Ontology Development: Difference between revisions
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**[[Apoptosis]] | **[[Apoptosis]] | ||
*Medium Priority | *Medium Priority | ||
**[[Non-symbiotic multi-organism processes]] | |||
**[[Neurobiology Project]] (David, Tanya, Jane, Paola) | **[[Neurobiology Project]] (David, Tanya, Jane, Paola) | ||
**[[:Category:Content MENGO|MENGO collaboration]] (Jane) | **[[:Category:Content MENGO|MENGO collaboration]] (Jane) | ||
**[[Signaling |Signaling overhaul]] (Becky, signaling WG) | **[[Signaling |Signaling overhaul]] (Becky, signaling WG) | ||
**[[Kidney Physiology]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group) | **[[Kidney Physiology]] (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group) | ||
**[[Cardiac conduction]] (David, Ruth, Doug, Tanya, Becky, Paola, Stan) | **[[Cardiac conduction]] (David, Ruth, Doug, Tanya, Becky, Paola, Stan) | ||
*Low priority | *Low priority | ||
**Peripheral nervous system development | **Peripheral nervous system development | ||
**[[Polyketide synthases]] | **[[Polyketide synthases]] | ||
| Line 39: | Line 38: | ||
[[2011 Timeline]] | [[2011 Timeline]] | ||
===Completed content work=== | ===Completed content work=== | ||
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* [[Bile formation and secretion processes]] | * [[Bile formation and secretion processes]] | ||
* [[multi-organism processes v/s cellular processes]] | * [[multi-organism processes v/s cellular processes]] | ||
* [[Polyketide synthases]] | |||
* [[protein and peptidyl amino acid modification / protein processing]] | |||
* [[Response to drug]] | |||
==Other Ontology Development Group Activities== | ==Other Ontology Development Group Activities== | ||
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*[[Ontology meeting 2011-12-14|Dec 14]] | *[[Ontology meeting 2011-12-14|Dec 14]] | ||
*[[Ontology meeting 2011-12-21|Dec 21]] | *[[Ontology meeting 2011-12-21|Dec 21]] | ||
[[Category:Ontology]] | [[Category:Ontology]] | ||
Revision as of 09:22, 26 October 2011
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 (Jane, Alex, Chris, others?)
- Chebi cross-products (David, Jane, Tanya, Chris, Harold, Midori)
- Function-Process Links
- part_of links between function and process (David, Tanya)
- has_part links between function and process (Harold, Jen)
- Chemical terms in GO(Part of the CHEbi alignment process)
- Transcription & transcription factor activity overhaul (Karen, David)
- Virus-related term overhaul (Michelle Gwinn Giglio, Jane Lomax, Candace Collmer, Ariane Toussaint, Brenley McIntosh, Alexander Diehl & others)
- Apoptosis
- Cross-products - see Category:Cross_Products and Cross_Product_Guide
- Medium Priority
- Non-symbiotic multi-organism processes
- Neurobiology Project (David, Tanya, Jane, Paola)
- MENGO collaboration (Jane)
- Signaling overhaul (Becky, signaling WG)
- Kidney Physiology (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
- Cardiac conduction (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
- Low priority
- Peripheral nervous system development
- Polyketide synthases
- cell growth/proliferation/division
- oxidoreductases
- Uberon alignment
Timeline
Completed content work
- Generic GO slim overhaul (Jane & Val)
- Kidney Development (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
- PAMGO collaboration (Jane)
- Heart Development (David, Ruth, Varsha, Doug, Susan, Yasmin, Becky)
- Cellular component processes (Jane, David, Midori, Val, ad hoc others)
- Transporters (Jen and community experts)
- 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
- plasma lipoprotein particle ontology - done Sept. 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.
- 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
- multi-organism processes v/s cellular processes
- Polyketide synthases
- protein and peptidyl amino acid modification / protein processing
- Response to drug
Other Ontology Development Group Activities
- Ongoing work on Quality control reports; see Ontology_Quality_Control (David, Jane, Chris, Tanya)
- Tracker wishlist
- Webinar Software Investigation
- Content Meeting Documentation
- Curator guides
- Ontology Documentation Drafts - for working on documentation of ontology content that will become part of the web-based documentation
- microbial ontology development and annotation
- New Ontology Editor Training
- Cell-type specific GO terms
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.
- Nov 2006 - Nov 2010 Ontology Development reports
- Jul 2005 - Oct 2006 GO Editorial Office reports