BioRemPP Database: A Curated Compound-Centric Resource for Bioremediation Potential Profiling

Description

Overview

The BioRemPP Database (Bioremediation Potential Profile Database) is a curated, integrated resource designed to support environmental bioremediation research by systematically linking chemical compounds, genes, enzymes, and regulatory frameworks. This database addresses a critical gap in bioremediation science: the absence of a unified, standardized resource connecting priority pollutant with their potential biodegradation pathways across multiple knowledge bases and regulatory contexts.

Scientific Rationale

Environmental contamination by xenobiotic compounds—including chlorinated solvents, polyaromatic hydrocarbons, pesticides, and heavy metals—poses significant ecological and public health challenges. While substantial knowledge exists regarding microbial biodegradation capabilities, this information remains fragmented across databases and regulatory frameworks. BioRemPP systematically integrates these sources into a unified, FAIR-compliant (Findable, Accessible, Interoperable, Reusable) framework.

Database Contents (v1.0.0)

This release contains:

10,869 database entries linking compounds to functional annotations

384 unique chemical compounds with standardized identifiers (CAS, ChEBI, SMILES)

1,541 KEGG Orthology (KO) identifiers for functional annotation

12 chemical compound classes for classification

Data Sources and Integration

Data were curated from multiple authoritative sources:

Regulatory Frameworks:

ATSDR (Agency for Toxic Substances and Disease Registry) Substance Priority List

EPA (U.S. Environmental Protection Agency) National Priorities List

CONAMA (Brazilian National Environment Council) Regulations

IARC (International Agency for Research on Cancer) Classifications (Groups 1, 2A, 2B)

EU Water Framework Directive Priority Substances

Canadian Environmental Protection Act Priority Substances List

Functional Annotations:

KEGG (Kyoto Encyclopedia of Genes and Genomes) — KO identifiers, pathways, enzymes

HADEG (Hydrocarbon Aerobic Degradation Enzymes and Genes) — degradation-specific coverage

BlastKOALA (v3.0) and EggNOG-mapper (v2) — sequence-based functional assignments

Chemical Classification:

ChEBI (Chemical Entities of Biological Interest) — standardized identifiers, SMILES, compound classes

Toxicological Annotations:

ToxCSM — machine learning-based multi-endpoint toxicity predictions (mutagenicity, carcinogenicity, environmental hazard)

Integration Framework and External Database Contributions

BioRemPP is not a copy or aggregation of existing databases. Rather, it is an integration layer that establishes compound-centric relationships across independent external resources, each contributing distinct and complementary information. BioRemPP does not redistribute primary data from these sources; instead, it provides standardized cross-references and relational mappings that enable users to navigate between resources through a unified analytical framework.

The data architecture organizes compound-gene-enzyme relationships within a centralized core containing 1,541 unique KOs and 384 compounds. This core is linked to three external resources that expand functional and toxicological coverage through cross-references, not data duplication.

The following external databases contribute specific layers of information to BioRemPP:

External Resource
Contribution to BioRemPP
Quantitative Coverage
Relationship Type

KEGG (Kyoto Encyclopedia of Genes and Genomes)
KO identifiers, gene symbols, enzyme classifications (EC), and pathway associations for functional annotation
855 entries from 20 canonical xenobiotic metabolism pathways
Cross-reference via KO identifiers

HADEG (Hydrocarbon Aerobic Degradation Enzymes and Genes)
Extends degradation-specific gene coverage for hydrocarbons, polymers, and biosurfactant-related pathways
867 entries across 71 sub-pathways
Cross-reference via KO identifiers

ChEBI (Chemical Entities of Biological Interest)
Standardized chemical identifiers, SMILES representations, and compound class assignments
384 compounds with validated identifiers
Cross-reference via ChEBI IDs

ToxCSM
Machine learning-based toxicity predictions as annotation layers
370 compounds with 31 toxicity endpoints (nuclear, stress-response, genomic, environmental, dose-related)
Cross-reference via CPD identifiers

Regulatory Frameworks (ATSDR, EPA, CONAMA, IARC, EU-WFD, CEPA-PSL)
Priority compound lists and hazard classifications defining the scope of environmentally relevant compounds
9 international regulatory references
Compound inclusion criteria

What BioRemPP adds:

Compound-centric relational structure — Links compounds to genes, enzymes, pathways, and regulatory status through standardized identifiers (CAS, ChEBI, KO, SMILES), analogous to toxicogenomic frameworks that prioritize chemical-gene interactions

Cross-database harmonization — Resolves identifier inconsistencies and synonym mappings across sources, ensuring interoperability between KEGG, ChEBI, HADEG, and ToxCSM

Regulatory context integration — Associates functional annotations with environmental priority status from multiple international frameworks, structuring the database around environmentally prioritized pollutants rather than pathway catalogs alone

Analytical framework — Provides structured tidy data tables (10,869 entries with 100% completeness across core fields) optimized for bioremediation potential profiling, functional coverage analysis, and sample comparison

Users seeking primary sequence data, pathway diagrams, or detailed toxicological reports should consult the original databases directly. BioRemPP facilitates this navigation by maintaining traceable cross-references to source identifiers.

Reference Genomes

For demonstration and validation purposes, the database includes functional annotations from nine representative RefSeq genomes spanning principal bioremediation-relevant groups:

Bacteria: Acinetobacter baumannii, Enterobacter asburiae, Pseudomonas aeruginosa

Fungi: Aspergillus nidulans, Fusarium graminearum, Cryptococcus gattii

Microalgae/Cyanobacteria: Chlorella variabilis, Nannochloropsis gaditana, Synechocystis sp.

File Formats

All data tables are provided in CSV format with UTF-8 encoding. Detailed field descriptions and data dictionaries are included in the accompanying documentation (biorempp-schemas).

Associated Web Server

The BioRemPP web server (https://bioinfo.imd.ufrn.br/biorempp/) provides interactive visualization and analysis tools for exploring this database across.eight analytical modules (56 use cases) supporting hypothesis generation.

License

This dataset is released under Creative Commons Attribution 4.0 International (CC BY 4.0). Third-party data sources retain their original licenses.

Version History

v1.0.0: Initial release

Contact

For questions or feedback, please contact [e-mail] or submit issues via the project repository https://github.com/BioRemPP/biorempp_web/issues.

Keywords 

bioremediation, biodegradation, xenobiotics, environmental microbiology, functional genomics, KEGG, pollutants, regulatory compounds, compound-gene associations, toxicology, environmental biotechnology, metagenomics

Metadata Fields

Field
Value

Resource Type
Dataset

Title
BioRemPP Database: A Curated Compound-Centric Resource for Bioremediation Potential Profiling

Version
1.0.0

License
Creative Commons Attribution 4.0 International (CC BY 4.0)

Language
English

Subjects
Environmental Sciences, Bioinformatics, Microbiology, Biotechnology