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SGD
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Saccharomyces Genome Database (SGD) is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae.
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CYGD
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The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis. |
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Yeast snoRNA Database
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Small Nucleolar RNAs (snoRNAs) from the Yeast Saccharomyces cerevisiae: A comprehensive database of S. cerevisiae H/ACA and C/D box snoRNAs.
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YMPD
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The Yeast Mitochondrial Protein Database (YMPD) presents a compilation of information concerning budding yeast mitoproteins - proteins of Saccharomyces cerevisiae that are: encoded within the mitochondrial genome (mtDNA), encoded within the nuclear genome and after synthesis imported into the mitochondria, or encoded within the nuclear genome and having an extra-mitochondrial (nuclear or cytoplasmic) role connected with mitochondrial biogenesis or function. |
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HMDB
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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.
The database contains three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular
biology/biochemistry data. HMDB contains information on more than 6500 metabolites. Additionally,
approximately 1500 protein (and DNA) sequences are linked to these metabolite entries. Each MetaboCard
entry contains more than 100 data fields with 2/3 of the information being devoted to chemical/clinical
data and the other 1/3 devoted to enzymatic or biochemical data. Many data fields are hyperlinked to
other databases (KEGG, PubChem, MetaCyc, ChEBI, PDB, Swiss-Prot, and GenBank) and a variety of
structure and pathway viewing applets.
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BiGG
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BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions.
The BiGG database contains metabolic reconstructions for Yeast, Human, E. coli and other microrganism
metabolism designed for systems biology simulation and metabolic flux balance modeling.
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SYSTOMONAS
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SYSTOMONAS (SYSTems biology of pseudOMONAS) is a database for systems biology studies of
Pseudomonas species. It contains extensive transcriptomic, proteomic and metabolomic
data as well as metabolic reconstructions of this pathogen. Reconstruction of metabolic
networks in SYSTOMONAS was achieved via comparative genomics. Broad data integration with
well established databases BRENDA, KEGG and PRODORIC is also maintained. Several tools for
the analysis of stored data and for the visualization of the corresponding results are provided,
enabling a quick understanding of metabolic pathways, genomic arrangements or promoter structures
of interest.
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SMPDB
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SMPDB (Small Molecule Pathway Database) is a comprehensive database of metabolic, drug, and disease pathways.
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KEGG
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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). These pathways are hyperlinked to metabolite and protein/enzyme information.
Currently KEGG has >15,000 compounds (from animals, plants and bacteria), 7742 drugs (including
different salt forms and drug carriers) and nearly 11,000 glycan structures.
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MetaCyc
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MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc
contains more than 1,100 pathways from more than 1,500 different organisms. MetaCyc is curated
from the scientific experimental literature and contains pathways involved in both primary and
secondary metabolism, as well as associated compounds, enzymes, and genes.
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HumanCyc
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HumanCyc is a bioinformatics database that describes the human metabolic pathways and the human
genome. The current version of HumanCyc was constructed using Build 31 of the human genome.
The resulting pathway/genome database (PGDB) includes information on 28,783 genes,
their products and the metabolic reactions and pathways they catalyze.
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BioCyc
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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. The databases within the
BioCyc collection are organized into tiers according to the amount of manual review and
updating they have received. Tier 1 DBs have been created through intensive manual efforts and
include EcoCyc, MetaCyc and the BioCyc Open Compounds Database (BOCD). BOCD includes metabolites,
enzyme activators, inhibitors, and cofactors derived from hundreds of organisms. Tier 2 and Tier 3
databases contain computationally predicted metabolic pathways, as well as predictions as to which
genes code for missing enzymes in metabolic pathways, and predicted operons.
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Reactome
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Reactome is a curated, peer-reviewed knowledgbase of biological pathways, including metabolic
pathways as well as protein trafficking and signaling pathways. Reactome includes several
types of reactions in its pathway diagram collection including experimentally confirmed, manually
inferred and electronically inferred reactions. Reactome has pathway data on more than 20
different organisms but the primary organism of interest is Homo sapiens. Reactome has data
and pathway diagrams for >2700 proteins, 2800 reactions and 860 pathways for humans.
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PubChem
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PubChem is a freely available database of chemical structures of small organic molecules and
information on their biological activities. It contains structure, nomenclature and calculated
physico-chemical data and is linked with NIH PubMed/Entrez information. PubChem is organized
as three linked databases within the NCBI's Entrez information retrieval system. These are
PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast
chemical structure similarity search tool. PubChem has >19 million unique chemical structures.
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ChEBI
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Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular
entities focused on 'small' chemical compounds. The chemical entities in ChEBI are either
products of nature (metabolites) or synthetic products used to intervene in the processes of
living organisms (drugs or toxins). ChEBI contains structure and nomenclature information along
with hyperlinks to many well-regarded databases. ChEBI uses a carefully developed ontological
classification, whereby the relationships between molecular entities or classes of entities and
their parents and/or children are precisely specified. ChEBI has >15,500 chemical entities in
its database.
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ChemSpider
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ChemSpider is an aggregated database of organic molecules containing more than 20 million compounds
from many different providers. At present the database contains information from such diverse sources
as a marine natural products database, ACD-Labs chemical databases, the EPA's DSSTox databases and from
a series of chemical vendors. It has extensive search utilities and most compounds have a large number
of calculated physico-chemical property values.
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KEGG Glycan
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The KEGG GLYCAN database is a collection of experimentally determined glycan structures. It contains
all unique structures taken from CarbBank, structures entered from recent publications, and structures
present in KEGG pathways. KEGG Glycan has >11,000 glycan structures from a large number of
eukaryotic and prokaryotic sources.
