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Jim Hu's presentation at the Biocurator 2012 conference: Developing an Ontology for Microbial Phenotypes...

Jim Hu's presentation at the Biocurator 2012 conference: Developing an Ontology for Microbial Phenotypes

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  • 1. Developing an Ontology for Microbial Phenotypes #41 Jim Hu
  • 2. "Before the physical basis of genes wasunderstood, associating phenotypes with a heritableunit laid the foundation of modern genetics" - Nicholset al 2011
  • 3. Goals• Build a classification system (ontology) for microbial phenotypes• Build an annotation system and annotate microbial phenotypes – Given a phenotype, identify kinds of genes and functions likely to be involved – Given a gene, identify phenotypes that may aid understanding of function – Correlate phenotypes to each other – Connect genotypes and phenotypes• Not there yet!
  • 4. What’s a phenotype? • Observable characteristics • Individual • Genotype • Environmenthttp://www.flickr.com/photos/max_westby/54275159/
  • 5. Building OMP (Ontology of Microbial Phenotypes)Expertise Literature Annotation Examples Ontology system Draft annotations
  • 6. Building OMP (Ontology of Microbial Phenotypes)Expertise Literature Annotation Examples Ontology system Draft annotations
  • 7. Entities and Qualities• Existing phenotype ontologies are based on the PATO entity-quality system – Entity: a trait, object, process – Quality: a property of an entity – Example from mouse phenotype ontology:
  • 8. Entities and Qualities• Making this work for microbes – In some cases the entities are analogous to anatomy terms for microbial cells
  • 9. Entities and Qualities• Making this work for microbes – Other cases are population behaviors Budrene and Berg (1991) Nature 349:630 Courtesy of Bonnie Bassler
  • 10. State vs Relative Phenotypes• Characteristics of a species/type strain• Changes relative to a reference strain – Not necessarily relative to wild-type
  • 11. What do we mean by observable?• Observations vs. inferences – Lac-• Where do we draw the line? – Loss of enzyme activity in an extract: yes – Altered folding of a purified protein: no – Expression patterns of specific genes: yes? – Specific transcriptome patterns: no
  • 12. Building OMP (Ontology of Microbial Phenotypes)Expertise Literature Annotation Examples Ontology system Draft annotations
  • 13. What is the object of annotation?• Individuals/populations?• Genes?• Genotypes? – “relevant genotypes”? – Genotype differences?
  • 14. Things the annotation system needs to express• Properties of wt type strains: – 1. E. coli wt has_phenotype lactose utilization• Mutant phenotypes – 2. E. coli cya has_phenotype decreased lactose utilization • relative_to 1• Environmental dependence – 3. E. coli cya has_phenotype increased lactose utilization in Environment: + cAMP • relative_to 2• Genetic interaction – 3. E. coli cya, crp* has_phenotype increased lactose utilization • relative_to 2
  • 15. Components needed• Unique annotation ID• Accessions for genotypes for all species/strains – Genes and alleles in a pangenome context• OMP• Relationships for relative phenotypes• Environments• ECO for evidence• Reference
  • 16. Future• Build the needed components – OMP in progress – ECO in progress – Universal genotype database?! – Environment ontology?• Build infrastructure – OMP wiki: http://microbialphenotypes.org – Sourceforge SVN for OMP• Coordination with other phenotype projects• Example annotation set for E. coli
  • 17. Acknowledgements etc.• TAMU – Debby Siegele – Adrienne Zweifel • NIH R01 GM089636 – Jon Herrera – Will Meza • http://microbialphenotypes.org – Whitley Lanier • micropheno• IGS/Maryland – Michelle Gwinn Giglio – Marcus Chibucos• Virginia Commonwealth – Peter Uetz – Kelly OBriant – Matt Feltz – Robel Hailu Wolde