Ontology Development progress report for March 2010 meetings

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)

• "Aging Report" for past year
• "Distribution by Resolution" for past year

Ontology Quality Control

Ontology QC procedures are still used as reported previously. 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

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)

• Chemical terms in GO are being reviewed and revised for
  1. Internal consistency
  2. Consistency with ChEBI

Kidney development

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

Additional biological topics

• Progress on virus-related terms
• Transcription and transcription factors
• New PAMGO terms

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