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

An ontology for microbial phenotypes.

Author information

1
Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA. mchibucos@som.umaryland.edu.
2
Department of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX, USA. adrienne.zweifel@ucsf.edu.
3
Current address: University of California, San Francisco, CA, USA. adrienne.zweifel@ucsf.edu.
4
Department of Biology, Texas A&M University, College Station, TX, USA. jherrera@bio.tamu.edu.
5
Department of Biology, Texas A&M University, College Station, TX, USA. wmeza@bio.tamu.edu.
6
Department of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX, USA. shabnam127@hotmail.com.
7
Virginia Commonwealth University, Richmond, VA, USA. phuetz@vcu.edu.
8
Department of Biology, Texas A&M University, College Station, TX, USA. d-siegele@tamu.edu.
9
Department of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX, USA. jimhu@tamu.edu.
10
Institute for Genome Sciences and Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA. mgiglio@som.umaryland.edu.

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.

PMID:
25433798
PMCID:
PMC4287307
DOI:
10.1186/s12866-014-0294-3
[Indexed for MEDLINE]
Free PMC Article

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