Development of a literature web search tool and knowledgebase for microbiome functional analysis and annotation

Authors

• Y Zhang
• A Biragyn
• J Engel
• KG Becker

Abstract

Interest in the Microbiome is growing exponentially with research applications in obesity, cancer, aging, immunity, neurodegeneration as well as population and environmental studies, among many others. Like most other Omics approaches, 16S and metagenomic bacterial sequencing produces an enormous amount of data. After pipeline sequencing analysis, taxonomic assignment, bacterial quantitation and classification, much of these data need to be put into biological context. We are developing a web tool/knowledgebase (PubBug?) with the goal to aid in placing lists of bacteria names into biological context. It has two parts: 1) a simple web-based PubMed search tool which enables automated multiplex searching of PubMed with user-supplied lists of bacterial names and biologically relevant keywords; and 2) a growing knowledgebase of bacterial annotation such as taxonomy, disease associations, anatomical or environmental site, bacterial characteristics, antibiotic resistance, PubMed Keywords and MESH headings. These two elements of the web tool will be linked where the user will be able to input lists of bacterial names from their experiment, search Pubmed efficiently, and get functional annotation for that list. In addition, this system will be especially useful in post-publication inquiry where any reader of a microbiome publication can cut and paste lists of bacterial names and explore their biological and disease contexts.

Scientific Focus Area: Microbiology and Infectious Diseases

This page was last updated on Friday, March 26, 2021