Ontology Development progress report for October 2008 meetings
From GO Public
Contents |
Ontology Development Progress Report
Metrics
GO term statistics
April 16, 2008
| Current | Defined | Obsolete | Total | |
|---|---|---|---|---|
| Function | 8262 | 7909 | 566 | 8828 |
| Process | 14702 | 14564 | 470 | 15172 |
| Component | 2077 | 2077 | 117 | 2194 |
| All | 25041 | 25703 | 1153 | 26194 |
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 |
SourceForge statistics (April 17 - Oct. 15) (to fill in)
- items opened: 539
- items closed: 587
SourceForge reports (on SF site)
Ontology Quality Control
New procedures are in place, and others are planned, to facilitate ontology QC.
- See XP:Progress_2008
- Consistency checks for regulation have been completed in bulk, and are now done for new regulation terms and regulates relationships.
- Curators are now going through the report on terms with multiple part_of parents.
- Chris has additional reports using cross-products that can be used for QC.
- Ontology_QC_Metrics are now recorded.
Completed work
- Another set of new terms have been added for PAMGO.
- MF terms for peptidase activities have been reorganized.
Work in progress
The ontology development group (including "core" members and ad hoc participants) has made a great deal of progress in several areas.
MF-BP links
- Overview of function-process (MF-BP) links
- GO curators conducted two pilot projects aimed at manually curating MF-links, in the areas of electron transport and core metabolism (glycolysis and the [[TCA_Cycle_Process-Function_Links|TCA cycle). Slides from the October 2008 GOC meeting are available for the electron transport links.
- The plan to add links between MF and BP to represent Regulation of molecular function has been announced on the GO Friends list, and is scheduled to be implemented on February xx, 2009.
- Additional sources of MF-BP links include Single-step biological processes and mining pathway databases such as Reactome and MetaCyc.
Signal transduction
- As part of an overhaul of functions and processes involved in signal transduction, a new set of high-level terms are ready for comment. Slides from the meeting are vailable.
Other work in progress
- We are reorganizing terms representing Processes affecting cellular components, including defining "organization" and "biogenesis" in the context of CCs.
- Interest in taxon correlations (e.g. relevant to a taxon, only found in a taxon, etc.) has led to the curation of a set of taxon-based "triggers" that will be used for annotation quality control. Additions and a pilot test are in progress.
- An overhaul of transcription and transcription factors has begun.
