SyBA 0.0.5

SyBA: a tool and database for standardizing gene names from the main bacterial pathogens causing food contamination

Contents Overview

• System Overview
• Getting Started with SyBA
  • Prerequisites
  • Installation Guide
• Efficiency of SyBA
• SyBA Class Functions
  • init
  • SyBA Update
  • SyBA fixName
  • SyBA buildQuery
• Example Codes
• Web Form for SyBA
• License Information
• Development Team
• Citing SyBA

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System Overview

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SyBA (Synonymous of BActerial Genes) is a tool and database for standardizing gene names in bacterial genomes. It provides a consistent nomenclature for gene names, allowing researchers to accurately search for genes from bacteria that cause human diseases, improving public health research on foodborne illnesses (Figure 1).

Figure 1. Global snapshot of the Food Contamination Monitoring and Assessment Programme, highlighting the top 10 countries and various regions. The data is sourced from the Global Environment Monitoring System, avaliable at https://apps.who.int/foscollab/Download/DownloadConta

The SyBA database is constructed using gene symbols and gene products (proteins) present in 1,215,109 functional bacterial genomes, based on the genera Campylobacter, Clostridium, Escherichia, Listeria, Salmonella, Shigella, Staphylococcus, and Vibrio.

SyBA includes a Python class for standardizing gene names, which can automatically find and change different name variations into a standard form. The class also generates search commands for specific genes or papers in GenBank or PubMedCentral with different bacterial gene names.

Additionally, SyBA provides a web form that is easy-to-use for researchers to search for specific genes or papers in GenBank or PubMedCentral.

The SyBA repository, hosted on GitHub and licensed under MIT, is a freely accessible resource for the scientific community. It offers comprehensive analysis results of bacterial gene names. In addition, it includes thorough guidelines and sample scripts to assist researchers in their work.

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Getting Started with SyBA

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• Prerequisites

Before you run SyBA, make sure you have the following prerequisites installed on your system:

• Python Environment
  • Python version 3.6 or higher
  • conda (optional)
• Dependencies (these will be automatically installed with pip)
  • requests
  • pandas
  • openpyxl
  • numpy

• Installation Guide

There are tree ways to install SyBA:

1. Through pip: Install SyBA directly using pip:

pip install SyBA

• This will install SyBA and its dependencies in your Python environment.  
   

2. By cloning the GitHub repository: Clone the source code of SyBA from GitHub:

git clone https://github.com/luanrabelo/SyBA.git
cd SyBA  
pip install -r requirements.txt

• This command will clone the repository, and then you should navigate to the cloned directory to install SyBA and its dependencies using pip.  
   

3. Installation via conda: You can also install SyBA using conda with the following commands:

conda create -n SyBA -c conda-forge -c bioconda SyBA
conda activate SyBA 

• This method will set up SyBA along with its dependencies in a new conda environment.  

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Efficiency of SyBA

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Figure 2. (a) Comparison between the number of gene name variations in the SyBA database (v1.0.0) and the number of proteins without a gene name. (b) The 15 genes with the most name variations in the SyBA database (v1.0.0). (c) By applying the names of proteins that do not have a gene name, it is possible to recover this information in up to 55.3% of cases. (d) The time required for the SyBA class to standardize gene names in 1000 bacterial genomes, with the possibility of executing the function asynchronously to further reduce processing time. (e) The time required to generate 1000 search commands with gene name variations.  

Figure 3. A comparative analysis of search results in March 2024, contrasting the efficiency of the SyBA web form against conventional searches in GenBank (a) and PubMedCentral (b). The comparison underscores the enhanced efficiency attained through the use of combined gene nomenclature and variation in gene nomenclature for genes birA, folD, fruA, hsdM, hsdR, hsdS, kdpD, mtlA, potD, pstS, putA, tnp, tnpA, wzy and wzx.  

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SyBA Class Functions

SyBA init

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__init__(self, **kwargs)

The SyBA class is initialized with this function. This function serves as the constructor for the class and is invoked when a new SyBA class instance is created.

Upon the creation of a SyBA class instance, the constructor verifies the existence of the SyBA_database.tsv database at the given path. If the database is not found, it will strive to establish the SyBA directory and procure the database from the GitHub repository.

If the verbose parameter is set to True, progress updates will be displayed in the terminal to keep the user informed about the ongoing operations.

Parameters:

• verbose (bool): If True, messages will be printed during execution. The default is True.

Returns:

• None

Notes:

• This function requires the requests and pandas library to be imported.
• The SyBA database is available at github.com/luanrabelo/SyBA.

Usage Example:

# Import the SyBA class from the SyBA module.
from SyBA import SyBA
# This function initializes the class and downloads the database from the GitHub repository.
sb = SyBA(verbose=True)

Output

############################## SyBA ##############################
SyBA Class has been initialized!
Version: 0.0.1
Status: Stable
Author: Luan Rabelo
License: MIT
GitHub Page: https://github.com/luanrabelo/SyBA
Consult the documentation in github page for more information.
############################## SyBA ##############################

 

SyBA update

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update(self, **kwargs)

The update method updates the SyBA database by fetching it from the GitHub repository's stable branch. If a database already exists, it's removed before the new one is downloaded.

This method checks for the SyBA_database.tsv database file on the user's system. If found, the file is removed. Then, it downloads the latest database from the GitHub repository URL.

If verbose is True, console messages inform the user about the progress, including the old database's removal and the new one's download.

Parameters:

• verbose (bool): If True, messages will be printed during execution. The default is True.

Returns:

• The updated SyBA database saved in the SyBA folder.

