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
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)
- UBERON page on OBO
- Multi-species anatomy ontology
- Originally reated to compare phenotype descriptions across species
- Now being used for XPs for GO development terms
CHEBI
- XP:biological_process_xp_chebi
- We are still missing links to many CHEBI terms
- Basic text-matching methods don't work because CHEBI uses a different terminology 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