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Toxin, Toxin Target Database (T3DB)
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T3DB is a database of common toxins and their associated toxin targets. It contains detailed target and compound
information similar to DrugBank, including structure, properties, mechanism of action, gene/protein sequence,
and associated SNPs.
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HMDB
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The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed
information about small molecule metabolites found in the human body. It contains experimental
MS/MS data for 800 compounds, experimental 1H and 13C NMR data (and assignments) for 790 compounds
and GC/MS spectral and retention index data for 260 compounds. Additionally, predicted 1H and 13C
NMR spectra have been generated for 3100 compounds. All spectral databases are downloadable and
searchable.
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BMRB
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The BioMagResBank (BMRB) is the central repository for experimental NMR spectral data, primarily for
macromolecules. The BMRB also contains a recently established subsection for metabolite data.
The current metabolomics database contains structures, structure viewing applets, nomenclature data,
extensive 1D and 2D spectral peak lists (from 1D, TOCSY, DEPT, HSQC experiments), raw spectra and FIDs
for nearly 500 molecules. The data is both searchable and downloadable.
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MMCD
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The Madison Metabolomics Consortium Database (MMCD) is a database on small molecules of biological
interest gathered from electronic databases and the scientific literature. It contains approximately
10,000 metabolite entries and experimental spectral data on about 500 compounds. Each metabolite
entry in the MMCD is supported by information in an average of 50 separate data fields, which provide
the chemical formula, names and synonyms, structure, physical and chemical properties, NMR and MS
data on pure compounds under defined conditions where available, NMR chemical shifts determined by
empirical and/or theoretical approaches, information on the presence of the metabolite in different
biological species, and extensive links to images, references, and other public databases.
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MassBank
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MassBank is a mass spectral database of experimentally acquired high resolution MS spectra of metabolites.
Maintained and supported by he JST-BIRD project, it offers various query methods for standard spectra
obtained from Keio University, RIKEN PSC, and other Japanese research institutions. It is officially
sanctioned bythe Mass Spectrometry Society of Japan. The database has very detailed MS data and
excellent spectral/structure searching utilities. More than 13,000 spectra from 1900 different
compounds are available.
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Golm Metabolome Database
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The Golm Metabolome Database provides public access to custom GC/MS libraries which are stored
as Mass Spectral (MS) and Retention Time Index (RI) Libraries (MSRI). These libraries of mass
spectral and retention time indices can be used with the NIST/AMDIS software to identify metabolites
according their spectral tags and RI's. The libraries are both searchable and downloadable and have
been carefully collected under defined conditions on several types of GC/MS instruments (quadrupole and TOF).
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Metlin
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The METLIN Metabolite Database is a repository for mass spectral metabolite data. All metabolites are
neutral or free acids. It is a collaborative effort between the Siuzdak and Abagyan groups and Center
for Mass Spectrometry at The Scripps Research Institute. METLIN is searchable by compound name, mass,
formula or structure. It contains 15,000 structures, including more than 8000 di and tripeptides.
METLIN contains MS/MS, LC/MS and FTMS data that can be searched by peak lists, mass range, biological
source or disease.
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Fiehn GC-MS Database
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This library contains data on 713 compounds (name, structure, CAS ID, other links) for which GC/MS
data (spectra and retention indices) have been collected by the Fiehn laboratory. A locally
maintain program called BinBase/Bellerophon filters input GC/MS spectra and uses the spectral
library to identify compounds. The actual GC/MS library is available from several different GC/MS vendors.
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OMIM
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Online Mendelian Inheritance in Man (OMIM) is a comprehensive compendium of human genes and genetic
phenotypes. The full-text, referenced overviews in OMIM contain information on all known Mendelian
disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype.
It is updated daily, and the entries contain many links to other genetics resources. OMIM contains
379 diseases with associated gene sequence data as well as 2385 conditions with a disease phenotype
and a known genetic cause.
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METAGENE
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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. It has data on 431 genetic diseases.
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OMMBID
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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. It also contains extensive reviews,
detailed pathways, chemical structures, physiological data and tables that are particularly
useful for clinical biochemists. Most university libraries have subscriptions to this resource.
OMMBID was originally developed by Charles Scriver at McGill.
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DrugBank
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The 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. The database contains nearly 4800 drug entries including
>1,350 FDA-approved small molecule drugs, 123 FDA-approved biotech (protein/peptide) drugs,
71 nutraceuticals and >3,243 experimental drugs. DrugBank also contains extensive SNP-drug data that
is useful for pharmacogenomics studies.
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Therapeutic Target DB
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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, the targeted disease conditions,
the pathway information and the corresponding drugs/ligands directed at each of these targets. The database
currently contains 1535 targets and 2107 drugs/ligands.
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PharmGKB
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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. The data
includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the
cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. Its aim is to aid researchers
in understanding how genetic variation among individuals contributes to differences in reactions to drugs.
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.
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STITCH
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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. Text mining and chemical structure similarity is used to predict relations between chemicals.
Each proposed interaction can be traced back to the original data sources. The database contains interaction
information for over 68 000 different chemicals, including 2200 drugs, and connects them to 1.5 million
genes across 373 genomes.
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SuperTarget
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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. SuperTarget provides tools
for 2D drug screening and sequence comparison of the targets. The database contains more than 2500 target
proteins, which are annotated with about 7300 relations to 1500 drugs; the vast majority of entries have
pointers to the respective literature source. A subset of 775 more extensively annotated drugs is provided
separately through the
Matador database (Manually Annotated Targets And Drugs Online Resource.
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