Ontology Development progress report for March 2010 meetings

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Ontology Development Progress Report

Metrics

GO term statistics

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


March 29, 2010

Current Defined Obsolete Total
Function 8703 8525 798 9501
Process 18747 18691 516 19263
Component 2727 2727 119 2846
All 30177 31376 1433 31610

Note that, in the tables above, "defined" counts include obsolete terms.

SourceForge statistics (September 16, 2009 - March 29, 2010)

  • items opened: 775
  • items closed: 790 (23 deleted, mainly duplicates)
  • 239 items open as of March 29, 2010

SourceForge reports (on SF site)

Ontology Quality Control

Ontology QC procedures are still used as reported previously. These include:

Progress is summarized on the Ontology_QC_Metrics page.

Completed work

Regulates cross-products

  • The first internal cross-products, for regulation terms, have been released into gene_ontology_write.obo and gene_ontology_ext.obo.

Kidney development

  • A very successful content meeting on kidney development was held in January.
    • Generic terms added during and just after meeting

Signaling

  • Revisions to the high-level signaling terms committed

Other completed work

  • Terms added based on discussions at the 2009 American Society for Cell Biology meeting
  • Taxon triggers for annotation quality control are now in use; a manuscript is in preparation
  • Further expansion of the ontology for heart development
  • Branching organ development
  • Axon-related CC terms

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

  • We are continuing to review and release internal cross-products according to the plan we developed earlier.
    • The next additions will be the BP-xp-self and CC-xp-self cross-products that use has_part as the discriminating relationship.
    • We've added process-specific function cross-product definitions to the list.
    • Background on the cross-products within GO and implementation plan pages.

GO and chemicals (ChEBI cross-products)

Kidney development

  • Metanephros term additions in progress
  • Terms for pronephros and mesonephros planned

Additional biological topics

Other work in progress

  • A review of the generic GO slim, with accompanying refinement of high-level terms, is continuing.
  • Further work to add MF-BP part_of links