Ontology Development: Difference between revisions

Revision as of 07:26, 19 November 2013

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.

Content Development

Projects

High Priority

Cell Cycle (Val, Pombe experts, GOEds)
Ongoing 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)
- Adding missing CHEBI xps
Signaling overhaul (Becky, signaling WG)
Virus-related term overhaul, Phage Terms (Jane Lomax, Brenley McIntosh, Rebecca Foulger & others)
Enzymes and EC mappings

Medium Priority

Non-symbiotic multi-organism processes (Jane)
Neurobiology Project (David, Tanya, Jane, Paola, DavidOS)

Low priority

Neuro Behaviour Ontology (NBO)-GO alignment (Jane, George Gkoutos, Chris, DavidOS)
Peripheral nervous system development
Uberon alignment (DavidOS)
microbial ontology development and annotation

Recently completed projects

Apoptosis (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
Transcription & transcription factor activity overhaul (Karen, David) - 2012
Kidney Physiology (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
Cardiac conduction (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
Rework disjoint terms as concluded in discussion on GO list (Jane).
MENGO collaboration (Jane)

Proposed content work

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.
Overhaul translation, similar to what's being done for transcription. 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
protein and peptidyl amino acid modification / protein processing
Response to drug
Polyketide synthases
cell growth/proliferation/division
oxidoreductases

Guides, Training and Documentation

Guidance for organizing content meetings
Curator guides
Ontology Documentation Drafts - for working on documentation of ontology content that will become part of the web-based documentation
New Ontology Editor Training
Ontology Editing Examples: Regulation of a pathway by regulation of enzyme activity

Other Ontology Development Group Activities

QC

Ongoing work on Quality control reports; see Ontology_Quality_Control (David, Jane, Chris, Tanya)
Jenkins

Meetings

Cambridge Editors' meetings - weekly Tuesday 10-11 AM

SourceForge Meetings: Fortnightly, Wednesdays, 4:30-5:15pm BST

Editor's Conference calls-weekly NOW ON THURSDAYS, 8:30-9:15 AM PST

Jul 4 No call (vacation day in the US)
Jul 11
Jul 18
Jul 25
Aug 1
Aug 8
Aug 15
Aug 22
Aug 29
Sep 5
Sep 12
Sep 19
Sep 26
Oct 10
Oct 17
Oct 24
Oct 31
Nov 7
Nov 14
Nov 20 (Wed. instead of Thu. bcs EBIers have a retreat on Thu.)
Nov 28 NO CALL (Thanksgiving)

Useful Links

Completed ontology content work
SF Rota for Gene Ontology requests
TermGenie1 Gatekeeper Rota
Ontology Development Reports (discontinued Nov 2010)

Administrative

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 *[[Ontology meeting 2013-11-07|Nov 7]]
 *[[Ontology meeting 2013-11-14|Nov 14]]
-*[[Ontology meeting 2013-11-21|Nov 21]]
+*[[Ontology meeting 2013-11-20|Nov 20]] (Wed. instead of Thu. bcs EBIers have a retreat on Thu.)
 *[[Ontology meeting 2013-11-28|Nov 28]] NO CALL (Thanksgiving)