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. 2019 Jul 15;10(1):13.
doi: 10.1186/s13326-019-0205-5.

Phenotype annotation with the ontology of microbial phenotypes (OMP)

Deborah A Siegele  1 , Sandra A LaBonte  2 , Peter I-Fan Wu  2 , Marcus C Chibucos  3 , Suvarna Nandendla  3 , Michelle G Giglio  3 , James C Hu  4
Affiliations

Phenotype annotation with the ontology of microbial phenotypes (OMP)

Deborah A Siegele et al. J Biomed Semantics. .

Abstract

Background: Microbial genetics has formed a foundation for understanding many aspects of biology. Systematic annotation that supports computational data mining should reveal further insights for microbes, microbiomes, and conserved functions beyond microbes. The Ontology of Microbial Phenotypes (OMP) was created to support such annotation.

Results: We define standards for an OMP-based annotation framework that supports the capture of a variety of phenotypes and provides flexibility for different levels of detail based on a combination of pre- and post-composition using OMP and other Open Biomedical Ontology (OBO) projects. A system for entering and viewing OMP annotations has been added to our online, public, web-based data portal.

Conclusions: The annotation framework described here is ready to support projects to capture phenotypes from the experimental literature for a variety of microbes. Defining the OMP annotation standard should support the development of new software tools for data mining and analysis in comparative phenomics.

Keywords: Annotation; Biomedical ontologies; Curation; Microbial genetics; Microbial phenotypes; Microbiology; Ontology; Phenotypes.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Phenotypes in the OMP wiki. a An Annotations table on a Strain page. Two annotations are shown. The interface calculates differences in the genotype and conditions for each annotation compared to the reference annotation. In the second row, the comparison is to a strain that is not isogenic, so multiple allele differences are shown where only one is likely to be causative. b Editing interface using TableEdit. This shows how an existing annotation can be edited. OMP and ECO term names are filled in from the IDs by a database lookup. Conditions are entered as multiple key-value pairs where allowed keys are selected from a pull-down menu. These include, ENVO term, temperature, pH, medium, and other. Extensions and Notes are entered as free text
Fig. 2
Fig. 2
Phenotypes in the OMP wiki. a An Annotations table on a Strain page. Two annotations are shown. The interface calculates differences in the genotype and conditions for each annotation compared to the reference annotation. In the second row, the comparison is to a strain that is not isogenic, so multiple allele differences are shown where only one is likely to be causative. b Editing interface using TableEdit. This shows how an existing annotation can be edited. OMP and ECO term names are filled in from the IDs by a database lookup. Conditions are entered as multiple key-value pairs where allowed keys are selected from a pull-down menu. These include, ENVO term, temperature, pH, medium, and other. Extensions and Notes are entered as free text.
Fig. 3
Fig. 3
Post-composition with the extensions field. a Example of OMP terms with pre-composed groupings at the level of resistance to chemicals. b Use of an extension to specify increased resistance to acriflavine hydrochloride using the Relations Ontology term RO:0002503 (towards) to link the ChEBI term CHEBI:74728 (acriflavine hydrochloride) to the OMP term for increased resistance to a chemical. c Other uses of the RO:0002503 (towards) relationship include specifying increased resistance to a beta-lactam (ampicillin), decreased organic carbon source utilization (lactose), and decreased sensitivity to a bacteriophage (bacteriophage Chi)
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