# overview
Phenotypes are observable characteristics of an organism that result from the expression of a particular genotype in a particular environment. Examples of phenotypic traits in microbes are motility, sporulation, ability to perform anaerobic respiration, and resistance/sensitivity to an antibiotic.

Until recently, phenotypic information has been captured as free text descriptions in research papers. Ambiguities in natural language confound attempts to retrieve information across sources. For example, "serotype" and "serovar" both refer to the same phenotype, but a simple text-based query with either word alone would miss the other. Or a single term, such as "sporulation" is used to refer to multiple, distinct processes in different organisms. Issues such as these hamper the ability to integrate different phenotypic data sets for the same organism or to use phenotypic information in one organism to predict possible phenotypes in another organism. Ideally, phenotype information should be stored in a consistent, computable format for ease of data integration and mining.

Controlled vocabularies are used to provide both consistent terminology and a structured data format for the capture of biological information. Ontologies are controlled vocabularies of defined terms with unique identifiers and precise relationships to each other. There are phenotype ontologies available for many eukaryotic organisms, including fungi. However, when the OMP project was initiated, none of the existing ontologies was appropriate to comprehensively capture phenotypes for Bacteria or Archaea or to enable comparisons across microbial taxa.

The Siegele lab and our collaborators at TAMU and the Univ. of Maryland (IGS) are developing a formal Ontology of Microbial Phenotypes (OMP). Our lab is focused on term development and annotating microbial phenotypes. OMP can be accessed at microbialphenotypes.org. Releases of OMP are available at github.com/microbialphenotypes.

# educationAndTraining[].organization.label
Harvard University - (Cambridge, Massachusetts, United States)

# educationAndTraining[].organization.label
University of Wisconsin - Madison - (Madison, Wisconsin, United States)

# educationAndTraining[].organization.label
Northwestern University - (Evanston, Illinois, United States)

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GONUTS: the Gene Ontology Normal Usage Tracking System.

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The stationary phase of the bacterial life cycle.

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A functional domain of bacteriophage lambda terminase for prohead binding.

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The stationary-phase-exit defect of cydC (surB) mutants is due to the lack of a functional terminal cytochrome oxidase.

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Proteome analysis of Escherichia coli K-12 by two-dimensional native-state chromatography and MALDI-MS

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Expansion of the Gene Ontology knowledgebase and resources.

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Green fluorescent protein as a reporter of transcriptional activity in a prokaryotic system

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PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools.

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Gene Ontology Consortium: going forward.

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Genetic analysis of the stationary phase-induced mcb operon promoter in Escherichia coli.

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Global analysis of Escherichia coli gene expression during the acetate-induced acid tolerance response.

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The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.

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Mutations in rpoD, the gene encoding the sigma 70 subunit of Escherichia coli RNA polymerase, that increase expression of the lac operon in the absence of CAP-cAMP.

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ESCHERICHIA-COLI FUNCTIONS REQUIRED FOR RESUMING GROWTH AFTER STARVATION

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ECO, the Evidence & Conclusion Ontology: community standard for evidence information.

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The Gene Ontology's Reference Genome Project: a unified framework for functional annotation across species.

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The ontology of microbial phenotypes (OMP): A precomposed ontology based on cross products from multiple external ontologies that is used for guiding microbial phenotype annotation

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Microbial competition: Escherichia coli mutants that take over stationary phase cultures.

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American Association for the Advancement of Science (AAAS)

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Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase.

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High-throughput, quantitative analyses of genetic interactions in E. coli.

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Proteome analysis of Escherichia coli K-12 by two-dimensional native-state chromatography and MALDI-MS.

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Bacteriophage lambda and 21 packaging specificities.

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Gene expression from plasmids containing the araBAD promoter at subsaturating inducer concentrations represents mixed populations.

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Proceedings of the National Academy of Sciences

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Use of a Fluorescence-Based Assay To Measure Escherichia coli Membrane Potential Changes in High Throughput.

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Packaging of the bacteriophage lambda chromosome: dependence of cos cleavage on chromosome length.

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Isolation and characterization of an Escherichia coli mutant defective in resuming growth after starvation.

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The Gene Ontology in 2010: extensions and refinements.

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Insights from the reanalysis of high-throughput chemical genomics data for Escherichia coli K-12.

# publications[].publisher
American Association for the Advancement of Science (AAAS)

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The regulation of transcription initiation in bacteria.

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Mutations in the flhD gene of Escherichia coli K-12 do not cause the reported effect on cell division.

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PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools (vol 42, pg D677, 2014)

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The Gene Ontology resource: enriching a GOld mine.

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Heterogeneous Distribution of Proton Motive Force in Nonheritable Antibiotic Resistance.

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Gene Ontology annotations and resources.

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Heat shock transcription factor 32 co-opts the signal recognition particle to regulate protein homeostasis in E. coli.

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Escherichia coli proteins synthesized during recovery from starvation.

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Packaging of the bacteriophage lambda chromosome: a role for base sequences outside cos.

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The Gene Ontology Resource: 20 years and still GOing strong.

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Phenotype annotation with the ontology of microbial phenotypes (OMP).

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MOPAC: motif finding by preprocessing and agglomerative clustering from microarrays.

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Universal stress proteins in Escherichia coli.

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A previously uncharacterized gene, yjfO (bsmA), influences Escherichia coli biofilm formation and stress response.

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Bacteria-to-Human Protein Networks Reveal Origins of Endogenous DNA Damage.

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What we can learn about Escherichia coli through application of Gene Ontology.

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The terminase of bacteriophage lambda. Functional domains for cosB binding and multimer assembly.

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The Gene Ontology: enhancements for 2011.

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Cloning and sequencing of Escherichia coli murZ and purification of its product, a UDP-N-acetylglucosamine enolpyruvyl transferase.

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Construction of an inducible, pfkA and pfkB deficient strain of Escherichia coli for the expression and purification of phosphofructokinase from bacterial sources.

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EcoliWiki: a wiki-based community resource for Escherichia coli.

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Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO).

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Physiological Role for Cation Channels in Bacteria

# researcherOn[].awardedBy.label
National Institutes of Health - (Bethesda, Maryland, United States)

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DHHS-NIH-National Institute of General Medical Science

# researcherOn[].awardedBy.label
National Institutes of Health - (Bethesda, Maryland, United States)

# streetAddress
Texas A&M University; Biology; 3258 TAMU

# etdChairOf[].label
Holland, Jill Diane (1999-02). Starvation and outgrowth response in Escherichia coli. Master's Thesis.

# etdChairOf[].label
Bain, Sherrie Valarie (2005-08). An unknown regulator affects cell division and the timing of entry into stationary phase in Escherichia coli. Master's Thesis.

# etdChairOf[].label
Kalyanaraman, Gayathri (2004-09). Construction and characterization of yciGFE mutants in Escherichia coli. Master's Thesis.

# etdChairOf[].label
Mao, Weimin (1997-02). Genetic analysis of the stationary-phase induced and [sigma]S-independent promoter of the mcb operon in Escherichia coli. Master's Thesis.