Ontology Development progress report for March 2009 meetings
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)
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
- A content meeting on lung development was held in December 2007.
- Met with experts in Boston; who did not want anatomical terms in the lung development in the ontology. So David made two files, one with and one without anatomical structures.
- Until last week, lung development only had one child, and Dimitry (MGI) has been requesting new terms; interestingly those include anatomical terms
- This also leads to the expansion of the 'morphogenesis of a branching structure' branch of the GO
- Chris asks whether the lung development is being analyzed from the mouse/mammalian point of view: David says, for lung development, yes, but for branching morphogenesis he is trying to capture different organs and species
- Alex: makes the point that this is analogous to the mitochondrial/cytoplasmic translation issue: all those branching types of development are different to some level, so we might need to add much more terms to describe this?
- David: we've asked this question since the beginning of GO
- Judy: we need to provide the information that researchers need
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.
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.