=Paper=
{{Paper
|id=Vol-2931/ICBO_2019_paper_46
|storemode=property
|title=OGG-Bac: Ontological Representation of Orthologous Bacterial Genes
|pdfUrl=https://ceur-ws.org/Vol-2931/ICBO_2019_paper_46.pdf
|volume=Vol-2931
|authors=Meng Liu,Hong-Yu Ou,Yongqun He
|dblpUrl=https://dblp.org/rec/conf/icbo/0012OH19a
}}
==OGG-Bac: Ontological Representation of Orthologous Bacterial Genes==
https://ceur-ws.org/Vol-2931/ICBO_2019_paper_46.pdf
OGG-Bac: Ontological Representation of Orthologous Bacterial Genes
Meng Liua,b, Hong-Yu Oua, Yongqun Heb
a
State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai,
China. bUniversity of Michigan Medical School, Ann Arbor, MI 48109, USA
Abstract
Different from eukaryotic organisms that turn to have one set of
gene annotations, bacteria are usually annotated with strain-
specific genome annotations within which a large number of
genes (e.g., DNA replication initiation factor dnaA gene) may be
orthologs. To systematically integrate and analyze bacterial
genes, we developed a bacterial branch of the Ontology of Genes
and Genomes (OGG-Bac) with a focus on standardized
orthologous gene representation and annotations. Figure 1. Representation of dnaA gene in OGG-Bacteria
Keywords: Our representation strategy principles: (i) Use unique gene IDs
for different levels of dnaA. (ii) Strain-specific genes are asserted
OGG; ortholog; bacteria gene based on their taxonomy hierarchy. (iii) For annotation, use the
most common gene name as the gene label, and includes other
Introduction gene labels (if different) as the alternative labels (Figure 1).
We are first representing the genes in the synthetic minimal bac-
Eukaryotic organisms usually have one set of gene annotations terial genomes (1) and their orthologous genes in other bacteria.
for each species (e.g., human). For bacteria, each bacterial species
turns to have decades and even hundreds of strains with
Conclusions
sequenced genomes, and each genome is individually annotated.
Therefore, it is very difficult to integrate the huge number of
bacterial genes in the same species or at higher taxonomy levels. OGG-Bac was developed to ontologically represent and annotate
bacterial genes based on the ortholog gene hierarchy at different
Orthologous genes have evolved from a common ancestral gene. taxonomical levels.
Using the OGG (an OBO Foundry library ontology) as a platform,
an ontological representation of the hierarchy and properties of
the bacterial orthologs at different taxonomic levels can facilitate Acknowledgments
the standardization and better understanding of the complex
relations among various bacterial genes. National Key R&D Program of China [2017YFC1600100 to
H.Y.O.]; ML was supported by a jointly funded Ph.D.-
Methods studentship of the China Scholarship Council and University of
Michigan Medical School (Grant No. 201806230209).
OGG-Bac was aligned with the OGG-core. The web servers
Ontobee (http://www.ontobee.org/) and Ontofox Address for correspondence
(http://ontofox.hegroup.org) were applied to check and import the
related existing terms from reliable ontologies. The Protégé-OWL YH and HYO are the co-corresponding authors. Email addresses:
editor was used for manually ontology editing. yongqunh@med.umich.edu and hyou@sjtu.edu.cn.
Results References
Figure 1 uses gene dnaA to illustrate how OGG-Bac represents 1. Hutchison,C.A., Chuang,R.-Y., Noskov,V.N., Assad-
different levels of bacterial orthologs. The dnaA gene encodes the Garcia,N., Deerinck,T.J., Ellisman,M.H., Gill,J., Kannan,K.,
DNA replication initiation factor in bacteria. It is the first gene in Karas,B.J., Ma,L., et al. (2016) Design and synthesis of a minimal
the synthetic minimal bacterial genomes (1) and conserved in bacterial genome. Science, 351, aad6253.
various bacteria (e.g., Brucella and E. coli).
Copyright © 2019 for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).