Notes:

• This function requires the requests library to be imported.
• The SyBA database is available at github.com/luanrabelo/SyBA.

Usage Example:

# Import the SyBA class from the SyBA module.
from SyBA import SyBA
# This function initializes the class and downloads the database from the GitHub repository.
sb = SyBA(verbose=True)
# This function update SyBA database
sb.update(verbose=True)

Output

2024/03/05 - 16:20:57 - SyBA database found in the current directory!
2024/03/05 - 16:20:57 - SyBA database found in /home/luanrabelo/SyBA/ !
2024/03/05 - 16:20:57 - Removing old SyBA database...
2024/03/05 - 16:20:57 - Old SyBA database removed successfully!
2024/03/05 - 16:20:57 - Downloading SyBA database from https://github.com/luanrabelo/SyBA, please wait...
2024/03/05 - 16:21:00 - Download SyBA database successfully!

 

SyBA fixName

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fixName(self, **kwargs)

Corrects the gene name according to the SyBA database, ensuring it adheres to the standardized nomenclature.

The fixName function takes a gene name and corrects it based on the entries in the SyBA database. If the provided gene name is found in the database, it is replaced with the standardized short name. If not found, the original name is returned, and a log entry is created. The function provides verbose output if the verbose parameter is set to True.

Parameters:

• dscp (str): The gene description, for example, lcl|AASOAZ010000001.1_cds_EFE7820019.1_2 [locus_tag=F6Q14_00010] [protein=pflagellum-specific ATP synthase FliL] [protein_id=EFE7820019.1] [location=complement(1576..1932)] [gbkey=CDS].
• verbose (bool): If set to True, messages will be printed during execution. The default is True.

Returns:

• ShortName (str): The corrected gene name.

Notes:

• This function requires the pandas and numpy library to be imported.
• The SyBA database can be found at github.com/luanrabelo/SyBA.

Usage Example:

# Import the SyBA class from the SyBA module.
from SyBA import SyBA
# This function initializes the class and downloads the database from the GitHub repository.
sb = SyBA(verbose=True)
# This function fixes the gene name.
geneName = sb.fixName(dscp='[protein=flagellum-specific ATP synthase FliL]', verbose=True)
print(geneName)

Output

fliL

 

SyBA buildQuery

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buildQuery(self, **kwargs)

Constructs a query for Entrez search in GenBank or PubMed using the SyBA database.

The buildQuery function creates a query string that can be utilized to search for specific gene information in the GenBank or PubMed databases.

The search type is validated against a list of acceptable formats.

The list of acceptable formats includes "Title", "Abstract", "All Fields", "MeSH Terms".

If the verbose parameter is set to True, the function will output informative messages during the process of query construction.

Parameters:

• geneName: The gene name, for example, rpoB.
• specieName: The specie name, for example, Salmonella.
• searchType: The search type, for example, All Fields.
• verbose: If True, the class will print the status of the database and the download process. If False, the class will not print anything. Default is False.

Returns:

• query (str): The query for Entrez search in GenBank or PubMed.

Notes:

• This function requires the pandas library to be imported.
• The SyBA database is available at github.com/luanrabelo/SyBA.
• The _listTypes contains the valid formats for the search type.

Usage Example:

from SyBA import SyBA
sb = SyBA()
query = sb.buildQuery(specieName='Salmonella', geneName='mntB', searchType='All Fields', verbose=True)
print(query)

Output

2024/03/05 - 18:17:37 - SyBA database found in the current directory!
2024/03/05 - 18:17:37 - Gene: 'mntB' found in SyBA database!
("Salmonella"[Organism] OR "Salmonella"[Title]) AND ("mntB"[All Fields] OR "zinc transport system permease protein"[All Fields] OR "manganese abc transporter (atp-binding protein)"[All Fields] OR "cation abc transporter permease protein"[All Fields] OR "putative manganese transport system membrane protein mntb"[All Fields] OR "manganese transport system membrane protein mntb"[All Fields] OR "manganese transport system membrane protein"[All Fields] OR "cation abc transporter"[All Fields] OR "abc-transporter membrane protein"[All Fields] OR "afed"[All Fields] OR "manganese abc transporter inner membrane permease sitd"[All Fields] OR "chelated iron transport system membrane protein yfed,manganese transport system membrane protein mntb,high-affinity zinc transporter membrane component,anchored repeat-type abc transporter, permease subunit,abc 3 transport family"[All Fields] OR "metal cation abc transporter membrane protein"[All Fields] OR "mn2+/zn2+ abc transporter permease"[All Fields])

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Example Codes

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Navigate to the Examples folder to view a notebook file that showcases examples of how to implement the commands of SyBA. This notebook serves as a practical guide, providing step-by-step instructions and examples to help you understand and utilize the functionalities of SyBA effectively.

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Web Form for SyBA

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We’ve created an intuitive web form, accessible at SyBA web form, designed for researchers interested in conducting individual searches using different names linked to the same gene. This web form produces a command that includes multiple names, facilitating accurate searches on platforms like the National Center for Biotechnology Information (NCBI) - GenBank and PubMed Central.
 

 

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License Information

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SyBA is released under the MIT License. This license permits reuse within proprietary software provided that all copies of the licensed software include a copy of the MIT License terms and the copyright notice.

For more details, please see the MIT License.  

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Development Team

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• Luan Rabelo
• Marcelo Vallinoto
• Iracilda Sampaio
• Davidson Sodré
• Luiza Helena Meller da Silva
• Grazielle Gomes  

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Citing SyBA

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