Integrating phenotype ontologies across multiple species
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Integrating phenotype ontologies across multiple species
- 1. Integrating phenotype ontologies across multiple speciesCaltech 2009 Chris Mungall
- 3. How do we compare phenotypes across species? Multiple project or species specific phenotype ontologies MP: mouse HP: human WP: worm TO: plant APO: fungi Data is not comparable How do we know they are built according to the same principles?
- 4. Anatomical and structural entities in OBO
- 7. Examples
- 8. Relational Qualities Have a bearer - have an additional dependency on some type of entity
- 9. EQ expressions can be written in obo format Why? Formal semantics Edit within OBO-Edit as genus-differentia definitions Use the OBO-Edit reasoner Can also be translated to OWL
- 10. EQ expressions can be written in obo format Why? Formal semantics Edit within OBO-Edit as genus-differentia definitions Use the OBO-Edit reasoner Can also be translated to OWL
- 11. EQ expressions can be written in obo format
- 12. EQ vs dedicated phenotype ontology Some groups pre-compose phenotype descriptions terms generated in advance by ontology editor ontology editors adds defs etc dedicated phenotype ontology often species-specific Other groups post-compose phenotype descriptions descriptions composed as needed by annotators no dedicated phenotype ontology
- 13. Methodologies
- 14. Unifying descriptions Equivalence Mappings between term EQ expression
- 15. Methods Use obol to generate first pass and updates parses term name assumes semi-controlled syntax Manually edit obo xp file
- 16. Results
- 17. Advantages Reuse PATO across ontologies Make sure we’re saying the same thing We can use the OBO-Edit reasoner to compute the is_a hierarchy We can enhance queries within species. E.g. find all genes that have a phenotype affecting sperm (CL:0000019 / WBbt:0006798) We can compare across species
- 18. Reasoning
- 20. Comparing across species Requirements: Phenotype ontology mappings Mappings between anatomy ontologies Uberon Multi-species anatomy ontology No assumption of homology Analogy is useful to; e.g. eyes Scope: metazoans Applicability outside vertebrates controversial Better to focus on cells (CL)
- 21. Mapping AOs to Uberon
- 22. Phenoblast: Quantifying similarity SimJ: 0.42 MaxIC: 13.4 SimJ: 0.17 MaxIC: 6.2 SimJ: 0.32 MaxIC: 12.1
- 23. Recovering pathway members by phenotypic similarity
- 24. Conclusions Sharing ontologies is good PATO / EQs can be used to help build ontologies as well as in annotation Find mistakes Automatically build DAG (reasoning) Mapping a phenotype ontology to EQs gives you the best of both worlds Control over the terms used in annotation Comparing data across species Where anatomical similarities permit..