Ontology Development: Difference between revisions
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A list of topics that we propose to address, but for which a timeline has not been set | A list of topics that we propose to address, but for which a timeline has not been set | ||
*Revamp | *Revamp embryonic and post-embryonic terms to be logically defined with cross products to stage ontology. | ||
*Rework disjoint terms as [[http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F#Conclusion concluded]]. | *Rework disjoint terms as [[http://gocwiki.geneontology.org/index.php/Are_multi-organism_process_and_cellular_process_disjoint%3F#Conclusion concluded in discussion on GO list]]. | ||
Revision as of 11:41, 28 January 2010
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
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?)
- Cross-products - see Category:Cross_Products and Cross_Product_Guide
- 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)
- Ion homeostasis (SF 1751898)
- Cytokine receptor binding (SF 1751924)
- Peripheral nervous system development
- Formation/assembly/biogenesis/etc. rationalization (SF 1733770)
- Polyketide synthases
Timeline
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
- 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
- Notes on Sourceforge items in progress
Future content work
- Generic GO slim overhaul - summer 2009
- Ion homeostasis (SF 1751898)
- Cytokine receptor binding (SF 1751924)
- Response to drug
- Peripheral nervous system development
- Formation/assembly/biogenesis/etc. rationalization (SF 1733770)
- Polyketide synthases
Selected SourceForge links
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
- 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
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
- Editor Guide
- Ontology Documentation Drafts - for working on documentation of ontology content that will become part of the web-based documentation
Agenda Items
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