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Environments for annotation with the Ontology for Microbial Phenotypes

Environments for annotation with the Ontology for Microbial Phenotypes. Phenotype RCN 2014 Jim Hu. What’s a phenotype?. What’s a phenotype?. What’s a phenotype?.

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Environments for annotation with the Ontology for Microbial Phenotypes

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  1. Environments for annotation with the Ontology for Microbial Phenotypes Phenotype RCN 2014 Jim Hu

  2. What’s a phenotype?

  3. What’s a phenotype?

  4. What’s a phenotype?

  5. "Before the physical basis of genes was understood, associating phenotypes with a heritable unit laid the foundation of modern genetics" - Nichols et al 2011

  6. OMP issues not directly about environment • Genotypes not genes or alleles • State phenotypes vs relative phenotypes • Population phenotypes • Observations vs inferences short of GO • Lac- as a phenotype Budrene and Berg (1991) Nature 349:630

  7. Things the annotation system needs to express • Properties of wt type strains: • 1. E. coli wthas_phenotypelactose utilization • Mutant phenotypes • 2. E. coli cyahas_phenotypedecreased lactose utilization • relative_to 1 • Environmental dependence • 3. E. coli cyahas_phenotypeincreased lactose utilization inEnvironment: + cAMP • relative_to 2 • Genetic interaction • 3. E. coli cya, crp* has_phenotypeincreased lactose utilization • relative_to 2

  8. Planned annotation components • Unique annotation ID • Accessions for genotypes for all species/strains • Genes and alleles in a pangenome context • OMP for phenotype • Relationships for relative phenotypes • Environments • ECO for evidence • Reference

  9. Environment issues • Capturing environment vs. relevant environment • Analogy to relevant genotypes • How granular do we want to be? • Gray area between phenotype and environment • Option 1: OMP: Drug resistance ENVO: medium term • Option 2: OMP: Growth/Death ENVO: medium + drug • Environment vs “relevant environment”

  10. Future • Build the needed components • OMP in progress • ECO in progress • Universal bacterial/microbial genotype database?! • Environment: from this workshop • Build infrastructure • OMP wiki: http://microbialphenotypes.org+ Sourceforge SVN • Coordination with other phenotype projects • RCN, APO, FYPO etc. • Example annotation sets for • E. coli • B. subtilis • bacteriophage

  11. TAMU Debby Siegele ShabnamEslamfam Adrienne Zweifel Jon Herrera Will Meza Whitley Lanier IGS/Maryland Michelle Gwinn Giglio Marcus Chibucos NIH R01 GM089636 http://microbialphenotypes.org micropheno Acknowledgements etc.

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