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:

Progress is summarized on the Ontology_QC_Metrics page.

Completed work

Function-process links

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

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

Function-process links

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:

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