Environments for annotation with the Ontology for Microbial Phenotypes
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Environments for annotation with the Ontology for Microbial Phenotypes Phenotype RCN 2014 Jim Hu
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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?. - PowerPoint PPT Presentation
Transcript of Environments for annotation with the Ontology for Microbial Phenotypes
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
