Ontology Development: Difference between revisions
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=Content Development = | =Content Development = | ||
==Ongoing | ==Ongoing Projects== | ||
*[[Transcription 2018]] (Pascale, Ruth, Astrid, Marcio, Paul T) | *[[Transcription 2018]] (Pascale, Ruth, Astrid, Marcio, Paul T) | ||
*[[Cell Cycle]] (Val, Pombe experts, GOEds) | *[[Cell Cycle]] (Val, Pombe experts, GOEds) |
Revision as of 10:08, 9 April 2019
Group's focus
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. With the help of the software team the group create rules to ensure the ontology's integrity.
Group Leader
David Hill (MGI)
Communication
Editor's Conference calls
When
- Calls are held weekly on Mondays, 12:00PM-1:00PM EST
- Calls are scheduled on the GO's Google calendar. Please request access to the calendar if you don't have it.
- Reminder emails are sent out to the go-ontology mailing list (see Internal_email_lists to register).
Agenda and Minutes
- 2019
- Past Annotation Call Minutes: 2005-2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 | 2017 | 2018 |
Documentation
Setting up Protege for GO editors
Installing and Using git
Ontology Editors Daily Workflow
Editing the Ontology
Relations General Relations Documentation Draft To be reviewed
Website - to be moved to the wiki?
Identifiers To be reviewed
Guidance for organizing content meetings
(old doc, but basic principles still apply)
Content Development
Ongoing Projects
- Transcription 2018 (Pascale, Ruth, Astrid, Marcio, Paul T)
- Cell Cycle (Val, Pombe experts, GOEds)
- Enzymes and EC mappings
- Non-symbiotic multi-organism processes (Jane, David OS)
- Signaling: 2017 Cambridge GOC Signalling Workshop
- Protein_Complexes:_who,_what,_where
Low priority
- Neuro Behaviour Ontology (NBO)-GO alignment (Jane, George Gkoutos, Chris, DavidOS)
- microbial ontology development and annotation
Completed projects
- Adding missing CHEBI xps
- Cell cross-products, Cell-type specific GO terms (Jane, Paola, Alex, Chris, DavidOS)
- Addition of cross-products - see Category:Cross_Products and Cross_Product_Guide
- Uberon alignment (DavidH)
- MENGO collaboration (Jane)
- PAMGO collaboration (Jane)
- PAMGO collaboration, phase 1
- PAMGO collaboration, phase 2 (as of Jan. 2007)
- Apoptosis (Emily, Becky, Paola, Pablo and community experts) - Feb 2013
- Autophagy (Paul D, Marc F, David H, Ruth, Paola and community experts) - Denny et al 2018
- ASCB 2009
- Binding discussion - mainly annotation issues, but with some ontology content points
- Cardiac conduction (David, Ruth, Doug, Tanya, Becky, Paola, Stan)
- Cardiovascular physiology/development - implemented Oct 2007
- Cellular component processes (Jane, David, Midori, Val, ad hoc others) - started summer 2008
- Central Nervous System Development
- Chaperones(completed by working group at Cambridge GOC meeting Sept. 2009)
- Ciliary components and processes (Paola, Karen Christie, SYSCILIA experts) Roncaglia et al 2017
- Collaboration with MIT GO-Engineering - Manuscript written
- Electron transport
- Extracellular RNA-containing vesicles (Paola, Aleks and community experts) Cheung et al 2016
- regulates links between function and process (David, Tanya)
- Gene expression (SF 1418820)
- Function-Process Links
- Heart Development (David, Ruth, Varsha, Doug, Susan, Yasmin, Becky)
- Lung_Development (David, Jen, community experts)
- Immunology Revisions
- is_a complete biological process
- Kidney Development (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
- Kidney Physiology (David, Yasmin, Doug, Tanya, Becky, Edinburgh GUDMAP group)
- Morphogenesis (David, Tanya)
- Muscle Biology - Started Feb. 2007; meeting July 2007; Done Oct 2007
- Neurobiology Project (David, Tanya, Jane, Paola, DavidOS)
- plasma lipoprotein particle ontology - done Sept. 2010
- Peptidase & protease activity overhaul begun June 2008; essentially completed August 2008
- Regulation Main Page live March 2008
- Regulator, activator and inhibitor MF terms (David, Tanya)
- RNA processing
- SDB 2009
- Sensu revamp
- Signaling overhaul (Becky, signaling WG)
- Synapse project (Synapse experts, DavidOS, Becky Foulger) - completed 2018
- Transcription & transcription factor activity overhaul (Karen, David) - 2012
- Transporters (Jen and community experts) - Started Feb. 2007
- Utilization - done March 2010
- Virus-related term overhaul, Phage Terms (Jane Lomax, Brenley McIntosh, Rebecca Foulger & others)
- Generic GO slim overhaul (Jane & Val)
- Make cc part_of tree complete (i.e. find homes for the children of 'unlocalized protein complex')
- regulates links- Dec 2008 (David, Tanya)
- Correct disjointness violations
- Rework disjoint terms as concluded in discussion on GO list (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
Quality Control
SPARQL checks on the ontology
[|SPARQL checks on the ontology]
Ontology release pipeline
TO BE REPLACED
- Ongoing work on Quality control reports; see Ontology_Quality_Control (David, Jane, Chris, Tanya)