Difference between revisions of "Ontology Development"

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===Completed projects===
 
===Completed projects===
*[http://wiki.geneontology.org/index.php/Extensions/x-metazoan-anatomy Uberon alignment] (DavidH)
+
**[[Adding missing CHEBI xps]]
*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)
 
**[[Cell cross-products]], [[Cell-type specific GO terms]] (Jane, Paola, Alex, Chris, DavidOS)
**[[Adding missing CHEBI xps]]
+
*[[: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
 +
*[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
 +
*[[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)
 +
*[[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)
 +
*[[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)
 +
*[[Collaboration with MIT GO-Engineering]] - Manuscript written
 +
*[[Electron transport]]
 +
*[[FP-regulates| regulates links between function and process]] (David, Tanya)
 +
*[[Function-Process Links]]
 +
*[[Heart_Development_workshop|Heart Development]] (David, Ruth, Varsha, Doug, Susan, Yasmin, Becky)
 +
*[[http://wiki.geneontology.org/index.php/Lung_Development Lung Development|Lung_Development 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)
 +
*[[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)
 +
*[[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)
 
*[[Signaling |Signaling overhaul]] (Becky, signaling WG)
 +
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David) - 2012
 +
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David) - 2012
 +
*[[Transporters]] (Jen and community experts)
 +
*[[Transporters]] - 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)
 
*[[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)
+
*[http://wiki.geneontology.org/index.php/Extensions/x-metazoan-anatomy Uberon alignment] (DavidH)
*[[Apoptosis]] (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
+
*Addition of cross-products - see [[:Category:Cross_Products]] and [[Cross_Product_Guide]]
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David) - 2012
+
*Correct disjointness violations
*[[Kidney Physiology]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)  
+
*Gene expression ([https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1418820&group_id=36855| SF 1418820])
*[[Cardiac conduction]] (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
+
*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)
 
*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).
 
*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===
 
===Proposed content work===

Revision as of 06:11, 9 April 2019

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

David Hill (MGI)

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

Setting up Protege for GO editors

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)
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 Taxon Restrictions
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

Projects

High Priority/Ongoing

  • Transcription 2018 (Pascale, Ruth, Astrid, Marcio, Paul T)
  • Cell Cycle (Val, Pombe experts, GOEds)
  • Enzymes and EC mappings
  • 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

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

Completed ontology content work

Quality Control

SPARQL checks on the ontology

[|SPARQL checks on the ontology]

Ontology release pipeline

TO BE REPLACED