Bioinformatics Resources and Tools

The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body. It is intended to be used for applications in metabolomics, clinical chemistry, biomarker discovery and general education. The database is designed to contain or link three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data.

KEGG LIGAND contains our knowledge on the universe of chemical substances and reactions that are relevant to life. It is a composite database consisting of COMPOUND, GLYCAN, REACTION, RPAIR, RCLASS, and ENZYME databases, whose entries are identified by C, G, R, RP, RC, and EC numbers, respectively.

The purpose of the KNApSAcK Metabolomics is to search metabolites from MS peak, molecular
weight and molecular formula, and species. It consists of KNApSAcK Metabolomics Search Engine and KNApSAcK Core System.

LIPID Metabolites And Pathways Strategy (LIPID MAPS®) is a multi-institutional effort created in 2003 to identify and quantitate, using a systems biology approach and sophisticated mass spectrometers, all of the major — and many minor — lipid species in mammalian cells, as well as to quantitate the changes in these species in response to perturbation.

MassBank data are useful for the chemical identification and structure elucidation of chemical compounds detected by mass spectrometry.

MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2453 pathways from 2788 different organisms. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes.

The METLIN metabolite database is a repository of metabolite information and tandem mass spectrometry data designed to facilitate metabolite identification in metabolomics.

BioGRID is an interaction repository with data compiled through comprehensive curation efforts. The current index is version 3.4.137 and searches 56,733 publications for 1,067,443 protein and genetic interactions, 27,501 chemical associations and 38,559 post translational modifications from major model organism species. All data are freely provided via our search index and available for download in standardized formats.

DAVID bioinformatics resources consists of an integrated biological knowledgebase and analytic tools aimed at systematically extracting biological meaning from large gene/protein lists. It provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.

KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks for: 1. Metabolism, 2. Genetic Information Processing, 3. Environmental Information Processing, 4. Cellular Processes, 5. Organismal Systems, 6. Human Diseases and also on the structure relationships (KEGG drug structure maps) in: 7. Drug Development

Pathguide is a meta-database that provides an overview of more than 190 web-accessible biological pathway and network databases. These include databases on metabolic pathways, signaling pathways, transcription factor targets, gene regulatory networks, genetic interactions, protein–compound interactions, and protein–protein interactions.

Pathway Commons is a collection of publicly available pathway information from multiple organisms. It provides researchers with convenient access to a comprehensive collection of biological pathways from multiple sources represented in a common language for gene and metabolic pathway analysis.

PhosphoSitePlus® (PSP) is an online systems biology resource providing comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, ubiquitination, acetylation and methylation.