XP:Progress 2008

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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


  • 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)

External Cross Products

  • Cross-products that refer to terms outside GO

Uber Anatomy Ontology (new)


  • XP:biological_process_xp_chebi
  • We are still missing links to many CHEBI terms
    • Basic text-matching methods don't work because CHEBI uses different terminological principles from GO
  • Pilot project using CHEBI to align GO with pathway dbs


  • ..

Goals for 2009

  • More curation of XP files
  • More automation, better integration with day to day ontology development