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Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

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BNDb--Biomolecules Nucleus Database: an integrated proteomics and transcriptomics database.

A C Faria-Campos¹, R R Gomes, F S Moratelli

¹Laboratório de Genética Bioquímica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil. alessa@icb.ufmg.br

Genetics and Molecular Research : GMR

|December 7, 2007

Summary

Researchers developed BNDb, an integrated proteomics and transcriptomics database, to store and retrieve raw and processed data. This database aids protein identification by consolidating information from multiple experiments and repositories.

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An Integrated Approach for Microprotein Identification and Sequence Analysis

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An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

Proteomics and Transcriptomics
Bioinformatics
Database Development

Background:

Proteomics analysis involves identifying and quantifying proteins, often requiring complex experimental workflows and comparison with existing databases.
Current proteomics databases typically store processed data or are limited to specific experiment types, necessitating the use of multiple repositories for comprehensive analysis.
Researchers face challenges in accessing and integrating raw and processed data from diverse proteomics experiments.

Purpose of the Study:

To propose and implement an integrated database, BNDb (Biomolecules Nucleus Database), for storing both raw and processed proteomics and transcriptomics data.
To facilitate the retrieval of combined or individual data types, thereby streamlining protein identification and analysis.
To provide a centralized resource for the scientific community, supporting research on various organisms.

Main Methods:

Development of a relational database using MySQL server.
Implementation of data indexing for efficient retrieval of raw and processed data.
Design of a data model with grouped tables for different data subtypes, including experimental details, raw data, analysis results, and publications.

Main Results:

The BNDb database successfully integrates proteomics and transcriptomics data.
The database is capable of storing raw and processed data, along with associated metadata and publications.
BNDb is currently being used to store data from Schistosoma mansoni, Tittyus serrulatus, and Phoneutria nigriventer.

Conclusions:

The integrated BNDb database offers a valuable resource for proteomics and transcriptomics research.
By consolidating diverse data types, BNDb simplifies protein identification and analysis.
The database aims to serve as a useful tool for the broader scientific community involved in biomolecular research.