Biomedical Science

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Metabolomics Resources

Metabolomics Databases

  • HMDB The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found (and experimentally verified) in the human body.
  • BiGG The BiGG database is a metabolic reconstruction of human metabolism designed for systems biology simulation and metabolic flux balance modeling. It is a comprehensive literature-based genome-scale metabolic reconstruction that accounts for the functions of 1,496 ORFs, 2,004 proteins, 2,766 metabolites, and 3,311 metabolic and transport reactions. It was assembled from build 35 of the human genome.
  • MetaboLights database MetaboLights is a database for metabolomics experiments and derived information. 

Metabolic Pathway Databases

  • KEGG KEGG (Kyoto Encyclopedia of Genes and Genomes) is one of the most complete and widely used databases containing metabolic pathways (372 reference pathwasy) from a wide variety of organisms (>700).
  • MetaCyc MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways.
  • HumanCyc HumanCyc is a bioinformatics database that describes the human metabolic pathways and the human genome.
  • BioCyc BioCyc is a collection of 371 Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism.
  • Reactome - Reactome is a curated, peer-reviewed knowledgebase of biological pathways, including metabolic pathways as well as protein trafficking and signaling pathways.
  • WikiPathways WikiPathways is an open, collaborative platform for capturing and disseminating models of biological pathways for data visualization and analysis. The database has pathway for more than 20 species and more than 100 pathways for seven species. . More info in this paper:

Compound or Compound-Specific Databases

  • PubChem PubChem is a freely available database of chemical structures of small organic molecules and information on their biological activities.
  • ChEBI Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. ChEBI has >15,500 chemical entities in its database.
  • ChemSpider
    ChemSpider is an aggregated database of organic molecules containing more than 20 million compounds from many different providers.
  • KEGG Glycan
    The KEGG GLYCAN database is a collection of experimentally determined glycan structures. KEGG Glycan has >11,000 glycan structures from a large number of eukaryotic and prokaryotic sources.

Drug Databases

  • DrugBankThe DrugBank database is a blended bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.
  • Therapeutic Target Database The Therapeutic Target Database (TTD) is a drug database designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature.
  • PharmGKB The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. PharmGKB contains searchable data on genes (>20,000), diseases (>3000), drugs (>2500) and pathways (53). It also has detailed information on 470 genetic variants (SNP data) affecting drug metabolism.
  • STITCH STITCH ('search tool for interactions of chemicals') is a searchable database that integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. 
  • SuperTarget SuperTarget is a database that contains a core dataset of about 7300 drug-target relations of which 4900 interactions have been subjected to a more extensive manual annotation effort. 

Disease & Physiology Databases

  • OMIM Online Mendelian Inheritance in Man (OMIM) is a comprehensive compendium of human genes and genetic phenotypes.
  • METAGENE METAGENE is a knowledgebase for inborn errors of metabolism providing information about the disease, genetic cause, treatment and the characteristic metabolite concentrations or clinical tests that may be used to diagnose or monitor the condition.
  • OMMBID OMMBID or the On-Line Metabolic and Molecular Basis to Inherited Disease is an web-accessible book/encyclopedia describing the genetics, metabolism, diagnosis and treatment of hundreds of metabolic disorders contributed from hundreds of experts. .



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