XP:Progress 2008

Progress as of 2008/10/20

Motivation and Goals

• GO has become too large and complex to manage manually
• Errors of omission and commission negatively impact users in many ways
• Provide connections between GO and other ontologies

Methods

• Create computable logical definitions (Cross Products) for GO terms using (a) other GO terms (b) terms from other ontologies
• Use logic-based reasoning to find inconsistencies and errors

Results 2008

• We have XP defs for 10712/27589 of GO terms
• 1500-2000 links added or moved in GO based on reasoner results

The table below shows the number of XP defs that have been curated

GO XP Results 2008

	dynamic		spatial
	bioprocess		anatomic			chemical
	biological_process	molecular_function	cell	cellular_component	uberon	chebi
biological_process	4133 go_xp_regulation bp_xp_bp		527 bp_xp_cell	724 bp_xp_cc	516 bp_xp_uberon	2901 bp_xp_chebi
molecular_function	134 mf_xp_regulators	84 mf_xp_regulators				360 mf_xp_chebi
cellular_component	24 cc_xp_go	148 cc_xp_go		715 cc_xp_cc

Internal Cross Products

• Cross-products that do not refer to terms outside GO

Regulation Cross Products

• Performed two batch updates on GO, fixing 1000 and 500 links respectively
• Moving towards automation of is_a link management

Cellular Component internal xps (new)

• New spatial relations:
  • surrounded_by
  • adjacent_to

BP XP CC (new)

• XP:biological_process_xp_cellular_component