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Table 3 List of the representative databases with potential for application of the machine learning in microbiome field

From: Irritable bowel syndrome and microbiome; Switching from conventional diagnosis and therapies to personalized interventions

Database Reference (URL) Description
BacDive https://bacdive.dsmz.de/ BacDive offers data on 81,827 bacterial and archaeal strains, including 14,091 type strains and thereby covers approx. 90% of the validly described species
Gold https://gold.jgi.doe.gov/ Gold is a World Wide Web resource for comprehensive access to information regarding genome and metagenome sequencing projects, and their associated metadata
NCBI Microbial Genomes https://www.ncbi.nlm.nih.gov/genome/microbes/ Microbial Genomes resource presents public data from prokaryotic genome sequencing projects
EnsemblBacteria http://bacteria.ensembl.org/index.html Ensembl Bacteria is a browser for bacterial and archaeal genomes
European Nucleotide Archive https://www.ebi.ac.uk/ena/browser/home The European Nucleotide Archive (ENA) provides a comprehensive record of the world’s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation
DrugBank https://go.drugbank.com/ DrugBank, the world's most comprehensive and structured drug and molecular drug information resource
Super Natural http://bioinf-applied.charite.de/supernatural_new/index.php?site=home Super Natural II, a database of natural products. It contains 325,508 natural compounds (NCs), including information about the corresponding 2d structures, physicochemical properties, predicted toxicity class and potential vendors
ChEMBL https://www.ebi.ac.uk/chembl/ ChEMBL is a manually curated database of bioactive molecules with drug-like properties
ChemSpider http://www.chemspider.com/ ChemSpider is a free chemical structure database providing fast text and structure search access to over 100 million structures from hundreds of data sources
BindingDB http://www.bindingdb.org/bind/index.jsp BindingDB is a public, web-accessible database of measured binding affinities. BindingDB contains 41,328 Entries, each with a DOI, containing 2,259,122 binding data for 8,516 protein targets and 977,487 small molecules
MicrobiomeDB https://microbiomedb.org/mbio/app/ A data-mining platform for interrogating microbiome experiments
UniProt https://www.uniprot.org/ UniProt provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information
Virtual Metabolic Human https://www.vmh.life/#home The VMH database captures information on human and gut microbial metabolism and links this information to hundreds of diseases and nutritional data
Disbiome https://disbiome.ugent.be/home Disbiome® is a database covering microbial composition changes in different kinds of diseases, managed by Ghent University
eHOMD http://www.homd.org/ eHOMD provides comprehensive curated information on the bacterial species present in the human aerodigestive tract (ADT), which encompasses the upper digestive and upper respiratory tracts, including the oral cavity, pharynx, nasal passages, sinuses and esophagus
HMDB https://hmdb.ca/ The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body
MDB https://db.cngb.org/microbiome/ Microbiome database involves the sequencing resource and metadata of ecological community samples of microorganisms, including both host-associated or environmental microbes
MGnify https://www.ebi.ac.uk/metagenomics/ MGnify provides amplicon, assemblies,metabarcoding, metagenomes and metatranscriptomes data on human and environmental biomes
Human Microbiome Project https://www.hmpdacc.org/ Genomic characterization of microbiota at five body sites (HMP1), and information on microbiota-human interactions in disease (iHMP)