Ontology Development: Difference between revisions

Revision as of 12:56, 14 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/Ongoing

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

Non-symbiotic multi-organism processes (Jane, David OS)

Low priority

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

Recently completed projects

Uberon alignment (DavidH)
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)
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

Peripheral nervous system development
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

Template-able Requests Prior To TG

Website

Editorial-type sections copied over from the GO website ontology documentation: MF

Protege

LEGO

Regulation

Modelling complex annotations in LEGO/noctua - meeting 140929

Annotation extensions

Terms that could be obsoleted if information was collected as annotation extension

Meetings

Cambridge Editors' meetings - weekly Tuesday 10-11 AM

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

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

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)

Jan 7 First call of 2016
Jan 14
Jan 21
Jan 28

Useful Links

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

Administrative

@@ Line 16: / Line 16: @@
 ====Low priority====
 *[[Neuro Behaviour Ontology (NBO)-GO alignment]] (Jane, George Gkoutos, Chris, DavidOS)
-*Peripheral nervous system development
 *[[microbial ontology development and annotation]]
@@ Line 37: / Line 36: @@
 A list of topics that  we propose to address, but for which a timeline has not been set
+*Peripheral nervous system development
 *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. [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1891512&group_id=36855| SF 1891512] is closed, but notes some issues for consideration. (midori 2010-10-04)