Ontology Development progress report for March 2009 meetings
From GO Wiki
Revision as of 07:55, 20 August 2009 by Midori
- 1 Ontology Development Progress Report
- 1.1 Metrics
- 1.2 Ontology Quality Control
- 1.3 Completed work
- 1.4 Work in progress
Ontology Development Progress Report
GO term statistics
October 15, 2008
March 27, 2009
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)
Ontology Quality Control
- 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.
- 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.
- The overhaul of functions and processes involved in signal transduction has continued, with plans for a content meeting in the works.
- 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.
- 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
- 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.