Environments for annotation with the Ontology for Microbial

PhenotypesPhenotype 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

• 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• 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– 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– Debby Siegele– Shabnam Eslamfam– Adrienne Zweifel– Jon Herrera– Will Meza– Whitley Lanier

• IGS/Maryland– Michelle Gwinn Giglio– Marcus Chibucos

• NIH R01 GM089636

• http://microbialphenotypes.org• micropheno