Ontology Development progress report for March 2009 meetings

From GO Public

Contents 1 Ontology Development Progress Report 1.1 Metrics 1.1.1 GO term statistics 1.1.2 SourceForge statistics (Oct. 15, 2008 - March 27, 2009) 1.1.3 SourceForge reports (on SF site) 1.2 Ontology Quality Control 1.3 Completed work 1.4 Work in progress 1.4.1 Lung development 1.4.2 Signal transduction 1.4.3 Cellular component organization 1.4.4 Internal cross-products 1.4.5 MF-BP links 1.4.6 Other work in progress

Ontology Development Progress Report

Metrics

GO term statistics

October 15, 2008

	Current	Defined	Obsolete	Total
Function	8421	8116	765	9186
Process	15565	15436	479	16044
Component	2226	2226	117	2343
All	26212	27139	1361	27573

March 27, 2009

	Current	Defined	Obsolete	Total
Function	8522	8272	780	9302
Process	16207	16110	480	16687
Component	2315	2315	117	2432
All	27044	28074	1377	28421

SourceForge statistics (Oct. 15, 2008 - March 27, 2009)

• items opened: 453
• items closed: more than 335 (new SF tracker has lost the feature that made counting straightforward; estimate about 420-430)

SourceForge reports (on SF site)

• "Aging Report" for past year
• "Distribution by Resolution" for past year

Ontology Quality Control

We're continuing to use the ontology QC procedures we reported in October. These include:

• Consistency checks for new regulation terms and regulates relationships;
• A report on terms with multiple part_of parents;
• Cross-product reports that can be used for QC; also see Progress_2008.

Progress is summarized on the Ontology_QC_Metrics page.

Completed work

• New regulates relationships have been added within MF, and between MF and BP, to represent Regulation of molecular function.
• Another set of new terms have been added for PAMGO.

Work in progress

The ontology development group (including "core" members and ad hoc participants) has made a great deal of progress in several areas.

Lung development

Signal transduction

• The overhaul of functions and processes involved in signal transduction has continued, with plans for a content meeting in the works.

(Jennifer)

• This wiki new will be linked from the comments field of the ontology, so that the users can easily give feedback
• New mailing list : signaling @genome
• This is just starting; look for feedback from as many people as possible and members of the community

Cellular component organization

• We have done a lot of work to reorganize terms representing Processes affecting cellular components, including defining "organization" and "biogenesis" in the context of CCs. Progress and the tasks remaining to be completed will be presented.

Internal cross-products

• We have done extensive work on cross-products within GO, vetting autogenerated cross-products and estabilshing a plan for releasing them in the "extended" GO OBO file.
• David and Tanya: working on on regulates

MF-BP links

• There is a new proposal to add process-specific MF terms to support part_of links between MF and BP.
• MF-BP link items reported in October remain relevant:
  • Overview of function-process (MF-BP) links
  • Pilot projects for manually curating MF-BP links for electron transport and core metabolism (glycolysis and the [[TCA_Cycle_Process-Function_Links|TCA cycle).
  • Additional sources of MF-BP links include Single-step biological processes and mining pathway databases such as Reactome and MetaCyc.

Other work in progress

• An overhaul of virus-related terms has begun.
• Work on transcription and transcription factors continues.
• Plans are being made for a small content meeting on electron transport in prokaryotes, organized by Rob Gunsalus at UCLA.