Ontology Development

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.

Administrative

• Ontology Development group summary
• Miscellaneous meeting minutes

Content Development

Priority ranking

• Ongoing work on Quality control reports; see Ontology_Quality_Control (David, Jane, Chris, Tanya)
• High Priority
  • Cross-products - see Category:Cross_Products and Cross_Product_Guide
    • Cell cross-products (David, Jane, Tanya, Alex, Chris, others?)
    • Chebi cross-products (David, Jane, Tanya, Chris, others?)
  • Cellular component processes (Jane, David, Midori, Val, ad hoc others)
  • Taxon data (Note: sensu revamp complete) (Jen)
  • Function-Process Links
    • part_of links between function and process (David, Tanya)
    • has_part links between function and process (Harold, Jen)
  • Transporters(Jen and community experts)
  • Filling in metabolism terms (Jane, David, Chris, Midori)
  • Generic GO slim overhaul (Jane, Val, others?)
  • Chemical terms in GO
• Medium Priority
  • PAMGO collaboration (Jane)
  • Virus-related term overhaul (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh, Alexander Diehl & others)
  • IMG mapping (Jane)
  • Signaling overhaul (Jen, Alex Diehl)
  • Transcription & transcription factor activity overhaul (Karen)
  • Kidney Development (David, Midori, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
• Low priority
  • Response to drug (Jen)
  • Peripheral nervous system development
  • Polyketide synthases

Timeline

Current content work

• Chemical terms in GO - manually curate GOCHE (April 2010), fix relationships in GOCHE (May 2010), align GOCHE with ChEBI (July 2010), submit paper (sept 2010).
• Internal cross-products (first set Jan 2010, cc x cc (po) March 2010, bp x bp (po) July 2010
• Virus-related term overhaul (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh & others)(waiting on file from Philipe le Mercier - some time 2010)
• Signaling overhaul (high-level terms committed Feb 2010), Becky clean-up until May 2010
• Transcription & transcription factor activity overhaul - started June 2008
• Taxon data (file committed Feb 2010, Jane maintaining file until UniProt new person takes it over in summer)
• IMG mapping (open ended - needs more personnel)
• Function-Process Links - pilot projects begun Feb. 2008; first links added May 2009, transporters->transport finished May 2010, catalytic activities end 2010
• Generic GO slim overhaul - (finished first round, needs refining)
• kidney development (generic kidney finished March 2010, metanephros April 2010, pronephros May 2010, mesonephros, June 2010, fly renal, July 2010, Sept 2010 write paper)
• PAMGO collaboration - ongoing
• QC - ongoing
• SF ongoing

Future content work

• Polyketide synthases

Completed content work

• PAMGO collaboration, phase 2 (as of Jan. 2007)
• Immunology Revisions
• Central Nervous System Development
• is_a complete biological process
• PAMGO collaboration, phase 1
• Correct disjointness violations
• RNA processing
• Collaboration with MIT GO-Engineering - Manuscript written
• Muscle Development - Started Feb. 2007; meeting July 2007; Done Oct 2007
• Cardiovascular physiology/development - implemented Oct 2007
• Make cc part_of tree complete (i.e. find homes for the children of 'unlocalized protein complex')
• Sensu revamp
• Regulation Main Page live March 2008
• Gene expression (SF 1418820)
• Electron transport
• Peptidase & protease activity overhaul begun June 2008; essentially completed August 2008
• SDB 2009
• ASCB 2009
• Function-Process Links
  • regulates links between function and process (David, Tanya)
• Morphogenesis (David, Tanya)
• regulates links- Dec 2008 (David, Tanya)
• Regulator, activator and inhibitor MF terms (David, Tanya)
• Chaperones(completed by working group at Cambridge GOC meeting Sept. 2009)
• Lung Development (David, Jen, community experts)
• Binding discussion - mainly annotation issues, but with some ontology content points
• Cellular component processes (Jane, David, Midori, Val, ad hoc others) - started summer 2008
• Transporters - Started Feb. 2007
• Utilization - done March 2010

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.
• Rework disjoint terms as [concluded in discussion on GO list].

Other Ontology Development Group Activities

• Ontology development timeline and release pipeline
• Ongoing work on Quality control reports; see Ontology_Quality_Control (David, Jane, Chris, Tanya)
• Tracker wishlist
• Webinar Software Investigation
• Content Meeting Documentation
  • Content meeting participants' information
• Editor Guide
• Ontology Documentation Drafts - for working on documentation of ontology content that will become part of the web-based documentation

Agenda Items

• Agenda items for next content conference call

Reports

Beginning with the November 2006 document, reports emphasize ontology development work. Reports issued between November 2006 and December 2009 also include a section that gives an overview of other GO Editorial Office staff activities, with the emergence of regular reports from other management groups, the second section has become redundant. Reports issued prior to November 2006 are not divided into parts, and have a GO Editorial Office-centric perspective, but do cover a substantial portion of the GOC's ontology development work.

• November 2006-present Ontology Development reports
• July 2005-October 2006 GO Editorial Office reports

GO Clinics

• GO clinic late 2009
• GO clinic spring 2010