Ontology Development

From GO Public

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.

Contents 1 Administrative 2 Content Development 2.1 Priority ranking 2.2 Timeline 2.2.1 Current content work 2.2.2 Future content work 2.3 Selected SourceForge links 2.4 Completed content work 3 Other Ontology Development Group Activities 4 Agenda Items 5 Reports

[edit] Administrative

• Ontology Development group summary
• Miscellaneous meeting minutes

[edit] Content Development

[edit] 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
    • regulates links between function and process (David, Tanya)
    • part_of links between function and process
    • has_part links between function and process (Harold, Jen)
  • Transporters(Jen and community experts)
  • Filling in metabolism terms (Jane, David, Chris, Midori)
  • Regulator, activator and inhibitor MF terms (David, Tanya)
  • Generic GO slim overhaul (Jane, Val, others?)
• Medium Priority
  • Lung Development (David, Jen, community experts)
  • PAMGO collaboration (Jane)
  • Virus-related term overhaul (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh, Alexander Diehl & others)
  • IMG mapping (Jane)
  • Morphogenesis (David, Tanya? need a plant person)
  • Signaling overhaul (David, Jen)
  • Transcription & transcription factor activity overhaul (Karen)
  • Binding discussion - mainly annotation issues, but with some ontology content points
• Low priority
  • Response to drug (Jen)
  • Ion homeostasis (SF 1751898)
  • Cytokine receptor binding (SF 1751924)
  • Peripheral nervous system development
  • Formation/assembly/biogenesis/etc. rationalization (SF 1733770)
  • Polyketide synthases
  • Kidney Development (David)

[edit] Timeline

[edit] Current content work

• Virus-related term overhaul (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh & others)
• Signaling overhaul
• Cellular component processes (Jane, David, Midori, Val, ad hoc others) - started summer 2008
• Transcription & transcription factor activity overhaul - started June 2008
• Taxon data
• Transporters - Started Feb. 2007
• Electron transport
• IMG mapping
• Function-Process Links - pilot projects begun Feb. 2008; first links added May 2009
  • regulates links- Dec 2008
  • kinases, phosphatases, transporters, and other 1:1- May/June 2009
• Cell cross-products - TBD
• Plant terms
• Filling in metabolism terms - face-to-face meeting July 9, 2008

[edit] Future content work

• Generic GO slim overhaul - summer 2009
• Lung Development
• Ion homeostasis (SF 1751898)
• Cytokine receptor binding (SF 1751924)
• Response to drug
• Peripheral nervous system development
• Chaperones
• Formation/assembly/biogenesis/etc. rationalization (SF 1733770)
• Polyketide synthases
• Regulator, activator and inhibitor MF terms
• Morphogenesis
• Binding discussion - mainly annotation issues, but with some ontology content points

[edit] Selected SourceForge links

[edit] 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

[edit] 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

[edit] Agenda Items

• Agenda items for next content conference call

[edit] Reports

Beginning with the November 2006 document, reports include two sections: the first focuses on ontology development work, and the second gives an overview of the rest of the GO Editorial Office staff activities (to avoid redundancy, the latter may cross-reference other management group reports). Reports issued earlier are not so divided, and have a GO Editorial Office-centric perspective, but do cover a substantial portion of the GOC's ontology development work.

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