Ontology Development progress report for September 2009 meetings
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Ontology Development Progress Report
Metrics
GO term statistics
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 |
September 15, 2009
Current | Defined | Obsolete | Total | |
---|---|---|---|---|
Function | 8646 | 8433 | 798 | 9444 |
Process | 17109 | 17032 | 506 | 17615 |
Component | 2450 | 2450 | 118 | 2568 |
All | 28205 | 29337 | 1422 | 29627 |
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
We are still using 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
Function-process links
- 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.
Has_part
- The has_part relation is now in use
- Background
- Documentation is available
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.
Internal cross-products
- The plan to add internal cross-products to the extended GO file has matured. The 'regulates' cross-products will be released first.
- Background on cross-products within GO
- The earlier draft of the implementation plan is still relevant.
Function-process links
- Further work to add MF-BP part_of links will use sources noted at the last two meetings:
- Single-step biological processes
- Mining pathway databases such as Reactome and MetaCyc.
- Previously reported pilot projects for manually curating MF-BP links for electron transport and core metabolism (glycolysis and the TCA cycle).
GO slims
A review of the generic GO slim is under way, and is guiding some refinement of high-level terms .
Biological topics
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
Other work in progress
- Evaluating new link suggestions and mismatches from ChEBI cross-products
- Work on relationships among multi-organism process regulation terms
- Taxon triggers for annotation quality control
- New workflow
- "Sensu" information moving from synonyms to definitions
- Meeting notes