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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological

Shuai Zeng1,2, Zhen Lyu1,3, Siva Ratna Kumari Narisetti1

  • 1Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, USA.

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|December 21, 2019
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Summary

Knowledge Base Commons (KBCommons) is a web framework for storing, sharing, and analyzing multi-omics data across species. It supports biological discovery through integrated data access and visualization tools for diverse research communities.

Keywords:
GenomicsKnowledge BaseMulti-omics dataOrganism-specific databaseVisualization and analysis

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Area of Science:

  • Bioinformatics
  • Genomics
  • Multi-omics Data Integration

Background:

  • Knowledge Base Commons (KBCommons) v1.1 is a universal web-based framework.
  • It provides generic functionalities for storing, sharing, analyzing, exploring, integrating, and visualizing genomics and integrative omics data for multiple organisms.
  • KBCommons aims to integrate diverse multi-level omics data to support biological discoveries across all species on a common platform.

Purpose of the Study:

  • To present KBCommons v1.1 as a comprehensive framework for multi-omics data management and analysis.
  • To highlight its capabilities in supporting biological discoveries for diverse research communities.
  • To provide a centralized platform for accessing and analyzing genomic and omics data.

Main Methods:

  • KBCommons is structured into four modules: data storage, data processing, data accessing, and a web interface.
  • It supports the creation of species-specific or disease-specific knowledge bases (KBs).
  • The framework allows for the addition of new genome versions and multi-omics data to existing KBs and exploration of datasets.

Main Results:

  • KBCommons offers tools for data visualization and analytics, including gene/metabolite search, function annotation, differential gene expression analysis, and bulk data download.
  • It features a robust data privilege management system for secure data sharing (public, private, pre-publication).
  • Users can perform data analysis via in-house workflows linked to high-performance computing resources (XSEDE) through an intuitive web interface.

Conclusions:

  • KBCommons meets the needs of diverse research communities for a comprehensive multi-level omics web resource.
  • It facilitates data retrieval, sharing, analysis, and visualization for all organisms.
  • KBCommons is publicly accessible at http://kbcommons.org/.