-ontology-guidelines  Biological-process-ontology-guidelines]


[[2010 Timeline]]
=[[Identifiers]] To be reviewed=


[[2011 Timeline]]
=[[Content Meeting Documentation|Guidance for organizing content meetings]]=
====Current content work====
(old doc, but basic principles still apply)
*[[Chemical terms in GO]] - manually curate GOCHE (June 2010), fix relationships in GOCHE (June/July 2010), align GOCHE with ChEBI (July 2010), submit paper (sept 2010).
*Internal cross-products (first set Jan 2010, cc x cc (po) May 2010, bp x bp (po) June 2010
*[[Virus terms|Virus-related term overhaul]] (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh & others)(waiting on file from Philipe le Mercier - some time 2010)
*[[Signaling |Signaling overhaul]] (high-level terms committed Feb 2010), Becky clean-up until May 2010
*[[Transcription |Transcription & transcription factor activity overhaul]] - started June 2008 completion target July 2010
*[[Taxon and sensu|Taxon data]] (file committed Feb 2010, Jane maintaining file until UniProt new person takes it over in summer)
*[[Function-Process Links]] - pilot projects begun Feb. 2008; first links added May 2009, transporters->transport finished May 2010, catalytic activities end 2010
*Generic [[GO slim overhaul]] - (finished first round, needs refining)
*kidney development (generic kidney finished March 2010, metanephros April 2010, pronephros May 2010, mesonephros, June 2010, fly renal, July 2010, Sept 2010 write paper)
*[[Non-symbiotic multi-organism processes]]
*QC - ongoing
*SF ongoing
*Enzyme reaction mappings to EC, MetaCyc, KEGG, other dbs? - ongoing


====Future content work====
*[[Polyketide synthases]]


===[[Selected SourceForge links]]===
=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]]


===Completed content work===
===Low priority===
*[[Heart_Development_workshop|Heart Development]] (David, Ruth, Varsha, Doug, Susan, Yasmin, Becky)
*[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris, DavidOS)
*[[Cellular component processes]] (Jane, David, Midori, Val, ad hoc others)
*[[microbial ontology development and annotation]]
*[[Transporters]] (Jen and community experts)
 
===Completed projects===
*[[Adding missing CHEBI xps]]
*[[Cell cross-products]], [[Cell-type specific GO terms]] (Jane, Paola, Alex, Chris, DavidOS)
*Addition of cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]
*[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)
*[[:Category:Content PAMGO|PAMGO collaboration]], phase 2 (as of Jan. 2007)
*[[Immunology Revisions]]
*[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
*[[Autophagy 2015-2016]] (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]]
*[[Central Nervous System Development]]
*[[Isa-complete_BP|is_a complete biological process]]
*[[Chaperones]](completed by working group at Cambridge GOC meeting Sept. 2009)
*[[:Category:Content PAMGO|PAMGO collaboration]], phase 1
*Ciliary components and processes (Paola, Karen Christie, SYSCILIA experts) [https://www.ncbi.nlm.nih.gov/pubmed/29177046 Roncaglia et al 2017]
*Correct disjointness violations
*[[RNA processing]]
*[[Collaboration with MIT GO-Engineering]] - Manuscript written
*[[Collaboration with MIT GO-Engineering]] - Manuscript written
*[[Muscle Development]] - Started Feb. 2007; meeting July 2007; Done Oct 2007
*[[Electron transport]]
*[[Cardiovascular physiology/development]] - implemented Oct 2007
*Extracellular RNA-containing vesicles (Paola, Aleks and community experts) [https://www.ncbi.nlm.nih.gov/pubmed/27076901 Cheung et al 2016]
*Make cc part_of tree complete (i.e. find homes for the children of 'unlocalized protein complex')
*[[FP-regulates| regulates links between function and process]] (David, Tanya)
*[[Sensu Main Page|Sensu revamp]]
*[[Regulation Main Page]] live March 2008
*Gene expression ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1418820&group_id=36855| SF 1418820])
*Gene expression ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1418820&group_id=36855| SF 1418820])
*[[Electron transport]]
*[[Proteases |Peptidase & protease activity overhaul]] begun June 2008; essentially completed August 2008
*[[SDB 2009]]
*[[ASCB 2009]]
*[[Function-Process Links]]
*[[Function-Process Links]]
**[[FP-regulates| regulates links between function and process]] (David, Tanya)
*[[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)
*[[Morphogenesis]] (David, Tanya)
*regulates links- Dec 2008 (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)
*[[Regulators |Regulator, activator and inhibitor MF terms]] (David, Tanya)
*[[Chaperones]](completed by working group at Cambridge GOC meeting Sept. 2009)
*[[RNA processing]]
*[http://wiki.geneontology.org/index.php/Lung_Development Lung Development] (David, Jen, community experts)
*[[SDB 2009]]
*[[Binding_terms_working_group|Binding]] discussion - mainly annotation issues, but with some ontology content points
*[[Sensu Main Page|Sensu revamp]]
*[[Cellular component processes]] (Jane, David, Midori, Val, ad hoc others) - started summer 2008
*[[Signaling |Signaling overhaul]] (Becky, signaling WG)
*[[Transporters]] - Started Feb. 2007
*[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
*[[Utilization]] - done March 2010
*[[plasma lipoprotein particle ontology]] - done Sept. 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===
===Proposed content work===
A list of topics that we propose to address, but for which a timeline has not been set
A list of topics that we propose to address, but for which a timeline has not been set
 
*Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology.
*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].
*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]]
 
==Other Ontology Development Group Activities==
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)
*[[Tracker wishlist]]
*[[Webinar Software Investigation]]
*[[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]]


==Reports==
* [[protein and peptidyl amino acid modification / protein processing]]
Beginning with the November 2006 document, reports emphasize ontology development work. Reports issued between November 2006 and December 2009 also include a section that gives an overview of other GO Editorial Office staff activities, with the emergence of regular reports from other management groups, the second section has become redundant. Reports issued prior to November 2006 are not divided into parts, and have a GO Editorial Office-centric perspective, but do cover a substantial portion of the GOC's ontology development work.
* [[Response to drug]]
* [[Polyketide synthases]]


*Nov 2006 - Nov 2010 [[Ontology_Development_reports|Ontology Development reports]]
=Quality Control=
*Jul 2005 - Oct 2006 [[GO Editorial Office reports]]
==SPARQL checks on the ontology==
[https://github.com/rctauber/robot/tree/reporting/robot-core/src/main/resources/queries SPARQL checks on the ontology]


==Editor's Conference calls-weekly 7-7.30 AM PST==
==Ontology release pipeline==
*[[July 6]]
* [[Release Pipeline]]
*[[July 20]]
* [http://current.geneontology.org/reports/gorule-report.html GO Rules rrrors reports]
*[[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 2011-11-23|Nov 30]]
*[[Ontology meeting 2011-11-23|Dec 7]]
*[[Ontology meeting 2011-11-23|Dec 14]]
*[[Ontology meeting 2011-11-23|Dec 21]]


==GO Clinics==
'''TO BE REPLACED'''
*Ongoing work on Quality control reports; see [[Ontology_Quality_Control]] (David, Jane, Chris, Tanya)


*[[GO clinic late 2009]]
*[[GO clinic spring 2010]]




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

Revision as of 02:37, 22 June 2020

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.

Pascale Gaudet (GOC); GitHub: @pgaudet

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

Documentation

Protégé 5.5 setup

Installing and Using git

Ontology Editors Daily Workflow

Editing the Ontology

General Gene Ontology Principles
New terms
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 (to be written)
Guidelines for creating a Regulation Term
Guidelines for GO textual definitions (being reviewed)
Guidelines for equivalence axioms (being reviewed) --- Also Logical_Definitions (being reviewed)
Guidelines for new Molecular Functions (new)
Guidelines for new Biological Processes (new)
Guidelines for new Cellular Components (new)
Guidelines for 'database cross references' and 'definition database cross references' (new)
Modifying existing terms
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 and Removing Taxon Restrictions
Adding References to GitHub tickets
Term obsoletion
Principles for term obsoletion Obsoleting an Existing Ontology Term
Restoring an Obsolete Ontology Term
Term merges
Principles for merging terms (being reviewed) Merging Ontology Terms
Subsets
Subset documentation (to add) Adding and Removing GO Subsets (Slims)
Import Files
Principles for GO import files Adding Terms and Regenerating the Import Files

Relations General Relations Documentation Draft To be reviewed

Website - to be moved to the wiki?

Identifiers To be reviewed

Guidance for organizing content meetings

(old doc, but basic principles still apply)


Content Development

Ongoing Projects

Low priority

Completed projects

Proposed content work

A list of topics that we propose to address, but for which a timeline has not been set

Quality Control

SPARQL checks on the ontology

SPARQL checks on the ontology

Ontology release pipeline

TO BE REPLACED