Ontology Development progress report for May 2011 meeting

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Ontology Development Progress Report

GOC Meeting May 2011

Prepared and Submitted by David Hill


  • David Hill (MGI)
  • Tanya Berardini (TAIR)
  • Karen Christie (SGD)
  • Harold Drabkin (MGI)
  • Becky Foulger (EBI, joined October 2010)
  • Midori Harris (left in Jan 2011)
  • Amelia Ireland (MGI)
  • Jane Lomax (EBI, maternity leave until mid-June)
  • Chris Mungall (LBL)
  • Paola Roncaglia (EBI, joined March 2011)

Ontology Editing

SourceForge Requests (Paola, Becky and rest of team):

SF items opened (SF items closed) 
Sept 2010    104 (162) 
Oct 2010     97 (127) 
Nov 2010    97 (117) 
Dec 2010    44 (62) 
Jan 2011    90 (76) 
Feb 2011    83 (72) 
March 2011    120 (110) 
April 2011    86 (88) 

Term Statistics

Total number of GO terms added Sept 2010 to April 2011 (inclusive): 2026 
Total number of GO terms obsoleted Sept 2010 to April 2011 (inclusive): 128

TermGenie (Tanya)

More than 680 terms added via this mechanism.
Can add regulates and ‘part_of’ terms

Quality Control (David, Tanya)

Review implied is_a regulation term links.

Major Projects

Transcription overhaul (Karen, David):

Terms with the GOC:txnOH definition dbxref
new term?	BP	CC	MF	Total
Yes.....	38	1	149	188
No......	34	-	17	51
Total	72	1	166	239

Heart Development (David, Doug, Susan, Tanya with Ruth, Varsha, community experts):

Paper written and published: PMID:21419760.

Kidney Development (Becky, David, Doug, Emily, Midori, Rachael, Susan with Yasmin, community experts)

Term additions complete: 446 new terms covering flies, amphibians, fish, mammals.
Paper Draft written.

Chemicals in GO (Amelia, Chris, David, Harold, Jane, Midori, Tanya)

Synchronized over 1500 reactions with MetaCyc, KEGG, RHEA and EC, and converted reaction text to reflect ChEBI names (Amelia)
GOCHE ontology complete (Chris, David, Harold, Tanya and ChEBI staff)
GOCHE/ChEBI alignment underway (David, Tanya)
Paper almost ready for submission (Chris, David, Harold, Jane, Midori, Tanya and ChEBI staff and Mike Bada)

Signaling (Becky, Ruth, Sandra, Varsha, Alex, Peter, Susan and community experts

2-day meeting at the EBI (2 experts, 3 editors, 8 annotators, Chris)
Defined and housed existing terms rather than creating new terms. 
Key topics: 
*'signaling', 'signal transduction', 'signal transmission' and 'signaling pathway'. 
*Connecting the cell surface receptors with intracellular modules. 
*Dealing with ligand-receptor signaling that is not 1:1.
*How to link signaling with receptor-mediated endocytosis.

Linking MF and BP (David, Tanya)

Most of the obvious branches are done. 
728 MF terms (7% of MF terms) have part_of links to BP.

Apoptosis (Paola, Becky, Emily, Ruth, and community experts)

Several conference calls so far.
Meeting planned for early June.

Viral work (Becky, Jane and curators from SIB)

Creating GO terms for existing SP keywords.