An ontology for microbial phenotypes

BMC Microbiology

Michelle G Giglio³  James C Hu⁴  Deborah A Siegele¹  Peter Uetz⁵  Shabnam Eslamfam⁴  William Meza¹  Jonathan C Herrera¹  Adrienne E Zweifel⁶  Marcus C Chibucos² 

[1] Department of Biology, Texas A&M University, College Station, TX, USA;Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA;Institute for Genome Sciences and Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA;Department of Biochemistry and Biophysics, Texas A&M University and Texas AgriLife Research, College Station, TX, USA;Virginia Commonwealth University, Richmond, VA, USA;Current address: University of California, San Francisco, CA, USA

关键词: Wiki;    Phenotypic evidence;    Phenotype annotation;    Microbial genetics;    Escherichia coli;    Controlled vocabulary;    Biological ontologies;    Bacterial phenotype;    Annotation capture;   

Others  :  1137704
DOI  :  10.1186/s12866-014-0294-3

 received in 2014-08-22, accepted in 2014-11-11,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Chibucos et al.; licensee BioMed Central.

【 图 表 】

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