Difference between revisions of "Ontology Development"

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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 <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]]
== Ontology editors==
**[[Cell cross-products]] (Jane, Alex, Chris, others?)
Karen Christie, Harold Drabkin, Raymond Lee, Pascale Gaudet
**[[XP:biological_process_xp_chebi |Chebi cross-products]] (David, Jane, Tanya, Chris, Harold, Midori)
 
*[[Function-Process Links]]
==Software support==
*[[Chemical terms in GO]](Part of the CHEbi alignment process)
Jim Balhoff
*[[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)
== Other group members==
*[[Apoptosis]]
Peter D'Eustachio, Tanya Berardini, Kimberly VanAuken, David Hill, 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 ===
* [[Ontology editors' conference call minutes 2022|2022]]
* 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]]
 
= Documentation=
Useful reference: [https://oboacademy.github.io/obook/ On becoming an OBO Semantic Engineer], by James Overton, Becky Jackson, Nicole Vasilevsky, Nicolas Matentzoglu, and Shawn Tan.
 
This book provides best practices as recommended by OBO Foundry. Note that some parts of this book may be more general than the documentation presented in this wiki.
 
==[[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
|
|-
! colspan="3" |'''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]]
|
|
|-
|[[Guidelines for 'database cross references' and 'definition database cross references' |Database cross references and definition database cross references]] (dbxrefs)
|
|
|-
|[[External ontologies]]
|
|
|}
 
 
{| class="wikitable"
! Guidelines for specific terms
! Status
! Last reviewed
|-
| [[Principles for catalytic activity terms]]
| Draft
| 2022-05-16
|-
|
|
|
|}
 
===How-to:Protégé instructions===
 
 
{| class="wikitable"
!Topic
! Status
! Last reviewed
|-
! colspan="3" | New terms
|-
|[[Guidelines for creating a GO term |GO term creation procedure]]
| Current
| 2022-05-17
|-
|[[Guidelines for creating a Regulation Term|Procedure for creation of 'Regulation' terms]]
|
|
|-
|[[Guidelines for creating relationships between terms]]
| Under review
|
|-
|[[Guidelines for equivalence axioms]]  (being reviewed) ---  Also [[Logical_Definitions]]
| Under review
|
|-
|[[Disjoint_Documentation |Guidelines for creating disjoint terms]]
| Under review
|
|-
|[[Guidelines for using ChEBI terms]]
|
|
|-
! colspan="3" |Term annotations
|-
|[[Adding or Deleting Asserted Subclasses]]
|
|
|-
|[[Adding Term Comments]]
|
|
|-
|[[Synonyms]]
|
|
|-
|[[Adding a Term to a GO Subset (Slim)]]
|
|
|-
|[[Adding Taxon Restrictions| Adding and Removing Taxon Restrictions]]
|
|
|-
! colspan="3" |Term obsoletion
|-
|[[Obsoleting an Existing Ontology Term]]
|
|
|-
|[[Restoring an Obsolete Ontology Term]]
|
|
|-
! colspan="3" |Term merges
|-
|[[Merging Ontology Terms]]
|
|
|-
! colspan="3" |Subsets
|-
|[[Adding and Removing GO Subsets (Slims)]]
|
|
|-
! colspan="3" |[[GO import files]]
|-
|[[Adding Terms and Regenerating the Import Files]]
|}


====Medium Priority====
=[[Identifiers]] To be reviewed=
*[[Non-symbiotic multi-organism processes]]
*[[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====
=[[Content Meeting Documentation|Guidance for organizing content meetings]]=
*Peripheral nervous system development
(old doc, but basic principles still apply)
*[[Uberon alignment]]


===Timeline===


[[2010 Timeline]]
=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]]


[[2011 Timeline]]
===Low priority===
*[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris, DavidOS)
*[[microbial ontology development and annotation]]
 
===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)
*[[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===
===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]]
* [[protein and peptidyl amino acid modification / protein processing]]
* [[protein and peptidyl amino acid modification / protein processing]]
* [[Response to drug]]
* [[Response to drug]]
* [[Polyketide synthases]]
* [[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]


==Other Ontology Development Group Activities==
==Ontology 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)
*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==
*[[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]]
[[Category:Ontology]][[Category:GO Editors]]

Latest revision as of 08:09, 30 June 2022

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

Karen Christie, Harold Drabkin, Raymond Lee, Pascale Gaudet

Software support

Jim Balhoff

Other group members

Peter D'Eustachio, Tanya Berardini, Kimberly VanAuken, David Hill, 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

Documentation

Useful reference: On becoming an OBO Semantic Engineer, by James Overton, Becky Jackson, Nicole Vasilevsky, Nicolas Matentzoglu, and Shawn Tan.

This book provides best practices as recommended by OBO Foundry. Note that some parts of this book may be more general than the documentation presented in this wiki.

Protégé 5.5 setup

Installing and Using git

Ontology Editors Daily Workflow

Editing the Ontology

Ontology editing principles

Topic Status Last reviewed
General Gene Ontology Principles Under review
Creating a new GO term - by aspect
*  New Molecular Functions
*  New Binding terms
*  New Biological Processes
*  New Cellular Components
Guidelines for GO textual definitions
Relations
Merging terms
Obsoleting terms
Database cross references and definition database cross references (dbxrefs)
External ontologies


Guidelines for specific terms Status Last reviewed
 Principles for catalytic activity terms  Draft 2022-05-16

How-to:Protégé instructions

Topic Status Last reviewed
New terms
GO term creation procedure  Current 2022-05-17
Procedure for creation of 'Regulation' terms
Guidelines for creating relationships between terms Under review
Guidelines for equivalence axioms (being reviewed) --- Also Logical_Definitions Under review
Guidelines for creating disjoint terms Under review
Guidelines for using ChEBI terms
Term annotations
Adding or Deleting Asserted Subclasses
Adding Term Comments
Synonyms
Adding a Term to a GO Subset (Slim)
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

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