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. 2014 Nov 30:14:294.
doi: 10.1186/s12866-014-0294-3.

An ontology for microbial phenotypes

Marcus C Chibucos  1 , Adrienne E Zweifel  2   3 , Jonathan C Herrera  4 , William Meza  5 , Shabnam Eslamfam  6 , Peter Uetz  7 , Deborah A Siegele  8 , James C Hu  9 , Michelle G Giglio  10
Affiliations

An ontology for microbial phenotypes

Marcus C Chibucos et al. BMC Microbiol. .

Abstract

Background: Phenotypic data are routinely used to elucidate gene function in organisms amenable to genetic manipulation. However, previous to this work, there was no generalizable system in place for the structured storage and retrieval of phenotypic information for bacteria.

Results: The Ontology of Microbial Phenotypes (OMP) has been created to standardize the capture of such phenotypic information from microbes. OMP has been built on the foundations of the Basic Formal Ontology and the Phenotype and Trait Ontology. Terms have logical definitions that can facilitate computational searching of phenotypes and their associated genes. OMP can be accessed via a wiki page as well as downloaded from SourceForge. Initial annotations with OMP are being made for Escherichia coli using a wiki-based annotation capture system. New OMP terms are being concurrently developed as annotation proceeds.

Conclusions: We anticipate that diverse groups studying microbial genetics and associated phenotypes will employ OMP for standardizing microbial phenotype annotation, much as the Gene Ontology has standardized gene product annotation. The resulting OMP resource and associated annotations will facilitate prediction of phenotypes for unknown genes and result in new experimental characterization of phenotypes and functions.

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Figures

Figure 1
Figure 1
Using a phenotype ontology to elucidate gene function.
Figure 2
Figure 2
Ontology of Microbial Phenotypes (OMP) in the context of Basic Formal Ontology (BFO), Phenotypic Quality Ontology (PATO), and Gene Ontology (GO). Terms from respective ontologies are rendered in different color type: BFO, black; PATO, blue; GO, red; and OMP, purple. (Note that “quality” exists in both BFO and PATO, and PATO instantiates the concept of “process quality”.) Asserted relationships are indicated by solid lines, and relationships inferred by a reasoner are indicated by dotted lines. Abbreviations: I, is_a; IH, inheres_in; PI, participates_in; Q, has_quality.
Figure 3
Figure 3
Root class and high-level grouping terms of the Ontology of Microbial Phenotypes.
Figure 4
Figure 4
Example annotations of chemotaxis phenotypes reported by Hazelbauer, et al. [ 40 ]. A) an independent annotation showing chemotaxis in the parent strain based on a swimming assay in semisolid medium. B) a dependent annotation for a chemotaxis deficient mutant characterized by decreased swim diameter in the same soft agar assay. Decreased positive chemotaxis is relative to the genotype/environment combination specified in the annotation in A.
See this image and copyright information in PMC

References

    1. Nichols RJ, Sen S, Choo YJ, Beltrao P, Zietek M, Chaba R, Lee S, Kazmierczak KM, Lee KJ, Wong A, Shales M, Lovett S, Winkler ME, Krogan NJ, Typas A, Gross CA. Phenotypic landscape of a bacterial cell. Cell. 2011;144(1):143–156. doi: 10.1016/j.cell.2010.11.052. - DOI - PMC - PubMed
    1. Hannon GJ. RNA interference. Nature. 2002;418(6894):244–251. doi: 10.1038/418244a. - DOI - PubMed
    1. Holt JG. Bergey’s Manual of Determinative Microbiology. 9. Hagerstown, MD: Lippincott Williams & Wilkins; 1994.
    1. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Leontis N, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007;25(11):1251–1255. doi: 10.1038/nbt1346. - DOI - PMC - PubMed
    1. Blom EJ, Breitling R, Hofstede KJ, Roerdink JB, Van Hijum SA, Kuipers OP. Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and multiple gene annotation sources. BMC Genomics. 2008;9:495. doi: 10.1186/1471-2164-9-495. - DOI - PMC - PubMed

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