Ontology Development: Difference between revisions
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*[[Ontology editor's conference call minutes Jan-June 2014|Jan-June 2014 minutes]] | *[[Ontology editor's conference call minutes Jan-June 2014|Jan-June 2014 minutes]] | ||
*[[Ontology meeting 2014-07-03|Jul 3]] | *[[Ontology meeting 2014-07-03|Jul 3]] | ||
*[[Ontology meeting 2014-07-10|Jul 10]] | *[[Ontology meeting 2014-07-10|Jul 10]] | ||
Revision as of 10:52, 3 July 2014
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
- Editor_Guide
- 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
TermGenie
Website
Protege
LEGO
Annotation extensions
Meetings
Cambridge Editors' meetings - weekly Tuesday 10-11 AM
SourceForge Meetings: Fortnightly, Wednesdays, 4:30-5:15pm BST
- July 24
- Sept 4
- Sept 11
- Sept 25
- Oct 9
- Oct 30
- Dec 11th
- Jan 29th
- Feb 12th
- Feb 26th
- Apr 23rd
- May 14th
- June 25th
Editor's Conference calls-weekly NOW ON THURSDAYS, 8:30-9:15 AM PST
- 2011 minutes
- Jan-June 2012 minutes
- July-Dec 2012 minutes
- Jan-June 2013 minutes
- July-Dec 2013 minutes
- Jan-June 2014 minutes
Useful Links
- Completed ontology content work
- SF + TG Rota for Gene Ontology requests
- Ontology Development Reports (discontinued Nov 2010)