Transcript E. coli (Jim Hu)

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?
"Before the physical basis of genes was understood,
associating phenotypes with a heritable unit laid the
foundation of modern genetics" - Nichols et al 2011
OMP issues not directly about environment
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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
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
Planned annotation components
• Unique annotation ID
• Accessions for genotypes for all species/strains
– Genes and alleles in a pangenome context
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OMP for phenotype
Relationships for relative phenotypes
Environments
ECO for evidence
Reference
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”
Future
• Build the needed components
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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
Acknowledgements etc.
• TAMU
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Debby Siegele
Shabnam Eslamfam
Adrienne Zweifel
Jon Herrera
Will Meza
Whitley Lanier
• IGS/Maryland
– Michelle Gwinn Giglio
– Marcus Chibucos
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NIH R01 GM089636
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http://microbialphenotypes.org
micropheno