Ontology Development progress report for September 2009 meetings
- 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
March 27, 2009
September 15, 2009
Note that, in the tables above, "defined" counts include obsolete terms.
SourceForge statistics (March 27 - September 15, 2009)
- items opened: 548
- items closed: 534
- 277 items open as of Sept. 15
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.
- The first part_of links between the MF and BP ontologies have been added. Work continues to add more links -- see below.
Cellular component organization
- We have reorganized terms representing Processes affecting cellular components, including defining "organization" and "biogenesis" in the context of CCs. Small refinements are made as term requests and other questions arise.
Other completed work
- Terms added based on discussions at the 2009 Society for Developmental Biology meeting
- S. pombe GO slim created
- OBO-Edit 2.0 released; more details in software report
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 plan to add internal cross-products to the extended GO file has matured. The 'regulates' cross-products will be released first.
- Further work to add MF-BP part_of links will use sources noted at the last two meetings:
A review of the generic GO slim is under way, and is guiding some refinement of high-level terms .
Much work is going on in several areas of biology:
- The overhaul of functions and processes involved in signal transduction has continued, with plans for a content meeting in the works. (Jennifer)
- Considerable progress on virus-related terms
- Further expansion of the ontology for heart development
- Branching organ development
- Transcription and transcription factors