DOI: 10.5281/zenodo.14795254
title: BIOSYSMOdb: Curated Database for Biodegradation and Bioremediation

description: BIOSYSMOdb is a comprehensive and integrative database developed as part of BIOSYSMO project. This resource centralizes data on metabolic pathways, reactions, enzymes, and degradative organisms to address soil contamination caused by industrial, agricultural, and urban activities. BIOSYSMOdb serves as a bridge between computational and experimental research, offering a unified platform to accelerate bioremediation solutions.

 

Dataset Description

BIOSYSMOdb integrates curated and synthesized data from major public repositories: EAWAG BBD, MibPOPdb, MetaCyc, Uniprot, and KEGG. The database includes:





Chemical level: Details on compounds relevant for biodegradation.

Metabolic level: Data on pathways, reactions, enzymes, and organisms associated with degradation.

Organism level: Information on degradative organisms and their genomic data.

Protein level: Information on enzymes in charge of each reaction and their sequence data associates (if available)



Data Structure

The following files are included in the dataset:



BIOSYSMOdb_Compounds_chemical_iden_v1.0.csv: Compounds identifiers iferred for other databases

BIOSYSMOdb_Compounds_chemical_info_v1.0.csv: Compounds information collected from public sources

BIOSYSMOdb_Compounds_onthology_cod_v1.0.csv: Compounds onthology codes derived from Classyfire

BIOSYSMOdb_Compounds_onthology_term_v1.0.csv: Compounds onthology terms derived from Classyfire

BIOSYSMOdb_Pathways_v1.0.csv: Pathways dataset

BIOSYSMOdb_Reactions_v1.0.csv: Reactions dataset (containing substrates, products, enzymes and pathways associated)

BIOSYSMOdb_Enzymes_v1.0.csv: Reactions dataset (containing reactions associated)

BIOSYSMOdb_Compounds_v1.0.csv: Compounds principal dataset

BIOSYSMOdb_Organisms_v1.0.csv: Organisms principal dataset (containing pathways associated and NCBI Genome ID when available)


 

CSV Descriptions



Compound ID: Unique identifier for each compound.

Pathway Name: Name of the metabolic pathway.

Reaction ID: Identifier for individual reactions.

Enzyme/Protein ID: Unique identifier for associated enzymes.

Organism Name: Name of the degradative organism.


Jupyter Notebook for querying BIOSYSMOdbTo facilitate data exploration and connections within the CSV files, a Jupyter Notebook, BIOSYSMO_database_queries, has been created. This notebook enables users to analyze relationships between different datasets and execute relevant queries efficiently.

 

Data Sources & Licenses

This database includes data derived from diverse databases:



EAWAG BBD: Data on biodegradation of persistent organic pollutants. Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)

MibPOPdb: Focused on microbial degradation of xenobiotics. Creative Commons Attribution 4.0 International (CC BY 4.0) license.

MetaCyc: Comprehensive metabolic pathway database. Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)

KEGG: Genomic integration and metabolic networks. Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)

UniProt: Protein sequences. Creative Commons Attribution 4.0 International (CC BY 4.0) license.

NCBI Genome: Organism Genomes. This database is public.

Pubchem: Chemical Compounds. this database is public.

CHebi: Chemical Compounds. Creative Commons Attribution 4.0 International (CC BY 4.0) license.


Licensing and Attribution

This dataset is shared under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0). Please credit BIOSYSMOdb and the original sources (EAWAG BBD, MibPOPdb, MetaCyc, ChEBI, Pubchem and KEGG) in any use or derivative works.

 

BIOSYSMOdb was developed as part of the BIOSYSMO project, which has received funding from the European Union’s Horizon Europe research and innovation programme under grant agreement No. 101060211.

Acknowledgments- MetaCyc, KEGG, EAWAG BBD, UniProt, NCBI Genome, PubChem, ChEBI, and MibPOPdb – For providing essential data that supported the curation of BIOSYSMOdb.- BIOSYSMO consortium – For their contributions to the database’s design and development.

We extend our gratitude to the Horizon Europe programme and the European Union for their support in advancing research on bioremediation and biodegradation.

Contact

For inquiries, please contact:

- Contact Name: Main Researcher: Marta Franco de Benito, MsC or Project Coordinator: Sara Gil Guerrero, PhD

- Email: marta.franco@idener.ai // sara.gil@idener.ai

- Institution: IDENER.AI