Developing an Ontology for Microbial            Phenotypes                 #41               Jim Hu
"Before the physical basis of genes wasunderstood, associating phenotypes with a heritableunit laid the foundation of mode...
Goals• Build a classification system (ontology) for microbial  phenotypes• Build an annotation system and annotate microbi...
What’s a phenotype?                                                    •   Observable characteristics                     ...
Building OMP (Ontology of Microbial Phenotypes)Expertise            Literature                                     Annotat...
Building OMP (Ontology of Microbial Phenotypes)Expertise            Literature                                     Annotat...
Entities and Qualities• Existing phenotype ontologies are based on the  PATO entity-quality system   – Entity: a trait, ob...
Entities and Qualities• Making this work for microbes   – In some cases the entities are analogous to anatomy terms     fo...
Entities and Qualities• Making this work for microbes   – Other cases are population behaviors    Budrene and Berg (1991) ...
State vs Relative Phenotypes• Characteristics of a species/type strain• Changes relative to a reference strain   – Not nec...
What do we mean by observable?• Observations vs. inferences   – Lac-• Where do we draw the line?   –   Loss of enzyme acti...
Building OMP (Ontology of Microbial Phenotypes)Expertise            Literature                                     Annotat...
What is the object of annotation?• Individuals/populations?• Genes?• Genotypes?   – “relevant genotypes”?   – Genotype dif...
Things the annotation system needs to              express• Properties of wt type strains:   – 1. E. coli wt has_phenotype...
Components needed• Unique annotation ID• Accessions for genotypes for all species/strains    – Genes and alleles in a pang...
Future• Build the needed components   –   OMP in progress   –   ECO in progress   –   Universal genotype database?!   –   ...
Acknowledgements etc.• TAMU   –   Debby Siegele   –   Adrienne Zweifel      •   NIH R01 GM089636   –   Jon Herrera   –   W...
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Jim Hu's presentation at the Biocurator 2012 conference: Developing an Ontology for Microbial Phenotypes

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Biocurator2012.41.hu

  1. 1. Developing an Ontology for Microbial Phenotypes #41 Jim Hu
  2. 2. "Before the physical basis of genes wasunderstood, associating phenotypes with a heritableunit laid the foundation of modern genetics" - Nicholset al 2011
  3. 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. 4. What’s a phenotype? • Observable characteristics • Individual • Genotype • Environmenthttp://www.flickr.com/photos/max_westby/54275159/
  5. 5. Building OMP (Ontology of Microbial Phenotypes)Expertise Literature Annotation Examples Ontology system Draft annotations
  6. 6. Building OMP (Ontology of Microbial Phenotypes)Expertise Literature Annotation Examples Ontology system Draft annotations
  7. 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. 8. Entities and Qualities• Making this work for microbes – In some cases the entities are analogous to anatomy terms for microbial cells
  9. 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. 10. State vs Relative Phenotypes• Characteristics of a species/type strain• Changes relative to a reference strain – Not necessarily relative to wild-type
  11. 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. 12. Building OMP (Ontology of Microbial Phenotypes)Expertise Literature Annotation Examples Ontology system Draft annotations
  13. 13. What is the object of annotation?• Individuals/populations?• Genes?• Genotypes? – “relevant genotypes”? – Genotype differences?
  14. 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. 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. 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. 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
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