Ontology Development: Difference between revisions
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==Guides, Training and Documentation== | ==Guides, Training and Documentation== | ||
*[[:Category:Curator Guides|Curator guides]] | *[[:Category:Curator Guides|Curator guides]] | ||
*[[Editor_Guide]] | *[[Editor_Guide]] | ||
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*[[Ontology Editing Examples|Ontology Editing Examples: Regulation of a pathway by regulation of enzyme activity]] | *[[Ontology Editing Examples|Ontology Editing Examples: Regulation of a pathway by regulation of enzyme activity]] | ||
*[[Guidelines on 'protein complex' terms]] | *[[Guidelines on 'protein complex' terms]] | ||
*[[Content Meeting Documentation|Guidance for organizing content meetings]] (old doc, but basic principles still apply) | |||
==Other Ontology Development Group Activities== | ==Other Ontology Development Group Activities== | ||
Revision as of 09:37, 11 January 2016
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
- Synapse project (Synapse experts, DavidOS, Becky Foulger)
Medium Priority
- Non-symbiotic multi-organism processes (Jane, David OS)
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
- Neurobiology Project (David, Tanya, Jane, Paola, DavidOS)
- 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
- 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
- Guidelines on 'protein complex' terms
- Guidance for organizing content meetings (old doc, but basic principles still apply)
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 - now fortnightly, Mondays, 4-5pm 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
- Sept 10th
- Sept 24th
- Oct 22nd
- Feb 11th
- Feb 25th
- Mar 11th
- Mar 25th
- Apr 22nd
- Apr 29th
- Jun 22nd
- Dec 14th
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
- July-Dec 2014 minutes
- Jan 6 First call of 2015
- Jan 13
- Jan 20
- Jan 27
- Feb 5
- Feb 12
- Feb 19
- Feb 26
- Mar 5
- Mar 12
- Mar 19
- Mar 26
- Apr 2
- Apr 9
- Apr 16
- Apr 23
- Apr 30
- May 7
- May 14
- May 21 Cancelled
- May 28
- Jun 4
- Jun 11
- Jun 18
- Jun 25
- Jul 2
- Jul 9 Cancelled
- Jul 16
- Jul 23
- Jul 30
- Aug 6
- Aug 13
- Aug 20
- Aug 27
- Sep 3 Cancelled (traveling back from GOC meeting)
- Sep 10
- Sep 17
- Sep 24
- Oct 1
- Oct 8
- Oct 15
- Oct 22
- Oct 29
- Nov 5
- Nov 12
- Nov 19
- Nov 26 Cancelled (Thanksgiving)
- Dec 3
- Dec 10 Cancelled (several conflicting meetings)
- Dec 17
- Dec 24 Cancelled (Special leave day at EBI)
- Dec 31 Cancelled (Special leave day at EBI)
Useful Links
- Completed ontology content work
- SF + TG Rota for Gene Ontology requests
- Ontology Development Reports (discontinued Nov 2010)