The document discusses several databases related to human metabolism and pharmacology. It describes the contents and purpose of each database, including the Human Metabolome Database (HMDB), KEGG, MetaCyc, PubChem, ChEBI, DrugBank, the Therapeutic Target Database (TTD), PharmGKB, and Chemical Entities of Biological Interest (ChEBI). These databases contain chemical, clinical, molecular biology, pathway, and genomic data on human metabolites, drugs, and targets.

1. BY :
Sachin Kumar

2.  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.
 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.
 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.

3. 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.

4.  setupX, developed by the Fiehn laboratory at
UC Davis, is a web-based metabolomics LIMS.
 It is XML compatible and built around a
relational database management core.
 It is particularly oriented towards the capture
and display of GC-MS metabolomic data
through its metabolic annotation database
called BinBase.
 for free download of database and source
code

5.  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.

6. 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.

7. 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.

8.  PubChem
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.

9.  ChEBI
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.

10. Drug bank
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.

11. 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.

12.  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.

13. 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.