Ontology Development progress report for September 2009 meetings

From GO Public

Contents 1 Ontology Development Progress Report 1.1 Metrics 1.1.1 GO term statistics 1.1.2 SourceForge statistics (March 27 - September 15, 2009) 1.1.3 SourceForge reports (on SF site) 1.2 Ontology Quality Control 1.3 Completed work 1.3.1 Function-process links 1.3.2 Cellular component organization 1.3.3 Has_part 1.3.4 Other completed work 1.4 Work in progress 1.4.1 Internal cross-products 1.4.2 Function-process links 1.4.3 GO slims 1.4.4 Biological topics 1.4.5 Other work in progress

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)

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

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