Introduction

The mbPPCPdb database is a manually curated integrative resource dedicated to microbial biodegradation of pharmaceuticals and personal care products (PPCPs) research. Data are systematically and manually collected from the scientific literature. It is a freely accessible platform providing information on a collection of resources such as key gene, strain and their systematic taxonomy, and scientific literature citations derived from published and experimentally validated pharmaceuticals and personal care products biodegradation datasets. It is an integrated resource that provides tools for predicting the biodegradability of compounds, generating automated structures of compounds, predicting the toxicity of chemicals, and bioinformatics utilities for PPCPs degrading microbial sequence analysis. By providing and consolidating high-level curated information on microbial biodegradation of PPCPs into a single resource, mbPPCPdb will be an important web resource that can foster studies into PPCP degrading microbial communities and help enhance our understanding of microbial biodegradation of pharmaceuticals and personal care products.

Organism included

The database contains data on algal, bacterial, and fungal microbial isolates experimentally validated in the published literature to degrade pharmaceuticals and personal care products.

Content

• • Emerging Contaminants information
• • Compound description (Compound name, Structure, SMILES, Physiochemical properties, External links to numerical identifiers, etc.)
• • Publications (scientific literature)
• • Compound metabolized (PPCPs metabolized, Biodegradation pathway map)
• • Degradation gene information (Strain ID, Taxonomy of organisms, encoding gene, Nucleotide, and Protein external links, FASTA links, etc.)
• • General information of strain (Strain ID, taxonomy, GenBank ID, FASTA sequence)
• • Biodegradation information (PPCPs metabolized, Biodegradation rate, Primary intermediates, Final product, degradation technique, Enzyme activity detected)
• • Sample collection information (Continent, Country, Isolation source, Habitat)
• • Publication Information (Title, PMID, Reference, External links to research, Abstract)
• • External links (BRENDA, Uniprot, AlgaeBase, KEGG, EAWAG-BBD, WoRMS, etc.)

Version

This is the first release of mbPPCPdb, and it is in its infancy and thus is incomplete. The database will be updated periodically, and article curation is ongoing, as new articles related to microbial biodegradation of pharmaceuticals and personal care products are continuously published. Bi-yearly updates will be carried out on the database.

Data constraints

The mbPPCPdb database was developed to assist environmental scientists and engineers working to understand microbial degradation of pharmaceuticals and personal care products by providing genes, strains that are important for PPCPs remediation research and also includes toolkits for users to input their datasets in the context of the database. As such, one is reminded that this database is not the ultimate source of microbial biodegradation of pharmaceuticals and personal care products.

Please note that datasets displayed in this manually curated resource it is not error-free. When making use of this data, users are urged to verify the authenticity and validity of the datasets provided before using them.

Data queries

Users can search for specific genes, strains, keywords, or a combination of concurrent conditions related to microbial biodegradation of PPCPs. See the mbPPCPdb Tutorial section for more details about all the query options.

Any queries or data misrepresentation-related issues concerning the mbPPCPdb can be reported via the contact feature incorporated into the mbPPCPdb. The administrator will respond to their queries.

Recommended Web-Browser for navigation

In order to appreciate the functionality and visualization of the mbPPCPdb database, we recommend users use the latest versions of Google Chrome, Mozilla Firefox, and Microsoft Edge browsers.

Data sources

Where appropriate sources from which the data included in mbPPCPdb was extracted were cited. For example, citing the relevant sources such as NCBI, WoRMS, AlgaeBase, FungiDB, and relevant literature sources from which valid data was extracted were also cited for each data entry.