New Metabolomic Data Resources: MiMeDB and ChemFOnt

Both resources were developed by Dr. Wishart’s group

The Human Microbial Metabolome Database (MiMeDB)

The Human Microbial Metabolome Database (MiMeDB) represents the kind of integrated, multi-omic or systems biology database that is needed to enable comprehensive multi-omic integration.

It is a comprehensive, multi-omic, microbiome resource that connects:

  • microbes to microbial genomes;
  • microbial genomes to microbial metabolites;
  • microbial metabolites to the human exposome and
  • all of these ‘omes’ to human health.

The related open-access article was just published last month in the Nucleic Acids Research

Screenshot of MiMeDB main webpage

The database contains comprehensive information about all the known metabolites generated by these microbes, their structural, chemical and spectral properties, the reactions and enzymes responsible for these metabolites and the primary exposome sources (food, drug, cosmetic, pollutant, etc.) that lead to the observed microbial metabolites in humans.

In simple terms, MiMeDB contains data about human microbes, their associated metabolites and the effects these metabolites have on humans. There is the graphic showing the data’s relational structure in MiMeDB’s backend.

One of the main features in MiMeDB is the Visualize tab, which offers two data visualization options: (i) Chromosome Viewer and (ii) Network Viewer.

Screenshots showing the (A) MiMeDB Chromosome Viewer for a portion of the Pseudomonas aeruginosa genome and (B) the MiMeDB Network Viewer highlighting connections with L-tryptophan metabolism.

6.4 million genes, 7.6 billion DNA bases, 1904 microorganisms, 3112 references, 22,054 reactions, 24,254 metabolites, and 648,861 MS and NMR spectra are among the data now present in MiMeDB. [MS- Mass Spectroscopy and NMR- Nuclear Magnetic Resonance]

ChemFOnt: the chemical functional ontology resource

The Chemical Functional Ontology (ChemFOnt), which may be found online at, is a hierarchical, OWL-compliant ontology that describes the actions and functions of more than 341,000 biologically important chemicals, including primary and secondary metabolites as well as natural products, food chemicals, synthetic food additives, drugs, herbicides, pesticides and environment-related chemicals. [OWL − Web Ontology Language].

The related open-access article was also published in the Nucleic Acids Research, check out further here!

Nucleic Acids Res,

The goal of ChemFOnt, a FAIR-compliant resource, is to give the same rigor, standardization, and formal structure to the terms and terminology used in biochemistry, food chemistry, and environmental chemistry as the gene ontology (GO) as given to molecular biology. Both a free, web-enabled database and a Web Ontology Language (OWL) file can be downloaded for ChemFOnt. [FAIR − findability, accessibility, interoperability, and reusability].

ChemFOnt currently contains 3.9 million protein-chemical relationships and ∼10.3 million chemical-functional relationships. The long-term objective of ChemFOnt is to be adopted by databases and software tools utilised by the metabolomics, exposomics, metagenomics, genomics, and proteomics communities in addition to the general chemistry community.

Find out more about other Databases and Web Servers & Data Analysis

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