Difference between revisions of "Ontology Development"

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m (Completed ontology content work)
m (Projects)
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*[[Cell Cycle]] (Val, Pombe experts, GOEds)
 
*[[Cell Cycle]] (Val, Pombe experts, GOEds)
 
*[[Enzymes and EC mappings]]
 
*[[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)
 
*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===
 
===Medium Priority===
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*[[:Category:Content PAMGO|PAMGO collaboration]], phase 2 (as of Jan. 2007)
 
*[[: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
 +
*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]]
 
*[[ASCB 2009]]
 
*[[Binding_terms_working_group|Binding]] discussion - mainly annotation issues, but with some ontology content points
 
*[[Binding_terms_working_group|Binding]] discussion - mainly annotation issues, but with some ontology content points
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*[[Central Nervous System Development]]
 
*[[Central Nervous System Development]]
 
*[[Chaperones]](completed by working group at Cambridge GOC meeting Sept. 2009)
 
*[[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
 
*[[Collaboration with MIT GO-Engineering]] - Manuscript written
 
*[[Electron transport]]
 
*[[Electron transport]]
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*[[Sensu Main Page|Sensu revamp]]
 
*[[Sensu Main Page|Sensu revamp]]
 
*[[Signaling |Signaling overhaul]] (Becky, signaling WG)
 
*[[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
 
*[[Transcription |Transcription & transcription factor activity overhaul]] (Karen, David) - 2012
 
*[[Transporters]] (Jen and community experts) - Started Feb. 2007
 
*[[Transporters]] (Jen and community experts) - Started Feb. 2007

Revision as of 06:25, 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


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

Quality Control

SPARQL checks on the ontology

[|SPARQL checks on the ontology]

Ontology release pipeline

TO BE REPLACED